diff --git a/Makefile b/Makefile index d1701459e..08ee2c064 100644 --- a/Makefile +++ b/Makefile @@ -1,7 +1,7 @@ SHELL := /bin/bash MONOREPO_URI := https://github.com/Opentrons/opentrons.git -OT2_VERSION_TAG := v4.3.0 +OT2_VERSION_TAG := v6.1.0 OT2_MONOREPO_DIR := ot2monorepoClone # Parsers output to here diff --git a/protoBuilds/007992/rna_isolation.ot2.apiv2.py.json b/protoBuilds/007992/rna_isolation.ot2.apiv2.py.json index d6f858e13..9fd86cd7c 100644 --- a/protoBuilds/007992/rna_isolation.ot2.apiv2.py.json +++ b/protoBuilds/007992/rna_isolation.ot2.apiv2.py.json @@ -4449,5 +4449,18 @@ "protocolName": "Viral RNA Isolation (Magnetic Beads)", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw isolation plate on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw elution plate on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/00f7b1_part2/00f7b1_part2.ot2.apiv2.py.json b/protoBuilds/00f7b1_part2/00f7b1_part2.ot2.apiv2.py.json index cdc3f84f7..34cb2a72c 100644 --- a/protoBuilds/00f7b1_part2/00f7b1_part2.ot2.apiv2.py.json +++ b/protoBuilds/00f7b1_part2/00f7b1_part2.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "# flake8: noqa\n\n\"\"\"OPENTRONS.\"\"\"\nfrom opentrons import protocol_api\nimport math\nimport threading\nfrom time import sleep\nfrom opentrons import types\n\nmetadata = {\n 'protocolName': 'NEBNext Ultra II Directional RNA Library Prep Kit for Illumina Part 2: RNA Isolation',\n 'author': 'John C. Lynch ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.13' # CHECK IF YOUR API LEVEL HERE IS UP TO DATE\n # IN SECTION 5.2 OF THE APIV2 \"VERSIONING\"\n}\n\n# Definitions for deck light flashing\n\n\nclass CancellationToken:\n \"\"\"FLASH SETUP.\"\"\"\n\n def __init__(self):\n \"\"\"FLASH SETUP.\"\"\"\n self.is_continued = False\n\n def set_true(self):\n \"\"\"FLASH SETUP.\"\"\"\n self.is_continued = True\n\n def set_false(self):\n \"\"\"FLASH SETUP.\"\"\"\n self.is_continued = False\n\n\ndef turn_on_blinking_notification(hardware, pause):\n \"\"\"FLASH SETUP.\"\"\"\n while pause.is_continued:\n hardware.set_lights(rails=True)\n sleep(1)\n hardware.set_lights(rails=False)\n sleep(1)\n\n\ndef create_thread(ctx, cancel_token):\n \"\"\"FLASH SETUP.\"\"\"\n t1 = threading.Thread(target=turn_on_blinking_notification,\n args=(ctx._hw_manager.hardware, cancel_token))\n t1.start()\n return t1\n\n\ndef run(ctx: protocol_api.ProtocolContext):\n \"\"\"PROTOCOLS.\"\"\"\n [\n num_samples,\n m300_mount, flash\n ] = get_values( # noqa: F821 (<--- DO NOT REMOVE!)\n \"num_samples\", \"m300_mount\", \"flash\")\n\n 'Global variables'\n TEST_MODE = True\n bead_delay_time = 7\n wash_delay_time = 7\n supernatant_headspeed_modulator = 10\n mag_height = 8\n ctx.max_speeds['Z'] = 125\n ctx.max_speeds['A'] = 125\n # Setup for flashing lights notification to empty trash\n cancellationToken = CancellationToken()\n\n # define all custom variables above here with descriptions:\n num_columns = math.ceil(num_samples/8)\n if m300_mount == 'right':\n m20_mount = 'left'\n else:\n m20_mount = 'right'\n # load modules\n mag_deck = ctx.load_module('magnetic module gen2', '1')\n mag_deck.disengage()\n temp_deck = ctx.load_module('temperature module gen2', '3')\n print(num_columns)\n\n # load labware\n mag_plate = mag_deck.load_labware('thermofisher_96_wellplate_200ul') # changed from thermofisher_96_wellplate_200ul\n temp_plate = temp_deck.load_labware('opentrons_96_aluminumblock_generic_'\n 'pcr_strip_200ul')\n dwp = ctx.load_labware('nest_96_wellplate_2ml_deep', '4')\n final_plate = ctx.load_labware('thermofisher_96_wellplate_200ul', '2') # changed from thermofisher_96_wellplate_200ul\n trash = ctx.load_labware('nest_1_reservoir_195ml', '9').wells()[0].top()\n # load tipracks\n\n tips300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)\n for slot in ['7', '10']]\n tips20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', slot)\n for slot in ['11']]\n # load instrument\n\n m300 = ctx.load_instrument(\n 'p300_multi_gen2', m300_mount, tip_racks=tips300)\n\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=tips20)\n\n # pipette functions # INCLUDE ANY BINDING TO CLASS\n\n def pick_up(pip):\n try:\n pip.pick_up_tip()\n except protocol_api.labware.OutOfTipsError:\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n pip.home()\n ctx.pause('\\n\\n~~~~~~~~~~~~~~PLEASE REPLACE TIPRACKS~~~~~~~~~~~~~~~\\n') # noqa: E501\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n pip.reset_tipracks()\n pick_up(pip)\n\n tips_dropped = 0\n\n def drop_tip(pip, home=True):\n nonlocal tips_dropped\n pip.drop_tip(home_after=home)\n if pip == m300:\n tips_dropped += 8\n else:\n tips_dropped += 1\n if tips_dropped == 288:\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n pip.home()\n ctx.pause('\\n\\n~~~~~~~~~~~~~~PLEASE EMPTY TRASH~~~~~~~~~~~~~~~\\n')\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n tips_dropped = 0\n\n def bead_mixing(well, pip, mvol, side_disp=0, mix_reps=10):\n \"\"\"bead_mixing.\"\"\"\n \"\"\"\n 'bead_mixing' will mix liquid that contains beads. This will be done by\n aspirating from the middle of the well & dispensing from the bottom to\n mix the beads with the other liquids as much as possible. Aspiration &\n dispensing will also be reversed to ensure proper mixing.\n param well: The current well that the mixing will occur in.\n param pip: The pipet that is currently attached/ being used.\n param mvol: The volume that is transferred before the mixing steps.\n param reps: The number of mix repetitions that should occur. Note~\n During each mix rep, there are 2 cycles of aspirating from bottom,\n dispensing at the top and 2 cycles of aspirating from middle,\n dispensing at the bottom\n \"\"\"\n\n ctx.comment('MIXING\\n')\n vol = mvol * .8\n\n pip.move_to(well.center())\n for _ in range(mix_reps):\n pip.aspirate(vol, dest.bottom().move(types.Point(x=-side_disp,\n y=0, z=3)), rate=2)\n pip.dispense(vol, dest.bottom().move(types.Point(x=-side_disp,\n y=0, z=5)), rate=2)\n\n def remove_supernatant(vol):\n for i, dest in enumerate(samples):\n side = -1 if i % 2 == 0 else 1\n pick_up(m300)\n m300.move_to(dest.top())\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(vol-20, dest.bottom().move(types.Point(x=side, y=0, z=1)),\n rate=0.1)\n ctx.delay(seconds=1)\n m300.move_to(dest.top())\n m300.aspirate(10, dest.top())\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(m300.current_volume, trash)\n m300.blow_out()\n m300.air_gap(50)\n drop_tip(m300)\n\n pick_up(m20)\n m20.move_to(dest.top())\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m20.aspirate(19, dest.bottom().move(types.Point(x=side, y=0, z=1)),\n rate=0.1)\n ctx.delay(seconds=1)\n m20.move_to(dest.top())\n m20.aspirate(1, dest.top())\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m20.dispense(m20.current_volume, trash)\n m20.blow_out()\n m20.aspirate(10, trash)\n drop_tip(m20)\n ctx.comment('\\n')\n\n def wash_beads(vol, source, dest, side_disp, mix_reps=15):\n pick_up(m300)\n m300.aspirate(vol, source)\n m300.dispense(vol, dest.bottom().move(types.Point(x=-side_disp, y=0, z=5)), rate=2)\n # bead_mixing(dest, m300, vol, reps=6)\n for _ in range(mix_reps):\n m300.aspirate(vol, dest.bottom().move(types.Point(x=-side_disp, y=0, z=3)), rate=2)\n m300.dispense(vol, dest.bottom().move(types.Point(x=-side_disp, y=0, z=5)), rate=2)\n drop_tip(m300)\n\n # reagents\n\n samples = mag_plate.rows()[0][:num_columns]\n beads = temp_plate.rows()[0][:math.ceil(num_columns/2)]*12\n wash_1 = dwp.rows()[0][0]\n wash_2 = dwp.rows()[0][2]\n tris = dwp.rows()[0][6]\n wash_3 = dwp.rows()[0][4]\n strand_primer_mix = temp_plate.rows()[0][-1]\n rna_wash = temp_plate.rows()[0][6:6+math.ceil(num_columns/3)]*12\n final_dest = final_plate.rows()[0][:num_columns]\n\n # protocol\n ctx.comment('\\n~~~~~~~~~~~~~~ADDING BEADS~~~~~~~~~~~~~~\\n')\n for i, (dest, bead_col) in enumerate(zip(samples, beads)):\n pick_up(m300)\n if i < math.ceil(num_columns/2):\n m300.mix(5, 65, bead_col)\n m300.aspirate(50, bead_col, rate=0.5)\n ctx.delay(seconds=1.5)\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.move_to(bead_col.top())\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(50, dest, rate=0.5)\n m300.mix(5, 80, dest)\n # bead_mixing(dest, m300, 100, reps=5)\n drop_tip(m300)\n\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n m300.home()\n ctx.pause(\"\"\"\n MOVE PLATE IN SLOT 1 TO OFF-DECK THERMOCYCLER\n REFER TO 1.2.12 FOR SPECIFIC HEATING/COOLING CYCLE\n RETURN PLATE TO SLOT 1 WHEN FINISHED. ENSURE SAMPLE PLATE IS\n FLAT AND SECURE WHEN RETURNING TO MAGNETIC MODULE!\n \"\"\")\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n\n ctx.comment('\\n~~~~~~~~~~~~~~MIXING~~~~~~~~~~~~~~\\n')\n for dest in samples:\n pick_up(m300)\n m300.mix(6, 80, dest)\n # bead_mixing(dest, m300, 100, reps=6)\n drop_tip(m300)\n if TEST_MODE:\n ctx.delay(seconds=5)\n else:\n ctx.delay(minutes=5)\n\n ctx.comment('\\n~~~~~~~~~~~~~~ENGAGING MAGNET~~~~~~~~~~~~~~\\n')\n mag_deck.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(minutes=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n ctx.comment('\\n~~~~~~~~~~~~~~REMOVING SUPERNATANT~~~~~~~~~~~~~~\\n')\n remove_supernatant(95)\n\n mag_deck.disengage()\n\n ctx.comment('\\n~~~~~~~~~~~~~WASHING BEADS TWICE WITH BUFFER~~~~~~~~~~~~\\n')\n for wash in [wash_1, wash_2]:\n for i, dest in enumerate(samples):\n side = -1 if i % 2 == 0 else 1\n wash_beads(180, wash, dest, side)\n\n mag_deck.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(minutes=wash_delay_time)\n else:\n ctx.delay(minutes=wash_delay_time)\n\n ctx.comment('\\n~~~~~~~~~~~~~~REMOVING SUPERNATANT~~~~~~~~~~~~~~\\n')\n remove_supernatant(190)\n\n mag_deck.disengage()\n\n ctx.comment('\\n~~~~~~~~~~~~~ADDING TRIS BUFFER~~~~~~~~~~~~\\n')\n for dest in samples:\n pick_up(m300)\n m300.aspirate(50, tris)\n m300.dispense(50, dest)\n m300.mix(6, 40, dest)\n # bead_mixing(dest, m300, 50, reps=6)\n drop_tip(m300)\n\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n m300.home()\n ctx.pause(\"\"\"\\n\\nMOVE PLATE IN SLOT 1 TO OFF-DECK THERMOCYCLER\n REFER TO 1.2.24 FOR SPECIFIC HEATING/COOLING CYCLE\n RETURN PLATE TO SLOT 1 WHEN FINISHED. ENSURE SAMPLE PLATE IS\n FLAT AND SECURE WHEN RETURNING TO MAGNETIC MODULE!\"\"\")\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n\n ctx.comment('\\n~~~~~~~~~~~~~ADDING BINDING BUFFER~~~~~~~~~~~~\\n')\n for i, (source, dest) in enumerate(zip(rna_wash, samples)):\n side = -1 if i % 2 == 0 else 1\n pick_up(m300)\n m300.aspirate(50, source)\n m300.dispense(50, dest)\n # m300.mix(6, 80, dest)\n bead_mixing(dest, m300, 100, side, mix_reps=15)\n drop_tip(m300)\n\n ctx.comment('\\n~~~~~~~~~~~~~INCUBATING 5 MINUTES~~~~~~~~~~~~\\n')\n if TEST_MODE:\n ctx.delay(seconds=5)\n else:\n ctx.delay(minutes=5)\n\n ctx.comment('\\n~~~~~~~~~~~~~ENGAGING MAGNETIC MODULE~~~~~~~~~~~~\\n')\n mag_deck.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(minutes=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n ctx.comment('\\n~~~~~~~~~~~~~REMOVING SUPERNATANT~~~~~~~~~~~~\\n')\n remove_supernatant(150)\n mag_deck.disengage()\n ctx.comment('\\n~~~~~~~~~~~~~WASHING BEADS WITH BUFFER~~~~~~~~~~~~\\n')\n for i, dest in enumerate(samples):\n side = -1 if i % 2 == 0 else 1\n wash_beads(180, wash_3, dest, side)\n\n mag_deck.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(minutes=wash_delay_time)\n else:\n ctx.delay(minutes=wash_delay_time)\n\n ctx.comment('\\n~~~~~~~~~~~~~REMOVING SUPERNATANT~~~~~~~~~~~~\\n')\n remove_supernatant(190)\n mag_deck.disengage()\n\n ctx.comment('\\n~~~~~~~~~~~~~ADDING MASTER MIX ELUTION~~~~~~~~~~~~\\n')\n for i, dest in enumerate(samples):\n side = -1 if i % 2 == 0 else 1\n pick_up(m20)\n m20.aspirate(11.5, strand_primer_mix)\n m20.dispense(11.5, dest.bottom().move(types.Point(x=-side, y=0, z=3)))\n bead_mixing(dest, m20, 11, side)\n drop_tip(m20)\n\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n m300.home()\n ctx.pause(\"\"\"\\n\\nMOVE PLATE IN SLOT 1 TO OFF-DECK THERMOCYCLER\n REFER TO 1.2.37 FOR SPECIFIC HEATING/COOLING CYCLE\n SPIN PLATE DOWN BEFORE RETURNING TO DECK\n RETURN PLATE TO SLOT 1 WHEN FINISHED. ENSURE SAMPLE PLATE IS\n FLAT AND SECURE WHEN RETURNING TO MAGNETIC MODULE!\"\"\")\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n\n ctx.comment('\\n~~~~~~~~~~~~~SEPARATING RNA SOLUTION~~~~~~~~~~~~\\n')\n mag_deck.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(minutes=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n ctx.comment('\\n~~~~~~~~~~~~~MOVING RNA TO NEW PLATE~~~~~~~~~~~~\\n')\n for s, d in zip(samples, final_dest):\n pick_up(m20)\n m20.aspirate(10, s)\n m20.dispense(10, d)\n drop_tip(m20)\n\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n m300.home()\n ctx.pause('\\n\\n~~~~~~~~~~~~~~PROTOCOL COMPLETE~~~~~~~~~~~~~~~\\n')\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n\n for c in ctx.commands():\n print(c)\n", + "content": "# flake8: noqa\n\n\"\"\"OPENTRONS.\"\"\"\nfrom opentrons import protocol_api\nimport math\nimport threading\nfrom time import sleep\nfrom opentrons import types\n\nmetadata = {\n 'protocolName': 'NEBNext Ultra II Directional RNA Library Prep Kit for Illumina Part 2: RNA Isolation',\n 'author': 'John C. Lynch ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.13' # CHECK IF YOUR API LEVEL HERE IS UP TO DATE\n # IN SECTION 5.2 OF THE APIV2 \"VERSIONING\"\n}\n\n# Definitions for deck light flashing\n\n\nclass CancellationToken:\n \"\"\"FLASH SETUP.\"\"\"\n\n def __init__(self):\n \"\"\"FLASH SETUP.\"\"\"\n self.is_continued = False\n\n def set_true(self):\n \"\"\"FLASH SETUP.\"\"\"\n self.is_continued = True\n\n def set_false(self):\n \"\"\"FLASH SETUP.\"\"\"\n self.is_continued = False\n\n\ndef turn_on_blinking_notification(hardware, pause):\n \"\"\"FLASH SETUP.\"\"\"\n while pause.is_continued:\n hardware.set_lights(rails=True)\n sleep(1)\n hardware.set_lights(rails=False)\n sleep(1)\n\n\ndef create_thread(ctx, cancel_token):\n \"\"\"FLASH SETUP.\"\"\"\n t1 = threading.Thread(target=turn_on_blinking_notification,\n args=(ctx._hw_manager.hardware, cancel_token))\n t1.start()\n return t1\n\n\ndef run(ctx: protocol_api.ProtocolContext):\n \"\"\"PROTOCOLS.\"\"\"\n [\n num_samples,\n m300_mount, flash\n ] = get_values( # noqa: F821 (<--- DO NOT REMOVE!)\n \"num_samples\", \"m300_mount\", \"flash\")\n\n 'Global variables'\n TEST_MODE = False\n bead_delay_time = 7\n wash_delay_time = 7\n supernatant_headspeed_modulator = 10\n mag_height = 8\n ctx.max_speeds['Z'] = 125\n ctx.max_speeds['A'] = 125\n # Setup for flashing lights notification to empty trash\n cancellationToken = CancellationToken()\n\n # define all custom variables above here with descriptions:\n num_columns = math.ceil(num_samples/8)\n if m300_mount == 'right':\n m20_mount = 'left'\n else:\n m20_mount = 'right'\n # load modules\n mag_deck = ctx.load_module('magnetic module gen2', '1')\n mag_deck.disengage()\n temp_deck = ctx.load_module('temperature module gen2', '3')\n print(num_columns)\n\n # load labware\n mag_plate = mag_deck.load_labware('thermofisher_96_wellplate_200ul') # changed from thermofisher_96_wellplate_200ul\n temp_plate = temp_deck.load_labware('opentrons_96_aluminumblock_generic_'\n 'pcr_strip_200ul')\n dwp = ctx.load_labware('nest_96_wellplate_2ml_deep', '4')\n final_plate = ctx.load_labware('thermofisher_96_wellplate_200ul', '2') # changed from thermofisher_96_wellplate_200ul\n trash = ctx.load_labware('nest_1_reservoir_195ml', '9').wells()[0].top()\n # load tipracks\n\n tips300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)\n for slot in ['7', '10']]\n tips20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', slot)\n for slot in ['11']]\n # load instrument\n\n m300 = ctx.load_instrument(\n 'p300_multi_gen2', m300_mount, tip_racks=tips300)\n\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=tips20)\n\n # pipette functions # INCLUDE ANY BINDING TO CLASS\n\n def pick_up(pip):\n try:\n pip.pick_up_tip()\n except protocol_api.labware.OutOfTipsError:\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n pip.home()\n ctx.pause('\\n\\n~~~~~~~~~~~~~~PLEASE REPLACE TIPRACKS~~~~~~~~~~~~~~~\\n') # noqa: E501\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n pip.reset_tipracks()\n pick_up(pip)\n\n tips_dropped = 0\n\n def drop_tip(pip, home=True):\n nonlocal tips_dropped\n pip.drop_tip(home_after=home)\n if pip == m300:\n tips_dropped += 8\n else:\n tips_dropped += 1\n if tips_dropped == 288:\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n pip.home()\n ctx.pause('\\n\\n~~~~~~~~~~~~~~PLEASE EMPTY TRASH~~~~~~~~~~~~~~~\\n')\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n tips_dropped = 0\n\n def bead_mixing(well, pip, mvol, side_disp=0, mix_reps=10):\n \"\"\"bead_mixing.\"\"\"\n \"\"\"\n 'bead_mixing' will mix liquid that contains beads. This will be done by\n aspirating from the middle of the well & dispensing from the bottom to\n mix the beads with the other liquids as much as possible. Aspiration &\n dispensing will also be reversed to ensure proper mixing.\n param well: The current well that the mixing will occur in.\n param pip: The pipet that is currently attached/ being used.\n param mvol: The volume that is transferred before the mixing steps.\n param reps: The number of mix repetitions that should occur. Note~\n During each mix rep, there are 2 cycles of aspirating from bottom,\n dispensing at the top and 2 cycles of aspirating from middle,\n dispensing at the bottom\n \"\"\"\n\n ctx.comment('MIXING\\n')\n vol = mvol * .8\n\n pip.move_to(well.center())\n for _ in range(mix_reps):\n pip.aspirate(vol, dest.bottom().move(types.Point(x=-side_disp,\n y=0, z=3)), rate=2)\n pip.dispense(vol, dest.bottom().move(types.Point(x=-side_disp,\n y=0, z=5)), rate=2)\n\n def remove_supernatant(vol):\n for i, dest in enumerate(samples):\n side = -1 if i % 2 == 0 else 1\n pick_up(m300)\n m300.move_to(dest.top())\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(vol-20, dest.bottom().move(types.Point(x=side, y=0, z=1)),\n rate=0.1)\n ctx.delay(seconds=1)\n m300.move_to(dest.top())\n m300.aspirate(10, dest.top())\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(m300.current_volume, trash)\n m300.blow_out()\n m300.air_gap(50)\n drop_tip(m300)\n\n pick_up(m20)\n m20.move_to(dest.top())\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m20.aspirate(19, dest.bottom().move(types.Point(x=side, y=0, z=1)),\n rate=0.1)\n ctx.delay(seconds=1)\n m20.move_to(dest.top())\n m20.aspirate(1, dest.top())\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m20.dispense(m20.current_volume, trash)\n m20.blow_out()\n m20.aspirate(10, trash)\n drop_tip(m20)\n ctx.comment('\\n')\n\n def wash_beads(vol, source, dest, side_disp, mix_reps=15):\n pick_up(m300)\n m300.aspirate(vol, source)\n m300.dispense(vol, dest.bottom().move(types.Point(x=-side_disp, y=0, z=5)), rate=2)\n # bead_mixing(dest, m300, vol, reps=6)\n for _ in range(mix_reps):\n m300.aspirate(vol, dest.bottom().move(types.Point(x=-side_disp, y=0, z=3)), rate=2)\n m300.dispense(vol, dest.bottom().move(types.Point(x=-side_disp, y=0, z=5)), rate=2)\n drop_tip(m300)\n\n # reagents\n\n samples = mag_plate.rows()[0][:num_columns]\n beads = temp_plate.rows()[0][:math.ceil(num_columns/2)]*12\n wash_1 = dwp.rows()[0][0]\n wash_2 = dwp.rows()[0][2]\n tris = dwp.rows()[0][6]\n wash_3 = dwp.rows()[0][4]\n strand_primer_mix = temp_plate.rows()[0][-1]\n rna_wash = temp_plate.rows()[0][6:6+math.ceil(num_columns/3)]*12\n final_dest = final_plate.rows()[0][:num_columns]\n\n # protocol\n ctx.comment('\\n~~~~~~~~~~~~~~ADDING BEADS~~~~~~~~~~~~~~\\n')\n for i, (dest, bead_col) in enumerate(zip(samples, beads)):\n pick_up(m300)\n if i < math.ceil(num_columns/2):\n m300.mix(5, 65, bead_col)\n m300.aspirate(50, bead_col, rate=0.5)\n ctx.delay(seconds=1.5)\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.move_to(bead_col.top())\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(50, dest, rate=0.5)\n m300.mix(5, 80, dest)\n # bead_mixing(dest, m300, 100, reps=5)\n drop_tip(m300)\n\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n m300.home()\n ctx.pause(\"\"\"\n MOVE PLATE IN SLOT 1 TO OFF-DECK THERMOCYCLER\n REFER TO 1.2.12 FOR SPECIFIC HEATING/COOLING CYCLE\n RETURN PLATE TO SLOT 1 WHEN FINISHED. ENSURE SAMPLE PLATE IS\n FLAT AND SECURE WHEN RETURNING TO MAGNETIC MODULE!\n \"\"\")\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n\n ctx.comment('\\n~~~~~~~~~~~~~~MIXING~~~~~~~~~~~~~~\\n')\n for dest in samples:\n pick_up(m300)\n m300.mix(6, 80, dest)\n # bead_mixing(dest, m300, 100, reps=6)\n drop_tip(m300)\n if TEST_MODE:\n ctx.delay(seconds=5)\n else:\n ctx.delay(minutes=5)\n\n ctx.comment('\\n~~~~~~~~~~~~~~ENGAGING MAGNET~~~~~~~~~~~~~~\\n')\n mag_deck.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(minutes=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n ctx.comment('\\n~~~~~~~~~~~~~~REMOVING SUPERNATANT~~~~~~~~~~~~~~\\n')\n remove_supernatant(95)\n\n mag_deck.disengage()\n\n ctx.comment('\\n~~~~~~~~~~~~~WASHING BEADS TWICE WITH BUFFER~~~~~~~~~~~~\\n')\n for wash in [wash_1, wash_2]:\n for i, dest in enumerate(samples):\n side = -1 if i % 2 == 0 else 1\n wash_beads(180, wash, dest, side)\n\n mag_deck.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(minutes=wash_delay_time)\n else:\n ctx.delay(minutes=wash_delay_time)\n\n ctx.comment('\\n~~~~~~~~~~~~~~REMOVING SUPERNATANT~~~~~~~~~~~~~~\\n')\n remove_supernatant(190)\n\n mag_deck.disengage()\n\n ctx.comment('\\n~~~~~~~~~~~~~ADDING TRIS BUFFER~~~~~~~~~~~~\\n')\n for dest in samples:\n pick_up(m300)\n m300.aspirate(50, tris)\n m300.dispense(50, dest)\n m300.mix(6, 40, dest)\n # bead_mixing(dest, m300, 50, reps=6)\n drop_tip(m300)\n\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n m300.home()\n ctx.pause(\"\"\"\\n\\nMOVE PLATE IN SLOT 1 TO OFF-DECK THERMOCYCLER\n REFER TO 1.2.24 FOR SPECIFIC HEATING/COOLING CYCLE\n RETURN PLATE TO SLOT 1 WHEN FINISHED. ENSURE SAMPLE PLATE IS\n FLAT AND SECURE WHEN RETURNING TO MAGNETIC MODULE!\"\"\")\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n\n ctx.comment('\\n~~~~~~~~~~~~~ADDING BINDING BUFFER~~~~~~~~~~~~\\n')\n for i, (source, dest) in enumerate(zip(rna_wash, samples)):\n side = -1 if i % 2 == 0 else 1\n pick_up(m300)\n m300.aspirate(50, source)\n m300.dispense(50, dest)\n # m300.mix(6, 80, dest)\n bead_mixing(dest, m300, 100, side, mix_reps=15)\n drop_tip(m300)\n\n ctx.comment('\\n~~~~~~~~~~~~~INCUBATING 5 MINUTES~~~~~~~~~~~~\\n')\n if TEST_MODE:\n ctx.delay(seconds=5)\n else:\n ctx.delay(minutes=5)\n\n ctx.comment('\\n~~~~~~~~~~~~~ENGAGING MAGNETIC MODULE~~~~~~~~~~~~\\n')\n mag_deck.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(minutes=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n ctx.comment('\\n~~~~~~~~~~~~~REMOVING SUPERNATANT~~~~~~~~~~~~\\n')\n remove_supernatant(150)\n mag_deck.disengage()\n ctx.comment('\\n~~~~~~~~~~~~~WASHING BEADS WITH BUFFER~~~~~~~~~~~~\\n')\n for i, dest in enumerate(samples):\n side = -1 if i % 2 == 0 else 1\n wash_beads(180, wash_3, dest, side)\n\n mag_deck.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(minutes=wash_delay_time)\n else:\n ctx.delay(minutes=wash_delay_time)\n\n ctx.comment('\\n~~~~~~~~~~~~~REMOVING SUPERNATANT~~~~~~~~~~~~\\n')\n remove_supernatant(190)\n mag_deck.disengage()\n\n ctx.comment('\\n~~~~~~~~~~~~~ADDING MASTER MIX ELUTION~~~~~~~~~~~~\\n')\n for i, dest in enumerate(samples):\n side = -1 if i % 2 == 0 else 1\n pick_up(m20)\n m20.aspirate(11.5, strand_primer_mix)\n m20.dispense(11.5, dest.bottom().move(types.Point(x=-side, y=0, z=3)))\n bead_mixing(dest, m20, 11, side)\n drop_tip(m20)\n\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n m300.home()\n ctx.pause(\"\"\"\\n\\nMOVE PLATE IN SLOT 1 TO OFF-DECK THERMOCYCLER\n REFER TO 1.2.37 FOR SPECIFIC HEATING/COOLING CYCLE\n SPIN PLATE DOWN BEFORE RETURNING TO DECK\n RETURN PLATE TO SLOT 1 WHEN FINISHED. ENSURE SAMPLE PLATE IS\n FLAT AND SECURE WHEN RETURNING TO MAGNETIC MODULE!\"\"\")\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n\n ctx.comment('\\n~~~~~~~~~~~~~SEPARATING RNA SOLUTION~~~~~~~~~~~~\\n')\n mag_deck.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(minutes=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n ctx.comment('\\n~~~~~~~~~~~~~MOVING RNA TO NEW PLATE~~~~~~~~~~~~\\n')\n for s, d in zip(samples, final_dest):\n pick_up(m20)\n m20.aspirate(10, s)\n m20.dispense(10, d)\n drop_tip(m20)\n\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n m300.home()\n ctx.pause('\\n\\n~~~~~~~~~~~~~~PROTOCOL COMPLETE~~~~~~~~~~~~~~~\\n')\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n\n for c in ctx.commands():\n print(c)\n", "custom_labware_defs": [ { "brand": { diff --git a/protoBuilds/010526/010526.ot2.apiv2.py.json b/protoBuilds/010526/010526.ot2.apiv2.py.json index b1544c4c5..9552b92db 100644 --- a/protoBuilds/010526/010526.ot2.apiv2.py.json +++ b/protoBuilds/010526/010526.ot2.apiv2.py.json @@ -859,5 +859,18 @@ "description": "Custom Protocol Request", "protocolName": "Restriction Digests" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw Opentrons 24 Well Aluminum Block with Variant Tubes on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/04eeb1-part-2/04eeb1-part-2.ot2.apiv2.py.json b/protoBuilds/04eeb1-part-2/04eeb1-part-2.ot2.apiv2.py.json index 2cd45e381..887f95e5c 100644 --- a/protoBuilds/04eeb1-part-2/04eeb1-part-2.ot2.apiv2.py.json +++ b/protoBuilds/04eeb1-part-2/04eeb1-part-2.ot2.apiv2.py.json @@ -105,5 +105,12 @@ "description": "Custom Protocol Request", "protocolName": "Illumina COVIDSeq Test: Synthesize First Strand cDNA" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw Master Mix Reservoir on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/04eeb1-part-3/04eeb1-part-3.ot2.apiv2.py.json b/protoBuilds/04eeb1-part-3/04eeb1-part-3.ot2.apiv2.py.json index 756fea7fd..584f617a0 100644 --- a/protoBuilds/04eeb1-part-3/04eeb1-part-3.ot2.apiv2.py.json +++ b/protoBuilds/04eeb1-part-3/04eeb1-part-3.ot2.apiv2.py.json @@ -190,5 +190,12 @@ "description": "Custom Protocol Request", "protocolName": "Illumina COVIDSeq Test: Amplify cDNA" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw Master Mix Reservoir on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/04eeb1-part-4/04eeb1-part-4.ot2.apiv2.py.json b/protoBuilds/04eeb1-part-4/04eeb1-part-4.ot2.apiv2.py.json index f1e47d16e..365fb74ec 100644 --- a/protoBuilds/04eeb1-part-4/04eeb1-part-4.ot2.apiv2.py.json +++ b/protoBuilds/04eeb1-part-4/04eeb1-part-4.ot2.apiv2.py.json @@ -135,5 +135,12 @@ "description": "Custom Protocol Request", "protocolName": "Illumina COVIDSeq Test: Tagment PCR Amplicons" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw Master Mix Reservoir on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/04eeb1-part-5/04eeb1-part-5.ot2.apiv2.py.json b/protoBuilds/04eeb1-part-5/04eeb1-part-5.ot2.apiv2.py.json index 42b70c96b..7c892ab66 100644 --- a/protoBuilds/04eeb1-part-5/04eeb1-part-5.ot2.apiv2.py.json +++ b/protoBuilds/04eeb1-part-5/04eeb1-part-5.ot2.apiv2.py.json @@ -123,5 +123,18 @@ "description": "Custom Protocol Request", "protocolName": "Illumina COVIDSeq Test: Post Tagmentation Clean Up" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw Master Mix Reservoir on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 3 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/04eeb1-part-6/04eeb1-part-6.ot2.apiv2.py.json b/protoBuilds/04eeb1-part-6/04eeb1-part-6.ot2.apiv2.py.json index da598773d..9354612ea 100644 --- a/protoBuilds/04eeb1-part-6/04eeb1-part-6.ot2.apiv2.py.json +++ b/protoBuilds/04eeb1-part-6/04eeb1-part-6.ot2.apiv2.py.json @@ -123,5 +123,18 @@ "description": "Custom Protocol Request", "protocolName": "Illumina COVIDSeq Test: Amplify Tagmented Amplicons" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw Master Mix Reservoir on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 3 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/04eeb1-part-7/04eeb1-part-7.ot2.apiv2.py.json b/protoBuilds/04eeb1-part-7/04eeb1-part-7.ot2.apiv2.py.json index 5b4b72c9d..c9c4626d5 100644 --- a/protoBuilds/04eeb1-part-7/04eeb1-part-7.ot2.apiv2.py.json +++ b/protoBuilds/04eeb1-part-7/04eeb1-part-7.ot2.apiv2.py.json @@ -87,5 +87,12 @@ "description": "Custom Protocol Request", "protocolName": "Illumina COVIDSeq Test: Pool and Clean Up Libraries" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 3 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/04eeb1/04eeb1.ot2.apiv2.py.json b/protoBuilds/04eeb1/04eeb1.ot2.apiv2.py.json index 0ccaacd37..3681ac236 100644 --- a/protoBuilds/04eeb1/04eeb1.ot2.apiv2.py.json +++ b/protoBuilds/04eeb1/04eeb1.ot2.apiv2.py.json @@ -99,5 +99,12 @@ "description": "Custom Protocol Request", "protocolName": "Illumina COVIDSeq Test: Anneal RNA" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw Master Mix Reservoir on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/0556be-covid-mm-qc-v3/0556be-covid-mm-qc-v3.ot2.apiv2.py.json b/protoBuilds/0556be-covid-mm-qc-v3/0556be-covid-mm-qc-v3.ot2.apiv2.py.json index 4e0fb060d..7bbbc054d 100644 --- a/protoBuilds/0556be-covid-mm-qc-v3/0556be-covid-mm-qc-v3.ot2.apiv2.py.json +++ b/protoBuilds/0556be-covid-mm-qc-v3/0556be-covid-mm-qc-v3.ot2.apiv2.py.json @@ -74,5 +74,12 @@ "description": "Custom Protocol Request", "protocolName": "COVID MM-QC-v3 Protocol" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 10 lw Opentrons 24 Well Aluminum Block with Generic 2 mL Screwcap on Temperature Module GEN2 on 10", + "share": false, + "slot": "10", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/0556be-covid-mm-qc/0556be-covid-mm-qc.ot2.apiv2.py.json b/protoBuilds/0556be-covid-mm-qc/0556be-covid-mm-qc.ot2.apiv2.py.json index de15d3b85..8991828e8 100644 --- a/protoBuilds/0556be-covid-mm-qc/0556be-covid-mm-qc.ot2.apiv2.py.json +++ b/protoBuilds/0556be-covid-mm-qc/0556be-covid-mm-qc.ot2.apiv2.py.json @@ -147,5 +147,12 @@ "description": "Custom Protocol Request", "protocolName": "COVID MM-QC Protocol" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 10 lw Opentrons 24 Well Aluminum Block with Generic 2 mL Screwcap on Temperature Module GEN2 on 10", + "share": false, + "slot": "10", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/060c4f/060c4f.ot2.apiv2.py.json b/protoBuilds/060c4f/060c4f.ot2.apiv2.py.json index eee21ce4d..5e8c6a91b 100644 --- a/protoBuilds/060c4f/060c4f.ot2.apiv2.py.json +++ b/protoBuilds/060c4f/060c4f.ot2.apiv2.py.json @@ -4773,5 +4773,12 @@ "protocolName": "96-well to 384-well transfer", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 4 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN1 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/08878b/08878b.ot2.apiv2.py.json b/protoBuilds/08878b/08878b.ot2.apiv2.py.json index be7692207..18cd77c9c 100644 --- a/protoBuilds/08878b/08878b.ot2.apiv2.py.json +++ b/protoBuilds/08878b/08878b.ot2.apiv2.py.json @@ -51,7 +51,7 @@ ], "labware": [ { - "name": "Bio-Rad 96 Well Plate 200 \u00b5L PCR on Temperature Module GEN1 on 4", + "name": "Bio-Rad 96 Well Plate 200 \u00b5L PCR on Temperature Module on 4", "share": false, "slot": "4", "type": "biorad_96_wellplate_200ul_pcr" @@ -99,5 +99,12 @@ "protocolName": "Transfer with Temperature Module", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module on 4 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Temperature Module on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/0944e4/ngs_cleanup.ot2.apiv2.py.json b/protoBuilds/0944e4/ngs_cleanup.ot2.apiv2.py.json index 5dfd7e4ca..3694a329a 100644 --- a/protoBuilds/0944e4/ngs_cleanup.ot2.apiv2.py.json +++ b/protoBuilds/0944e4/ngs_cleanup.ot2.apiv2.py.json @@ -1297,5 +1297,12 @@ "protocolName": "NGS Library Cleanup with Ampure XP Beads", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw magnetic plate on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/0a23c6/0a23c6.ot2.apiv2.py.json b/protoBuilds/0a23c6/0a23c6.ot2.apiv2.py.json index 846574120..0b66fbb77 100644 --- a/protoBuilds/0a23c6/0a23c6.ot2.apiv2.py.json +++ b/protoBuilds/0a23c6/0a23c6.ot2.apiv2.py.json @@ -81,5 +81,12 @@ "protocolName": "", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 9 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN2 on 9", + "share": false, + "slot": "9", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/0bf4f4-pt2/0bf4f4-pt2.ot2.apiv2.py.json b/protoBuilds/0bf4f4-pt2/0bf4f4-pt2.ot2.apiv2.py.json index 21d79a3e2..d9f76e474 100644 --- a/protoBuilds/0bf4f4-pt2/0bf4f4-pt2.ot2.apiv2.py.json +++ b/protoBuilds/0bf4f4-pt2/0bf4f4-pt2.ot2.apiv2.py.json @@ -1328,5 +1328,12 @@ "protocolName": "Ilumina DNA Prep Part 2 - Post Tagmentation Cleanup", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/0bf4f4-pt3/0bf4f4-pt3.ot2.apiv2.py.json b/protoBuilds/0bf4f4-pt3/0bf4f4-pt3.ot2.apiv2.py.json index aa24eb981..288259152 100644 --- a/protoBuilds/0bf4f4-pt3/0bf4f4-pt3.ot2.apiv2.py.json +++ b/protoBuilds/0bf4f4-pt3/0bf4f4-pt3.ot2.apiv2.py.json @@ -214,5 +214,12 @@ "protocolName": "Ilumina DNA Prep Part 3 - Clean up Libraries", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/0e8e3/0e8e3.ot2.apiv2.py.json b/protoBuilds/0e8e3/0e8e3.ot2.apiv2.py.json index 5a625e039..256e7499f 100644 --- a/protoBuilds/0e8e3/0e8e3.ot2.apiv2.py.json +++ b/protoBuilds/0e8e3/0e8e3.ot2.apiv2.py.json @@ -2457,5 +2457,12 @@ "protocolName": "PCR Prep", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 10 lw Plate B (DNAse Dilution Plate) on Temperature Module GEN2 on 10", + "share": false, + "slot": "10", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/0f4405/extraction.ot2.apiv2.py.json b/protoBuilds/0f4405/extraction.ot2.apiv2.py.json deleted file mode 100644 index f2a4ee89d..000000000 --- a/protoBuilds/0f4405/extraction.ot2.apiv2.py.json +++ /dev/null @@ -1,2406 +0,0 @@ -{ - "content": "from opentrons.types import Point\nimport json\nimport os\nimport math\n\nmetadata = {\n 'protocolName': 'NEB NExt Ultra II Illumina Library Prep',\n 'author': 'Opentrons ',\n 'apiLevel': '2.11'\n}\n\n\n# Start protocol\ndef run(ctx):\n\n [num_samples, _ratio_beads_dna, time_mag_incubation,\n mount_m300, mount_m20] = get_values( # noqa: F821\n 'num_samples', '_ratio_beads_dna', 'time_mag_incubation', 'mount_m300',\n 'mount_m20')\n park_tips = True\n tip_track = False\n mag_height = 11\n x_offset = 2.0\n z_offset_beads = 2.0\n z_offset_supernatant = 1.0\n\n \"\"\"\n Here is where you can change the locations of your labware and modules\n (note that this is the recommended configuration)\n \"\"\"\n magdeck = ctx.load_module('magnetic module gen2', '1')\n magdeck.disengage()\n mag_plate = magdeck.load_labware('eppendorftwin.tec_96_wellplate_150ul')\n tips20 = [\n ctx.load_labware('opentrons_96_filtertiprack_20ul', slot)\n for slot in ['2', '4', '5']]\n tempdeck = ctx.load_module('Temperature Module Gen2', '3')\n tempdeck.set_temperature(4)\n elution_plate = tempdeck.load_labware(\n 'eppendorftwin.tec_96_aluminumblock_150ul')\n tc = ctx.load_module('thermocycler')\n tc.open_lid()\n tc.set_block_temperature(20)\n tc.set_lid_temperature(105)\n tc_plate = tc.load_labware('eppendorftwin.tec_96_wellplate_150ul',\n 'DNA plate')\n tips300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)\n for slot in ['6']]\n reservoir = ctx.load_labware('nest_96_wellplate_2ml_deep', '9',\n 'reagent reservoir')\n\n num_cols = math.ceil(num_samples/8)\n if park_tips:\n parking_spots300 = tips300[0].rows()[0][:num_cols]\n parking_spots20 = tips20[0].rows()[0][:num_cols]\n else:\n parking_spots300 = [None for none in range(12)]\n parking_spots20 = [None for none in range(12)]\n\n # load pipette\n m300 = ctx.load_instrument(\n 'p300_multi_gen2', mount_m300, tip_racks=tips300)\n m20 = ctx.load_instrument(\n 'p20_multi_gen2', mount_m20, tip_racks=tips20)\n\n tip_log = {val: {} for val in ctx.loaded_instruments.values()}\n\n \"\"\"\n Here is where you can define the locations of your reagents.\n \"\"\"\n mastermix = reservoir.rows()[0][0]\n adaptor = reservoir.rows()[0][1]\n mastermix2 = reservoir.rows()[0][2]\n user = reservoir.rows()[0][3]\n etoh = reservoir.rows()[0][4]\n elution_buffer = reservoir.rows()[0][5]\n waste = reservoir.rows()[0][-1]\n\n mag_samples_m = mag_plate.rows()[0][:num_cols]\n elution_samples_m = elution_plate.rows()[0][:num_cols]\n tc_samples_m = tc_plate.rows()[0][:num_cols]\n\n magdeck.disengage() # just in case\n tempdeck.set_temperature(4)\n\n m300.flow_rate.aspirate = 50\n m300.flow_rate.dispense = 150\n m300.flow_rate.blow_out = 300\n\n folder_path = '/data/B'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n data = json.load(json_file)\n for pip in tip_log:\n if pip.name in data:\n tip_log[pip]['count'] = data[pip.name]\n else:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n\n for pip in tip_log:\n if pip.type == 'multi':\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.rows()[0]]\n else:\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.wells()]\n tip_log[pip]['max'] = len(tip_log[pip]['tips'])\n\n def _pick_up(pip, loc=None):\n if tip_log[pip]['count'] == tip_log[pip]['max'] and not loc:\n ctx.pause('Replace ' + str(pip.max_volume) + '\u00b5l tipracks before \\\nresuming.')\n pip.reset_tipracks()\n tip_log[pip]['count'] = 0\n if loc:\n pip.pick_up_tip(loc)\n else:\n pip.pick_up_tip(tip_log[pip]['tips'][tip_log[pip]['count']])\n tip_log[pip]['count'] += 1\n\n switch = True\n drop_count = 0\n # number of tips trash will accommodate before prompting user to empty\n drop_threshold = 120\n\n def _drop(pip, loc=None):\n nonlocal switch\n nonlocal drop_count\n if loc:\n pip.drop_tip(loc)\n else:\n side = 30 if switch else -18\n drop_loc = ctx.loaded_labwares[12].wells()[0].top().move(\n Point(x=side))\n pip.drop_tip(drop_loc)\n switch = not switch\n if pip.type == 'multi':\n drop_count += 8\n else:\n drop_count += 1\n if drop_count == drop_threshold:\n ctx.pause('Please empty tips from waste before \\\n resuming.')\n drop_count = 0\n\n def remove_supernatant(vol, pip=m300, park=False):\n pip.flow_rate.aspirate /= 5\n parking_spots = parking_spots300 if pip == m300 else parking_spots20\n for i, (m, p) in enumerate(zip(mag_samples_m, parking_spots)):\n if park:\n _pick_up(pip, p)\n else:\n _pick_up(pip)\n side = -1 if i % 2 == 0 else 1\n loc = m.bottom(0).move(Point(x=side, z=z_offset_supernatant))\n pip.move_to(m.center())\n pip.transfer(vol, loc, waste, new_tip='never',\n air_gap=pip.min_volume)\n pip.blow_out(waste)\n pip.air_gap(pip.min_volume)\n _drop(pip)\n pip.flow_rate.aspirate *= 5\n\n \"\"\" 1. NEBNext End Prep \"\"\"\n for t in tc_samples_m:\n _pick_up(m20)\n m20.transfer(10, mastermix, t, mix_after=(10, 20), new_tip='never')\n _drop(m20)\n\n profile = [\n {'temperature': 20, 'hold_time_minutes': 30},\n {'temperature': 65, 'hold_time_minutes': 30}]\n tc.close_lid()\n tc.execute_profile(steps=profile, repetitions=1, block_max_volume=60)\n tc.set_block_temperature(4)\n tc.open_lid()\n\n \"\"\" 2. Adapter Ligation \"\"\"\n for t in tc_samples_m:\n _pick_up(m20)\n m20.transfer(2.5, adaptor, t, mix_after=(10, 20), new_tip='never')\n _drop(m20)\n\n for t in tc_samples_m:\n _pick_up(m300)\n m300.transfer(31, mastermix2, t, mix_after=(10, 50), new_tip='never')\n _drop(m300)\n\n tc.close_lid()\n tc.set_block_temperature(20, hold_time_minutes=15)\n tc.open_lid()\n\n for t in tc_samples_m:\n _pick_up(m20)\n m20.transfer(3, user, t, mix_after=(10, 20), new_tip='never')\n _drop(m20)\n\n tc.close_lid()\n tc.set_block_temperature(37, hold_time_minutes=15)\n tc.set_block_temperature(4)\n tc.open_lid()\n\n \"\"\" 3. Clean Up \"\"\"\n dna_vol_total = 96.5\n elution_vol_total = 17\n num_washes = math.ceil(_ratio_beads_dna/0.9)\n dna_vol_wash = dna_vol_total/num_washes\n elution_vol_wash = elution_vol_total/num_washes\n elution_vol_final = 15/num_washes\n\n for wash_ind in range(num_washes):\n # add sample\n for t, m, p in zip(tc_samples_m, mag_samples_m, parking_spots300):\n if wash_ind == 0:\n _pick_up(m300)\n else:\n _pick_up(m300, p)\n m300.transfer(dna_vol_wash, t, m, mix_after=(10, 50),\n new_tip='never')\n _drop(m300, p)\n ctx.delay(minutes=time_mag_incubation, msg=f'Incubating off magnet for \\\n{time_mag_incubation} minutes.')\n magdeck.engage(height=mag_height)\n ctx.delay(minutes=time_mag_incubation, msg=f'Incubating on magnet for \\\n{time_mag_incubation} minutes.')\n remove_supernatant(200, pip=m300, park=True)\n\n # wash 2x\n for _ in range(2):\n _pick_up(m300)\n for i, m in enumerate(mag_samples_m):\n m300.aspirate(200, etoh)\n m300.dispense(200, m.top())\n ctx.delay(seconds=30, msg='Incubating on magnet for 30 seconds.')\n m300.drop_tip()\n remove_supernatant(200, pip=m300, park=True)\n\n # remove residual\n remove_supernatant(20, pip=m20, park=False)\n\n # air dry\n ctx.delay(minutes=5, msg='Air drying for 5 minutes.')\n magdeck.disengage()\n\n # elute\n for i, m in enumerate(mag_samples_m):\n _pick_up(m20)\n side = 1 if i % 2 == 0 else -1\n loc = m.bottom().move(Point(x=x_offset*side, z=z_offset_beads))\n m20.aspirate(elution_vol_wash, elution_buffer)\n m20.move_to(m.center())\n m20.dispense(elution_vol_wash, loc)\n for _ in range(10): # custom mix\n m20.aspirate(20, m.bottom(1))\n m20.dispense(20, loc)\n _drop(m20)\n\n ctx.delay(minutes=time_mag_incubation, msg=f'Incubating off magnet for \\\n{time_mag_incubation} minutes.')\n magdeck.engage(height=mag_height)\n ctx.delay(minutes=time_mag_incubation, msg=f'Incubating on magnet for \\\n{time_mag_incubation} minutes.')\n\n # elute\n for m, e in zip(mag_samples_m, elution_samples_m):\n _pick_up(m20)\n m20.flow_rate.aspirate /= 5\n m20.transfer(elution_vol_final, m.bottom(0.5), e, new_tip='never')\n m20.flow_rate.aspirate *= 5\n m20.mix(10, 20, e)\n _drop(m20)\n\n magdeck.disengage()\n tc.deactivate_lid()\n tc.deactivate_block()\n\n # track final used tip\n if not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n data = {pip.name: tip_log[pip]['count'] for pip in tip_log}\n with open(tip_file_path, 'w') as outfile:\n json.dump(data, outfile)\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "Eppendorf twin.tec", - "brandId": [] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.75, - "yDimension": 85.5, - "zDimension": 21.2 - }, - "groups": [ - { - "metadata": { - "displayCategory": "wellPlate", - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8", - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9", - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10", - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11", - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - } - ], - "metadata": { - "displayCategory": "aluminumBlock", - "displayName": "Eppendorf Twin.tec 96 Aluminum Block 150 \u00b5L", - "displayVolumeUnits": "\u00b5L", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1" - ], - [ - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - 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{ - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p300_multi_gen2" - }, - { - "mount": "right", - "name": "p20_multi_gen2" - } - ], - "labware": [ - { - "name": "Eppendorf Twin.tec 96 Well Plate 150 \u00b5L on Magnetic Module GEN2 on 1", - "share": false, - "slot": "1", - "type": "eppendorftwin.tec_96_wellplate_150ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 2", - "share": false, - "slot": "2", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Eppendorf Twin.tec 96 Aluminum Block 150 \u00b5L on Temperature Module GEN2 on 3", - "share": false, - "slot": "3", - "type": "eppendorftwin.tec_96_aluminumblock_150ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 4", - "share": false, - "slot": "4", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "DNA plate on Thermocycler Module on 7", - "share": false, - "slot": "7", - "type": "eppendorftwin.tec_96_wellplate_150ul" - }, - { - "name": "reagent reservoir on 9", - "share": false, - "slot": "9", - "type": "nest_96_wellplate_2ml_deep" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Opentrons ", - "protocolName": "NEB NExt Ultra II Illumina Library Prep" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/10bf60-station-B/extraction.ot2.apiv2.py.json b/protoBuilds/10bf60-station-B/extraction.ot2.apiv2.py.json index 6bddc035b..02395cf66 100644 --- a/protoBuilds/10bf60-station-B/extraction.ot2.apiv2.py.json +++ b/protoBuilds/10bf60-station-B/extraction.ot2.apiv2.py.json @@ -196,5 +196,18 @@ "author": "Opentrons ", "protocolName": "COVID-19 Station B RNA Extraction" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw deepwell plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw elution strips on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/10bf60-station-C/generic_station_C.ot2.apiv2.py.json b/protoBuilds/10bf60-station-C/generic_station_C.ot2.apiv2.py.json index 3ead02655..68fb43b7e 100644 --- a/protoBuilds/10bf60-station-C/generic_station_C.ot2.apiv2.py.json +++ b/protoBuilds/10bf60-station-C/generic_station_C.ot2.apiv2.py.json @@ -1234,5 +1234,12 @@ "protocolName": "Covid-19 qPCR Setup Protocol", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 7 lw mastermix (tube A1) on Temperature Module GEN2 on 7", + "share": false, + "slot": "7", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/111210-part-10/111210-part-10.ot2.apiv2.py.json b/protoBuilds/111210-part-10/111210-part-10.ot2.apiv2.py.json index a9e805098..712d08f5d 100644 --- a/protoBuilds/111210-part-10/111210-part-10.ot2.apiv2.py.json +++ b/protoBuilds/111210-part-10/111210-part-10.ot2.apiv2.py.json @@ -111,5 +111,24 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung RNA Fusion UMI Panel Kit:\n Cleanup of Universal PCR with QIAseq Beads" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Screwcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/111210-part-2/111210-part-2.ot2.apiv2.py.json b/protoBuilds/111210-part-2/111210-part-2.ot2.apiv2.py.json index 0be049afb..84b5901c6 100644 --- a/protoBuilds/111210-part-2/111210-part-2.ot2.apiv2.py.json +++ b/protoBuilds/111210-part-2/111210-part-2.ot2.apiv2.py.json @@ -68,5 +68,18 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung RNA Fusion UMI Panel Kit:\n Reverse Transcription" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/111210-part-3/111210-part-3.ot2.apiv2.py.json b/protoBuilds/111210-part-3/111210-part-3.ot2.apiv2.py.json index 372fe92cc..1792ac098 100644 --- a/protoBuilds/111210-part-3/111210-part-3.ot2.apiv2.py.json +++ b/protoBuilds/111210-part-3/111210-part-3.ot2.apiv2.py.json @@ -68,5 +68,18 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung RNA Fusion UMI Panel Kit:\n Second strand synthesis" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/111210-part-4/111210-part-4.ot2.apiv2.py.json b/protoBuilds/111210-part-4/111210-part-4.ot2.apiv2.py.json index 2a2419f02..21907a76e 100644 --- a/protoBuilds/111210-part-4/111210-part-4.ot2.apiv2.py.json +++ b/protoBuilds/111210-part-4/111210-part-4.ot2.apiv2.py.json @@ -93,5 +93,18 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung RNA Fusion UMI Panel Kit:\n End repair / dA tailing" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/111210-part-5/111210-part-5.ot2.apiv2.py.json b/protoBuilds/111210-part-5/111210-part-5.ot2.apiv2.py.json index 3098026bf..4016db899 100644 --- a/protoBuilds/111210-part-5/111210-part-5.ot2.apiv2.py.json +++ b/protoBuilds/111210-part-5/111210-part-5.ot2.apiv2.py.json @@ -93,5 +93,18 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung RNA Fusion UMI Panel Kit:\n Adaptor ligation" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw None", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/111210-part-6/111210-part-6.ot2.apiv2.py.json b/protoBuilds/111210-part-6/111210-part-6.ot2.apiv2.py.json index 58b7ecd71..77d440e3c 100644 --- a/protoBuilds/111210-part-6/111210-part-6.ot2.apiv2.py.json +++ b/protoBuilds/111210-part-6/111210-part-6.ot2.apiv2.py.json @@ -117,5 +117,24 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung RNA Fusion UMI Panel Kit:\n Cleanup of Adapter-ligated DNA with QIAseq Beads" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Screwcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/111210-part-7/111210-part-7.ot2.apiv2.py.json b/protoBuilds/111210-part-7/111210-part-7.ot2.apiv2.py.json index cc9e9950e..08ae49f21 100644 --- a/protoBuilds/111210-part-7/111210-part-7.ot2.apiv2.py.json +++ b/protoBuilds/111210-part-7/111210-part-7.ot2.apiv2.py.json @@ -68,5 +68,18 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung RNA Fusion UMI Panel Kit:\n Target Enrichment PCR" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Screwcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/111210-part-8/111210-part-8.ot2.apiv2.py.json b/protoBuilds/111210-part-8/111210-part-8.ot2.apiv2.py.json index 4c35cdd09..d98e67f16 100644 --- a/protoBuilds/111210-part-8/111210-part-8.ot2.apiv2.py.json +++ b/protoBuilds/111210-part-8/111210-part-8.ot2.apiv2.py.json @@ -111,5 +111,24 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung RNA Fusion UMI Panel Kit:\n Cleanup of Target Enrichment PCR with QIAseq Beads" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Screwcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/111210-part-9/111210-part-9.ot2.apiv2.py.json b/protoBuilds/111210-part-9/111210-part-9.ot2.apiv2.py.json index 2a175ba37..829f5cc01 100644 --- a/protoBuilds/111210-part-9/111210-part-9.ot2.apiv2.py.json +++ b/protoBuilds/111210-part-9/111210-part-9.ot2.apiv2.py.json @@ -93,5 +93,18 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung RNA Fusion UMI Panel Kit:\n Universal PCR Amplification" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Screwcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/111210/111210.ot2.apiv2.py.json b/protoBuilds/111210/111210.ot2.apiv2.py.json index 029625ddb..4c85baa34 100644 --- a/protoBuilds/111210/111210.ot2.apiv2.py.json +++ b/protoBuilds/111210/111210.ot2.apiv2.py.json @@ -89,5 +89,18 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung RNA Fusion UMI Panel Kit:\n First strand cDNA synthesis" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/1185d3/1185d3.ot2.apiv2.py.json b/protoBuilds/1185d3/1185d3.ot2.apiv2.py.json index fecb1a8ab..aac7e7a66 100644 --- a/protoBuilds/1185d3/1185d3.ot2.apiv2.py.json +++ b/protoBuilds/1185d3/1185d3.ot2.apiv2.py.json @@ -88,5 +88,12 @@ "protocolName": "MagMAX Viral/Pathogen Nucleic Acid Isolation Kit wash", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw deepwell plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/118e8c/118e8c.ot2.apiv2.py.json b/protoBuilds/118e8c/118e8c.ot2.apiv2.py.json index 073e447b9..190b19e12 100644 --- a/protoBuilds/118e8c/118e8c.ot2.apiv2.py.json +++ b/protoBuilds/118e8c/118e8c.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "from opentrons.protocol_api.labware import Well\nfrom opentrons import types\nimport math\nimport csv\nimport os\n\nmetadata = {\n 'protocolName': 'FluoGene HLA NX 96-Well or 384-Well Setup',\n 'author': 'Steve ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.9'\n}\n\n\ndef run(ctx):\n\n [use_384, p20_blowout_height, disposal_volume, p300_transfer_height,\n dispense_volume, p300_mixing_height,\n p20_tube_height, relative_height, tracking_reset,\n p20_reservoir_height, tip_max, water_volume, fluomix_volume,\n dna_volume, reservoir_fill_volume] = get_values( # noqa: F821\n \"use_384\", \"p20_blowout_height\", \"disposal_volume\",\n \"p300_transfer_height\", \"dispense_volume\", \"p300_mixing_height\",\n \"p20_tube_height\", \"relative_height\", \"tracking_reset\",\n \"p20_reservoir_height\", \"tip_max\", \"water_volume\", \"fluomix_volume\",\n \"dna_volume\", \"reservoir_fill_volume\")\n\n ctx.set_rail_lights(True)\n ctx.delay(seconds=10)\n\n # constant values\n reduced_pick_up_current = 0.15\n touch_radius = 0.75\n touch_v_offset = -3\n touch_speed = 10\n\n # constrain reduced_pick_up_current value to acceptable range\n if reduced_pick_up_current < 0.1 or reduced_pick_up_current > 0.15:\n raise Exception('''Invalid value for reduced_pick_up_current parameter\n (must be between 0.1 and 0.15).''')\n\n \"\"\"\n for reservoir column tracking between protocol runs\n \"\"\"\n # for reservoir column tracking between protocol runs\n # if ctx.is_simulating(): # logic reversed for simulation\n if not ctx.is_simulating():\n file_path = '/data/temporary/columnandtiptracking.csv'\n file_dir = os.path.dirname(file_path)\n # check for file directory\n if not os.path.exists(file_dir):\n os.makedirs(file_dir)\n # check for file; if not there, create initial csv\n if (not os.path.isfile(file_path) or tracking_reset):\n with open(file_path, 'w') as outfile:\n outfile.write(\",\".join([\n \"0\", \"A1 of Opentrons 96 Filter Tip Rack 20 \u00b5L on 10\",\n \"A1 of Opentrons 96 Filter Tip Rack 200 \u00b5L on 11\", \"\\n\"]))\n\n current_data_list = []\n # if not ctx.is_simulating(): # logic reversed for simulation\n if ctx.is_simulating():\n current_data_list = [0,\n \"A1 of Opentrons 96 Filter Tip Rack 20 \u00b5L on 10\",\n \"A1 of Opentrons 96 Filter Tip Rack 200 \u00b5L on 11\"]\n else:\n with open(file_path) as csv_file:\n csv_reader = csv.reader(csv_file, delimiter=',')\n current_data_list = next(csv_reader)\n\n current_col_index = int(current_data_list[0])\n [current_starting_tip_20, current_starting_tip_300] = [\n current_data_list[i] for i in range(1, 3)]\n\n if current_col_index == 0:\n ctx.pause(\"Please place an unused, clean source plate in deck slot 7.\")\n\n # reservoir with column tracking between protocol runs\n reservoir = ctx.load_labware('nunc_96_wellplate_500ul', '7')\n\n # increment column index for future protocol run\n if current_col_index < len(reservoir.columns()) - 1:\n new_col_index = current_col_index + 1\n else:\n new_col_index = 0\n \"\"\"\n protocol steps using tracked reservoir column\n \"\"\"\n # reagent mix in reservoir column tracked across protocol runs\n reservoir_col = reservoir.columns()[current_col_index]\n ctx.set_rail_lights(True)\n\n # tips and p300 multi\n tips300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', '11')]\n tips20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', '10')]\n p300s = ctx.load_instrument('p300_single_gen2', 'left', tip_racks=tips300)\n p20m = ctx.load_instrument('p20_multi_gen2', 'right', tip_racks=tips20)\n\n # trays\n if not use_384:\n trays = [\n ctx.load_labware(labware, slot) for labware, slot in zip(\n ['innotrainot2pcrplate_96_wellplate_200ul',\n 'innotrainot22pcrplate_96_wellplate_200ul'], ['5', '6'])]\n else:\n trays = [ctx.load_labware('custom_384_well_tray', '5')]\n\n # tube rack rxn components: water in A1, pcr mix in A2, DNA dilution in A3\n tube_rack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap', '4')\n [w, p, d] = [\n tube_rack.wells_by_name()[well] for well in ['A1', 'A2', 'A3']]\n\n class WellH(Well):\n def __init__(self, well, min_height=5, comp_coeff=1.15,\n current_volume=0):\n super().__init__(well._impl)\n self.well = well\n self.min_height = min_height\n self.comp_coeff = comp_coeff\n self.current_volume = current_volume\n if self.diameter is not None:\n self.radius = self.diameter/2\n cse = math.pi*(self.radius**2)\n elif self.length is not None:\n cse = self.length*self.width\n self.height = current_volume/cse\n if self.height < min_height:\n self.height = min_height\n elif self.height > well.parent.highest_z:\n raise Exception(\"\"\"Specified liquid volume\n can not exceed the height of the labware.\"\"\")\n\n def height_dec(self, vol):\n if self.diameter is not None:\n cse = math.pi*(self.radius**2)\n elif self.length is not None:\n cse = self.length*self.width\n dh = (vol/cse)*self.comp_coeff\n if self.height - dh > self.min_height:\n self.height = self.height - dh\n else:\n self.height = self.min_height\n if self.current_volume - vol > 0:\n self.current_volume = self.current_volume - vol\n else:\n self.current_volume = 0\n return(self.well.bottom(self.height))\n\n def height_inc(self, vol, top=False):\n if self.diameter is not None:\n cse = math.pi*(self.radius**2)\n elif self.length is not None:\n cse = self.length*self.width\n ih = (vol/cse)*self.comp_coeff\n if self.height < self.min_height:\n self.height = self.min_height\n if self.height + ih < self.depth:\n self.height = self.height + ih\n else:\n self.height = self.depth\n self.current_volume += vol\n if top is False:\n return(self.well.bottom(self.height))\n else:\n return(self.well.top())\n\n # to track liquid height\n water = WellH(w, min_height=1, current_volume=water_volume)\n pcr_mix = WellH(p, min_height=1, current_volume=0.9*fluomix_volume)\n dna_dilution = WellH(d, min_height=1, current_volume=dna_volume)\n\n \"\"\"\n pick_up() function to use only the rear-most channel of the p20 multi\n \"\"\"\n num_channels_per_pickup = 1 # (only pickup tips on rear-most channel)\n tips_ordered = [\n tip for rack in tips20\n for row in rack.rows(\n )[len(rack.rows())-num_channels_per_pickup::-1*num_channels_per_pickup]\n for tip in row]\n\n tip_count = tips_ordered.index(\n tips20[0].wells_by_name()[\n current_starting_tip_20.split()[0].replace('A', 'H')])\n\n def pick_up(pip):\n nonlocal tip_count\n pip.pick_up_tip(tips_ordered[tip_count])\n tip_count += 1\n\n # one-tip transfer water, fluomix to 1st col last well\n p20m.flow_rate.aspirate = 3.8\n p20m.flow_rate.dispense = 3.8\n\n # capture and report original value for p20m pick_up_current\n default_current = ctx._implementation._hw_manager.hardware.\\\n _attached_instruments[p20m._implementation.get_mount()].\\\n config.pick_up_current\n ctx.comment(\"\"\"Tip pick-up current for the p20 multi-channel pipette\n initially configured to {} mAmp.\"\"\".format(str(default_current)))\n\n # temporarily reduce p20m pick_up_current for one-channel tip pickup\n ctx._implementation._hw_manager.hardware._attached_instruments[\n p20m._implementation.get_mount()].update_config_item(\n 'pick_up_current', reduced_pick_up_current)\n ctx.comment(\"\"\"Tip pick-up current configuration for the p20 multi-channel\n pipette temporarily reduced to {} mAmp for one-tip pickup.\"\"\".format(\n str(reduced_pick_up_current)))\n\n # one-tip pickup with p20m\n pick_up(p20m)\n\n # reset p20m pick_up_current to original value\n ctx._implementation._hw_manager.hardware._attached_instruments[\n p20m._implementation.get_mount()].update_config_item(\n 'pick_up_current', default_current)\n ctx.comment(\"\"\"Tip pick-up current for the p20 multi-channel pipette\n restored to initial value of {} mAmp for standard 8-tip pickup.\"\"\".format(\n str(ctx._implementation._hw_manager.hardware._attached_instruments[\n p20m._implementation.get_mount()].config.pick_up_current)))\n\n # water then fluomix to last well of 1st col each tray\n for reagent in [water, pcr_mix]:\n for tray in trays:\n p20m.aspirate(4, reagent.height_dec(4))\n p20m.dispense(4, reagent.height_inc(4))\n p20m.aspirate(4, reagent.height_dec(4))\n d_height = -3 if use_384 else -11.2\n p20m.dispense(\n 4, tray.columns()[0][-1].top(d_height))\n p20m.touch_tip(\n tray.columns()[0][-1], radius=touch_radius,\n v_offset=touch_v_offset, speed=touch_speed)\n p20m.drop_tip()\n\n # helper function for repeat large vol transfers\n def repeat_max_transfer(current_pipette, remaining, source, dest,\n flowrate, touch=False):\n while remaining > tip_max:\n current_pipette.aspirate(\n tip_max, source.height_dec(tip_max), rate=flowrate)\n current_pipette.dispense(\n tip_max, dest.height_inc(tip_max), rate=flowrate)\n remaining -= tip_max\n if touch:\n ctx.delay(seconds=0.5)\n current_pipette.blow_out()\n current_pipette.touch_tip(radius=0.75, v_offset=-2, speed=10)\n current_pipette.aspirate(\n remaining, source.height_dec(remaining), rate=flowrate)\n current_pipette.dispense(\n remaining, dest.height_inc(remaining), rate=flowrate)\n if touch:\n ctx.delay(seconds=0.5)\n current_pipette.blow_out()\n current_pipette.touch_tip(radius=0.75, v_offset=-2, speed=10)\n\n # combine DNA dilution with pcr mix\n p300s.starting_tip = tips300[0].wells_by_name()[\n current_starting_tip_300.split()[0]]\n p300s.pick_up_tip()\n for rep in range(10):\n p300s.aspirate(200, dna_dilution.height_dec(200).move(\n types.Point(x=0, y=0, z=-dna_dilution.height*(relative_height))),\n rate=3.2)\n p300s.dispense(200, dna_dilution.height_inc(200).move(\n types.Point(x=0, y=0, z=-dna_dilution.height*(relative_height))),\n rate=3.2)\n repeat_max_transfer(p300s, dna_volume, dna_dilution, pcr_mix, 0.5)\n for rep in range(20):\n p300s.aspirate(200, pcr_mix.height_dec(200).move(\n types.Point(x=0, y=0, z=-pcr_mix.height*(relative_height))), rate=3.2)\n p300s.dispense(200, pcr_mix.height_inc(200).move(\n types.Point(x=0, y=0, z=-pcr_mix.height*(relative_height))), rate=3.2)\n\n # reservoir filling\n reservoir_mix = [WellH(well, min_height=3) for well in reservoir_col]\n for well in reservoir_mix:\n for rep in range(2):\n repeat_max_transfer(\n p300s, reservoir_fill_volume / 16, pcr_mix,\n well, 0.5, touch=True)\n p300s.drop_tip()\n if tips300[0].next_tip(1, p300s.starting_tip) is not None:\n future_tip_300 = tips300[0].next_tip(1, p300s.starting_tip)\n else:\n future_tip_300 = \"A1 of Opentrons 96 Filter Tip Rack 200 \u00b5L on 11\"\n\n # 7-tip transfer 8 ul to wells A1-G1 if 96-well tray\n # 7-tip transfer 8 ul to wells B1, D1, F1, H1, J1, L1, N1 if 384\n p20m.flow_rate.dispense = 22\n p20m.reset_tipracks()\n p20m.starting_tip = tips20[0].wells_by_name()[\n current_starting_tip_20.split()[0]]\n p20m.pick_up_tip()\n for tray in trays:\n p20m.aspirate(dispense_volume, reservoir_mix[0].bottom(\n p20_reservoir_height))\n d_height = -3 if use_384 else -11.2\n d_well = 1 if use_384 else 0\n p20m.dispense(dispense_volume, tray.columns()[0][d_well].top(d_height))\n p20m.touch_tip(\n tray.columns()[0][d_well], radius=touch_radius,\n v_offset=touch_v_offset, speed=touch_speed)\n p20m.drop_tip()\n\n p20m.pick_up_tip()\n # 8-tip transfer 8 ul to wells A1, C1, E1, G1, I1, K1, M1, O1 if 384\n if use_384:\n for tray in trays:\n p20m.aspirate(dispense_volume, reservoir_mix[0].bottom(\n p20_reservoir_height))\n d_height = -3\n d_well = 0\n p20m.dispense(\n dispense_volume, tray.columns()[0][d_well].top(d_height))\n p20m.touch_tip(\n tray.columns()[0][d_well], radius=touch_radius,\n v_offset=touch_v_offset, speed=touch_speed)\n\n # 8-tip transfer 8 ul to columns 2-12 of each tray\n for tray in trays:\n for index, column in enumerate(tray.columns()[1:12]):\n if use_384:\n p20m.aspirate(2*dispense_volume + disposal_volume,\n reservoir_mix[0].bottom(p20_reservoir_height))\n else:\n if not index % 2:\n if index < len(tray.columns()[1:]) - 1:\n p20m.aspirate(\n 2*dispense_volume + disposal_volume, reservoir_mix[\n 0].bottom(p20_reservoir_height))\n else:\n p20m.aspirate(\n dispense_volume, reservoir_mix[0].bottom(\n p20_reservoir_height))\n d_height = -3 if use_384 else -11.2\n p20m.dispense(dispense_volume, column[0].top(d_height))\n p20m.touch_tip(\n column[0], radius=touch_radius,\n v_offset=touch_v_offset, speed=touch_speed)\n if use_384:\n p20m.dispense(dispense_volume, column[1].top(d_height))\n p20m.touch_tip(\n column[1], radius=touch_radius,\n v_offset=touch_v_offset, speed=touch_speed)\n p20m.dispense(\n disposal_volume, reservoir_mix[0].bottom(p20_blowout_height))\n else:\n if index % 2:\n p20m.dispense(disposal_volume, reservoir_mix[0].bottom(\n p20_blowout_height))\n\n p20m.drop_tip()\n if tips20[0].next_tip(8, p20m.starting_tip) is not None:\n future_tip_20 = tips20[0].next_tip(8, p20m.starting_tip)\n else:\n future_tip_20 = \"A1 of Opentrons 96 Filter Tip Rack 20 \u00b5L on 10\"\n \"\"\"\n for reservoir column tracking between protocol runs\n \"\"\"\n # write future column and starting tips to csv for next protocol run\n new_data = \",\".join([\n str(new_col_index), str(future_tip_20), str(future_tip_300), '\\n'])\n # if ctx.is_simulating(): # logic reversed for simulation\n if not ctx.is_simulating():\n with open(file_path, 'w') as outfile:\n outfile.write(new_data)\n", + "content": "from opentrons.protocol_api.labware import Well\nfrom opentrons import types\nimport math\nimport csv\nimport os\n\nmetadata = {\n 'protocolName': 'FluoGene HLA NX 96-Well or 384-Well Setup',\n 'author': 'Steve ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.9'\n}\n\n\ndef run(ctx):\n\n [use_384, p20_blowout_height, disposal_volume, p300_transfer_height,\n dispense_volume, p300_mixing_height,\n p20_tube_height, relative_height, tracking_reset,\n p20_reservoir_height, tip_max, water_volume, fluomix_volume,\n dna_volume, reservoir_fill_volume] = get_values( # noqa: F821\n \"use_384\", \"p20_blowout_height\", \"disposal_volume\",\n \"p300_transfer_height\", \"dispense_volume\", \"p300_mixing_height\",\n \"p20_tube_height\", \"relative_height\", \"tracking_reset\",\n \"p20_reservoir_height\", \"tip_max\", \"water_volume\", \"fluomix_volume\",\n \"dna_volume\", \"reservoir_fill_volume\")\n\n ctx.set_rail_lights(True)\n ctx.delay(seconds=10)\n\n # constant values\n reduced_pick_up_current = 0.15\n touch_radius = 0.75\n touch_v_offset = -3\n touch_speed = 10\n\n # constrain reduced_pick_up_current value to acceptable range\n if reduced_pick_up_current < 0.1 or reduced_pick_up_current > 0.15:\n raise Exception('''Invalid value for reduced_pick_up_current parameter\n (must be between 0.1 and 0.15).''')\n\n \"\"\"\n for reservoir column tracking between protocol runs\n \"\"\"\n # for reservoir column tracking between protocol runs\n # if ctx.is_simulating(): # logic reversed for simulation\n if not ctx.is_simulating():\n file_path = '/data/temporary/columnandtiptracking.csv'\n file_dir = os.path.dirname(file_path)\n # check for file directory\n if not os.path.exists(file_dir):\n os.makedirs(file_dir)\n # check for file; if not there, create initial csv\n if (not os.path.isfile(file_path) or tracking_reset):\n with open(file_path, 'w') as outfile:\n outfile.write(\",\".join([\n \"0\", \"A1 of Opentrons 96 Filter Tip Rack 20 \u00b5L on 10\",\n \"A1 of Opentrons 96 Filter Tip Rack 200 \u00b5L on 11\", \"\\n\"]))\n\n current_data_list = []\n # if not ctx.is_simulating(): # logic reversed for simulation\n if ctx.is_simulating():\n current_data_list = [0,\n \"A1 of Opentrons 96 Filter Tip Rack 20 \u00b5L on 10\",\n \"A1 of Opentrons 96 Filter Tip Rack 200 \u00b5L on 11\"]\n else:\n with open(file_path) as csv_file:\n csv_reader = csv.reader(csv_file, delimiter=',')\n current_data_list = next(csv_reader)\n\n current_col_index = int(current_data_list[0])\n [current_starting_tip_20, current_starting_tip_300] = [\n current_data_list[i] for i in range(1, 3)]\n\n if current_col_index == 0:\n ctx.pause(\"Please place an unused, clean source plate in deck slot 7.\")\n\n # reservoir with column tracking between protocol runs\n reservoir = ctx.load_labware('nunc_96_wellplate_500ul', '7')\n\n # increment column index for future protocol run\n if current_col_index < len(reservoir.columns()) - 1:\n new_col_index = current_col_index + 1\n else:\n new_col_index = 0\n \"\"\"\n protocol steps using tracked reservoir column\n \"\"\"\n # reagent mix in reservoir column tracked across protocol runs\n reservoir_col = reservoir.columns()[current_col_index]\n ctx.set_rail_lights(True)\n\n # tips and p300 multi\n tips300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', '11')]\n tips20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', '10')]\n p300s = ctx.load_instrument('p300_single_gen2', 'left', tip_racks=tips300)\n p20m = ctx.load_instrument('p20_multi_gen2', 'right', tip_racks=tips20)\n\n # trays\n if not use_384:\n trays = [\n ctx.load_labware(labware, slot) for labware, slot in zip(\n ['innotrainot2pcrplate_96_wellplate_200ul',\n 'innotrainot22pcrplate_96_wellplate_200ul'], ['5', '6'])]\n else:\n trays = [ctx.load_labware('custom_384_well_tray', '5')]\n\n # tube rack rxn components: water in A1, pcr mix in A2, DNA dilution in A3\n tube_rack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap', '4')\n [w, p, d] = [\n tube_rack.wells_by_name()[well] for well in ['A1', 'A2', 'A3']]\n\n class WellH(Well):\n def __init__(self, well, min_height=5, comp_coeff=1.15,\n current_volume=0):\n super().__init__(well._impl)\n self.well = well\n self.min_height = min_height\n self.comp_coeff = comp_coeff\n self.current_volume = current_volume\n if self.diameter is not None:\n self.radius = self.diameter/2\n cse = math.pi*(self.radius**2)\n elif self.length is not None:\n cse = self.length*self.width\n self.height = current_volume/cse\n if self.height < min_height:\n self.height = min_height\n elif self.height > well.parent.highest_z:\n raise Exception(\"\"\"Specified liquid volume\n can not exceed the height of the labware.\"\"\")\n\n def height_dec(self, vol):\n if self.diameter is not None:\n cse = math.pi*(self.radius**2)\n elif self.length is not None:\n cse = self.length*self.width\n dh = (vol/cse)*self.comp_coeff\n if self.height - dh > self.min_height:\n self.height = self.height - dh\n else:\n self.height = self.min_height\n if self.current_volume - vol > 0:\n self.current_volume = self.current_volume - vol\n else:\n self.current_volume = 0\n return (self.well.bottom(self.height))\n\n def height_inc(self, vol, top=False):\n if self.diameter is not None:\n cse = math.pi*(self.radius**2)\n elif self.length is not None:\n cse = self.length*self.width\n ih = (vol/cse)*self.comp_coeff\n if self.height < self.min_height:\n self.height = self.min_height\n if self.height + ih < self.depth:\n self.height = self.height + ih\n else:\n self.height = self.depth\n self.current_volume += vol\n if top is False:\n return (self.well.bottom(self.height))\n else:\n return (self.well.top())\n\n # to track liquid height\n water = WellH(w, min_height=1, current_volume=water_volume)\n pcr_mix = WellH(p, min_height=1, current_volume=0.9*fluomix_volume)\n dna_dilution = WellH(d, min_height=1, current_volume=dna_volume)\n\n \"\"\"\n pick_up() function to use only the rear-most channel of the p20 multi\n \"\"\"\n num_channels_per_pickup = 1 # (only pickup tips on rear-most channel)\n tips_ordered = [\n tip for rack in tips20\n for row in rack.rows(\n )[len(rack.rows())-num_channels_per_pickup::-1*num_channels_per_pickup]\n for tip in row]\n\n tip_count = tips_ordered.index(\n tips20[0].wells_by_name()[\n current_starting_tip_20.split()[0].replace('A', 'H')])\n\n def pick_up(pip):\n nonlocal tip_count\n pip.pick_up_tip(tips_ordered[tip_count])\n tip_count += 1\n\n # one-tip transfer water, fluomix to 1st col last well\n p20m.flow_rate.aspirate = 3.8\n p20m.flow_rate.dispense = 3.8\n\n # capture and report original value for p20m pick_up_current\n default_current = ctx._hw_manager.hardware.\\\n _attached_instruments[p20m._implementation.get_mount()].\\\n config.pick_up_current\n ctx.comment(\"\"\"Tip pick-up current for the p20 multi-channel pipette\n initially configured to {} mAmp.\"\"\".format(str(default_current)))\n\n # temporarily reduce p20m pick_up_current for one-channel tip pickup\n ctx._hw_manager.hardware._attached_instruments[\n p20m._implementation.get_mount()].update_config_item(\n 'pick_up_current', reduced_pick_up_current)\n ctx.comment(\"\"\"Tip pick-up current configuration for the p20 multi-channel\n pipette temporarily reduced to {} mAmp for one-tip pickup.\"\"\".format(\n str(reduced_pick_up_current)))\n\n # one-tip pickup with p20m\n pick_up(p20m)\n\n # reset p20m pick_up_current to original value\n ctx._hw_manager.hardware._attached_instruments[\n p20m._implementation.get_mount()].update_config_item(\n 'pick_up_current', default_current)\n ctx.comment(\"\"\"Tip pick-up current for the p20 multi-channel pipette\n restored to initial value of {} mAmp for standard 8-tip pickup.\"\"\".format(\n str(ctx._hw_manager.hardware._attached_instruments[\n p20m._implementation.get_mount()].config.pick_up_current)))\n\n # water then fluomix to last well of 1st col each tray\n for reagent in [water, pcr_mix]:\n for tray in trays:\n p20m.aspirate(4, reagent.height_dec(4))\n p20m.dispense(4, reagent.height_inc(4))\n p20m.aspirate(4, reagent.height_dec(4))\n d_height = -3 if use_384 else -11.2\n p20m.dispense(\n 4, tray.columns()[0][-1].top(d_height))\n p20m.touch_tip(\n tray.columns()[0][-1], radius=touch_radius,\n v_offset=touch_v_offset, speed=touch_speed)\n p20m.drop_tip()\n\n # helper function for repeat large vol transfers\n def repeat_max_transfer(current_pipette, remaining, source, dest,\n flowrate, touch=False):\n while remaining > tip_max:\n current_pipette.aspirate(\n tip_max, source.height_dec(tip_max), rate=flowrate)\n current_pipette.dispense(\n tip_max, dest.height_inc(tip_max), rate=flowrate)\n remaining -= tip_max\n if touch:\n ctx.delay(seconds=0.5)\n current_pipette.blow_out()\n current_pipette.touch_tip(radius=0.75, v_offset=-2, speed=10)\n current_pipette.aspirate(\n remaining, source.height_dec(remaining), rate=flowrate)\n current_pipette.dispense(\n remaining, dest.height_inc(remaining), rate=flowrate)\n if touch:\n ctx.delay(seconds=0.5)\n current_pipette.blow_out()\n current_pipette.touch_tip(radius=0.75, v_offset=-2, speed=10)\n\n # combine DNA dilution with pcr mix\n p300s.starting_tip = tips300[0].wells_by_name()[\n current_starting_tip_300.split()[0]]\n p300s.pick_up_tip()\n for rep in range(10):\n p300s.aspirate(200, dna_dilution.height_dec(200).move(\n types.Point(x=0, y=0, z=-dna_dilution.height*(relative_height))),\n rate=3.2)\n p300s.dispense(200, dna_dilution.height_inc(200).move(\n types.Point(x=0, y=0, z=-dna_dilution.height*(relative_height))),\n rate=3.2)\n repeat_max_transfer(p300s, dna_volume, dna_dilution, pcr_mix, 0.5)\n for rep in range(20):\n p300s.aspirate(200, pcr_mix.height_dec(200).move(\n types.Point(x=0, y=0, z=-pcr_mix.height*(relative_height))), rate=3.2)\n p300s.dispense(200, pcr_mix.height_inc(200).move(\n types.Point(x=0, y=0, z=-pcr_mix.height*(relative_height))), rate=3.2)\n\n # reservoir filling\n reservoir_mix = [WellH(well, min_height=3) for well in reservoir_col]\n for well in reservoir_mix:\n for rep in range(2):\n repeat_max_transfer(\n p300s, reservoir_fill_volume / 16, pcr_mix,\n well, 0.5, touch=True)\n p300s.drop_tip()\n if tips300[0].next_tip(1, p300s.starting_tip) is not None:\n future_tip_300 = tips300[0].next_tip(1, p300s.starting_tip)\n else:\n future_tip_300 = \"A1 of Opentrons 96 Filter Tip Rack 200 \u00b5L on 11\"\n\n # 7-tip transfer 8 ul to wells A1-G1 if 96-well tray\n # 7-tip transfer 8 ul to wells B1, D1, F1, H1, J1, L1, N1 if 384\n p20m.flow_rate.dispense = 22\n p20m.reset_tipracks()\n p20m.starting_tip = tips20[0].wells_by_name()[\n current_starting_tip_20.split()[0]]\n p20m.pick_up_tip()\n for tray in trays:\n p20m.aspirate(dispense_volume, reservoir_mix[0].bottom(\n p20_reservoir_height))\n d_height = -3 if use_384 else -11.2\n d_well = 1 if use_384 else 0\n p20m.dispense(dispense_volume, tray.columns()[0][d_well].top(d_height))\n p20m.touch_tip(\n tray.columns()[0][d_well], radius=touch_radius,\n v_offset=touch_v_offset, speed=touch_speed)\n p20m.drop_tip()\n\n p20m.pick_up_tip()\n # 8-tip transfer 8 ul to wells A1, C1, E1, G1, I1, K1, M1, O1 if 384\n if use_384:\n for tray in trays:\n p20m.aspirate(dispense_volume, reservoir_mix[0].bottom(\n p20_reservoir_height))\n d_height = -3\n d_well = 0\n p20m.dispense(\n dispense_volume, tray.columns()[0][d_well].top(d_height))\n p20m.touch_tip(\n tray.columns()[0][d_well], radius=touch_radius,\n v_offset=touch_v_offset, speed=touch_speed)\n\n # 8-tip transfer 8 ul to columns 2-12 of each tray\n for tray in trays:\n for index, column in enumerate(tray.columns()[1:12]):\n if use_384:\n p20m.aspirate(2*dispense_volume + disposal_volume,\n reservoir_mix[0].bottom(p20_reservoir_height))\n else:\n if not index % 2:\n if index < len(tray.columns()[1:]) - 1:\n p20m.aspirate(\n 2*dispense_volume + disposal_volume, reservoir_mix[\n 0].bottom(p20_reservoir_height))\n else:\n p20m.aspirate(\n dispense_volume, reservoir_mix[0].bottom(\n p20_reservoir_height))\n d_height = -3 if use_384 else -11.2\n p20m.dispense(dispense_volume, column[0].top(d_height))\n p20m.touch_tip(\n column[0], radius=touch_radius,\n v_offset=touch_v_offset, speed=touch_speed)\n if use_384:\n p20m.dispense(dispense_volume, column[1].top(d_height))\n p20m.touch_tip(\n column[1], radius=touch_radius,\n v_offset=touch_v_offset, speed=touch_speed)\n p20m.dispense(\n disposal_volume, reservoir_mix[0].bottom(p20_blowout_height))\n else:\n if index % 2:\n p20m.dispense(disposal_volume, reservoir_mix[0].bottom(\n p20_blowout_height))\n\n p20m.drop_tip()\n if tips20[0].next_tip(8, p20m.starting_tip) is not None:\n future_tip_20 = tips20[0].next_tip(8, p20m.starting_tip)\n else:\n future_tip_20 = \"A1 of Opentrons 96 Filter Tip Rack 20 \u00b5L on 10\"\n \"\"\"\n for reservoir column tracking between protocol runs\n \"\"\"\n # write future column and starting tips to csv for next protocol run\n new_data = \",\".join([\n str(new_col_index), str(future_tip_20), str(future_tip_300), '\\n'])\n # if ctx.is_simulating(): # logic reversed for simulation\n if not ctx.is_simulating():\n with open(file_path, 'w') as outfile:\n outfile.write(new_data)\n", "custom_labware_defs": [ { "brand": { diff --git a/protoBuilds/11beaa/11beaa.ot2.apiv2.py.json b/protoBuilds/11beaa/11beaa.ot2.apiv2.py.json index f9bd398a1..51c31c802 100644 --- a/protoBuilds/11beaa/11beaa.ot2.apiv2.py.json +++ b/protoBuilds/11beaa/11beaa.ot2.apiv2.py.json @@ -6779,5 +6779,12 @@ "protocolName": "qPCR Prep with 384 Well Plate", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 4 lw Biorad 96 Aluminum Block 200 \u00b5L on Temperature Module GEN1 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/121d15-2-96/README.json b/protoBuilds/121d15-2-96/README.json deleted file mode 100644 index 035438011..000000000 --- a/protoBuilds/121d15-2-96/README.json +++ /dev/null @@ -1,28 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "Sample Prep": [ - "Cherrypicking" - ] - }, - "deck-setup": "\n", - "description": "Links:\n* Manual Cleave\n\n\n* Manual Cleave Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n* HPLC Picking\n\n\n* Redo Replacement Picking (96)\n\n\n* Redo Replacement Picking (384)\n\n\nThis protocol performs a custom Redo Replacement Picking protocol from a worklist. The worklist should be specified as follows:\nNumber of Redo\n8\npos TB_RCK_1,pos MTP_1,disposal_vol,transfer_vol\n1,1,200,200\n2,35,200,200\n3,2,150,200\n4,90,100,100\n5,84\n6,62\n7,42\n8,18\n...\n", - "internal": "121d15", - "labware": "\nCustom 48-tuberack\nGreiner MASTERBLOCK 96 Well Plate 500 \u00b5L\nOpentrons 300\u00b5L Tips\n", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* Sample Prep\n\t* Cherrypicking\n\n", - "deck-setup": "![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/121d15/deck2-96.png)\n\n---\n\n", - "description": "\nLinks:\n* [Manual Cleave](./121d15)\n
\n
\n* [Manual Cleave Elution (Off-deck Vacuum)](./121d15-4)\n
\n
\n* [Manual Cleave, ACN + Elution (Off-deck Vacuum)](./121d15-5)\n
\n
\n* [Manual Cleave, ACN + Elution (On-deck Vacuum)](./121d15-6)\n
\n
\n* [HPLC Picking](./121d15-3)\n
\n
\n* [Redo Replacement Picking (96)](./121d15-2-96)\n
\n
\n* [Redo Replacement Picking (384)](./121d15-2-384)\n
\n
\n\nThis protocol performs a custom Redo Replacement Picking protocol from a worklist. The worklist should be specified as follows:\n\n```\nNumber of Redo\n8\npos TB_RCK_1,pos MTP_1,disposal_vol,transfer_vol\n1,1,200,200\n2,35,200,200\n3,2,150,200\n4,90,100,100\n5,84\n6,62\n7,42\n8,18\n...\n```\n\n---\n\n", - "internal": "121d15\n", - "labware": "* Custom 48-tuberack\n* [Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L](https://shop.gbo.com/en/row/products/bioscience/microplates/polypropylene-storage-plates/96-well-masterblock-0-5ml/786201.html)\n* [Opentrons 300\u00b5L Tips](https://shop.opentrons.com/opentrons-300ul-tips-1000-refills/)\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "pipettes": "* [P300 Single Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/single-channel-electronic-pipette-p20/)\n\n---\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "title": "Redo Replacement Picking (96)" - }, - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "pipettes": "\nP300 Single Channel Electronic Pipette (GEN2)\n\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "title": "Redo Replacement Picking (96)" -} \ No newline at end of file diff --git a/protoBuilds/121d15-2-96/metadata.json b/protoBuilds/121d15-2-96/metadata.json deleted file mode 100644 index 6b3b15abb..000000000 --- a/protoBuilds/121d15-2-96/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "redoreplacementpicking.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": false, - "skip-tests": false - }, - "path": "protocols/121d15-2-96", - "slug": "121d15-2-96", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/121d15-2-96/redoreplacementpicking.ot2.apiv2.py.json b/protoBuilds/121d15-2-96/redoreplacementpicking.ot2.apiv2.py.json deleted file mode 100644 index bbf6b8e74..000000000 --- a/protoBuilds/121d15-2-96/redoreplacementpicking.ot2.apiv2.py.json +++ /dev/null @@ -1,16904 +0,0 @@ -{ - "content": "# metadata\nmetadata = {\n 'protocolName': 'Redo Replacement Picking (96)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [input_file, default_disposal_vol, default_transfer_vol,\n p300_mount] = get_values( # noqa: F821\n 'input_file', 'default_disposal_vol', 'default_transfer_vol',\n 'p300_mount')\n\n # load labware\n rack = ctx.load_labware('eurofins_96x2ml_tuberack', '2', 'tuberack')\n plate = ctx.load_labware('greinermasterblock_96_wellplate_500ul', '1')\n tips300 = [\n ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in ['4', '7']]\n\n # pipette\n p300 = ctx.load_instrument('p300_single_gen2', p300_mount,\n tip_racks=tips300)\n\n # parse\n data = [\n [val.strip() for val in line.split(',')]\n for line in input_file.splitlines()[3:]\n if line and line.split(',')[0].strip()]\n\n tubes_ordered = [\n well for i in range(2) for col in rack.columns()\n for well in col[i*8:(i+1)*8]]\n\n for line in data:\n tube = tubes_ordered[int(line[0])-1]\n well = plate.wells()[int(line[1])-1]\n if len(line) >= 3 and line[2]:\n disposal_vol = float(line[2])\n else:\n disposal_vol = default_disposal_vol\n if len(line) >= 4 and line[3]:\n transfer_vol = float(line[3])\n else:\n transfer_vol = default_transfer_vol\n\n # remove contents of well\n p300.pick_up_tip()\n ctx.max_speeds['A'] = 100 # slow descent\n ctx.max_speeds['Z'] = 100 # slow descent\n\n p300.aspirate(disposal_vol, well.bottom(0.2))\n del ctx.max_speeds['A'] # reset to default\n del ctx.max_speeds['Z'] # reset to default\n p300.drop_tip()\n\n # transfer tube to well\n p300.transfer(transfer_vol, tube, well.top(-1))\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "Greiner Masterblock", - "brandId": [ - "781270" - ] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.76, - "yDimension": 85.48, - "zDimension": 22 - }, - "groups": [ - { - "metadata": { - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "I1", - "J1", - "K1", - "L1", - "M1", - "N1", - "O1", - "P1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "I2", - "J2", - "K2", - "L2", - "M2", - "N2", - "O2", - "P2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "I3", - "J3", - "K3", - "L3", - "M3", - "N3", - "O3", - "P3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "I4", - "J4", - "K4", - "L4", - "M4", - "N4", - "O4", - "P4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "I5", - "J5", - "K5", - "L5", - "M5", - "N5", - "O5", - "P5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "I6", - "J6", - "K6", - "L6", - "M6", - "N6", - "O6", - "P6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "I7", - "J7", - "K7", - "L7", - "M7", - "N7", - "O7", - "P7", - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8", - "I8", - "J8", - "K8", - "L8", - "M8", - "N8", - "O8", - "P8", - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9", - "I9", - "J9", - "K9", - "L9", - "M9", - "N9", - "O9", - "P9", - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10", - "I10", - "J10", - "K10", - "L10", - "M10", - "N10", - "O10", - "P10", - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11", - "I11", - "J11", - "K11", - "L11", - "M11", - "N11", - "O11", - "P11", - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12", - "I12", - "J12", - "K12", - "L12", - "M12", - "N12", - "O12", - "P12", - "A13", - "B13", - "C13", - "D13", - "E13", - "F13", - "G13", - "H13", - "I13", - "J13", - "K13", - "L13", - "M13", - "N13", - "O13", - "P13", - "A14", - "B14", - "C14", - "D14", - "E14", - "F14", - "G14", - "H14", - "I14", - "J14", - "K14", - "L14", - "M14", - "N14", - "O14", - "P14", - "A15", - "B15", - "C15", - "D15", - "E15", - "F15", - "G15", - "H15", - "I15", - "J15", - "K15", - "L15", - "M15", - "N15", - "O15", - "P15", - "A16", - "B16", - "C16", - "D16", - "E16", - "F16", - "G16", - "H16", - "I16", - "J16", - "K16", - "L16", - "M16", - "N16", - "O16", - "P16", - "A17", - "B17", - "C17", - "D17", - "E17", - "F17", - "G17", - "H17", - "I17", - "J17", - "K17", - "L17", - "M17", - "N17", - "O17", - "P17", - "A18", - "B18", - "C18", - "D18", - "E18", - "F18", - "G18", - "H18", - "I18", - "J18", - "K18", - "L18", - "M18", - "N18", - "O18", - "P18", - "A19", - "B19", - "C19", - "D19", - "E19", - "F19", - "G19", - "H19", - "I19", - "J19", - "K19", - "L19", - "M19", - "N19", - "O19", - "P19", - "A20", - "B20", - "C20", - "D20", - "E20", - "F20", - "G20", - "H20", - "I20", - "J20", - "K20", - "L20", - "M20", - "N20", - "O20", - "P20", - "A21", - "B21", - "C21", - "D21", - "E21", - "F21", - "G21", - "H21", - "I21", - "J21", - "K21", - "L21", - "M21", - "N21", - "O21", - "P21", - "A22", - "B22", - "C22", - "D22", - "E22", - "F22", - "G22", - "H22", - "I22", - "J22", - "K22", - "L22", - "M22", - "N22", - "O22", - "P22", - "A23", - "B23", - "C23", - "D23", - "E23", - "F23", - "G23", - "H23", - "I23", - "J23", - "K23", - "L23", - "M23", - "N23", - "O23", - "P23", - "A24", - "B24", - "C24", - "D24", - "E24", - "F24", - "G24", - "H24", - "I24", - "J24", - "K24", - "L24", - "M24", - "N24", - "O24", - "P24" - ] - } - ], - "metadata": { - "displayCategory": "wellPlate", - "displayName": "Greiner Masterblock 384 Well Plate 225 \u00b5L", - "displayVolumeUnits": "\u00b5L", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "I1", - "J1", - "K1", - "L1", - "M1", - "N1", - "O1", - "P1" - ], - 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"x": 77.38, - "xDimension": 8.24, - "y": 11.26, - "yDimension": 8.24, - "z": 4.97 - }, - "H9": { - "depth": 39.23, - "shape": "rectangular", - "totalLiquidVolume": 2200, - "x": 86.38, - "xDimension": 8.24, - "y": 11.26, - "yDimension": 8.24, - "z": 4.97 - } - } - } - ], - "fields": [ - { - "default": "Number of Redo\n8\npos TB_RCK_1,pos MTP_1,disposal_vol,transfer_vol\n1,1,200,200\n2,35,200,200\n3,2,150,200\n4,90,100,100\n5,84\n6,62\n7,42\n8,18\n", - "label": "input file", - "name": "input_file", - "type": "textFile" - }, - { - "default": 200.0, - "label": "default initial disposal volume (\u00b5l)", - "name": "default_disposal_vol", - "type": "float" - }, - { - "default": 200.0, - "label": "default new transfer volume (\u00b5l)", - "name": "default_transfer_vol", - "type": "float" - }, - { - "label": "P300 single-channel pipette mount", - "name": "p300_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p300_single_gen2" - } - ], - "labware": [ - { - "name": "Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L on 1", - "share": false, - "slot": "1", - "type": "greinermasterblock_96_wellplate_500ul" - }, - { - "name": "tuberack on 2", - "share": false, - "slot": "2", - "type": "eurofins_96x2ml_tuberack" - }, - { - "name": "Opentrons 96 Tip Rack 300 \u00b5L on 4", - "share": false, - "slot": "4", - "type": "opentrons_96_tiprack_300ul" - }, - { - "name": "Opentrons 96 Tip Rack 300 \u00b5L on 7", - "share": false, - "slot": "7", - "type": "opentrons_96_tiprack_300ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Nick ", - "protocolName": "Redo Replacement Picking (96)", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/121d15-2/README.json b/protoBuilds/121d15-2/README.json deleted file mode 100644 index 23498780b..000000000 --- a/protoBuilds/121d15-2/README.json +++ /dev/null @@ -1,28 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "Sample Prep": [ - "Cherrypicking" - ] - }, - "deck-setup": "\n", - "description": "Links:\n* Manual Cleave\n\n\n* Manual Cleave Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n* Redo Replacement Picking\n\n\n* HPLC Picking\nThis protocol performs a custom Redo Replacement Picking protocol from a worklist. The worklist should be specified as follows:\nNumber of Redo\n9\npos TB_RCK_1,pos MTP_1,disposal_vol,transfer_vol\n1,1,200,200\n2,135,200,200\n3,2,150,200\n4,90,100,100\n5,84\n6,262\n7,242\n8,218\n9,219\n...\n", - "internal": "121d15", - "labware": "\nCustom 48-tuberack\nGreiner MASTERBLOCK 384 Well Plate 225 \u00b5L\nGreiner MASTERBLOCK 96 Well Plate 500 \u00b5L\nOpentrons 300\u00b5L Tips\n", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* Sample Prep\n\t* Cherrypicking\n\n", - "deck-setup": "![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/121d15/deck2-v2.png)\n\n---\n\n", - "description": "\nLinks:\n* [Manual Cleave](./121d15)\n
\n
\n* [Manual Cleave Elution (Off-deck Vacuum)](./121d15-4)\n
\n
\n* [Manual Cleave, ACN + Elution (Off-deck Vacuum)](./121d15-5)\n
\n
\n* [Manual Cleave, ACN + Elution (On-deck Vacuum)](./121d15-6)\n
\n
\n* [Redo Replacement Picking](./121d15-2)\n
\n
\n* [HPLC Picking](./121d15-3)\n\nThis protocol performs a custom Redo Replacement Picking protocol from a worklist. The worklist should be specified as follows:\n\n```\nNumber of Redo\n9\npos TB_RCK_1,pos MTP_1,disposal_vol,transfer_vol\n1,1,200,200\n2,135,200,200\n3,2,150,200\n4,90,100,100\n5,84\n6,262\n7,242\n8,218\n9,219\n...\n```\n\n---\n\n", - "internal": "121d15\n", - "labware": "* Custom 48-tuberack\n* [Greiner MASTERBLOCK 384 Well Plate 225 \u00b5L](https://shop.gbo.com/en/row/products/bioscience/microplates/polypropylene-storage-plates/384-deep-well-masterblock/781270.html)\n* [Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L](https://shop.gbo.com/en/row/products/bioscience/microplates/polypropylene-storage-plates/96-well-masterblock-0-5ml/786201.html)\n* [Opentrons 300\u00b5L Tips](https://shop.opentrons.com/opentrons-300ul-tips-1000-refills/)\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "pipettes": "* [P300 Single Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/single-channel-electronic-pipette-p20/)\n\n---\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "title": "Redo Replacement Picking" - }, - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "pipettes": "\nP300 Single Channel Electronic Pipette (GEN2)\n\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "title": "Redo Replacement Picking" -} \ No newline at end of file diff --git a/protoBuilds/121d15-2/metadata.json b/protoBuilds/121d15-2/metadata.json deleted file mode 100644 index cf0579d83..000000000 --- a/protoBuilds/121d15-2/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "redoreplacementpicking.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": false, - "skip-tests": false - }, - "path": "protocols/121d15-2", - "slug": "121d15-2", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/121d15-2/redoreplacementpicking.ot2.apiv2.py.json b/protoBuilds/121d15-2/redoreplacementpicking.ot2.apiv2.py.json deleted file mode 100644 index ec0ae3218..000000000 --- a/protoBuilds/121d15-2/redoreplacementpicking.ot2.apiv2.py.json +++ /dev/null @@ -1,16919 +0,0 @@ -{ - "content": "# metadata\nmetadata = {\n 'protocolName': 'Redo Replacement Picking',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [input_file, default_disposal_vol, default_transfer_vol, plate_type,\n p300_mount] = get_values( # noqa: F821\n 'input_file', 'default_disposal_vol', 'default_transfer_vol',\n 'plate_type', 'p300_mount')\n\n # load labware\n rack = ctx.load_labware('eurofins_96x2ml_tuberack', '2', 'tuberack')\n plate = ctx.load_labware(plate_type, '1')\n tips300 = [\n ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in ['4', '7']]\n\n # pipette\n p300 = ctx.load_instrument('p300_single_gen2', p300_mount,\n tip_racks=tips300)\n\n # parse\n data = [\n [val.strip() for val in line.split(',')]\n for line in input_file.splitlines()[3:]\n if line and line.split(',')[0].strip()]\n\n tubes_ordered = [\n well for i in range(2) for col in rack.columns()\n for well in col[i*8:(i+1)*8]]\n\n for line in data:\n tube = tubes_ordered[int(line[0])-1]\n well = plate.wells()[int(line[1])-1]\n if len(line) >= 3 and line[2]:\n disposal_vol = float(line[2])\n else:\n disposal_vol = default_disposal_vol\n if len(line) >= 4 and line[3]:\n transfer_vol = float(line[3])\n else:\n transfer_vol = default_transfer_vol\n\n # remove contents of well\n p300.pick_up_tip()\n ctx.max_speeds['A'] = 100 # slow descent\n ctx.max_speeds['Z'] = 100 # slow descent\n\n p300.aspirate(disposal_vol, well.bottom(0.2))\n del ctx.max_speeds['A'] # reset to default\n del ctx.max_speeds['Z'] # reset to default\n p300.drop_tip()\n\n # transfer tube to well\n p300.transfer(transfer_vol, tube, well.top(-1))\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "Greiner Masterblock", - "brandId": [ - "781270" - ] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.76, - "yDimension": 85.48, - "zDimension": 22 - }, - "groups": [ - { - "metadata": { - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "I1", - "J1", - "K1", - "L1", - "M1", - "N1", - "O1", - "P1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "I2", - "J2", - "K2", - "L2", - "M2", - "N2", - "O2", - "P2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "I3", - "J3", - "K3", - "L3", - "M3", - "N3", - "O3", - "P3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "I4", - "J4", - "K4", - "L4", - "M4", - "N4", - "O4", - "P4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "I5", - "J5", - "K5", - "L5", - "M5", - "N5", - "O5", - "P5", - "A6", - "B6", - "C6", - 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"x": 77.38, - "xDimension": 8.24, - "y": 11.26, - "yDimension": 8.24, - "z": 4.97 - }, - "H9": { - "depth": 39.23, - "shape": "rectangular", - "totalLiquidVolume": 2200, - "x": 86.38, - "xDimension": 8.24, - "y": 11.26, - "yDimension": 8.24, - "z": 4.97 - } - } - } - ], - "fields": [ - { - "default": "Number of Redo\n8\npos TB_RCK_1,pos MTP_1,disposal_vol,transfer_vol\n1,1,200,200\n2,135,200,200\n3,2,150,200\n4,90,100,100\n5,84\n6,262\n7,242\n8,218\n", - "label": "input file", - "name": "input_file", - "type": "textFile" - }, - { - "default": 200.0, - "label": "default initial disposal volume (\u00b5l)", - "name": "default_disposal_vol", - "type": "float" - }, - { - "default": 200.0, - "label": "default new transfer volume (\u00b5l)", - "name": "default_transfer_vol", - "type": "float" - }, - { - "label": "plate type", - "name": "plate_type", - "options": [ - { - "label": "Greiner MASTERBLOCK 384 Well Plate 225 \u00b5L", - "value": "greinermasterblock_384_wellplate_225ul" - }, - { - "label": "Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L", - "value": "greinermasterblock_96_wellplate_500ul" - } - ], - "type": "dropDown" - }, - { - "label": "P300 single-channel pipette mount", - "name": "p300_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p300_single_gen2" - } - ], - "labware": [ - { - "name": "Greiner Masterblock 384 Well Plate 225 \u00b5L on 1", - "share": false, - "slot": "1", - "type": "greinermasterblock_384_wellplate_225ul" - }, - { - "name": "tuberack on 2", - "share": false, - "slot": "2", - "type": "eurofins_96x2ml_tuberack" - }, - { - "name": "Opentrons 96 Tip Rack 300 \u00b5L on 4", - "share": false, - "slot": "4", - "type": "opentrons_96_tiprack_300ul" - }, - { - "name": "Opentrons 96 Tip Rack 300 \u00b5L on 7", - "share": false, - "slot": "7", - "type": "opentrons_96_tiprack_300ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Nick ", - "protocolName": "Redo Replacement Picking", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/121d15-4/manual_cleave.ot2.apiv2.py.json b/protoBuilds/121d15-4/manual_cleave.ot2.apiv2.py.json index 140d790c5..eb9b57a34 100644 --- a/protoBuilds/121d15-4/manual_cleave.ot2.apiv2.py.json +++ b/protoBuilds/121d15-4/manual_cleave.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "import json\nimport os\n\n# metadata\nmetadata = {\n 'protocolName': 'Manual Cleave Elution',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [occupied_well_csv1, occupied_well_csv2, occupied_well_csv3, reagent_scan,\n slot_scan, transfer_vol, m300_mount, p300_mount,\n tip_track] = get_values( # noqa: F821\n 'occupied_well_csv1', 'occupied_well_csv2', 'occupied_well_csv3',\n 'reagent_scan', 'slot_scan', 'transfer_vol', 'm300_mount',\n 'p300_mount', 'tip_track')\n\n # load labware\n racks = [\n ctx.load_labware('custom_96_tuberack_500ul', f'{slot}', f'plate {i+1}')\n for i, slot in enumerate(['4', '5', '6'])]\n tips300 = [\n ctx.load_labware('opentrons_96_tiprack_300ul', slot,\n '300ul tiprack')\n for slot in ['10', '11']]\n\n reagent_map = {\n 'WATER': {\n 'slot': '9',\n 'tips': tips300[1].columns()[5:6],\n 'flow-rate-asp': 100,\n 'flow-rate-disp': 100,\n 'flow-rate-blow-out': 100,\n 'blow-out': True,\n 'dispense-delay': 0,\n 'drop-tip': False\n }\n }\n\n # check for barcode scan\n reagent_scan_type = reagent_scan.split('_')[-1].upper().strip()\n slot_scan_type = slot_scan.upper().strip()\n if reagent_scan_type == 'REPLACE WITH SCAN' \\\n or slot_scan_type == 'REPLACE WITH SCAN':\n pass\n else:\n if not reagent_scan_type:\n raise Exception('Rescan reagent (empty reagent_scan)')\n if not slot_scan_type:\n raise Exception('Rescan slot (empty slot scan)')\n if not reagent_scan_type == slot_scan_type[:3]:\n raise Exception(f'Reagent mismatch: {reagent_scan_type} in slot \\\n {slot_scan_type}')\n if slot_scan_type not in reagent_map.keys():\n raise Exception(f'Invalid slot scan: {slot_scan_type}')\n\n reagent_type = slot_scan_type\n reagent = ctx.load_labware(\n 'test_1_reservoir_300000ul', reagent_map[reagent_type]['slot'],\n reagent_type).wells()[0]\n\n def all_tips_full():\n for rack in tips300:\n for well in rack.wells():\n well.has_tip = True\n\n folder_path = '/data/manual_cleave'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n tip_data = json.load(json_file)\n for slot in tip_data.keys():\n for well, tip_bool in tip_data[slot].items():\n ctx.loaded_labwares[int(slot)].wells_by_name()[\n well].has_tip = tip_bool\n else:\n all_tips_full()\n else:\n all_tips_full()\n\n # load pipette\n m300 = ctx.load_instrument(\n 'p300_multi_gen2', m300_mount, tip_racks=tips300)\n p300 = ctx.load_instrument(\n 'p300_single_gen2', p300_mount, tip_racks=tips300)\n\n # samples and reagents\n def slide_window(num_tips, col):\n num_slides = 9 - num_tips\n for slide in range(num_slides):\n window_start_index = 8 + -1*num_tips - slide\n window = col[window_start_index:(window_start_index+num_tips)]\n window_full = True\n for tip in window:\n if not tip.has_tip:\n window_full = False\n if window_full:\n return window[0]\n return False\n\n def scan_racks(num_tips, reagent_type):\n all_columns = reagent_map[reagent_type]['tips']\n for col in all_columns:\n pick_up_loc = slide_window(num_tips, col)\n if pick_up_loc:\n return pick_up_loc\n return False\n\n per_tip_pickup_current = .1\n\n def pick_up(num_tips, reagent_type):\n if not 1 <= num_tips <= 8:\n raise Exception(f'INVALID NUMBER OF TIPS: {num_tips}.')\n if num_tips > 1:\n pip = m300\n pick_up_current = num_tips*per_tip_pickup_current\n ctx._implementation._hw_manager.hardware._attached_instruments[\n pip._implementation.get_mount()].update_config_item(\n 'pick_up_current', pick_up_current)\n else:\n pip = p300\n scan_result = scan_racks(num_tips, reagent_type)\n if scan_result:\n pip.pick_up_tip(scan_result)\n else:\n ctx.pause('REFILL TIPRACKS BEFORE RESUMING.')\n [rack.reset() for rack in tips300]\n scan_result = scan_racks(num_tips, reagent_type)\n pip.pick_up_tip(scan_result)\n return scan_result, pip\n\n def return_tip(pip, tip_loc, chunk_len, reagent_type):\n pip.drop_tip(tip_loc)\n all_tips = [\n well\n for col in reagent_map[reagent_type]['tips'] for well in col]\n tip_ind = all_tips.index(tip_loc)\n for tip in all_tips[tip_ind:tip_ind+chunk_len]:\n tip.has_tip = True\n\n # parse wells into chunks\n chunk_map = {num: [] for num in range(1, 9)}\n for csv, rack in zip(\n [occupied_well_csv1, occupied_well_csv2, occupied_well_csv3],\n racks):\n occupied_wells = [\n rack.wells_by_name()[line.upper()]\n for line in csv.splitlines() if line]\n for col in rack.columns():\n running = None\n chunk_length = 0\n for well in col[::-1]:\n if well in occupied_wells:\n running = well\n chunk_length += 1\n else:\n if running:\n chunk_map[chunk_length].append(running)\n running = None\n chunk_length = 0\n if running:\n chunk_map[chunk_length].append(running)\n\n ctx.home()\n first_col = 0\n for i, col in enumerate(reagent_map[reagent_type]['tips']):\n if col[0].has_tip:\n first_col = i\n break\n col = reagent_map[\n reagent_type]['tips'][first_col][0].display_name.split(' ')[0][1:]\n ctx.pause(f'Ensure tips are in column {col}')\n\n num_chunks = len(\n [key for key, vals in chunk_map.items()\n if len(vals) > 0])\n accessed = 0\n num_centrifugations = 4\n\n for elution in range(num_centrifugations):\n for num_tips, dests in chunk_map.items():\n if len(dests) > 0:\n accessed += 1\n pick_up_loc, pip = pick_up(num_tips, reagent_type)\n for dest in dests:\n pip.aspirate(transfer_vol, reagent.bottom(2))\n pip.dispense(transfer_vol, dest.top(-1))\n ctx.delay(seconds=reagent_map[\n reagent_type]['dispense-delay'])\n if reagent_map[reagent_type]['blow-out']:\n pip.blow_out(dest.top(-1))\n\n if elution == num_centrifugations - 1 and \\\n reagent_map[reagent_type]['drop-tip'] and \\\n accessed == num_chunks:\n pip.drop_tip()\n else:\n # return tip and reset has_tip attribute\n return_tip(pip, pick_up_loc, num_tips, reagent_type)\n func = ctx.pause if elution < num_centrifugations - 1 \\\n else ctx.comment\n func('Centrifuge all plates. Replace and resume when finished.')\n\n # track final used tip\n # void partially full tip column\n for tiprack in tips300:\n for col in tiprack.columns():\n for well in col:\n if not well.has_tip:\n for well in col:\n well.has_tip = False\n break\n tip_data = {\n str(rack.parent):\n {well.display_name.split(' ')[0]: well.has_tip\n for well in rack.wells()}\n for rack in tips300\n }\n if not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n with open(tip_file_path, 'w') as outfile:\n json.dump(tip_data, outfile)\n\n ctx._implementation._hw_manager.hardware._attached_instruments[\n m300._implementation.get_mount()].update_config_item(\n 'pick_up_current', 1.0)\n", + "content": "import json\nimport os\n\n# metadata\nmetadata = {\n 'protocolName': 'Manual Cleave Elution',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [occupied_well_csv1, occupied_well_csv2, occupied_well_csv3, reagent_scan,\n slot_scan, transfer_vol, m300_mount, p300_mount,\n tip_track] = get_values( # noqa: F821\n 'occupied_well_csv1', 'occupied_well_csv2', 'occupied_well_csv3',\n 'reagent_scan', 'slot_scan', 'transfer_vol', 'm300_mount',\n 'p300_mount', 'tip_track')\n\n # load labware\n racks = [\n ctx.load_labware('custom_96_tuberack_500ul', f'{slot}', f'plate {i+1}')\n for i, slot in enumerate(['4', '5', '6'])]\n tips300 = [\n ctx.load_labware('opentrons_96_tiprack_300ul', slot,\n '300ul tiprack')\n for slot in ['10', '11']]\n\n reagent_map = {\n 'WATER': {\n 'slot': '9',\n 'tips': tips300[1].columns()[5:6],\n 'flow-rate-asp': 100,\n 'flow-rate-disp': 100,\n 'flow-rate-blow-out': 100,\n 'blow-out': True,\n 'dispense-delay': 0,\n 'drop-tip': False\n }\n }\n\n # check for barcode scan\n reagent_scan_type = reagent_scan.split('_')[-1].upper().strip()\n slot_scan_type = slot_scan.upper().strip()\n if reagent_scan_type == 'REPLACE WITH SCAN' \\\n or slot_scan_type == 'REPLACE WITH SCAN':\n pass\n else:\n if not reagent_scan_type:\n raise Exception('Rescan reagent (empty reagent_scan)')\n if not slot_scan_type:\n raise Exception('Rescan slot (empty slot scan)')\n if not reagent_scan_type == slot_scan_type[:3]:\n raise Exception(f'Reagent mismatch: {reagent_scan_type} in slot \\\n {slot_scan_type}')\n if slot_scan_type not in reagent_map.keys():\n raise Exception(f'Invalid slot scan: {slot_scan_type}')\n\n reagent_type = slot_scan_type\n reagent = ctx.load_labware(\n 'test_1_reservoir_300000ul', reagent_map[reagent_type]['slot'],\n reagent_type).wells()[0]\n\n def all_tips_full():\n for rack in tips300:\n for well in rack.wells():\n well.has_tip = True\n\n folder_path = '/data/manual_cleave'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n tip_data = json.load(json_file)\n for slot in tip_data.keys():\n for well, tip_bool in tip_data[slot].items():\n ctx.loaded_labwares[int(slot)].wells_by_name()[\n well].has_tip = tip_bool\n else:\n all_tips_full()\n else:\n all_tips_full()\n\n # load pipette\n m300 = ctx.load_instrument(\n 'p300_multi_gen2', m300_mount, tip_racks=tips300)\n p300 = ctx.load_instrument(\n 'p300_single_gen2', p300_mount, tip_racks=tips300)\n\n # samples and reagents\n def slide_window(num_tips, col):\n num_slides = 9 - num_tips\n for slide in range(num_slides):\n window_start_index = 8 + -1*num_tips - slide\n window = col[window_start_index:(window_start_index+num_tips)]\n window_full = True\n for tip in window:\n if not tip.has_tip:\n window_full = False\n if window_full:\n return window[0]\n return False\n\n def scan_racks(num_tips, reagent_type):\n all_columns = reagent_map[reagent_type]['tips']\n for col in all_columns:\n pick_up_loc = slide_window(num_tips, col)\n if pick_up_loc:\n return pick_up_loc\n return False\n\n per_tip_pickup_current = .1\n\n def pick_up(num_tips, reagent_type):\n if not 1 <= num_tips <= 8:\n raise Exception(f'INVALID NUMBER OF TIPS: {num_tips}.')\n if num_tips > 1:\n pip = m300\n pick_up_current = num_tips*per_tip_pickup_current\n ctx._hw_manager.hardware._attached_instruments[\n pip._implementation.get_mount()].update_config_item(\n 'pick_up_current', pick_up_current)\n else:\n pip = p300\n scan_result = scan_racks(num_tips, reagent_type)\n if scan_result:\n pip.pick_up_tip(scan_result)\n else:\n ctx.pause('REFILL TIPRACKS BEFORE RESUMING.')\n [rack.reset() for rack in tips300]\n scan_result = scan_racks(num_tips, reagent_type)\n pip.pick_up_tip(scan_result)\n return scan_result, pip\n\n def return_tip(pip, tip_loc, chunk_len, reagent_type):\n pip.drop_tip(tip_loc)\n all_tips = [\n well\n for col in reagent_map[reagent_type]['tips'] for well in col]\n tip_ind = all_tips.index(tip_loc)\n for tip in all_tips[tip_ind:tip_ind+chunk_len]:\n tip.has_tip = True\n\n # parse wells into chunks\n chunk_map = {num: [] for num in range(1, 9)}\n for csv, rack in zip(\n [occupied_well_csv1, occupied_well_csv2, occupied_well_csv3],\n racks):\n occupied_wells = [\n rack.wells_by_name()[line.upper()]\n for line in csv.splitlines() if line]\n for col in rack.columns():\n running = None\n chunk_length = 0\n for well in col[::-1]:\n if well in occupied_wells:\n running = well\n chunk_length += 1\n else:\n if running:\n chunk_map[chunk_length].append(running)\n running = None\n chunk_length = 0\n if running:\n chunk_map[chunk_length].append(running)\n\n ctx.home()\n first_col = 0\n for i, col in enumerate(reagent_map[reagent_type]['tips']):\n if col[0].has_tip:\n first_col = i\n break\n col = reagent_map[\n reagent_type]['tips'][first_col][0].display_name.split(' ')[0][1:]\n ctx.pause(f'Ensure tips are in column {col}')\n\n num_chunks = len(\n [key for key, vals in chunk_map.items()\n if len(vals) > 0])\n accessed = 0\n num_centrifugations = 4\n\n for elution in range(num_centrifugations):\n for num_tips, dests in chunk_map.items():\n if len(dests) > 0:\n accessed += 1\n pick_up_loc, pip = pick_up(num_tips, reagent_type)\n for dest in dests:\n pip.aspirate(transfer_vol, reagent.bottom(2))\n pip.dispense(transfer_vol, dest.top(-1))\n ctx.delay(seconds=reagent_map[\n reagent_type]['dispense-delay'])\n if reagent_map[reagent_type]['blow-out']:\n pip.blow_out(dest.top(-1))\n\n if elution == num_centrifugations - 1 and \\\n reagent_map[reagent_type]['drop-tip'] and \\\n accessed == num_chunks:\n pip.drop_tip()\n else:\n # return tip and reset has_tip attribute\n return_tip(pip, pick_up_loc, num_tips, reagent_type)\n func = ctx.pause if elution < num_centrifugations - 1 \\\n else ctx.comment\n func('Centrifuge all plates. Replace and resume when finished.')\n\n # track final used tip\n # void partially full tip column\n for tiprack in tips300:\n for col in tiprack.columns():\n for well in col:\n if not well.has_tip:\n for well in col:\n well.has_tip = False\n break\n tip_data = {\n str(rack.parent):\n {well.display_name.split(' ')[0]: well.has_tip\n for well in rack.wells()}\n for rack in tips300\n }\n if not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n with open(tip_file_path, 'w') as outfile:\n json.dump(tip_data, outfile)\n\n ctx._hw_manager.hardware._attached_instruments[\n m300._implementation.get_mount()].update_config_item(\n 'pick_up_current', 1.0)\n", "custom_labware_defs": [ { "brand": { diff --git a/protoBuilds/12213d/12213d.ot2.apiv2.py.json b/protoBuilds/12213d/12213d.ot2.apiv2.py.json index 621deb13d..af0bfb714 100644 --- a/protoBuilds/12213d/12213d.ot2.apiv2.py.json +++ b/protoBuilds/12213d/12213d.ot2.apiv2.py.json @@ -81,5 +81,12 @@ "protocolName": "Ethanol Transfer with User", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 4 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN1 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/13c0b8/13c0b8.ot2.apiv2.py.json b/protoBuilds/13c0b8/13c0b8.ot2.apiv2.py.json index 1acad9eb2..3d49dad3c 100644 --- a/protoBuilds/13c0b8/13c0b8.ot2.apiv2.py.json +++ b/protoBuilds/13c0b8/13c0b8.ot2.apiv2.py.json @@ -1146,7 +1146,7 @@ ], "labware": [ { - "name": "96-well BRANDplate with V-bottom on Temperature Module GEN1 on 1", + "name": "96-well BRANDplate with V-bottom on Temperature Module on 1", "share": false, "slot": "1", "type": "brandplates_96_wellplate_360ul" @@ -1206,5 +1206,12 @@ "protocolName": "Non-Sterile Cell Analysis", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module on 1 lw 96-well BRANDplate with V-bottom on Temperature Module on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/13ea1e-part1/13ea1e-part1.ot2.apiv2.py.json b/protoBuilds/13ea1e-part1/13ea1e-part1.ot2.apiv2.py.json deleted file mode 100644 index 83c721bd2..000000000 --- a/protoBuilds/13ea1e-part1/13ea1e-part1.ot2.apiv2.py.json +++ /dev/null @@ -1,139 +0,0 @@ -{ - "content": "metadata = {\n 'protodestName': 'Extraction Prep with Kingfisher Flex Extractor',\n 'author': 'Rami Farawi ',\n 'source': 'Custom Protodest Request',\n 'apiLevel': '2.7'\n}\n\n\ndef run(ctx):\n\n [num_samp, mix_reps, p300_mount, p1000_mount] = get_values( # noqa: F821\n \"num_samp\", \"mix_reps\", \"p300_mount\", \"p1000_mount\")\n\n if not 0 <= num_samp <= 96:\n raise Exception(\"Enter a sample number between 1-96\")\n\n # load labware\n reservoir = ctx.load_labware('nest_12_reservoir_15ml', '1')\n reservoir2 = ctx.load_labware('nest_12_reservoir_15ml', '2')\n npw4_block = ctx.load_labware('nest_96_wellplate_2ml_deep', '3')\n sample_block = ctx.load_labware('nest_96_wellplate_2ml_deep', '4')\n elution_block = ctx.load_labware('nest_96_wellplate_2ml_deep', '5')\n ethanol_block = ctx.load_labware('nest_96_wellplate_2ml_deep', '6')\n npw3_block = ctx.load_labware('nest_96_wellplate_2ml_deep', '7')\n\n tiprack300 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in ['9', '8']]\n tiprack1000 = [ctx.load_labware('opentrons_96_tiprack_1000ul', '10')]\n tuberack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '11')\n\n # load instrument\n p1000 = ctx.load_instrument('p1000_single_gen2', p1000_mount,\n tip_racks=tiprack1000)\n p300 = ctx.load_instrument('p300_multi_gen2', p300_mount,\n tip_racks=tiprack300)\n\n num_channels_per_pickup = 1 # (only pickup tips on front-most channel)\n tips_ordered = [\n tip for rack in tiprack300\n for row in rack.rows()[\n len(rack.rows())-num_channels_per_pickup::-1*num_channels_per_pickup]\n for tip in row]\n tip_count = 0\n\n def pick_up(pip):\n nonlocal tip_count\n pip.pick_up_tip(tips_ordered[tip_count])\n tip_count += 1\n\n # reagents\n mag_beads = reservoir.rows()[0][:4]\n ethanol = reservoir.rows()[0][4:8]\n npw3 = reservoir.rows()[0][8:12]\n npw4 = reservoir2.rows()[0][:4]\n\n proteinase_k = tuberack.rows()[0][:2]\n ntc = tuberack.rows()[1][0]\n hsc = tuberack.rows()[2][0]\n elution_buffer = tuberack.rows()[3][:4]\n\n # add controls\n p1000.pick_up_tip()\n p1000.transfer(400, ntc, sample_block.wells()[0], new_tip='never')\n p1000.drop_tip()\n\n p1000.pick_up_tip()\n p1000.transfer(400, hsc, sample_block.wells()[1], new_tip='never')\n p1000.drop_tip()\n ctx.comment('\\n\\n\\n\\n\\n')\n\n # add proteinase k and incubate for 15 minutes\n for s, d in zip(proteinase_k*num_samp, sample_block.wells()[:num_samp]):\n pick_up(p300)\n p300.aspirate(24, s)\n p300.dispense(24, d)\n p300.mix(mix_reps, 300, d)\n p300.drop_tip()\n ctx.delay(minutes=15)\n ctx.comment('\\n\\n\\n\\n\\n')\n\n # add magnetic beads\n p1000.pick_up_tip()\n for mag_well, dest in zip(mag_beads*num_samp,\n sample_block.wells()[:num_samp]):\n p1000.mix(5, 1000, mag_well)\n p1000.transfer(595, mag_well, dest.top(), new_tip='never')\n p1000.drop_tip()\n ctx.comment('\\n\\n\\n\\n\\n')\n\n # make npw3, npw4 and ethanol npw3_block\n # ethanol\n p1000.pick_up_tip()\n for ethanol_well, dest in zip(ethanol*num_samp,\n ethanol_block.wells()[:num_samp]):\n p1000.transfer(600, ethanol_well, dest.top(), new_tip='never')\n p1000.drop_tip()\n ctx.comment('\\n\\n\\n\\n\\n')\n\n # npw3\n p1000.pick_up_tip()\n for npw3_well, dest in zip(npw3*num_samp,\n npw3_block.wells()[:num_samp]):\n p1000.transfer(600, npw3_well, dest.top(), new_tip='never')\n p1000.drop_tip()\n ctx.comment('\\n\\n\\n\\n\\n')\n\n # npw4\n p1000.pick_up_tip()\n for npw4_well, dest in zip(npw4*num_samp, npw4_block.wells()[:num_samp]):\n p1000.transfer(600, npw4_well, dest.top(), new_tip='never')\n p1000.drop_tip()\n\n # elution buffer\n pick_up(p300)\n for elution_tubes, elution_well in zip(elution_buffer*num_samp,\n elution_block.wells()[:num_samp]):\n p300.aspirate(50, elution_tubes)\n p300.dispense(50, elution_well.top())\n p300.drop_tip()\n", - "custom_labware_defs": [], - "fields": [ - { - "default": 96, - "label": "Number of wells (1-96)", - "name": "num_samp", - "type": "int" - }, - { - "default": 15, - "label": "Mix Repetitions to Re-suspend beads", - "name": "mix_reps", - "type": "int" - }, - { - "label": "P1000 Single Channel Mount (GEN2)", - "name": "p1000_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - }, - { - "label": "P300 Multi Channel Mount (GEN2)", - "name": "p300_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p300_multi_gen2" - }, - { - "mount": "right", - "name": "p1000_single_gen2" - } - ], - "labware": [ - { - "name": "NEST 12 Well Reservoir 15 mL on 1", - "share": false, - "slot": "1", - "type": "nest_12_reservoir_15ml" - }, - { - "name": "NEST 12 Well Reservoir 15 mL on 2", - "share": false, - "slot": "2", - "type": "nest_12_reservoir_15ml" - }, - { - "name": "NEST 96 Deepwell Plate 2mL on 3", - "share": false, - "slot": "3", - "type": "nest_96_wellplate_2ml_deep" - }, - { - "name": "NEST 96 Deepwell Plate 2mL on 4", - "share": false, - "slot": "4", - "type": "nest_96_wellplate_2ml_deep" - }, - { - "name": "NEST 96 Deepwell Plate 2mL on 5", - "share": false, - "slot": "5", - "type": "nest_96_wellplate_2ml_deep" - }, - { - "name": "NEST 96 Deepwell Plate 2mL on 6", - "share": false, - "slot": "6", - "type": "nest_96_wellplate_2ml_deep" - }, - { - "name": "NEST 96 Deepwell Plate 2mL on 7", - "share": false, - "slot": "7", - "type": "nest_96_wellplate_2ml_deep" - }, - { - "name": "Opentrons 96 Tip Rack 300 \u00b5L on 8", - "share": false, - "slot": "8", - "type": "opentrons_96_tiprack_300ul" - }, - { - "name": "Opentrons 96 Tip Rack 300 \u00b5L on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_tiprack_300ul" - }, - { - "name": "Opentrons 96 Tip Rack 1000 \u00b5L on 10", - "share": false, - "slot": "10", - "type": "opentrons_96_tiprack_1000ul" - }, - { - "name": "Opentrons 24 Tube Rack with Eppendorf 1.5 mL Safe-Lock Snapcap on 11", - "share": false, - "slot": "11", - "type": "opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.7", - "author": "Rami Farawi ", - "protodestName": "Extraction Prep with Kingfisher Flex Extractor", - "source": "Custom Protodest Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/13ea1e-part1/README.json b/protoBuilds/13ea1e-part1/README.json deleted file mode 100644 index 022def778..000000000 --- a/protoBuilds/13ea1e-part1/README.json +++ /dev/null @@ -1,34 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "Sample Prep": [ - "Plate Filling" - ] - }, - "deck-setup": "\nDeck setup with samples loaded into all wells except A1 and B1.\n\n", - "description": "This protocol preps a sample plate as well as an ethanol, NPW3, NPW4, and elution buffer plate for further use in a Kingfisher Flex Extractor. Samples are pre-loaded onto the sample plate before the protocol begins. Mag beads are then added to sample, and after an incubation step, all other reagent plates are prepped. \nThe protocol is broken down into 3 main parts:\n Controls are added to sample plate\n Proteinase K is added to samples\n Magnetic Beads are added, incubate\n Sample blocks made\nNote: For all transfers between reservoirs/tubes to well plate, transfers will always iterate over all wells in the source. For example, magnetic beads will be transferred from A1 to plate, A2 to plate, A3 to plate, A4 to plate, A1 to plate, etc. Consequently, all reaction volumes should be split equally into respective wells as seen in the deck layout.\nExplanation of complex parameters below:\n Number of samples: Specify the number of populated wells (1-96, include controls) that the sample block, elution buffer block, ethanol block, NPW3 block, and NPW4 block will be filled.\n Mix repetitions to resuspend beads: Specify the amount of mix steps to re-suspend beads each time the pipette returns to the reservoir.\n P1000 Single Channel Mount (GEN2): Specify which mount the P1000 Single Channel pipette will be mounted.\n P300 Multi Channel Mount (GEN2): Specify which mount the P300 Multi Channel pipette will be mounted.\n", - "internal": "13ea1e", - "labware": "\nKingfisher 96 Well Plate\nNEST 12-Well Reservoirs, 15 mL\nOpentrons 20\u00b5L Tips\nOpentrons 300\u00b5L Tips\nOpentrons 4-in-1 tube rack with 1.5mL tubes\n", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* Sample Prep\n\t* Plate Filling\n\n", - "deck-setup": "* Deck setup with samples loaded into all wells except A1 and B1.\n\n![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/13ea1e/pt1/Screen+Shot+2021-05-26+at+11.24.55+AM.png)\n\n", - "description": "This protocol preps a sample plate as well as an ethanol, NPW3, NPW4, and elution buffer plate for further use in a Kingfisher Flex Extractor. Samples are pre-loaded onto the sample plate before the protocol begins. Mag beads are then added to sample, and after an incubation step, all other reagent plates are prepped. \n\nThe protocol is broken down into 3 main parts:\n* Controls are added to sample plate\n* Proteinase K is added to samples\n* Magnetic Beads are added, incubate\n* Sample blocks made\n\nNote: For all transfers between reservoirs/tubes to well plate, transfers will always iterate over all wells in the source. For example, magnetic beads will be transferred from A1 to plate, A2 to plate, A3 to plate, A4 to plate, A1 to plate, etc. Consequently, all reaction volumes should be split equally into respective wells as seen in the deck layout.\n\nExplanation of complex parameters below:\n* `Number of samples`: Specify the number of populated wells (1-96, include controls) that the sample block, elution buffer block, ethanol block, NPW3 block, and NPW4 block will be filled.\n* `Mix repetitions to resuspend beads`: Specify the amount of mix steps to re-suspend beads each time the pipette returns to the reservoir.\n* `P1000 Single Channel Mount (GEN2)`: Specify which mount the P1000 Single Channel pipette will be mounted.\n* `P300 Multi Channel Mount (GEN2)`: Specify which mount the P300 Multi Channel pipette will be mounted.\n---\n\n", - "internal": "13ea1e\n", - "labware": "* Kingfisher 96 Well Plate\n* [NEST 12-Well Reservoirs, 15 mL](https://shop.opentrons.com/collections/reservoirs/products/nest-12-well-reservoir-15-ml)\n* [Opentrons 20\u00b5L Tips](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-10ul-tips)\n* [Opentrons 300\u00b5L Tips](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips)\n* [Opentrons 4-in-1 tube rack with 1.5mL tubes](https://shop.opentrons.com/collections/racks-and-adapters/products/tube-rack-set-1)\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "partner": "[Partner Name](partner website link)\n\n", - "pipettes": "* [P1000 GEN2 Single Channel Pipette](https://shop.opentrons.com/collections/ot-2-robot/products/single-channel-electronic-pipette)\n* [P300 GEN2 Multi-Channel Pipette](https://shop.opentrons.com/collections/ot-2-robot/products/8-channel-electronic-pipette)\n\n\n---\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "protocol-steps": "1. Controls are added to sample plate\n2. Proteinase K is added to samples\n3. Magnetic beads are added to samples\n4. Incubate 15 minutes\n5. Ethanol block is prepped.\n6. NPW3 block is prepped.\n7. NPW4 block is prepped.\n10. Elution buffer block is prepped.\n\n", - "reagent-setup": "\n* Reservoir 1: Slot 1\n\n![reservoir 1](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/13ea1e/pt1/Screen+Shot+2021-05-24+at+9.08.52+AM.png)\n* Reservoir 2: Slot 2\n\n![reservoir 2](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/13ea1e/pt1/Screen+Shot+2021-05-24+at+9.14.53+AM.png)\n* Tube rack: Slot 11\n\n![tube rack](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/13ea1e/pt1/Screen+Shot+2021-05-24+at+9.09.13+AM.png)\n\n---\n\n", - "title": "Extraction Prep with Kingfisher Flex Extractor" - }, - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "partner": "Partner Name", - "pipettes": "\nP1000 GEN2 Single Channel Pipette\nP300 GEN2 Multi-Channel Pipette\n\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "protocol-steps": "\nControls are added to sample plate\nProteinase K is added to samples\nMagnetic beads are added to samples\nIncubate 15 minutes\nEthanol block is prepped.\nNPW3 block is prepped.\nNPW4 block is prepped.\nElution buffer block is prepped.\n", - "reagent-setup": "\nReservoir 1: Slot 1\n\n\n* Reservoir 2: Slot 2\n\n* Tube rack: Slot 11\n\n", - "title": "Extraction Prep with Kingfisher Flex Extractor" -} \ No newline at end of file diff --git a/protoBuilds/13ea1e-part1/metadata.json b/protoBuilds/13ea1e-part1/metadata.json deleted file mode 100644 index f9c279f16..000000000 --- a/protoBuilds/13ea1e-part1/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "13ea1e-part1.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": false, - "skip-tests": false - }, - "path": "protocols/13ea1e-part1", - "slug": "13ea1e-part1", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/13fd88/13fd88.ot2.apiv2.py.json b/protoBuilds/13fd88/13fd88.ot2.apiv2.py.json index 88926a10c..c194bf909 100644 --- a/protoBuilds/13fd88/13fd88.ot2.apiv2.py.json +++ b/protoBuilds/13fd88/13fd88.ot2.apiv2.py.json @@ -2341,5 +2341,12 @@ "protocolName": "Protein Purification with Magnetic NI Resin", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 7 lw Greiner BioOne 96 Well Microplate on Magnetic Module GEN2 on 7", + "share": false, + "slot": "7", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/141a1a/141a1a.ot2.apiv2.py.json b/protoBuilds/141a1a/141a1a.ot2.apiv2.py.json index 5e7e4cdee..a0f4528fc 100644 --- a/protoBuilds/141a1a/141a1a.ot2.apiv2.py.json +++ b/protoBuilds/141a1a/141a1a.ot2.apiv2.py.json @@ -4825,5 +4825,12 @@ "protocolName": "Cell-Free Gene Expression (TXTL) Test", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/1440ad/1440ad.ot2.apiv2.py.json b/protoBuilds/1440ad/1440ad.ot2.apiv2.py.json index 853d5ac91..1c7e3e790 100644 --- a/protoBuilds/1440ad/1440ad.ot2.apiv2.py.json +++ b/protoBuilds/1440ad/1440ad.ot2.apiv2.py.json @@ -225,5 +225,24 @@ "protocolName": "Extraction with Mag-Bind TotalPure NGS kit", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw MAG PLATE on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw SAMPLES on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 6 lw COOL REAGENTS on Temperature Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/14b685/14b685.ot2.apiv2.py.json b/protoBuilds/14b685/14b685.ot2.apiv2.py.json index 4c634f51b..3ab0c65e6 100644 --- a/protoBuilds/14b685/14b685.ot2.apiv2.py.json +++ b/protoBuilds/14b685/14b685.ot2.apiv2.py.json @@ -150,5 +150,12 @@ "protocolName": "PCR Clean-Up for Illumina 16S", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 10 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN1 on 10", + "share": false, + "slot": "10", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/1577-v2/custom_chip_PCR_prep.ot2.apiv2.py.json b/protoBuilds/1577-v2/custom_chip_PCR_prep.ot2.apiv2.py.json index 17b305c6a..8ecd36d51 100644 --- a/protoBuilds/1577-v2/custom_chip_PCR_prep.ot2.apiv2.py.json +++ b/protoBuilds/1577-v2/custom_chip_PCR_prep.ot2.apiv2.py.json @@ -1523,7 +1523,7 @@ "type": "opentrons_96_tiprack_300ul" }, { - "name": "2ml Eppendorf snapcap reagent tubes on Temperature Module GEN1 on 6", + "name": "2ml Eppendorf snapcap reagent tubes on Temperature Module on 6", "share": false, "slot": "6", "type": "opentrons_24_aluminumblock_nest_2ml_snapcap" @@ -1547,5 +1547,18 @@ "protocolName": "Custom Chip PCR Preparation", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw thermocycler plate on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module on 6 lw 2ml Eppendorf snapcap reagent tubes on Temperature Module on 6", + "share": false, + "slot": "6", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/1649b1/1649b1.ot2.apiv2.py.json b/protoBuilds/1649b1/1649b1.ot2.apiv2.py.json index bfa77b32a..2f3a851f7 100644 --- a/protoBuilds/1649b1/1649b1.ot2.apiv2.py.json +++ b/protoBuilds/1649b1/1649b1.ot2.apiv2.py.json @@ -1328,5 +1328,18 @@ "description": "Custom Protocol Request", "protocolName": "LGC Sbeadex Plant Maxi Kit Nucleic Acid Extraction" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/18d6a1/18d6a1.ot2.apiv2.py.json b/protoBuilds/18d6a1/18d6a1.ot2.apiv2.py.json index fa032290d..89200db46 100644 --- a/protoBuilds/18d6a1/18d6a1.ot2.apiv2.py.json +++ b/protoBuilds/18d6a1/18d6a1.ot2.apiv2.py.json @@ -1315,5 +1315,12 @@ "protocolName": "MGI Easy Nucleic Acid Extraction Kit", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 10 lw Extraction Plate on Magnetic Module GEN2 on 10", + "share": false, + "slot": "10", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/19313a/19313a.ot2.apiv2.py.json b/protoBuilds/19313a/19313a.ot2.apiv2.py.json index 6ed0ee830..7a4b114dc 100644 --- a/protoBuilds/19313a/19313a.ot2.apiv2.py.json +++ b/protoBuilds/19313a/19313a.ot2.apiv2.py.json @@ -1386,5 +1386,18 @@ "protocolName": "RNA Extraction with Magnetic Life", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 7 lw Mag Plate on Magnetic Module GEN2 on 7", + "share": false, + "slot": "7", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 10 lw Temperature tuberack on Temperature Module GEN2 on 10", + "share": false, + "slot": "10", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/19fc32/19fc32.ot2.apiv2.py.json b/protoBuilds/19fc32/19fc32.ot2.apiv2.py.json index de0b2fd51..b1b75c415 100644 --- a/protoBuilds/19fc32/19fc32.ot2.apiv2.py.json +++ b/protoBuilds/19fc32/19fc32.ot2.apiv2.py.json @@ -44,7 +44,7 @@ "type": "corning_384_wellplate_112ul_flat" }, { - "name": "Mag Plate on Magnetic Module GEN1 on 4", + "name": "Mag Plate on Magnetic Module on 4", "share": false, "slot": "4", "type": "biorad_96_wellplate_200ul_pcr" @@ -98,5 +98,12 @@ "protocolName": "Library Prep Clean Up", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 4 lw Mag Plate on Magnetic Module on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/1a2343/pcr_prep.ot2.apiv2.py.json b/protoBuilds/1a2343/pcr_prep.ot2.apiv2.py.json index e92bc37f4..7f3081fe1 100644 --- a/protoBuilds/1a2343/pcr_prep.ot2.apiv2.py.json +++ b/protoBuilds/1a2343/pcr_prep.ot2.apiv2.py.json @@ -63,7 +63,7 @@ "type": "opentrons_96_tiprack_20ul" }, { - "name": "reagent plate on Temperature Module GEN1 on 4", + "name": "reagent plate on Temperature Module on 4", "share": false, "slot": "4", "type": "usascientific_96_wellplate_2.4ml_deep" @@ -113,7 +113,7 @@ "type": "thermocycler" }, { - "name": "TemperatureModuleContext at Temperature Module GEN1 on 4 lw reagent plate on Temperature Module GEN1 on 4", + "name": "TemperatureModuleContext at Temperature Module on 4 lw reagent plate on Temperature Module on 4", "share": false, "slot": "4", "type": "tempdeck" diff --git a/protoBuilds/1bcd67/normalization.ot2.apiv2.py.json b/protoBuilds/1bcd67/normalization.ot2.apiv2.py.json index b61d3b8c1..67dc2e2c6 100644 --- a/protoBuilds/1bcd67/normalization.ot2.apiv2.py.json +++ b/protoBuilds/1bcd67/normalization.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "import math\nimport json\n\nmetadata = {\n 'protocolName': 'Normalization',\n 'author': 'Nick ',\n 'source': 'Protocol Library',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [dil_json_1, dil_json_2, dil_json_3, p1000_mount, m300_mount, final_vol\n ] = get_values( # noqa: F821\n 'dil_json_1', 'dil_json_2', 'dil_json_3', 'p1000_mount', 'm300_mount',\n 'final_vol')\n\n # labware\n dw_plate = ctx.load_labware('thermofisherabgene_96_wellplate_2200ul', '8',\n 'deepwell plate')\n final_dilution_plates = [\n ctx.load_labware('nunc_96_wellplate_500ul', slot,\n f'final dilution plate {i+1}')\n for i, slot in enumerate(['4', '5', '6'])]\n diluent = ctx.load_labware('thermofishernalgene_1_reservoir_300000ul',\n '9', 'diluent').wells()[0]\n tipracks1000 = [\n ctx.load_labware('opentrons_96_tiprack_1000ul', slot)\n for slot in ['10']]\n tipracks300 = [\n ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in ['7']]\n\n # pipettes\n if p1000_mount == m300_mount:\n raise Exception('Pipette mounts cannot match.')\n p1000 = ctx.load_instrument('p1000_single_gen2', p1000_mount,\n tip_racks=tipracks1000)\n p300 = ctx.load_instrument('p300_multi_gen2', m300_mount,\n tip_racks=tipracks300)\n\n tip_data = {\n 'single': {\n 'count': 0,\n 'tips': [\n well for rack in tipracks300[::-1]\n for col in rack.columns()[::-1]\n for well in col[::-1]]\n },\n 'multi': {\n 'count': 0,\n 'tips': [well for rack in tipracks300 for well in rack.rows()[0]]\n }\n }\n\n def pickup_p300(mode='single'):\n current = 0.1 if mode == 'single' else 0.5\n ctx._implementation._hw_manager.hardware._attached_instruments[\n p300._implementation.get_mount()].update_config_item(\n 'pick_up_current', current)\n\n p300.pick_up_tip(tip_data[mode]['tips'][tip_data[mode]['count']])\n tip_data[mode]['count'] += 1\n\n def extract_well_name(well_obj):\n return well_obj.display_name.split(' ')[0]\n\n def custom_transfer(vol, source, dest, pip=p300):\n num_trans = math.ceil(vol/pip.max_volume)\n vol_per_trans = vol/num_trans\n for n in range(num_trans):\n pip.aspirate(vol_per_trans, source)\n pip.dispense(vol_per_trans, dest)\n\n def determine_dil(col):\n rows = 'ABCDEFGH'\n col = dw_plate.rows()[0].index(col)\n dict = [dict1, dict2, dict3][col % 3]\n wells_to_check = [row + str(col+1) for row in rows]\n for well in wells_to_check:\n if dict[well]:\n return True\n return False\n\n # pre-parse `None` to `null`\n dil_json_1 = dil_json_1.replace('None', 'null')\n dil_json_2 = dil_json_2.replace('None', 'null')\n dil_json_3 = dil_json_3.replace('None', 'null')\n\n # read .json files as dictionaries\n dict1 = json.loads(dil_json_1)\n dict2 = json.loads(dil_json_2)\n dict3 = json.loads(dil_json_3)\n\n map_dil_wells = {\n well_set[0]: {\n well_set[0]: dict1[extract_well_name(well_set[0])],\n well_set[1]: dict2[extract_well_name(well_set[1])],\n well_set[2]: dict3[extract_well_name(well_set[2])]\n }\n for well_set in [\n row[i*3:(i+1)*3] for i in range(4) for row in dw_plate.rows()]\n }\n\n final_locations = []\n for key, dict in map_dil_wells.items():\n final_well = None\n for well, vol in dict.items():\n if vol:\n final_well = well\n final_locations.append(final_well)\n\n # pre-add diluent\n pickup_p300('multi')\n for col in dw_plate.rows()[0]:\n if determine_dil(col):\n for _ in range(4): # 4x 200ul = 800ul\n p300.transfer(200, diluent, col, new_tip='never')\n p300.drop_tip()\n\n # prompt user to transfer neat sample\n display_wells = [\n well for well, vol in dict1.items() if vol]\n display_vols = [\n round(vol, 2) for vol in dict1.values() if vol]\n sample_str = '\\n'.join([\n f'Transfer {display_vol}uL to well {display_well} of deepwell \\\nplate on slot 8.'\n for display_well, display_vol in zip(display_wells, display_vols)])\n ctx.pause(msg=sample_str)\n\n # perform dilutions\n for set in map_dil_wells.values():\n for i, (well, vol) in enumerate(set.items()):\n if i > 0 and vol: # neat is manually added\n if vol <= 200:\n pip = p300\n pickup_p300('single')\n else:\n pip = p1000\n p1000.pick_up_tip()\n custom_transfer(vol, list(set.keys())[i-1], well, pip)\n pip.mix(5, 200, well)\n pip.drop_tip()\n\n # final transfer\n final_targets = [\n well for plate in final_dilution_plates for well in plate.rows()[0]]\n\n for source, dest in zip(final_locations, final_targets):\n if source:\n col = int(source.display_name.split(' ')[0][1:])\n if col % 3 == 1:\n pip.mix(5, 200, source)\n p1000.transfer(final_vol, source, dest)\n", + "content": "import math\nimport json\n\nmetadata = {\n 'protocolName': 'Normalization',\n 'author': 'Nick ',\n 'source': 'Protocol Library',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [dil_json_1, dil_json_2, dil_json_3, p1000_mount, m300_mount, final_vol\n ] = get_values( # noqa: F821\n 'dil_json_1', 'dil_json_2', 'dil_json_3', 'p1000_mount', 'm300_mount',\n 'final_vol')\n\n # labware\n dw_plate = ctx.load_labware('thermofisherabgene_96_wellplate_2200ul', '8',\n 'deepwell plate')\n final_dilution_plates = [\n ctx.load_labware('nunc_96_wellplate_500ul', slot,\n f'final dilution plate {i+1}')\n for i, slot in enumerate(['4', '5', '6'])]\n diluent = ctx.load_labware('thermofishernalgene_1_reservoir_300000ul',\n '9', 'diluent').wells()[0]\n tipracks1000 = [\n ctx.load_labware('opentrons_96_tiprack_1000ul', slot)\n for slot in ['10']]\n tipracks300 = [\n ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in ['7']]\n\n # pipettes\n if p1000_mount == m300_mount:\n raise Exception('Pipette mounts cannot match.')\n p1000 = ctx.load_instrument('p1000_single_gen2', p1000_mount,\n tip_racks=tipracks1000)\n p300 = ctx.load_instrument('p300_multi_gen2', m300_mount,\n tip_racks=tipracks300)\n\n tip_data = {\n 'single': {\n 'count': 0,\n 'tips': [\n well for rack in tipracks300[::-1]\n for col in rack.columns()[::-1]\n for well in col[::-1]]\n },\n 'multi': {\n 'count': 0,\n 'tips': [well for rack in tipracks300 for well in rack.rows()[0]]\n }\n }\n\n def pickup_p300(mode='single'):\n current = 0.1 if mode == 'single' else 0.5\n ctx._hw_manager.hardware._attached_instruments[\n p300._implementation.get_mount()].update_config_item(\n 'pick_up_current', current)\n\n p300.pick_up_tip(tip_data[mode]['tips'][tip_data[mode]['count']])\n tip_data[mode]['count'] += 1\n\n def extract_well_name(well_obj):\n return well_obj.display_name.split(' ')[0]\n\n def custom_transfer(vol, source, dest, pip=p300):\n num_trans = math.ceil(vol/pip.max_volume)\n vol_per_trans = vol/num_trans\n for n in range(num_trans):\n pip.aspirate(vol_per_trans, source)\n pip.dispense(vol_per_trans, dest)\n\n def determine_dil(col):\n rows = 'ABCDEFGH'\n col = dw_plate.rows()[0].index(col)\n dict = [dict1, dict2, dict3][col % 3]\n wells_to_check = [row + str(col+1) for row in rows]\n for well in wells_to_check:\n if dict[well]:\n return True\n return False\n\n # pre-parse `None` to `null`\n dil_json_1 = dil_json_1.replace('None', 'null')\n dil_json_2 = dil_json_2.replace('None', 'null')\n dil_json_3 = dil_json_3.replace('None', 'null')\n\n # read .json files as dictionaries\n dict1 = json.loads(dil_json_1)\n dict2 = json.loads(dil_json_2)\n dict3 = json.loads(dil_json_3)\n\n map_dil_wells = {\n well_set[0]: {\n well_set[0]: dict1[extract_well_name(well_set[0])],\n well_set[1]: dict2[extract_well_name(well_set[1])],\n well_set[2]: dict3[extract_well_name(well_set[2])]\n }\n for well_set in [\n row[i*3:(i+1)*3] for i in range(4) for row in dw_plate.rows()]\n }\n\n final_locations = []\n for key, dict in map_dil_wells.items():\n final_well = None\n for well, vol in dict.items():\n if vol:\n final_well = well\n final_locations.append(final_well)\n\n # pre-add diluent\n pickup_p300('multi')\n for col in dw_plate.rows()[0]:\n if determine_dil(col):\n for _ in range(4): # 4x 200ul = 800ul\n p300.transfer(200, diluent, col, new_tip='never')\n p300.drop_tip()\n\n # prompt user to transfer neat sample\n display_wells = [\n well for well, vol in dict1.items() if vol]\n display_vols = [\n round(vol, 2) for vol in dict1.values() if vol]\n sample_str = '\\n'.join([\n f'Transfer {display_vol}uL to well {display_well} of deepwell \\\nplate on slot 8.'\n for display_well, display_vol in zip(display_wells, display_vols)])\n ctx.pause(msg=sample_str)\n\n # perform dilutions\n for set in map_dil_wells.values():\n for i, (well, vol) in enumerate(set.items()):\n if i > 0 and vol: # neat is manually added\n if vol <= 200:\n pip = p300\n pickup_p300('single')\n else:\n pip = p1000\n p1000.pick_up_tip()\n custom_transfer(vol, list(set.keys())[i-1], well, pip)\n pip.mix(5, 200, well)\n pip.drop_tip()\n\n # final transfer\n final_targets = [\n well for plate in final_dilution_plates for well in plate.rows()[0]]\n\n for source, dest in zip(final_locations, final_targets):\n if source:\n col = int(source.display_name.split(' ')[0][1:])\n if col % 3 == 1:\n pip.mix(5, 200, source)\n p1000.transfer(final_vol, source, dest)\n", "custom_labware_defs": [ { "brand": { diff --git a/protoBuilds/1ccd23-station-B/extraction.ot2.apiv2.py.json b/protoBuilds/1ccd23-station-B/extraction.ot2.apiv2.py.json index 5087349c8..d3fd2533e 100644 --- a/protoBuilds/1ccd23-station-B/extraction.ot2.apiv2.py.json +++ b/protoBuilds/1ccd23-station-B/extraction.ot2.apiv2.py.json @@ -205,5 +205,18 @@ "author": "Opentrons ", "protocolName": "COVID-19 Station B RNA Extraction" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw deepwell plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw elution plate on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/1eeb01/1eeb01.ot2.apiv2.py.json b/protoBuilds/1eeb01/1eeb01.ot2.apiv2.py.json index d9653be3b..0a5f68f3c 100644 --- a/protoBuilds/1eeb01/1eeb01.ot2.apiv2.py.json +++ b/protoBuilds/1eeb01/1eeb01.ot2.apiv2.py.json @@ -122,5 +122,18 @@ "protocolName": "Nucleic Acid Extraction Using 1.5mL Tubes", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 10 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 10", + "share": false, + "slot": "10", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 7 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Snapcap on Temperature Module GEN2 on 7", + "share": false, + "slot": "7", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/1f96ca-part-2/1f96ca-part-2.ot2.apiv2.py.json b/protoBuilds/1f96ca-part-2/1f96ca-part-2.ot2.apiv2.py.json index 79bd7d7ce..2a1455202 100644 --- a/protoBuilds/1f96ca-part-2/1f96ca-part-2.ot2.apiv2.py.json +++ b/protoBuilds/1f96ca-part-2/1f96ca-part-2.ot2.apiv2.py.json @@ -149,5 +149,12 @@ "author": "Steve Plonk ", "protocolName": "NGS Library Prep: KAPA Hyper Plus 96rx, cat#07962428001,\n ROCHE - part 2 of 2: post-PCR clean up and pooling" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 9 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 9", + "share": false, + "slot": "9", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/1f96ca/1f96ca.ot2.apiv2.py.json b/protoBuilds/1f96ca/1f96ca.ot2.apiv2.py.json index fa5aee002..2421aa72a 100644 --- a/protoBuilds/1f96ca/1f96ca.ot2.apiv2.py.json +++ b/protoBuilds/1f96ca/1f96ca.ot2.apiv2.py.json @@ -2492,5 +2492,18 @@ "author": "Steve Plonk ", "protocolName": "NGS Library Prep: KAPA Hyper Plus 96rx, cat#07962428001,\n ROCHE - part 1 of 2" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 9 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 9", + "share": false, + "slot": "9", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/203136/203136.ot2.apiv2.py.json b/protoBuilds/203136/203136.ot2.apiv2.py.json index 70f574329..b0ca0af60 100644 --- a/protoBuilds/203136/203136.ot2.apiv2.py.json +++ b/protoBuilds/203136/203136.ot2.apiv2.py.json @@ -69,7 +69,7 @@ "type": "opentrons_96_filtertiprack_200ul" }, { - "name": "Deep Well Plate on Magnetic Module GEN1 on 4", + "name": "Deep Well Plate on Magnetic Module on 4", "share": false, "slot": "4", "type": "usascientific_96_wellplate_2.4ml_deep" @@ -129,5 +129,12 @@ "protocolName": "Purification of Genomic DNA", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 4 lw Deep Well Plate on Magnetic Module on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/211fe1/mass_spec_sample_prep.ot2.apiv2.py.json b/protoBuilds/211fe1/mass_spec_sample_prep.ot2.apiv2.py.json index 47ff46c99..07dac4eff 100644 --- a/protoBuilds/211fe1/mass_spec_sample_prep.ot2.apiv2.py.json +++ b/protoBuilds/211fe1/mass_spec_sample_prep.ot2.apiv2.py.json @@ -80,5 +80,12 @@ "protocolName": "Mass Spec Sample Prep", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/21e4d8-pt2/21e4d8-pt2.ot2.apiv2.py.json b/protoBuilds/21e4d8-pt2/21e4d8-pt2.ot2.apiv2.py.json index 10e9bfbbd..34986fd52 100644 --- a/protoBuilds/21e4d8-pt2/21e4d8-pt2.ot2.apiv2.py.json +++ b/protoBuilds/21e4d8-pt2/21e4d8-pt2.ot2.apiv2.py.json @@ -1504,5 +1504,12 @@ "protocolName": "Twist Library Prep || Part 2: Ligate Adapters", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 10 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN1 on 10", + "share": false, + "slot": "10", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/21e4d8-pt3/21e4d8-pt3.ot2.apiv2.py.json b/protoBuilds/21e4d8-pt3/21e4d8-pt3.ot2.apiv2.py.json index 7f2d5f493..fe21fb756 100644 --- a/protoBuilds/21e4d8-pt3/21e4d8-pt3.ot2.apiv2.py.json +++ b/protoBuilds/21e4d8-pt3/21e4d8-pt3.ot2.apiv2.py.json @@ -1504,5 +1504,12 @@ "protocolName": "Twist Library Prep || Part 3: PCR Amplification", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 10 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN1 on 10", + "share": false, + "slot": "10", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/245eb2/245eb2.ot2.apiv2.py.json b/protoBuilds/245eb2/245eb2.ot2.apiv2.py.json index c7599dfd2..eb23726ff 100644 --- a/protoBuilds/245eb2/245eb2.ot2.apiv2.py.json +++ b/protoBuilds/245eb2/245eb2.ot2.apiv2.py.json @@ -1240,5 +1240,12 @@ "protocolName": "Nucleic Acid Extraction", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 6 lw Axygen 96 Well Plate 300 \u00b5L on Magnetic Module GEN1 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/269b21/pcr_prep.ot2.apiv2.py.json b/protoBuilds/269b21/pcr_prep.ot2.apiv2.py.json index 48990b5ef..a3e4ab71e 100644 --- a/protoBuilds/269b21/pcr_prep.ot2.apiv2.py.json +++ b/protoBuilds/269b21/pcr_prep.ot2.apiv2.py.json @@ -5513,7 +5513,7 @@ "type": "genmate_96_aluminumblock_20ul" }, { - "name": "Opentrons 24 Well Aluminum Block with NEST 1.5 mL Snapcap on Temperature Module GEN1 on 4", + "name": "Opentrons 24 Well Aluminum Block with NEST 1.5 mL Snapcap on Temperature Module on 4", "share": false, "slot": "4", "type": "opentrons_24_aluminumblock_nest_1.5ml_snapcap" @@ -5543,5 +5543,12 @@ "protocolName": "PCR Prep", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module on 4 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Snapcap on Temperature Module on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/280ea4/generic_station_C.ot2.apiv2.py.json b/protoBuilds/280ea4/generic_station_C.ot2.apiv2.py.json deleted file mode 100644 index 8b52b4cc0..000000000 --- a/protoBuilds/280ea4/generic_station_C.ot2.apiv2.py.json +++ /dev/null @@ -1,1280 +0,0 @@ -{ - "content": "from opentrons import protocol_api\nimport json\nimport os\nimport math\n\n# metadata\nmetadata = {\n 'protocolName': 'PCR Prep',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.9'\n}\n\n\ndef run(ctx: protocol_api.ProtocolContext):\n [num_samples, assay, prepare_mastermix, p300_mount,\n tip_track] = get_values( # noqa: F821\n 'num_samples', 'assay', 'prepare_mastermix',\n 'p300_mount', 'tip_track')\n\n # check source (elution) labware type\n source_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n '1', 'DNA source plate')\n tips300 = [\n ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)\n for slot in ['5', '6', '8', '9']]\n tips20 = []\n tempdeck = ctx.load_module('Temperature Module Gen2', '7')\n pcr_plate = tempdeck.load_labware('biorad_96_aluminumblock_200ul',\n 'PCR strips')\n tempdeck.set_temperature(4)\n tube_block = ctx.load_labware(\n 'opentrons_24_aluminumblock_nest_2ml_screwcap', '3',\n '2ml screw tube aluminum block for mastermix + reagents')\n\n # pipette\n p300 = ctx.load_instrument('p300_single_gen2', p300_mount,\n tip_racks=tips300)\n m20_mount = 'left' if p300_mount == 'right' else 'right'\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount)\n\n # setup up sample sources and destinations\n sources = source_plate.wells()[:num_samples]\n sample_dests = pcr_plate.wells()[:num_samples]\n\n tip_log = {'count': {}}\n folder_path = '/data/C'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n data = json.load(json_file)\n if 'tips20' in data:\n tip_log['count'][m20] = data['tips20']\n else:\n tip_log['count'][m20] = 0\n if 'tips300' in data:\n tip_log['count'][p300] = data['tips300']\n else:\n tip_log['count'][p300] = 0\n else:\n tip_log['count'] = {m20: 0, p300: 0}\n else:\n tip_log['count'] = {m20: 0, p300: 0}\n\n tip_log['tips'] = {\n m20: [tip for rack in tips20 for tip in rack.rows()[0]],\n p300: [tip for rack in tips300 for tip in rack.wells()]\n }\n tip_log['max'] = {\n pip: len(tip_log['tips'][pip])\n for pip in [m20, p300]\n }\n\n def pick_up(pip):\n nonlocal tip_log\n if tip_log['count'][pip] == tip_log['max'][pip]:\n ctx.pause('Replace ' + str(pip.max_volume) + '\u00b5l tipracks before \\\nresuming.')\n pip.reset_tipracks()\n tip_log['count'][pip] = 0\n pip.pick_up_tip(tip_log['tips'][pip][tip_log['count'][pip]])\n tip_log['count'][pip] += 1\n\n \"\"\" mastermix component maps \"\"\"\n mm_tubes = tube_block.wells()[:2]\n [mmx, enzyme, primer1, primer2, primer3, primer4, primer5, primer6, probe,\n other, nfh2o] = tube_block.wells()[2:13]\n mm_map = {\n '1': {\n 'sample_vol': 5,\n 'mm_vol': 50,\n 'components': {\n tube: vol for tube, vol in zip(\n [mmx, enzyme, primer1, primer2, primer3, primer4, primer5,\n primer6, nfh2o],\n [25, 2, 2, 2, 2, 2, 2, 2, 11])\n }\n },\n '2': {\n 'sample_vol': 5,\n 'mm_vol': 50,\n 'components': {\n tube: vol for tube, vol in zip(\n [mmx, enzyme, primer1, primer2, nfh2o],\n [25, 2, 1, 1, 21])\n }\n },\n '3': {\n 'sample_vol': 5,\n 'mm_vol': 22.5,\n 'components': {\n tube: vol for tube, vol in zip(\n [mmx, primer1, primer2, nfh2o],\n [12.5, 1.25, 1.25, 8.5])\n }\n },\n '4': {\n 'sample_vol': 5,\n 'mm_vol': 17,\n 'components': {\n tube: vol for tube, vol in zip(\n [mmx, enzyme, primer1, primer2, primer3, probe, nfh2o],\n [12.5, 1, 0.25, 0.25, 0.25, 0.25, 2.5])\n }\n },\n '5': {\n 'sample_vol': 5,\n 'mm_vol': 20,\n 'components': {\n tube: vol for tube, vol in zip(\n [mmx, primer1, primer2, probe, other, nfh2o],\n [6.25, 0.1, 0.2, 0.5, 1, 11.95])\n }\n }\n }\n mm_dict = mm_map[assay]\n sample_vol = mm_dict['sample_vol']\n mm_vol = mm_dict['mm_vol']\n\n vol_overage = 1.2 if num_samples > 48 else 1.1\n total_mm_vol = mm_vol*(num_samples+2)*vol_overage\n # translate total mastermix volume to starting height\n r = mm_tubes[0].diameter/2\n mm_heights = {\n tube: total_mm_vol/(math.pi*(r**2)) - 5\n for tube in mm_tubes\n }\n\n def h_track(vol, tube):\n dh = 1.1*vol/(math.pi*(r**2)) # compensate for 10% theoretical v loss\n h = mm_heights[tube]\n h = h - dh if h - dh > 2 else 2 # stop at 2mm\n mm_heights[tube] = h\n return tube.bottom(mm_heights[tube])\n\n def p300_transfer(vol, source, dest):\n if vol < 20:\n p300.air_gap(20-vol)\n p300.aspirate(vol, source)\n p300.dispense(vol, dest)\n p300.dispense(p300.current_volume, dest.top())\n else:\n num_trans = math.ceil(vol/260)\n vol_per_trans = vol/num_trans\n for _ in range(num_trans):\n p300.air_gap(20)\n p300.aspirate(vol_per_trans, source)\n ctx.delay(seconds=2)\n p300.touch_tip(source)\n p300.air_gap(20)\n p300.dispense(20, dest.top()) # void air gap\n p300.dispense(vol_per_trans, dest.bottom(2))\n p300.dispense(20, dest.top()) # void pre-loaded air gap\n # p300.blow_out(mm_tube.top())\n p300.touch_tip(dest)\n\n if prepare_mastermix:\n p300.flow_rate.aspirate = 15\n p300.flow_rate.dispense = 30\n vol_overage = 1.2 if num_samples > 48 else 1.1\n if mm_dict['mm_vol']*num_samples*vol_overage > 1700:\n num_mm_tubes = 2\n else:\n num_mm_tubes = 1\n for i, (tube, vol) in enumerate(mm_dict['components'].items()):\n comp_vol = vol*num_samples*vol_overage/num_mm_tubes\n pick_up(p300)\n for mm_tube in mm_tubes[:num_mm_tubes]:\n p300_transfer(comp_vol, tube, mm_tube)\n if i < len(mm_dict['components'].items()) - 1:\n p300.drop_tip()\n mm_total_vol_per_tube = mm_vol*(num_samples)*vol_overage/num_mm_tubes\n if not p300.hw_pipette['has_tip']:\n pick_up(p300)\n if mm_total_vol_per_tube / 2 <= 300:\n mix_vol = mm_total_vol_per_tube / 2\n else:\n mix_vol = 300\n for tube in mm_tubes[:num_mm_tubes]:\n if num_samples > 48:\n mix_loc = mm_tube.bottom(20)\n else:\n mix_loc = mm_tube.bottom(5)\n p300.mix(7, mix_vol, mix_loc)\n # p300.blow_out(mm_tube.top())\n p300.touch_tip()\n\n # transfer mastermix to plate\n if num_mm_tubes == 1:\n sample_dest_sets = [sample_dests]\n else:\n split_ind = math.ceil(num_samples/2)\n sample_dest_sets = [sample_dests[:split_ind], sample_dests[split_ind:]]\n for mm_tube, dest_set in zip(mm_tubes, sample_dest_sets):\n p300.distribute(mm_dict['mm_vol'], mm_tube, dest_set,\n new_tip='never')\n p300.drop_tip()\n\n # transfer samples to corresponding locations\n for s, d in zip(sources, sample_dests):\n pick_up(p300)\n p300_transfer(sample_vol, s, d)\n p300.drop_tip()\n\n # track final used tip\n if tip_track and not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n data = {\n 'tips20': tip_log['count'][m20],\n 'tips300': tip_log['count'][p300]\n }\n with open(tip_file_path, 'w') as outfile:\n json.dump(data, outfile)\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "Bio-Rad", - "brandId": [ - "TBS0201" - ] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.75, - "yDimension": 85.5, - "zDimension": 20 - }, - "groups": [ - { - "metadata": { - "displayCategory": "tubeRack", - "wellBottomShape": "flat" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8", - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9", - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10", - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11", - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - } - ], - "metadata": { - "displayCategory": "aluminumBlock", - "displayName": "Bio-Rad 96 Aluminum Block 200 \u00b5L", - "displayVolumeUnits": "\u00b5L", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1" - ], - [ - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2" - ], - [ - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3" - ], - [ - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4" - ], - [ - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5" - ], - [ - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6" - ], - [ - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7" - ], - [ - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8" - ], - [ - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9" - ], - [ - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10" - ], - [ - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11" - ], - [ - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - ], - "parameters": { - "format": "irregular", - "isMagneticModuleCompatible": false, - "isTiprack": false, - "loadName": "biorad_96_aluminumblock_200ul", - "quirks": [] - }, - "schemaVersion": 2, - "version": 1, - "wells": { - "A1": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 74.25, - "z": 5 - }, - "A10": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 95.38, - "y": 74.25, - "z": 5 - }, - "A11": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 104.38, - "y": 74.25, - "z": 5 - }, - "A12": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 113.38, - "y": 74.25, - "z": 5 - }, - "A2": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 23.38, - "y": 74.25, - "z": 5 - }, - "A3": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 32.38, - "y": 74.25, - "z": 5 - }, - "A4": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 74.25, - "z": 5 - }, - "A5": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 50.38, - "y": 74.25, - "z": 5 - }, - "A6": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 59.38, - "y": 74.25, - "z": 5 - }, - "A7": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 74.25, - "z": 5 - }, - "A8": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 74.25, - "z": 5 - }, - "A9": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 74.25, - "z": 5 - }, - "B1": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 65.25, - "z": 5 - }, - "B10": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 95.38, - "y": 65.25, - "z": 5 - }, - "B11": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 104.38, - "y": 65.25, - "z": 5 - }, - "B12": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 113.38, - "y": 65.25, - "z": 5 - }, - "B2": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 23.38, - "y": 65.25, - "z": 5 - }, - "B3": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 32.38, - "y": 65.25, - "z": 5 - }, - "B4": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 65.25, - "z": 5 - }, - "B5": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 50.38, - "y": 65.25, - "z": 5 - }, - "B6": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 59.38, - "y": 65.25, - "z": 5 - }, - "B7": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 65.25, - "z": 5 - }, - "B8": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 65.25, - "z": 5 - }, - "B9": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 65.25, - "z": 5 - }, - "C1": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 56.25, - "z": 5 - }, - "C10": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 95.38, - "y": 56.25, - "z": 5 - }, - "C11": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 104.38, - "y": 56.25, - "z": 5 - }, - "C12": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 113.38, - "y": 56.25, - "z": 5 - }, - "C2": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 23.38, - "y": 56.25, - "z": 5 - }, - "C3": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 32.38, - "y": 56.25, - "z": 5 - }, - "C4": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 56.25, - "z": 5 - }, - "C5": { - "depth": 15, - "diameter": 6, - "shape": 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"diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 11.25, - "z": 5 - }, - "H5": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 50.38, - "y": 11.25, - "z": 5 - }, - "H6": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 59.38, - "y": 11.25, - "z": 5 - }, - "H7": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 11.25, - "z": 5 - }, - "H8": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 11.25, - "z": 5 - }, - "H9": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 11.25, - "z": 5 - } - } - } - ], - "fields": [ - { - "default": 96, - "label": "Number of Samples", - "name": "num_samples", - "type": "int" - }, - { - "label": "assay type (see image above for reference)", - "name": "assay", - "options": [ - { - "label": "1", - "value": "1" - }, - { - "label": "2", - "value": "2" - }, - { - "label": "3", - "value": "3" - }, - { - "label": "4", - "value": "4" - }, - { - "label": "5", - "value": "5" - } - ], - "type": "dropDown" - }, - { - "label": "prepare mastermix", - "name": "prepare_mastermix", - "options": [ - { - "label": "yes", - "value": true - }, - { - "label": "no", - "value": false - } - ], - "type": "dropDown" - }, - { - "label": "P300 single-channel pipette GEN2 mount", - "name": "p300_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - }, - { - "label": "track tips across protocol runs", - "name": "tip_track", - "options": [ - { - "label": "no", - "value": false - }, - { - "label": "yes", - "value": true - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p20_multi_gen2" - }, - { - "mount": "right", - "name": "p300_single_gen2" - } - ], - "labware": [ - { - "name": "DNA source plate on 1", - "share": false, - "slot": "1", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "2ml screw tube aluminum block for mastermix + reagents on 3", - "share": false, - "slot": "3", - "type": "opentrons_24_aluminumblock_nest_2ml_screwcap" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "PCR strips on Temperature Module GEN2 on 7", - "share": false, - "slot": "7", - "type": "biorad_96_aluminumblock_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 8", - "share": false, - "slot": "8", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.9", - "author": "Nick ", - "protocolName": "PCR Prep", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/2905a4/2905a4.ot2.apiv2.py.json b/protoBuilds/2905a4/2905a4.ot2.apiv2.py.json index 05f51d159..847e69484 100644 --- a/protoBuilds/2905a4/2905a4.ot2.apiv2.py.json +++ b/protoBuilds/2905a4/2905a4.ot2.apiv2.py.json @@ -2381,5 +2381,24 @@ "description": "Custom Protocol Request", "protocolName": "RNA Purification with Magnetic Beads" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw Origin RNA Sample Plate on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 6 lw Recipient Cooled Plate on Temperature Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 9 lw Mag Deck Plate on Magnetic Module GEN2 on 9", + "share": false, + "slot": "9", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/295c73/295c73.ot2.apiv2.py.json b/protoBuilds/295c73/295c73.ot2.apiv2.py.json index 90463a474..c89e96f4f 100644 --- a/protoBuilds/295c73/295c73.ot2.apiv2.py.json +++ b/protoBuilds/295c73/295c73.ot2.apiv2.py.json @@ -86,5 +86,24 @@ "author": "Steve Plonk ", "protocolName": "swiftbiosci.com accel-amplicon-plus-egfr-pathway-panel" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 6 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN1 on 6", + "share": false, + "slot": "6", + "type": "tempdeck" + }, + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 9 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 9", + "share": false, + "slot": "9", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/29effa-mastermix/29effa-mastermix.ot2.apiv2.py.json b/protoBuilds/29effa-mastermix/29effa-mastermix.ot2.apiv2.py.json index eb6a2cac3..d515e1097 100644 --- a/protoBuilds/29effa-mastermix/29effa-mastermix.ot2.apiv2.py.json +++ b/protoBuilds/29effa-mastermix/29effa-mastermix.ot2.apiv2.py.json @@ -62,5 +62,12 @@ "protocolName": "Lyra Direct Covid-19 Mastermix Distribution", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/2a370c/2a370c.ot2.apiv2.py.json b/protoBuilds/2a370c/2a370c.ot2.apiv2.py.json index 91598f77b..8d6ca8a83 100644 --- a/protoBuilds/2a370c/2a370c.ot2.apiv2.py.json +++ b/protoBuilds/2a370c/2a370c.ot2.apiv2.py.json @@ -117,5 +117,12 @@ "description": "Custom Protocol Request", "protocolName": "Omega Mag-Bind Bacterial DNA 96 Kit" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/2aee74-2/README.json b/protoBuilds/2aee74-2/README.json deleted file mode 100644 index 0eace6f49..000000000 --- a/protoBuilds/2aee74-2/README.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "Proteins & Proteomics": [ - "Olink Target 96" - ] - }, - "deck-setup": "\nNote: all volumes for 96 samples (including controls)\n green on reservoir (slot 5): 10562.0\u00b5l extension mix\n blue on incubation plate (slot 2): samples\n", - "description": "Links:\n Part 1: Incubation\n Part 2: Extension\n* Part 3: Detection\nThis protocol accomplishes part 2/3: Extension for the Olink Target 96 protocol for protein biomarker discovery.\n", - "internal": "2aee74", - "labware": "\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nNEST 12-Well Reservoir, 15 mL\nOpentrons Filter Tips\n", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* Proteins & Proteomics\n\t* Olink Target 96\n\n", - "deck-setup": "![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/2aee74/deck2.png)\nNote: all volumes for 96 samples (including controls)\n* green on reservoir (slot 5): 10562.0\u00b5l extension mix\n* blue on incubation plate (slot 2): samples\n\n---\n\n", - "description": "\nLinks:\n* [Part 1: Incubation](./2aee74)\n* [Part 2: Extension](./2aee74-2)\n* [Part 3: Detection](./2aee74-3)\n\nThis protocol accomplishes part 2/3: Extension for the [Olink Target 96 protocol](https://www.olink.com/products-services/target/) for protein biomarker discovery.\n\n---\n\n", - "internal": "2aee74\n", - "labware": "* [NEST 0.1 mL 96-Well PCR Plate, Full Skirt](https://shop.opentrons.com/collections/verified-labware/products/nest-0-1-ml-96-well-pcr-plate-full-skirt)\n* [NEST 12-Well Reservoir, 15 mL](https://shop.opentrons.com/collections/verified-labware/products/nest-12-well-reservoir-15-ml)\n* [Opentrons Filter Tips](https://shop.opentrons.com/collections/opentrons-tips)\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "pipettes": "* [P300 8-Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/collections/ot-2-pipettes/products/8-channel-electronic-pipette)\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "reagents": "* [Olink Target 96](https://www.olink.com/products-services/target/)\n\n---\n\n", - "title": "Olink Target 96 Part 2/3: Extension" - }, - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "pipettes": "\nP300 8-Channel Electronic Pipette (GEN2)\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "reagents": [ - "Olink Target 96" - ], - "title": "Olink Target 96 Part 2/3: Extension" -} diff --git a/protoBuilds/2aee74-2/metadata.json b/protoBuilds/2aee74-2/metadata.json deleted file mode 100644 index ff28ad11f..000000000 --- a/protoBuilds/2aee74-2/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "olink.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": false, - "skip-tests": false - }, - "path": "protocols/2aee74-2", - "slug": "2aee74-2", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/2aee74-2/olink.ot2.apiv2.py.json b/protoBuilds/2aee74-2/olink.ot2.apiv2.py.json deleted file mode 100644 index 3caeaeb19..000000000 --- a/protoBuilds/2aee74-2/olink.ot2.apiv2.py.json +++ /dev/null @@ -1,1208 +0,0 @@ -{ - "content": "import math\n\nmetadata = {\n 'protocolName': 'Olink Target 96 Part 2/3: Extension',\n 'author': 'Nick ',\n 'description': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n num_samples, plate_type, m300_mount = get_values( # noqa: F821\n 'num_samples', 'plate_type', 'm300_mount')\n\n if not 1 <= num_samples <= 96:\n raise Exception('Invalid number of samples (1-96)')\n\n ext_mix = ctx.load_labware(\n 'nest_12_reservoir_15ml', '5',\n 'reservoir for extension mix (channel 1)').wells()[0]\n inc_plate = ctx.load_labware(plate_type, '2', 'incubation plate')\n tipracks300 = [ctx.load_labware('opentrons_96_tiprack_300ul', '6')]\n\n m300 = ctx.load_instrument('p300_multi_gen2', m300_mount,\n tip_racks=tipracks300)\n\n num_cols = math.ceil(num_samples/8)\n\n ctx.comment('Bring the Incubation Plate to room temperature, spin at 400 x \\\ng for 1 min. Preheat the PCR machine.')\n ctx.comment('Vortex the Extension mix and pour into a multi-channel \\\npipette reservoir.')\n\n m300.pick_up_tip()\n m300.aspirate(20, ext_mix)\n for col in inc_plate.rows()[0][:num_cols]:\n m300.aspirate(96, ext_mix)\n m300.dispense(96, col.top(-1))\n m300.drop_tip()\n\n ctx.comment('Seal the plate with an adhesive plastic film, vortex \\\nthoroughly ensuring that all wells are mixed, and spin down.')\n ctx.comment('Place the Incubation Plate in the thermal cycler, and start \\\nthe PEA program (50\u00b0C 20 min, 95\u00b0C 5 min (95\u00b0C 30s, 54\u00b0C 1 min, 60\u00b0C 1 min) \\\nx17, 10\u00b0C hold).')\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "Generic", - "brandId": [] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.75, - "yDimension": 85.5, - "zDimension": 25 - }, - "groups": [ - { - "metadata": { - "displayCategory": "wellPlate", - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8", - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9", - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10", - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11", - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - } - ], - "metadata": { - "displayCategory": "aluminumBlock", - "displayName": "Generic 96 Aluminum Block 350 \u00b5L", - "displayVolumeUnits": "\u00b5L", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1" - ], - [ - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2" - ], - [ - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3" - ], - [ - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4" - ], - [ - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5" - ], - [ - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6" - ], - [ - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7" - ], - [ - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8" - ], - [ - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9" - ], - [ - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10" - ], - [ - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11" - ], - [ - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - ], - "parameters": { - "format": "irregular", - "isMagneticModuleCompatible": false, - "isTiprack": false, - "loadName": "generic_96_aluminumblock_350ul", - 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"totalLiquidVolume": 350, - "x": 113.38, - "y": 11.25, - "z": 3 - }, - "H2": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 23.38, - "y": 11.25, - "z": 3 - }, - "H3": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 32.38, - "y": 11.25, - "z": 3 - }, - "H4": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 41.38, - "y": 11.25, - "z": 3 - }, - "H5": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 50.38, - "y": 11.25, - "z": 3 - }, - "H6": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 59.38, - "y": 11.25, - "z": 3 - }, - "H7": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 68.38, - "y": 11.25, - "z": 3 - }, - "H8": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 77.38, - "y": 11.25, - "z": 3 - }, - "H9": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 86.38, - "y": 11.25, - "z": 3 - } - } - } - ], - "fields": [ - { - "default": 96, - "label": "number of samples (1-96)", - "name": "num_samples", - "type": "int" - }, - { - "label": "PCR plate type", - "name": "plate_type", - "options": [ - { - "label": "NEST", - "value": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "label": "Custom on aluminum block", - "value": "generic_96_aluminumblock_350ul" - } - ], - "type": "dropDown" - }, - { - "label": "P300 multi-channel pipette mount", - "name": "m300_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p300_multi_gen2" - } - ], - "labware": [ - { - "name": "incubation plate on 2", - "share": false, - "slot": "2", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "reservoir for extension mix (channel 1) on 5", - "share": false, - "slot": "5", - "type": "nest_12_reservoir_15ml" - }, - { - "name": "Opentrons 96 Tip Rack 300 \u00b5L on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_tiprack_300ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Nick ", - "description": "Custom Protocol Request", - "protocolName": "Olink Target 96 Part 2/3: Extension" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/2aee74-3/README.json b/protoBuilds/2aee74-3/README.json deleted file mode 100644 index b90210230..000000000 --- a/protoBuilds/2aee74-3/README.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "Proteins & Proteomics": [ - "Olink Target 96" - ] - }, - "deck-setup": "\nNote: all volumes for 96 samples (including controls)\n purple on primer plate (slot 1): samples\n blue on sample plate (slot 5): samples from extension\n* green on tuberack (slot 9): 790.9\u00b5l detection mix\n", - "description": "Links:\n Part 1: Incubation\n Part 2: Extension\n* Part 3: Detection\nThis protocol accomplishes part 3/3: Detection for the Olink Target 96 protocol for protein biomarker discovery. Primers are transferred to the left 96 wells of the Fluidigm detection plate, and samples are transferred to the right 96 wells. The transfer mapping for these plates is shown in the following images:\n\n\n", - "internal": "2aee74", - "labware": "\nFluidigm 96.96 Dynamic Array\u2122 IFC for Gene Expression\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons 4-in-1 Tube Rack Set with NEST 1.5 mL Screwcap Tubes or equivalent\nOpentrons Filter Tips\n", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* Proteins & Proteomics\n\t* Olink Target 96\n\n", - "deck-setup": "![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/2aee74/deck3-5.png)\nNote: all volumes for 96 samples (including controls)\n* purple on primer plate (slot 1): samples\n* blue on sample plate (slot 5): samples from extension\n* green on tuberack (slot 9): 790.9\u00b5l detection mix\n\n---\n\n", - "description": "\nLinks:\n* [Part 1: Incubation](./2aee74)\n* [Part 2: Extension](./2aee74-2)\n* [Part 3: Detection](./2aee74-3)\n\nThis protocol accomplishes part 3/3: Detection for the [Olink Target 96 protocol](https://www.olink.com/products-services/target/) for protein biomarker discovery. Primers are transferred to the left 96 wells of the Fluidigm detection plate, and samples are transferred to the right 96 wells. The transfer mapping for these plates is shown in the following images: \n![scheme1](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/2aee74/scheme1-2.png)\n![scheme2](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/2aee74/scheme2-2.png)\n\n---\n\n", - "internal": "2aee74\n", - "labware": "* [Fluidigm 96.96 Dynamic Array\u2122 IFC for Gene Expression](https://store.fluidigm.com/Genomics/ApplicationsGenomics/GeneExpression/96-96%20Dynamic%20Array%E2%84%A2%20IFC%20for%20Gene%20Expression)\n* [NEST 0.1 mL 96-Well PCR Plate, Full Skirt](https://shop.opentrons.com/collections/verified-labware/products/nest-0-1-ml-96-well-pcr-plate-full-skirt)\n* [Opentrons 4-in-1 Tube Rack Set](https://shop.opentrons.com/collections/verified-labware/products/tube-rack-set-1) with [NEST 1.5 mL Screwcap Tubes](https://shop.opentrons.com/collections/verified-consumables/products/nest-1-5-ml-sample-vial) or equivalent\n* [Opentrons Filter Tips](https://shop.opentrons.com/collections/opentrons-tips)\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "pipettes": "* [P300 Single-Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/collections/ot-2-pipettes/products/single-channel-electronic-pipette?variant=5984549109789)\n* [P20 8-Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/collections/ot-2-pipettes/products/8-channel-electronic-pipette)\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "reagents": "* [Olink Target 96](https://www.olink.com/products-services/target/)\n\n---\n\n", - "title": "Olink Target 96 Part 3/3: Detection" - }, - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "pipettes": "\nP300 Single-Channel Electronic Pipette (GEN2)\nP20 8-Channel Electronic Pipette (GEN2)\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "reagents": [ - "Olink Target 96" - ], - "title": "Olink Target 96 Part 3/3: Detection" -} diff --git a/protoBuilds/2aee74-3/metadata.json b/protoBuilds/2aee74-3/metadata.json deleted file mode 100644 index 699cdc870..000000000 --- a/protoBuilds/2aee74-3/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "olink.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": false, - "skip-tests": false - }, - "path": "protocols/2aee74-3", - "slug": "2aee74-3", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/2aee74-3/olink.ot2.apiv2.py.json b/protoBuilds/2aee74-3/olink.ot2.apiv2.py.json deleted file mode 100644 index 2e6a4448f..000000000 --- a/protoBuilds/2aee74-3/olink.ot2.apiv2.py.json +++ /dev/null @@ -1,4794 +0,0 @@ -{ - "content": "from opentrons.types import Point\nimport json\nimport os\nimport math\n\nmetadata = {\n 'protocolName': 'Olink Target 96 Part 3/3: Detection',\n 'author': 'Nick ',\n 'description': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n num_samples, p300_mount, m20_mount = get_values( # noqa: F821\n 'num_samples', 'p300_mount', 'm20_mount')\n\n if not 1 <= num_samples <= 96:\n raise Exception('Invalid number of samples (1-96)')\n\n det_mix = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '9',\n 'tuberack for detection mix (A3)').wells_by_name()['A3']\n inc_plate = ctx.load_labware('generic_96_aluminumblock_350ul', '5',\n 'incubation plate')\n sample_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n '3', 'sample plate')\n strip = ctx.load_labware(\n 'genericstrips_96_wellplate_200ul', '6',\n 'strip for distribution (column 7)').columns_by_name()['7']\n primer_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n '1', 'primer plate')\n fluidigm = ctx.load_labware('fluidigm_192_wellplate_96x10ul_96x10ul', '2',\n 'Fluidigm 96.96 Dynamic Array')\n tipracks300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', '10')]\n tipracks20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', slot)\n for slot in ['7', '8', '11']]\n stationary_rack = ctx.load_labware('opentrons_96_filtertiprack_20ul', '4')\n\n p300 = ctx.load_instrument('p300_single_gen2', p300_mount,\n tip_racks=tipracks300)\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount,\n tip_racks=tipracks20)\n num_cols = math.ceil(num_samples/8)\n tip_track = True\n tip_count = 0\n\n folder_path = '/data/olink'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n data = json.load(json_file)\n if 'm20' in data:\n tip_count = data['m20']\n\n def m20_pick_up():\n nonlocal tip_count\n if tip_count == 12:\n ctx.pause('\\n\\n\\n\\n\\nPlease refill 20ul filter tiprack on slot 6 \\\nbefore resuming.\\n\\n\\n\\n\\n')\n m20.pick_up_tip(stationary_rack.rows()[0][tip_count])\n tip_count += 1\n\n side = 1\n\n def drop(pip):\n nonlocal side\n drop_loc = ctx.loaded_labwares[12].wells()[0].top().move(\n Point(x=30*side))\n pip.drop_tip(drop_loc)\n side = -1*side\n\n p300.default_speed = 100\n m20.default_speed = 100\n ctx.home()\n ctx.comment('\\n\\n\\n\\n\\nPrepare and prime a 96.96 Dynamic ArrayTM \\\nIntegrated Fluidic Circuit (IFC) according to the manufacturer\u2019s instructions.\\\n Briefly,inject one control line fluid syringe into each accumulator on the \\\nchip, and then prime the chip on the IFC Controller for approximately 20 \\\nminutes.\\n\\n\\n\\n\\n')\n ctx.comment('\\n\\n\\n\\n\\nThaw the Primer Plate, vortex and spin \\\nbriefly.\\n\\n\\n\\n\\n')\n ctx.pause(f'\\n\\n\\n\\n\\nP20 multi transfer will begin at column \\\n{tip_count+1} of tiprack on slot 6.\\n\\n\\n\\n\\n')\n\n # transfer detection mix to strip with reverse pipetting\n p300.pick_up_tip()\n p300.aspirate(5, det_mix)\n for well in strip:\n p300.aspirate(95, det_mix)\n p300.dispense(95, well)\n p300.dispense(p300.current_volume, det_mix)\n drop(p300)\n\n # transfer from strip to plate\n m20_pick_up()\n m20.aspirate(5, strip[0])\n for col in sample_plate.rows()[0][:num_cols]:\n m20.aspirate(7.2, strip[0])\n m20.dispense(7.2, col)\n drop(m20)\n\n # transfer samples\n for s, d in zip(inc_plate.rows()[0][:num_cols],\n sample_plate.rows()[0][:num_cols]):\n m20.pick_up_tip()\n m20.transfer(2.8, s, d, new_tip='never')\n drop(m20)\n\n ctx.pause('\\n\\n\\n\\n\\nSeal the plate with an adhesive plastic film, vortex \\\nand spin at 400 x g, 1 min at room temperature.\\n\\n\\n\\n\\n')\n\n # transfer primer and sample to fluidigm plate\n sample_destinations = [\n well for row in fluidigm.rows()[:2] for well in row[6:]]\n primer_destinations = [\n well for col in fluidigm.rows()[:2] for well in col[:6]]\n\n for source, dest in zip(\n primer_plate.rows()[0] + sample_plate.rows()[0][:num_cols],\n primer_destinations + sample_destinations[:num_cols]):\n m20.pick_up_tip()\n m20.aspirate(7, source.bottom(0.5))\n m20.dispense(5, dest.bottom(1))\n drop(m20)\n\n # track final used tip\n if tip_track and not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n data = {'m20': tip_count}\n with open(tip_file_path, 'w') as outfile:\n json.dump(data, outfile)\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "generic strips", - "brandId": [] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.76, - "yDimension": 85.48, - "zDimension": 20 - }, - "groups": [ - { - "metadata": { - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8", - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9", - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10", - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11", - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - } - ], - "metadata": { - "displayCategory": "wellPlate", - "displayName": "Generic Strips 96 Well Plate 200 \u00b5L", - "displayVolumeUnits": "\u00b5L", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1" - ], - [ - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2" - ], - [ - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3" - ], - [ - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4" - ], - [ - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5" - ], - [ - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6" - ], - [ - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7" - ], - [ - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8" - ], - [ - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9" - ], - [ - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10" - ], - [ - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11" - ], - [ - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - ], - "parameters": { - "format": "irregular", - "isMagneticModuleCompatible": false, - "isTiprack": false, - "loadName": "genericstrips_96_wellplate_200ul", - "quirks": [] - }, - "schemaVersion": 2, - "version": 1, - "wells": { - "A1": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 74.24, - "z": 4 - }, - "A10": { - "depth": 16, - "diameter": 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- "y": 20.25, - "z": 3 - }, - "G11": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 104.38, - "y": 20.25, - "z": 3 - }, - "G12": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 113.38, - "y": 20.25, - "z": 3 - }, - "G2": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 23.38, - "y": 20.25, - "z": 3 - }, - "G3": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 32.38, - "y": 20.25, - "z": 3 - }, - "G4": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 41.38, - "y": 20.25, - "z": 3 - }, - "G5": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 50.38, - "y": 20.25, - "z": 3 - }, - "G6": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 59.38, - "y": 20.25, - "z": 3 - }, - "G7": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 68.38, - "y": 20.25, - "z": 3 - }, - "G8": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 77.38, - "y": 20.25, - "z": 3 - }, - "G9": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 86.38, - "y": 20.25, - "z": 3 - }, - "H1": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 14.38, - "y": 11.25, - "z": 3 - }, - "H10": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 95.38, - "y": 11.25, - "z": 3 - }, - "H11": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 104.38, - "y": 11.25, - "z": 3 - }, - "H12": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 113.38, - "y": 11.25, - "z": 3 - }, - "H2": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 23.38, - "y": 11.25, - "z": 3 - }, - "H3": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 32.38, - "y": 11.25, - "z": 3 - }, - "H4": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 41.38, - "y": 11.25, - "z": 3 - }, - "H5": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 50.38, - "y": 11.25, - "z": 3 - }, - "H6": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 59.38, - "y": 11.25, - "z": 3 - }, - "H7": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 68.38, - "y": 11.25, - "z": 3 - }, - "H8": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 77.38, - "y": 11.25, - "z": 3 - }, - "H9": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 86.38, - "y": 11.25, - "z": 3 - } - } - } - ], - "fields": [ - { - "default": 96, - "label": "number of samples (1-96)", - "name": "num_samples", - "type": "int" - }, - { - "label": "P300 single-channel pipette mount", - "name": "p300_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - }, - { - "label": "P20 multi-channel pipette mount", - "name": "m20_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p20_multi_gen2" - }, - { - "mount": "right", - "name": "p300_single_gen2" - } - ], - "labware": [ - { - "name": "primer plate on 1", - "share": false, - "slot": "1", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "Fluidigm 96.96 Dynamic Array on 2", - "share": false, - "slot": "2", - "type": "fluidigm_192_wellplate_96x10ul_96x10ul" - }, - { - "name": "sample plate on 3", - "share": false, - "slot": "3", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 4", - "share": false, - "slot": "4", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "incubation plate on 5", - "share": false, - "slot": "5", - "type": "generic_96_aluminumblock_350ul" - }, - { - "name": "strip for distribution (column 7) on 6", - "share": false, - "slot": "6", - "type": "genericstrips_96_wellplate_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 7", - "share": false, - "slot": "7", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 8", - "share": false, - "slot": "8", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "tuberack for detection mix (A3) on 9", - "share": false, - "slot": "9", - "type": "opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 10", - "share": false, - "slot": "10", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 11", - "share": false, - "slot": "11", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Nick ", - "description": "Custom Protocol Request", - "protocolName": "Olink Target 96 Part 3/3: Detection" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/2aee74/README.json b/protoBuilds/2aee74/README.json deleted file mode 100644 index d2c828e68..000000000 --- a/protoBuilds/2aee74/README.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "Proteins & Proteomics": [ - "Olink Target 96" - ] - }, - "deck-setup": "\nNote: all volumes for 96 samples (including controls)\n blue on sample plate (slot 7): starting samples\n green on tuberack (slot 8): 400.0\u00b5l incubation mix\n", - "description": "Links:\n Part 1: Incubation\n Part 2: Extension\n* Part 3: Detection\nThis protocol accomplishes part 1/3: Incubation for the Olink Target 96 protocol for protein biomarker discovery.\n", - "internal": "2aee74", - "labware": "\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons 4-in-1 Tube Rack Set with NEST 1.5 mL Screwcap Tubes or equivalent\nOpentrons Filter Tips\n", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* Proteins & Proteomics\n\t* Olink Target 96\n\n", - "deck-setup": "![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/2aee74/deck1-5.png)\nNote: all volumes for 96 samples (including controls)\n* blue on sample plate (slot 7): starting samples\n* green on tuberack (slot 8): 400.0\u00b5l incubation mix\n\n---\n\n", - "description": "\nLinks:\n* [Part 1: Incubation](./2aee74)\n* [Part 2: Extension](./2aee74-2)\n* [Part 3: Detection](./2aee74-3)\n\nThis protocol accomplishes part 1/3: Incubation for the [Olink Target 96 protocol](https://www.olink.com/products-services/target/) for protein biomarker discovery.\n\n---\n\n", - "internal": "2aee74\n", - "labware": "* [NEST 0.1 mL 96-Well PCR Plate, Full Skirt](https://shop.opentrons.com/collections/verified-labware/products/nest-0-1-ml-96-well-pcr-plate-full-skirt)\n* [Opentrons 4-in-1 Tube Rack Set](https://shop.opentrons.com/collections/verified-labware/products/tube-rack-set-1) with [NEST 1.5 mL Screwcap Tubes](https://shop.opentrons.com/collections/verified-consumables/products/nest-1-5-ml-sample-vial) or equivalent\n* [Opentrons Filter Tips](https://shop.opentrons.com/collections/opentrons-tips)\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "pipettes": "* [P300 Single-Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/collections/ot-2-pipettes/products/single-channel-electronic-pipette?variant=5984549109789)\n* [P20 8-Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/collections/ot-2-pipettes/products/8-channel-electronic-pipette)\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "reagents": "* [Olink Target 96](https://www.olink.com/products-services/target/)\n\n---\n\n", - "title": "Olink Target 96 Part 1/3: Incubation" - }, - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "pipettes": "\nP300 Single-Channel Electronic Pipette (GEN2)\nP20 8-Channel Electronic Pipette (GEN2)\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "reagents": [ - "Olink Target 96" - ], - "title": "Olink Target 96 Part 1/3: Incubation" -} diff --git a/protoBuilds/2aee74/metadata.json b/protoBuilds/2aee74/metadata.json deleted file mode 100644 index bc53b1b57..000000000 --- a/protoBuilds/2aee74/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "olink.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": false, - "skip-tests": false - }, - "path": "protocols/2aee74", - "slug": "2aee74", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/2aee74/olink.ot2.apiv2.py.json b/protoBuilds/2aee74/olink.ot2.apiv2.py.json deleted file mode 100644 index 58e22e07c..000000000 --- a/protoBuilds/2aee74/olink.ot2.apiv2.py.json +++ /dev/null @@ -1,2361 +0,0 @@ -{ - "content": "from opentrons.types import Point\nimport json\nimport os\nimport math\n\nmetadata = {\n 'protocolName': 'Olink Target 96 Part 1/3: Incubation',\n 'author': 'Nick ',\n 'description': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n num_samples, p300_mount, m20_mount = get_values( # noqa: F821\n 'num_samples', 'p300_mount', 'm20_mount')\n\n if not 1 <= num_samples <= 96:\n raise Exception('Invalid number of samples (1-96)')\n\n inc_mix = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '8',\n 'tuberack for incubation mix (A1)').wells()[0]\n inc_plate = ctx.load_labware('generic_96_aluminumblock_350ul', '10',\n 'incubation plate')\n sample_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n '7', 'sample plate')\n strip = ctx.load_labware('genericstrips_96_wellplate_200ul', '11',\n 'strip for distribution (column 1)').columns()[0]\n tipracks300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', '9')]\n tipracks20 = [\n ctx.load_labware('opentrons_96_filtertiprack_20ul', slot)\n for slot in ['1']]\n stationary_rack = ctx.load_labware('opentrons_96_filtertiprack_20ul', '4')\n\n p300 = ctx.load_instrument('p300_single_gen2', p300_mount,\n tip_racks=tipracks300)\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount,\n tip_racks=tipracks20)\n\n num_cols = math.ceil(num_samples/8)\n tip_track = True\n tip_count = 0\n\n folder_path = '/data/olink'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n data = json.load(json_file)\n if 'm20' in data:\n tip_count = data['m20']\n\n def m20_pick_up():\n nonlocal tip_count\n if tip_count == 12:\n ctx.pause('\\n\\n\\n\\n\\nPlease refill 20ul filter tiprack on slot 6 \\\nbefore resuming.\\n\\n\\n\\n\\n')\n m20.pick_up_tip(stationary_rack.rows()[0][tip_count])\n tip_count += 1\n\n side = 1\n\n def drop(pip):\n nonlocal side\n drop_loc = ctx.loaded_labwares[12].wells()[0].top().move(\n Point(x=30*side))\n pip.drop_tip(drop_loc)\n side = -1*side\n\n p300.default_speed = 100\n m20.default_speed = 100\n\n ctx.home()\n ctx.pause(f'P20 multi transfer will begin at column {tip_count+1} of \\\ntiprack on slot 6.')\n\n # transfer incubation mix to strip with reverse pipetting\n p300.pick_up_tip()\n p300.aspirate(5, inc_mix)\n for well in strip:\n p300.aspirate(47, inc_mix)\n p300.dispense(47, well)\n p300.dispense(p300.current_volume, inc_mix)\n drop(p300)\n\n # transfer from strip to plate\n m20_pick_up()\n m20.aspirate(5, strip[0])\n for col in inc_plate.rows()[0][:num_cols]:\n m20.aspirate(3, strip[0])\n m20.dispense(3, col)\n # m20.dispense(m20.current_volume, strip[0])\n drop(m20)\n\n # transfer samples\n for s, d in zip(sample_plate.rows()[0][:num_samples],\n inc_plate.rows()[0][:num_samples]):\n m20.pick_up_tip()\n m20.transfer(1, s, d, new_tip='never')\n m20.blow_out(d.bottom(1))\n drop(m20)\n\n ctx.comment('\\n\\n\\n\\n\\nSeal the plate with an adhesive plastic film, spin \\\nat 400 x g, 1 min at room temperature. Incubate overnight at +4\u00b0C.\\n\\n\\n\\n\\n')\n\n # track final used tip\n if tip_track and not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n data = {'m20': tip_count}\n with open(tip_file_path, 'w') as outfile:\n json.dump(data, outfile)\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "generic strips", - "brandId": [] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.76, - "yDimension": 85.48, - "zDimension": 20 - }, - "groups": [ - { - "metadata": { - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "A7", - 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"right" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p20_multi_gen2" - }, - { - "mount": "right", - "name": "p300_single_gen2" - } - ], - "labware": [ - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 1", - "share": false, - "slot": "1", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 4", - "share": false, - "slot": "4", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "sample plate on 7", - "share": false, - "slot": "7", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "tuberack for incubation mix (A1) on 8", - "share": false, - "slot": "8", - "type": "opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "incubation plate on 10", - "share": false, - "slot": "10", - "type": "generic_96_aluminumblock_350ul" - }, - { - "name": "strip for distribution (column 1) on 11", - "share": false, - "slot": "11", - "type": "genericstrips_96_wellplate_200ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Nick ", - "description": "Custom Protocol Request", - "protocolName": "Olink Target 96 Part 1/3: Incubation" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/2b3642/2b3642.ot2.apiv2.py.json b/protoBuilds/2b3642/2b3642.ot2.apiv2.py.json index 789fb8191..6717c9023 100644 --- a/protoBuilds/2b3642/2b3642.ot2.apiv2.py.json +++ b/protoBuilds/2b3642/2b3642.ot2.apiv2.py.json @@ -159,5 +159,24 @@ "description": "Custom Protocol Request", "protocolName": "NEBNext Ultra II DNA Library Preparation Kit\n for Illumina E7645S" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 2 mL Screwcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + }, + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/2b9486/ngs_prep.ot2.apiv2.py.json b/protoBuilds/2b9486/ngs_prep.ot2.apiv2.py.json index a057a46b7..58631de43 100644 --- a/protoBuilds/2b9486/ngs_prep.ot2.apiv2.py.json +++ b/protoBuilds/2b9486/ngs_prep.ot2.apiv2.py.json @@ -4623,5 +4623,12 @@ "protocolName": "NGS Library Prep", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw ABGene 96 Well Plate 200\u00b5l on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/2c83f7/2c83f7.ot2.apiv2.py.json b/protoBuilds/2c83f7/2c83f7.ot2.apiv2.py.json index 3c050aa7d..194a93fe0 100644 --- a/protoBuilds/2c83f7/2c83f7.ot2.apiv2.py.json +++ b/protoBuilds/2c83f7/2c83f7.ot2.apiv2.py.json @@ -128,5 +128,12 @@ "protocolName": "Zymo Research Direct-zol-96 RNA MagPrep", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 4 lw deepwell block on Magnetic Module GEN1 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/2d9a0c/2d9a0c.ot2.apiv2.py.json b/protoBuilds/2d9a0c/2d9a0c.ot2.apiv2.py.json index de5a65253..11df18c6b 100644 --- a/protoBuilds/2d9a0c/2d9a0c.ot2.apiv2.py.json +++ b/protoBuilds/2d9a0c/2d9a0c.ot2.apiv2.py.json @@ -1257,5 +1257,12 @@ "protocolName": "PCR Workflow With Thermocycler", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw Thermo Scientific Non Skirted 96 Well Plate on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/2e84cc/2e84cc.ot2.apiv2.py.json b/protoBuilds/2e84cc/2e84cc.ot2.apiv2.py.json index dddc5511a..4d0965aee 100644 --- a/protoBuilds/2e84cc/2e84cc.ot2.apiv2.py.json +++ b/protoBuilds/2e84cc/2e84cc.ot2.apiv2.py.json @@ -81,5 +81,24 @@ "protocolName": "TG Nextera XT index kit v2 Set A to D", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw Opentrons 24 Well Aluminum Block with Generic 2 mL Screwcap on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/2ed4de-2/fluribogreen.ot2.apiv2.py.json b/protoBuilds/2ed4de-2/fluribogreen.ot2.apiv2.py.json index 2e297b576..115b541e2 100644 --- a/protoBuilds/2ed4de-2/fluribogreen.ot2.apiv2.py.json +++ b/protoBuilds/2ed4de-2/fluribogreen.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "import math\nfrom opentrons.types import Point\n\n\nmetadata = {\n 'protocolName': 'FluRibogreen Assay',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [num_samples, reagent_labware, starting_conc, prepare_standard,\n standard_type, p1000_mount, p300_mount] = get_values( # noqa: F821\n 'num_samples', 'reagent_labware', 'starting_conc', 'prepare_standard',\n 'standard_type', 'p1000_mount', 'p300_mount')\n\n final_transfer_vol = 100\n sample_vol = 25\n max_working_vol = 1000\n mix_reps = 10\n max_factor_1_dil = max_working_vol/sample_vol\n\n # load labwarex\n sample_rack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '11',\n 'sample tuberack')\n deepplate = ctx.load_labware('nest_96_wellplate_2ml_deep', '5',\n 'standard preparation plate')\n flatplate = ctx.load_labware('corning_96_wellplate_360ul_flat', '2',\n 'final plate')\n reagent_labware = ctx.load_labware(reagent_labware, '8',\n 'standards and buffers')\n tipracks1000 = ctx.load_labware('opentrons_96_filtertiprack_1000ul', '7')\n tipracks200 = ctx.load_labware('opentrons_96_filtertiprack_200ul', '6')\n tiprack200m = ctx.load_labware('opentrons_96_filtertiprack_200ul', '9')\n\n # load pipettes\n p1000 = ctx.load_instrument('p1000_single_gen2', p1000_mount,\n tip_racks=[tipracks1000])\n p300 = ctx.load_instrument('p300_multi_gen2', p300_mount,\n tip_racks=[tiprack200m])\n\n tip_data = {\n 'single': {\n 'count': 0,\n 'tips': [\n well for col in tipracks200.columns()[::-1]\n for well in col[::-1]]\n },\n 'multi': {\n 'count': 0,\n 'tips': tipracks200.rows()[0]\n }\n }\n\n def pickup_p300(mode='single'):\n current = 0.1 if mode == 'single' else 0.5\n ctx._implementation._hw_manager.hardware._attached_instruments[\n p300._implementation.get_mount()].update_config_item(\n 'pick_up_current', current)\n\n p300.pick_up_tip(tip_data[mode]['tips'][tip_data[mode]['count']])\n tip_data[mode]['count'] += 1\n\n side = 1\n\n def drop(pip):\n nonlocal side\n center = ctx.loaded_labwares[12].wells()[0].top()\n pip.drop_tip(center.move(Point(x=side*20)))\n side = side * -1\n\n working_standard_1 = reagent_labware.wells()[5]\n assay_buffer_1 = reagent_labware.wells()[6:9]\n starting_samples = sample_rack.wells()[:num_samples]\n num_sets = math.ceil(num_samples/8)\n all_samples = [\n deepplate.columns()[i*3:(i+1)*3]\n for i in range(1, 1+num_sets)]\n\n def standard_prep(standard, buffer, column):\n dilution_col = column[:7]\n for vol, dest in zip([900, 700, 500, 300, 100], dilution_col[:5]):\n p1000.pick_up_tip()\n p1000.transfer(vol, standard, dest, new_tip='never')\n drop(p1000)\n\n for vol, dest in zip([100, 300, 500, 700, 900, 950, 1000],\n dilution_col):\n p1000.pick_up_tip()\n p1000.transfer(vol, buffer[0], dest, mix_after=(5, 800),\n new_tip='never')\n drop(p1000)\n pickup_p300('single')\n p300.aspirate(50, standard.bottom(2))\n p300.dispense(50, dilution_col[5].bottom(3))\n p300.mix(1, 100, dilution_col[5].bottom(3))\n drop(p300)\n p1000.pick_up_tip()\n p1000.mix(mix_reps, 800, dilution_col[5])\n drop(p1000)\n\n def dilute(final_conc, dil_sets, buffer):\n dil_factor = starting_conc/final_conc\n # find necessary dilution factor(s)\n if dil_factor > max_factor_1_dil:\n factors = [10, dil_factor/10]\n else:\n factors = [dil_factor]\n\n # pre add diluent\n for i, factor in enumerate(factors):\n dil_vol = (factor-1)*sample_vol*(i+1)\n print(dil_vol)\n for j, set in enumerate(dil_sets):\n for k, well in enumerate(set[i]):\n if j*k+k < num_samples:\n p1000.pick_up_tip()\n p1000.transfer(dil_vol,\n buffer[1+int((j*8+k)//(num_samples/2))],\n well, new_tip='never')\n drop(p1000)\n\n p300.flow_rate.aspirate = 40\n p300.flow_rate.dispense = 40\n # transfer sample\n for i, s in enumerate(starting_samples):\n print(sample_vol)\n pickup_p300('single')\n well = dil_sets[i//8][0][i % 8]\n p300.aspirate(sample_vol, s.bottom(2))\n p300.dispense(sample_vol, well.bottom(3))\n p300.mix(1, 20, well.bottom(3))\n drop(p300)\n p300.flow_rate.aspirate = 94\n p300.flow_rate.dispense = 94\n\n # perform dilution\n for i, factor in enumerate(factors):\n for set in dil_sets:\n pickup_p300('multi')\n total_vol = sample_vol*(i+1)*factor\n mix_vol = total_vol*0.8 if total_vol*0.8 <= 175 else 175\n if i == 0:\n p300.mix(mix_reps, mix_vol, set[i][0])\n else:\n print(sample_vol*(i+1))\n p300.transfer(sample_vol*(i+1), set[i-1][0].bottom(3),\n set[i][0].bottom(3),\n mix_after=(5, mix_vol),\n new_tip='never')\n drop(p300)\n\n return int(len(factors)-1)\n\n \"\"\" PART 1 \"\"\"\n if prepare_standard:\n\n # standard preparation\n standard_prep(working_standard_1, assay_buffer_1,\n deepplate.columns()[0])\n\n \"\"\" PART 2 \"\"\"\n\n # sample normalization (TE or TR)\n sample_1_final_ind = dilute(standard_type, all_samples, assay_buffer_1)\n\n \"\"\" PART 3 \"\"\"\n\n # transfer to final black plate\n sources = [deepplate.rows_by_name()['A'][0]] + [\n set[sample_1_final_ind][0] for set in all_samples]\n for i, source in enumerate(sources):\n dest_set = flatplate.rows()[0][i*3:(i+1)*3]\n for dest in dest_set:\n p300.pick_up_tip()\n p300.transfer(final_transfer_vol, source.bottom(3), dest.bottom(3),\n mix_before=(mix_reps, 0.8*final_transfer_vol),\n new_tip='never')\n drop(p300)\n", + "content": "import math\nfrom opentrons.types import Point\n\n\nmetadata = {\n 'protocolName': 'FluRibogreen Assay',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [num_samples, reagent_labware, starting_conc, prepare_standard,\n standard_type, p1000_mount, p300_mount] = get_values( # noqa: F821\n 'num_samples', 'reagent_labware', 'starting_conc', 'prepare_standard',\n 'standard_type', 'p1000_mount', 'p300_mount')\n\n final_transfer_vol = 100\n sample_vol = 25\n max_working_vol = 1000\n mix_reps = 10\n max_factor_1_dil = max_working_vol/sample_vol\n\n # load labwarex\n sample_rack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '11',\n 'sample tuberack')\n deepplate = ctx.load_labware('nest_96_wellplate_2ml_deep', '5',\n 'standard preparation plate')\n flatplate = ctx.load_labware('corning_96_wellplate_360ul_flat', '2',\n 'final plate')\n reagent_labware = ctx.load_labware(reagent_labware, '8',\n 'standards and buffers')\n tipracks1000 = ctx.load_labware('opentrons_96_filtertiprack_1000ul', '7')\n tipracks200 = ctx.load_labware('opentrons_96_filtertiprack_200ul', '6')\n tiprack200m = ctx.load_labware('opentrons_96_filtertiprack_200ul', '9')\n\n # load pipettes\n p1000 = ctx.load_instrument('p1000_single_gen2', p1000_mount,\n tip_racks=[tipracks1000])\n p300 = ctx.load_instrument('p300_multi_gen2', p300_mount,\n tip_racks=[tiprack200m])\n\n tip_data = {\n 'single': {\n 'count': 0,\n 'tips': [\n well for col in tipracks200.columns()[::-1]\n for well in col[::-1]]\n },\n 'multi': {\n 'count': 0,\n 'tips': tipracks200.rows()[0]\n }\n }\n\n def pickup_p300(mode='single'):\n current = 0.1 if mode == 'single' else 0.5\n ctx._hw_manager.hardware._attached_instruments[\n p300._implementation.get_mount()].update_config_item(\n 'pick_up_current', current)\n\n p300.pick_up_tip(tip_data[mode]['tips'][tip_data[mode]['count']])\n tip_data[mode]['count'] += 1\n\n side = 1\n\n def drop(pip):\n nonlocal side\n center = ctx.loaded_labwares[12].wells()[0].top()\n pip.drop_tip(center.move(Point(x=side*20)))\n side = side * -1\n\n working_standard_1 = reagent_labware.wells()[5]\n assay_buffer_1 = reagent_labware.wells()[6:9]\n starting_samples = sample_rack.wells()[:num_samples]\n num_sets = math.ceil(num_samples/8)\n all_samples = [\n deepplate.columns()[i*3:(i+1)*3]\n for i in range(1, 1+num_sets)]\n\n def standard_prep(standard, buffer, column):\n dilution_col = column[:7]\n for vol, dest in zip([900, 700, 500, 300, 100], dilution_col[:5]):\n p1000.pick_up_tip()\n p1000.transfer(vol, standard, dest, new_tip='never')\n drop(p1000)\n\n for vol, dest in zip([100, 300, 500, 700, 900, 950, 1000],\n dilution_col):\n p1000.pick_up_tip()\n p1000.transfer(vol, buffer[0], dest, mix_after=(5, 800),\n new_tip='never')\n drop(p1000)\n pickup_p300('single')\n p300.aspirate(50, standard.bottom(2))\n p300.dispense(50, dilution_col[5].bottom(3))\n p300.mix(1, 100, dilution_col[5].bottom(3))\n drop(p300)\n p1000.pick_up_tip()\n p1000.mix(mix_reps, 800, dilution_col[5])\n drop(p1000)\n\n def dilute(final_conc, dil_sets, buffer):\n dil_factor = starting_conc/final_conc\n # find necessary dilution factor(s)\n if dil_factor > max_factor_1_dil:\n factors = [10, dil_factor/10]\n else:\n factors = [dil_factor]\n\n # pre add diluent\n for i, factor in enumerate(factors):\n dil_vol = (factor-1)*sample_vol*(i+1)\n print(dil_vol)\n for j, set in enumerate(dil_sets):\n for k, well in enumerate(set[i]):\n if j*k+k < num_samples:\n p1000.pick_up_tip()\n p1000.transfer(dil_vol,\n buffer[1+int((j*8+k)//(num_samples/2))],\n well, new_tip='never')\n drop(p1000)\n\n p300.flow_rate.aspirate = 40\n p300.flow_rate.dispense = 40\n # transfer sample\n for i, s in enumerate(starting_samples):\n print(sample_vol)\n pickup_p300('single')\n well = dil_sets[i//8][0][i % 8]\n p300.aspirate(sample_vol, s.bottom(2))\n p300.dispense(sample_vol, well.bottom(3))\n p300.mix(1, 20, well.bottom(3))\n drop(p300)\n p300.flow_rate.aspirate = 94\n p300.flow_rate.dispense = 94\n\n # perform dilution\n for i, factor in enumerate(factors):\n for set in dil_sets:\n pickup_p300('multi')\n total_vol = sample_vol*(i+1)*factor\n mix_vol = total_vol*0.8 if total_vol*0.8 <= 175 else 175\n if i == 0:\n p300.mix(mix_reps, mix_vol, set[i][0])\n else:\n print(sample_vol*(i+1))\n p300.transfer(sample_vol*(i+1), set[i-1][0].bottom(3),\n set[i][0].bottom(3),\n mix_after=(5, mix_vol),\n new_tip='never')\n drop(p300)\n\n return int(len(factors)-1)\n\n \"\"\" PART 1 \"\"\"\n if prepare_standard:\n\n # standard preparation\n standard_prep(working_standard_1, assay_buffer_1,\n deepplate.columns()[0])\n\n \"\"\" PART 2 \"\"\"\n\n # sample normalization (TE or TR)\n sample_1_final_ind = dilute(standard_type, all_samples, assay_buffer_1)\n\n \"\"\" PART 3 \"\"\"\n\n # transfer to final black plate\n sources = [deepplate.rows_by_name()['A'][0]] + [\n set[sample_1_final_ind][0] for set in all_samples]\n for i, source in enumerate(sources):\n dest_set = flatplate.rows()[0][i*3:(i+1)*3]\n for dest in dest_set:\n p300.pick_up_tip()\n p300.transfer(final_transfer_vol, source.bottom(3), dest.bottom(3),\n mix_before=(mix_reps, 0.8*final_transfer_vol),\n new_tip='never')\n drop(p300)\n", "custom_labware_defs": [], "fields": [ { diff --git a/protoBuilds/2ed4de/fluribogreen.ot2.apiv2.py.json b/protoBuilds/2ed4de/fluribogreen.ot2.apiv2.py.json index f81e3405c..ad2c1bde6 100644 --- a/protoBuilds/2ed4de/fluribogreen.ot2.apiv2.py.json +++ b/protoBuilds/2ed4de/fluribogreen.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "from opentrons.types import Point\n\n\nmetadata = {\n 'protocolName': 'Ribogreen Assay - 2 Standards and up to 8 Samples',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [num_samples, reagent_labware, starting_conc, prepare_standard,\n p1000_mount, p300_mount] = get_values( # noqa: F821\n 'num_samples', 'reagent_labware', 'starting_conc', 'prepare_standard',\n 'p1000_mount', 'p300_mount')\n\n final_transfer_vol = 100\n sample_vol = 25\n max_working_vol = 1000\n mix_reps = 10\n max_factor_1_dil = max_working_vol/sample_vol\n\n # load labwarex\n sample_rack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '11',\n 'sample tuberack')\n deepplate = ctx.load_labware('nest_96_wellplate_2ml_deep', '5',\n 'standard preparation plate')\n flatplate = ctx.load_labware('corning_96_wellplate_360ul_flat', '2',\n 'final plate')\n reagent_labware = ctx.load_labware(reagent_labware, '8',\n 'standards and buffers')\n tipracks1000 = ctx.load_labware('opentrons_96_filtertiprack_1000ul', '7')\n tipracks200 = ctx.load_labware('opentrons_96_filtertiprack_200ul', '6')\n tiprack200m = ctx.load_labware('opentrons_96_filtertiprack_200ul', '9')\n\n # load pipettes\n p1000 = ctx.load_instrument('p1000_single_gen2', p1000_mount,\n tip_racks=[tipracks1000])\n p300 = ctx.load_instrument('p300_multi_gen2', p300_mount,\n tip_racks=[tiprack200m])\n\n tip_data = {\n 'single': {\n 'count': 0,\n 'tips': [\n well for col in tipracks200.columns()[::-1]\n for well in col[::-1]]\n },\n 'multi': {\n 'count': 0,\n 'tips': tipracks200.rows()[0]\n }\n }\n\n def pickup_p300(mode='single'):\n current = 0.1 if mode == 'single' else 0.5\n ctx._implementation._hw_manager.hardware._attached_instruments[\n p300._implementation.get_mount()].update_config_item(\n 'pick_up_current', current)\n\n p300.pick_up_tip(tip_data[mode]['tips'][tip_data[mode]['count']])\n tip_data[mode]['count'] += 1\n\n side = 1\n\n def drop(pip):\n nonlocal side\n center = ctx.loaded_labwares[12].wells()[0].top()\n pip.drop_tip(center.move(Point(x=side*20)))\n side = side * -1\n\n working_standard_1 = reagent_labware.wells()[0]\n assay_buffer_1 = reagent_labware.wells()[1:3]\n working_standard_2 = reagent_labware.wells()[9]\n assay_buffer_2 = reagent_labware.wells()[10:12]\n starting_samples = sample_rack.wells()[:num_samples]\n samples_1 = deepplate.columns()[3:6]\n samples_2 = deepplate.columns()[9:]\n\n def standard_prep(standard, buffer, column):\n dilution_col = column[:7]\n for vol, dest in zip([900, 700, 500, 300, 100], dilution_col[:5]):\n p1000.pick_up_tip()\n p1000.transfer(vol, standard, dest, new_tip='never')\n drop(p1000)\n\n for i, (vol, dest) in enumerate(\n zip([100, 300, 500, 700, 900, 950, 1000], dilution_col)):\n p1000.pick_up_tip()\n p1000.transfer(vol, buffer[i//5], dest, mix_after=(5, 800),\n new_tip='never')\n drop(p1000)\n pickup_p300('single')\n p300.aspirate(50, standard.bottom(2))\n p300.dispense(50, dilution_col[5].bottom(3))\n p300.mix(1, 100, dilution_col[5].bottom(3))\n drop(p300)\n p1000.pick_up_tip()\n p1000.mix(mix_reps, 800, dilution_col[5])\n drop(p1000)\n\n def dilute(final_conc, dil_set, buffer):\n dil_factor = starting_conc/final_conc\n # find necessary dilution factor(s)\n if dil_factor > max_factor_1_dil:\n factors = [10, dil_factor/10]\n else:\n factors = [dil_factor]\n\n # pre add diluent\n for i, factor in enumerate(factors):\n dil_vol = (factor-1)*sample_vol*(i+1)\n for j, well in enumerate(dil_set[i][:num_samples]):\n p1000.pick_up_tip()\n p1000.transfer(dil_vol, buffer[j//5], well, new_tip='never')\n drop(p1000)\n\n p300.flow_rate.aspirate = 40\n # transfer sample\n for i, s in enumerate(starting_samples):\n pickup_p300('single')\n p300.aspirate(sample_vol, s.bottom(2))\n p300.dispense(sample_vol, dil_set[0][i].bottom(3))\n p300.mix(1, 20, dil_set[0][i].bottom(3))\n drop(p300)\n p300.flow_rate.aspirate = 94\n\n # perform dilution\n for i, factor in enumerate(factors):\n pickup_p300('multi')\n total_vol = sample_vol*(i+1)*factor\n mix_vol = total_vol*0.8 if total_vol*0.8 <= 175 else 175\n if i == 0:\n p300.mix(mix_reps, mix_vol, dil_set[i][0])\n else:\n p300.transfer(sample_vol*(i+1), dil_set[i-1][0].bottom(3),\n dil_set[i][0].bottom(3),\n\n\n mix_after=(5, mix_vol),\n new_tip='never')\n drop(p300)\n\n return dil_set[len(factors)-1][0]\n\n \"\"\" PART 1 \"\"\"\n if prepare_standard:\n\n # TE preparation\n standard_prep(working_standard_1, assay_buffer_1,\n deepplate.columns()[0])\n\n # TR preparation\n standard_prep(working_standard_2, assay_buffer_2,\n deepplate.columns()[6])\n\n \"\"\" PART 2 \"\"\"\n\n # sample normalization (TE)\n sample_1_final_loc = dilute(2.5, samples_1, assay_buffer_1)\n\n # sample normalization (TR)\n sample_2_final_loc = dilute(0.5, samples_2, assay_buffer_2)\n\n \"\"\" PART 3 \"\"\"\n\n # transfer to final black plate\n for i, source in enumerate(\n [deepplate.rows_by_name()['A'][0], sample_1_final_loc,\n deepplate.rows_by_name()['A'][6], sample_2_final_loc]):\n dest_set = flatplate.rows()[0][i*3:(i+1)*3]\n for dest in dest_set:\n p300.pick_up_tip()\n p300.transfer(final_transfer_vol, source.bottom(3), dest.bottom(3),\n mix_before=(mix_reps, 0.8*final_transfer_vol),\n new_tip='never')\n drop(p300)\n", + "content": "from opentrons.types import Point\n\n\nmetadata = {\n 'protocolName': 'Ribogreen Assay - 2 Standards and up to 8 Samples',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [num_samples, reagent_labware, starting_conc, prepare_standard,\n p1000_mount, p300_mount] = get_values( # noqa: F821\n 'num_samples', 'reagent_labware', 'starting_conc', 'prepare_standard',\n 'p1000_mount', 'p300_mount')\n\n final_transfer_vol = 100\n sample_vol = 25\n max_working_vol = 1000\n mix_reps = 10\n max_factor_1_dil = max_working_vol/sample_vol\n\n # load labwarex\n sample_rack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '11',\n 'sample tuberack')\n deepplate = ctx.load_labware('nest_96_wellplate_2ml_deep', '5',\n 'standard preparation plate')\n flatplate = ctx.load_labware('corning_96_wellplate_360ul_flat', '2',\n 'final plate')\n reagent_labware = ctx.load_labware(reagent_labware, '8',\n 'standards and buffers')\n tipracks1000 = ctx.load_labware('opentrons_96_filtertiprack_1000ul', '7')\n tipracks200 = ctx.load_labware('opentrons_96_filtertiprack_200ul', '6')\n tiprack200m = ctx.load_labware('opentrons_96_filtertiprack_200ul', '9')\n\n # load pipettes\n p1000 = ctx.load_instrument('p1000_single_gen2', p1000_mount,\n tip_racks=[tipracks1000])\n p300 = ctx.load_instrument('p300_multi_gen2', p300_mount,\n tip_racks=[tiprack200m])\n\n tip_data = {\n 'single': {\n 'count': 0,\n 'tips': [\n well for col in tipracks200.columns()[::-1]\n for well in col[::-1]]\n },\n 'multi': {\n 'count': 0,\n 'tips': tipracks200.rows()[0]\n }\n }\n\n def pickup_p300(mode='single'):\n current = 0.1 if mode == 'single' else 0.5\n ctx._hw_manager.hardware._attached_instruments[\n p300._implementation.get_mount()].update_config_item(\n 'pick_up_current', current)\n\n p300.pick_up_tip(tip_data[mode]['tips'][tip_data[mode]['count']])\n tip_data[mode]['count'] += 1\n\n side = 1\n\n def drop(pip):\n nonlocal side\n center = ctx.loaded_labwares[12].wells()[0].top()\n pip.drop_tip(center.move(Point(x=side*20)))\n side = side * -1\n\n working_standard_1 = reagent_labware.wells()[0]\n assay_buffer_1 = reagent_labware.wells()[1:3]\n working_standard_2 = reagent_labware.wells()[9]\n assay_buffer_2 = reagent_labware.wells()[10:12]\n starting_samples = sample_rack.wells()[:num_samples]\n samples_1 = deepplate.columns()[3:6]\n samples_2 = deepplate.columns()[9:]\n\n def standard_prep(standard, buffer, column):\n dilution_col = column[:7]\n for vol, dest in zip([900, 700, 500, 300, 100], dilution_col[:5]):\n p1000.pick_up_tip()\n p1000.transfer(vol, standard, dest, new_tip='never')\n drop(p1000)\n\n for i, (vol, dest) in enumerate(\n zip([100, 300, 500, 700, 900, 950, 1000], dilution_col)):\n p1000.pick_up_tip()\n p1000.transfer(vol, buffer[i//5], dest, mix_after=(5, 800),\n new_tip='never')\n drop(p1000)\n pickup_p300('single')\n p300.aspirate(50, standard.bottom(2))\n p300.dispense(50, dilution_col[5].bottom(3))\n p300.mix(1, 100, dilution_col[5].bottom(3))\n drop(p300)\n p1000.pick_up_tip()\n p1000.mix(mix_reps, 800, dilution_col[5])\n drop(p1000)\n\n def dilute(final_conc, dil_set, buffer):\n dil_factor = starting_conc/final_conc\n # find necessary dilution factor(s)\n if dil_factor > max_factor_1_dil:\n factors = [10, dil_factor/10]\n else:\n factors = [dil_factor]\n\n # pre add diluent\n for i, factor in enumerate(factors):\n dil_vol = (factor-1)*sample_vol*(i+1)\n for j, well in enumerate(dil_set[i][:num_samples]):\n p1000.pick_up_tip()\n p1000.transfer(dil_vol, buffer[j//5], well, new_tip='never')\n drop(p1000)\n\n p300.flow_rate.aspirate = 40\n # transfer sample\n for i, s in enumerate(starting_samples):\n pickup_p300('single')\n p300.aspirate(sample_vol, s.bottom(2))\n p300.dispense(sample_vol, dil_set[0][i].bottom(3))\n p300.mix(1, 20, dil_set[0][i].bottom(3))\n drop(p300)\n p300.flow_rate.aspirate = 94\n\n # perform dilution\n for i, factor in enumerate(factors):\n pickup_p300('multi')\n total_vol = sample_vol*(i+1)*factor\n mix_vol = total_vol*0.8 if total_vol*0.8 <= 175 else 175\n if i == 0:\n p300.mix(mix_reps, mix_vol, dil_set[i][0])\n else:\n p300.transfer(sample_vol*(i+1), dil_set[i-1][0].bottom(3),\n dil_set[i][0].bottom(3),\n\n\n mix_after=(5, mix_vol),\n new_tip='never')\n drop(p300)\n\n return dil_set[len(factors)-1][0]\n\n \"\"\" PART 1 \"\"\"\n if prepare_standard:\n\n # TE preparation\n standard_prep(working_standard_1, assay_buffer_1,\n deepplate.columns()[0])\n\n # TR preparation\n standard_prep(working_standard_2, assay_buffer_2,\n deepplate.columns()[6])\n\n \"\"\" PART 2 \"\"\"\n\n # sample normalization (TE)\n sample_1_final_loc = dilute(2.5, samples_1, assay_buffer_1)\n\n # sample normalization (TR)\n sample_2_final_loc = dilute(0.5, samples_2, assay_buffer_2)\n\n \"\"\" PART 3 \"\"\"\n\n # transfer to final black plate\n for i, source in enumerate(\n [deepplate.rows_by_name()['A'][0], sample_1_final_loc,\n deepplate.rows_by_name()['A'][6], sample_2_final_loc]):\n dest_set = flatplate.rows()[0][i*3:(i+1)*3]\n for dest in dest_set:\n p300.pick_up_tip()\n p300.transfer(final_transfer_vol, source.bottom(3), dest.bottom(3),\n mix_before=(mix_reps, 0.8*final_transfer_vol),\n new_tip='never')\n drop(p300)\n", "custom_labware_defs": [], "fields": [ { diff --git a/protoBuilds/313086-logixsmart-station-C/README.json b/protoBuilds/313086-logixsmart-station-C/README.json deleted file mode 100644 index dd9984253..000000000 --- a/protoBuilds/313086-logixsmart-station-C/README.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "Covid Workstation": [ - "qPCR Setup" - ] - }, - "deck-setup": "\ngreen: mastermix\npink: positive control\npurple: negative control \nblue: starting samples\n\n\n", - "description": "Links:\n Logix Smart Nasopharyngeal Covid-19 Plating (Station A)\n Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station C)\nThis protocol performs PCR prep in a NEST 96-well PCR plate. Samples with buffer pre-added should be arranged in a NEST 96-deepwell, and mastermix and controls should be loaded in 1.5ml microcentrifuge tubes in the Opentrons 4x6 tuberack. The transfer order is as shown below:\n\n", - "internal": "313086", - "labware": "\nNEST 2 mL 96-Well Deep Well Plate, V Bottom\nOpentrons 24 tuberack with NEST 1.5 mL Microcentrifuge Tubes\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons 10\u00b5l tipracks\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* Covid Workstation\n\t* qPCR Setup\n\n", - "deck-setup": "* green: mastermix\n* pink: positive control\n* purple: negative control \n* blue: starting samples\n![deck setup](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/313086-station-C/deck_setup2.png)\n\n---\n\n", - "description": "Links: \n* [Logix Smart Nasopharyngeal Covid-19 Plating (Station A)](./313086)\n* [Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station C)](./313086-station-C)\n\nThis protocol performs PCR prep in a NEST 96-well PCR plate. Samples with buffer pre-added should be arranged in a NEST 96-deepwell, and mastermix and controls should be loaded in 1.5ml microcentrifuge tubes in the Opentrons 4x6 tuberack. The transfer order is as shown below: \n![order](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/demo/order.png)\n\n---\n\n", - "internal": "313086\n", - "labware": "* [NEST 2 mL 96-Well Deep Well Plate, V Bottom](https://shop.opentrons.com/collections/verified-labware/products/nest-0-2-ml-96-well-deep-well-plate-v-bottom)\n* [Opentrons 24 tuberack](https://shop.opentrons.com/collections/verified-labware/products/tube-rack-set-1) with [NEST 1.5 mL Microcentrifuge Tubes](https://shop.opentrons.com/collections/verified-consumables/products/nest-microcentrifuge-tubes)\n* [NEST 0.1 mL 96-Well PCR Plate, Full Skirt](https://shop.opentrons.com/collections/verified-labware/products/nest-0-1-ml-96-well-pcr-plate-full-skirt)\n* [Opentrons 10\u00b5l tipracks](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-10ul-tips)\n\nTo purchase tips, reagents, or pipettes, please visit our [online store](https://shop.opentrons.com/) or contact our sales team at [info@opentrons.com](mailto:info@opentrons.com)\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "pipettes": "* [P10 Single-channel electronic pipette](https://shop.opentrons.com/collections/ot-2-pipettes/products/single-channel-electronic-pipette)\n* [P10 Multi-channel electronic pipette](https://shop.opentrons.com/collections/ot-2-pipettes/products/8-channel-electronic-pipette)\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "reagents": "* [Logix Smart Nasopharyngeal Covid-19 Kit](https://codiagnostics.com/products/diagnostic-solutions/logix-smart-covid19/)\n\n---\n\n", - "title": "Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station C)" - }, - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "pipettes": "\nP10 Single-channel electronic pipette\nP10 Multi-channel electronic pipette\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "reagents": [ - "Logix Smart Nasopharyngeal Covid-19 Kit" - ], - "title": "Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station C)" -} \ No newline at end of file diff --git a/protoBuilds/313086-logixsmart-station-C/generic_station_C.ot2.apiv2.py.json b/protoBuilds/313086-logixsmart-station-C/generic_station_C.ot2.apiv2.py.json deleted file mode 100644 index d46d1195c..000000000 --- a/protoBuilds/313086-logixsmart-station-C/generic_station_C.ot2.apiv2.py.json +++ /dev/null @@ -1,163 +0,0 @@ -{ - "content": "import json\nimport os\nimport math\n\n# metadata\nmetadata = {\n 'protocolName': 'Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep \\\n(Station C)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.10'\n}\n\n\ndef run(ctx):\n\n [sample_type, num_samples, p10_mount, m10_mount,\n tip_track] = get_values( # noqa: F821\n 'sample_type', 'num_samples', 'p10_mount', 'm10_mount', 'tip_track')\n\n # load labware\n source_plate = ctx.load_labware('nest_96_wellplate_2ml_deep', '1',\n '96-deepwell sample plate')\n dest_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n '2', '96-well PCR plate')\n tuberack = ctx.load_labware('opentrons_24_tuberack_nest_2ml_screwcap',\n '4', 'reagent tuberack')\n tipracks10s = [\n ctx.load_labware('opentrons_96_tiprack_10ul', slot,\n '300\u00b5l tiprack')\n for slot in ['7', '8', '10', '11']]\n tipracks10m = [ctx.load_labware('opentrons_96_tiprack_10ul', slot,\n '10\u00b5l tiprack')\n for slot in ['3', '5', '6', '9']]\n\n # load pipette\n p10 = ctx.load_instrument('p10_single', p10_mount, tip_racks=tipracks10s)\n m10 = ctx.load_instrument('p10_multi', m10_mount, tip_racks=tipracks10m)\n\n # setup samples and reagents\n source_multi = source_plate.rows()[0][:math.ceil((num_samples+2)/8)]\n all_dests = dest_plate.wells()[:2+num_samples]\n all_dests_multi = dest_plate.rows()[0][:math.ceil((num_samples+2)/8)]\n mm, pos_control, neg_control = tuberack.wells()[:3]\n\n tip_log = {val: {} for val in ctx.loaded_instruments.values()}\n\n folder_path = '/data/B'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n data = json.load(json_file)\n for pip in tip_log:\n if pip.name in data:\n tip_log[pip]['count'] = data[pip.name]\n else:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n\n for pip in tip_log:\n if pip.type == 'multi':\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.rows()[0]]\n else:\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.wells()]\n tip_log[pip]['max'] = len(tip_log[pip]['tips'])\n\n def _pick_up(pip, loc=None):\n if tip_log[pip]['count'] == tip_log[pip]['max'] and not loc:\n ctx.pause('Replace ' + str(pip.max_volume) + '\u00b5l tipracks before \\\nresuming.')\n pip.reset_tipracks()\n tip_log[pip]['count'] = 0\n if loc:\n pip.pick_up_tip(loc)\n else:\n pip.pick_up_tip(tip_log[pip]['tips'][tip_log[pip]['count']])\n tip_log[pip]['count'] += 1\n\n if sample_type == 'nasopharyngeal':\n vol_mm = 5\n vol_sample = 5\n else:\n vol_mm = 10\n vol_sample = 10\n\n # transfer mastermix\n _pick_up(p10)\n for d in all_dests:\n if vol_mm <= 7:\n p10.air_gap(2)\n p10.aspirate(vol_mm, mm)\n if vol_mm <= 7:\n p10.air_gap(1)\n p10.dispense(p10.current_volume, d.bottom(1))\n p10.drop_tip()\n\n # transfer sample\n for s, d in zip(source_multi, all_dests_multi):\n _pick_up(m10)\n if vol_mm <= 7:\n m10.air_gap(2)\n m10.aspirate(vol_sample, mm)\n if vol_mm <= 7:\n m10.air_gap(1)\n m10.dispense(p10.current_volume, d.bottom(1))\n m10.drop_tip()\n\n # transfer controls\n for s, d in zip([pos_control, neg_control], dest_plate.wells()[:2]):\n _pick_up(p10)\n if vol_mm <= 7:\n p10.air_gap(2)\n p10.aspirate(vol_sample, mm)\n if vol_mm <= 7:\n p10.air_gap(1)\n p10.dispense(p10.current_volume, d.bottom(1))\n p10.drop_tip()\n\n # track final used tip\n if tip_track and not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n data = {pip.name: tip_log[pip]['count'] for pip in tip_log}\n with open(tip_file_path, 'w') as outfile:\n json.dump(data, outfile)\n", - "custom_labware_defs": [], - "fields": [ - { - "label": "sample type", - "name": "sample_type", - "options": [ - { - "label": "nasopharyngeal (5\u00b5l sample, 5\u00b5l mix)", - "value": "nasopharyngeal" - }, - { - "label": "saliva (10\u00b5l sample, 10\u00b5l mix)", - "value": "saliva" - } - ], - "type": "dropDown" - }, - { - "default": 94, - "label": "number of samples (1-94)", - "name": "num_samples", - "type": "int" - }, - { - "label": "P10 single-channel GEN1 mount", - "name": "p10_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - }, - { - "label": "P10 multi-channel GEN2 mount", - "name": "m10_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - }, - { - "label": "track tips across protocol runs", - "name": "tip_track", - "options": [ - { - "label": "no", - "value": false - }, - { - "label": "yes", - "value": true - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p10_multi" - }, - { - "mount": "right", - "name": "p10_single" - } - ], - "labware": [ - { - "name": "96-deepwell sample plate on 1", - "share": false, - "slot": "1", - "type": "nest_96_wellplate_2ml_deep" - }, - { - "name": "96-well PCR plate on 2", - "share": false, - "slot": "2", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "10\u00b5l tiprack on 3", - "share": false, - "slot": "3", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "reagent tuberack on 4", - "share": false, - "slot": "4", - "type": "opentrons_24_tuberack_nest_2ml_screwcap" - }, - { - "name": "10\u00b5l tiprack on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "10\u00b5l tiprack on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 7", - "share": false, - "slot": "7", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 8", - "share": false, - "slot": "8", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "10\u00b5l tiprack on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 10", - "share": false, - "slot": "10", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 11", - "share": false, - "slot": "11", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.10", - "author": "Nick ", - "protocolName": "Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station C)", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/313086-logixsmart-station-C/metadata.json b/protoBuilds/313086-logixsmart-station-C/metadata.json deleted file mode 100644 index c15f027d0..000000000 --- a/protoBuilds/313086-logixsmart-station-C/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "generic_station_C.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": false, - "skip-tests": false - }, - "path": "protocols/313086-logixsmart-station-C", - "slug": "313086-logixsmart-station-C", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/313086-station-B/README.json b/protoBuilds/313086-station-B/README.json deleted file mode 100644 index 0d0a247ca..000000000 --- a/protoBuilds/313086-station-B/README.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "Covid Workstation": [ - "Sample Plating" - ] - }, - "deck-setup": "\ngreen: lysis/binding buffer (13ml per channel)\npink: elution buffer: (9ml per channel)\nblue: starting samples\n\n\n", - "description": "This protocol plates lysis/binding buffer, samples, and elution buffer in a NEST 96-deepwell plate. Samples should be arranged in up to 4x Opentrons tuberacks, and buffers should be loaded in a NEST 12-channel reservoir. The transfer order is as shown below:\n\nDeepwells A1 and B1 are left empty for controls to be added later on.\n", - "internal": "313086", - "labware": "\nLabware name\nNick is working on auto-filling these sections from the protocol (3/28/2021)\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* Covid Workstation\n\t* Sample Plating\n\n\n", - "deck-setup": "* green: lysis/binding buffer (13ml per channel)\n* pink: elution buffer: (9ml per channel)\n* blue: starting samples \n![deck setup](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/313086/deck_setup.png)\n\n---\n\n", - "description": "This protocol plates lysis/binding buffer, samples, and elution buffer in a NEST 96-deepwell plate. Samples should be arranged in up to 4x Opentrons tuberacks, and buffers should be loaded in a NEST 12-channel reservoir. The transfer order is as shown below: \n![order](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/demo/order.png)\n\nDeepwells A1 and B1 are left empty for controls to be added later on.\n\n---\n\n", - "internal": "313086\n", - "labware": "* [Labware name](link to labware on shop.opentrons.com when applicable)\n* Nick is working on auto-filling these sections from the protocol (3/28/2021)\n\nTo purchase tips, reagents, or pipettes, please visit our [online store](https://shop.opentrons.com/) or contact our sales team at [info@opentrons.com](mailto:info@opentrons.com)\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "pipettes": "* [P300](link to pipette on shop.opentrons.com)\n* Nick is working on auto-filling these sections from the protocol (3/28/2021)\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "reagents": "* [Logix Smart Nasopharyngeal Covid-19 Kit](https://codiagnostics.com/products/diagnostic-solutions/logix-smart-covid19/)\n\n---\n\n", - "title": "Logix Smart Nasopharyngeal Covid-19 Plating (Station A)" - }, - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "pipettes": "\nP300\nNick is working on auto-filling these sections from the protocol (3/28/2021)\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "reagents": [ - "Logix Smart Nasopharyngeal Covid-19 Kit" - ], - "title": "Logix Smart Nasopharyngeal Covid-19 Plating (Station A)" -} \ No newline at end of file diff --git a/protoBuilds/313086-station-B/generic_station_B.ot2.apiv2.py.json b/protoBuilds/313086-station-B/generic_station_B.ot2.apiv2.py.json deleted file mode 100644 index 099a86a1c..000000000 --- a/protoBuilds/313086-station-B/generic_station_B.ot2.apiv2.py.json +++ /dev/null @@ -1,2741 +0,0 @@ -{ - "content": "import json\nimport os\nimport math\n\n# metadata\nmetadata = {\n 'protocolName': 'Logix Smart Nasopharyngeal Covid-19 PCR Prep (Station B)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.10'\n}\n\n\ndef run(ctx):\n\n [sample_type, num_samples, p10_mount, m10_mount,\n tip_track] = get_values( # noqa: F821\n 'sample_type', 'num_samples', 'p10_mount', 'm10_mount', 'tip_track')\n\n # load labware\n source_plate = ctx.load_labware('nest_96_wellplate_2ml_deep', '1',\n '96-deepwell sample plate')\n dest_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n '2', '96-well PCR plate')\n tuberack = ctx.load_labware('opentrons_24_tuberack_nest_1.5ml_screwcap',\n '4', 'reagent tuberack')\n tipracks10s = [\n ctx.load_labware('opentrons_96_tiprack_10ul', slot,\n '300\u00b5l tiprack')\n for slot in ['7', '8', '10', '11']]\n tipracks10m = [ctx.load_labware('opentrons_96_tiprack_10ul', slot,\n '10\u00b5l tiprack')\n for slot in ['3', '5', '6', '9']]\n\n # load pipette\n p10 = ctx.load_instrument('p10_single', p10_mount, tip_racks=tipracks10s)\n m10 = ctx.load_instrument('p10_multi', m10_mount, tip_racks=tipracks10m)\n\n # setup samples and reagents\n source_multi = source_plate.rows()[0][:math.ceil((num_samples+2)/8)]\n all_dests = dest_plate.wells()[:2+num_samples]\n all_dests_multi = dest_plate.rows()[0][:math.ceil((num_samples+2)/8)]\n mm, pos_control, neg_control = tuberack.wells()[:3]\n\n tip_log = {val: {} for val in ctx.loaded_instruments.values()}\n\n folder_path = '/data/tip_track'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n data = json.load(json_file)\n for pip in tip_log:\n if pip.name in data:\n tip_log[pip]['count'] = data[pip.name]\n else:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n\n for pip in tip_log:\n if pip.type == 'multi':\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.rows()[0]]\n else:\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.wells()]\n tip_log[pip]['max'] = len(tip_log[pip]['tips'])\n\n def _pick_up(pip, loc=None):\n if tip_log[pip]['count'] == tip_log[pip]['max'] and not loc:\n ctx.pause('Replace ' + str(pip.max_volume) + '\u00b5l tipracks before \\\nresuming.')\n pip.reset_tipracks()\n tip_log[pip]['count'] = 0\n if loc:\n pip.pick_up_tip(loc)\n else:\n pip.pick_up_tip(tip_log[pip]['tips'][tip_log[pip]['count']])\n tip_log[pip]['count'] += 1\n\n if sample_type == 'nasopharyngeal':\n vol_mm = 5\n vol_sample = 5\n else:\n vol_mm = 10\n vol_sample = 10\n\n # transfer mastermix\n _pick_up(p10)\n for d in all_dests:\n if vol_mm <= 7:\n p10.air_gap(2)\n p10.aspirate(vol_mm, mm)\n if vol_mm <= 7:\n p10.air_gap(1)\n p10.dispense(p10.current_volume, d.bottom(1))\n p10.drop_tip()\n\n # transfer sample\n for s, d in zip(source_multi, all_dests_multi):\n _pick_up(m10)\n if vol_mm <= 7:\n m10.air_gap(2)\n m10.aspirate(vol_sample, mm)\n if vol_mm <= 7:\n m10.air_gap(1)\n m10.dispense(p10.current_volume, d.bottom(1))\n m10.drop_tip()\n\n # transfer controls\n for s, d in zip([pos_control, neg_control], dest_plate.wells()[:2]):\n _pick_up(p10)\n if vol_mm <= 7:\n p10.air_gap(2)\n p10.aspirate(vol_sample, mm)\n if vol_mm <= 7:\n p10.air_gap(1)\n p10.dispense(p10.current_volume, d.bottom(1))\n p10.drop_tip()\n\n # track final used tip\n if tip_track and not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n data = {pip.name: tip_log[pip]['count'] for pip in tip_log}\n with open(tip_file_path, 'w') as outfile:\n json.dump(data, outfile)\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "", - "brandId": [], - "links": [] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.76, - "yDimension": 85.47, - "zDimension": 85.35 - }, - "groups": [ - { - "metadata": { - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "A2", - "B2", - "C2", - "D2", - "A3", - "B3", - "C3", - "D3", - "A4", - "B4", - "C4", - "D4", - "A5", - "B5", - "C5", - "D5", - "A6", - "B6", - "C6", - "D6" - ] - } - ], - "metadata": { - "displayCategory": "tubeRack", - "displayName": "Opentrons 24 Tube Rack with Blood Tube 5mL Conical", - "displayVolumeUnits": "mL", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1", - "B1", - "C1", - "D1" - ], - [ - "A2", - "B2", - "C2", - "D2" - ], - [ - "A3", - "B3", - "C3", - "D3" - ], - [ - "A4", - "B4", - "C4", - "D4" - ], - [ - "A5", - "B5", - "C5", - "D5" - ], - [ - "A6", - "B6", - "C6", - "D6" - ] - ], - "parameters": { - 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"type": "int" - }, - { - "label": "P10 single-channel GEN1 mount", - "name": "p10_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - }, - { - "label": "P10 multi-channel GEN2 mount", - "name": "m10_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - }, - { - "label": "track tips across protocol runs", - "name": "tip_track", - "options": [ - { - "label": "no", - "value": false - }, - { - "label": "yes", - "value": true - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p10_multi" - }, - { - "mount": "right", - "name": "p10_single" - } - ], - "labware": [ - { - "name": "96-deepwell sample plate on 1", - "share": false, - "slot": "1", - "type": "nest_96_wellplate_2ml_deep" - }, - { - "name": "96-well PCR plate on 2", - "share": false, - "slot": "2", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "10\u00b5l tiprack on 3", - "share": false, - "slot": "3", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "reagent tuberack on 4", - "share": false, - "slot": "4", - "type": "opentrons_24_tuberack_nest_1.5ml_screwcap" - }, - { - "name": "10\u00b5l tiprack on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "10\u00b5l tiprack on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 7", - "share": false, - "slot": "7", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 8", - "share": false, - "slot": "8", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "10\u00b5l tiprack on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 10", - "share": false, - "slot": "10", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 11", - "share": false, - "slot": "11", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.10", - "author": "Nick ", - "protocolName": "Logix Smart Nasopharyngeal Covid-19 PCR Prep (Station B)", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/313086-station-B/metadata.json b/protoBuilds/313086-station-B/metadata.json deleted file mode 100644 index e46d9af95..000000000 --- a/protoBuilds/313086-station-B/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "generic_station_B.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": false, - "skip-tests": false - }, - "path": "protocols/313086-station-B", - "slug": "313086-station-B", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/313086-station-C/README.json b/protoBuilds/313086-station-C/README.json deleted file mode 100644 index dd9984253..000000000 --- a/protoBuilds/313086-station-C/README.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "Covid Workstation": [ - "qPCR Setup" - ] - }, - "deck-setup": "\ngreen: mastermix\npink: positive control\npurple: negative control \nblue: starting samples\n\n\n", - "description": "Links:\n Logix Smart Nasopharyngeal Covid-19 Plating (Station A)\n Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station C)\nThis protocol performs PCR prep in a NEST 96-well PCR plate. Samples with buffer pre-added should be arranged in a NEST 96-deepwell, and mastermix and controls should be loaded in 1.5ml microcentrifuge tubes in the Opentrons 4x6 tuberack. The transfer order is as shown below:\n\n", - "internal": "313086", - "labware": "\nNEST 2 mL 96-Well Deep Well Plate, V Bottom\nOpentrons 24 tuberack with NEST 1.5 mL Microcentrifuge Tubes\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons 10\u00b5l tipracks\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* Covid Workstation\n\t* qPCR Setup\n\n", - "deck-setup": "* green: mastermix\n* pink: positive control\n* purple: negative control \n* blue: starting samples\n![deck setup](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/313086-station-C/deck_setup2.png)\n\n---\n\n", - "description": "Links: \n* [Logix Smart Nasopharyngeal Covid-19 Plating (Station A)](./313086)\n* [Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station C)](./313086-station-C)\n\nThis protocol performs PCR prep in a NEST 96-well PCR plate. Samples with buffer pre-added should be arranged in a NEST 96-deepwell, and mastermix and controls should be loaded in 1.5ml microcentrifuge tubes in the Opentrons 4x6 tuberack. The transfer order is as shown below: \n![order](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/demo/order.png)\n\n---\n\n", - "internal": "313086\n", - "labware": "* [NEST 2 mL 96-Well Deep Well Plate, V Bottom](https://shop.opentrons.com/collections/verified-labware/products/nest-0-2-ml-96-well-deep-well-plate-v-bottom)\n* [Opentrons 24 tuberack](https://shop.opentrons.com/collections/verified-labware/products/tube-rack-set-1) with [NEST 1.5 mL Microcentrifuge Tubes](https://shop.opentrons.com/collections/verified-consumables/products/nest-microcentrifuge-tubes)\n* [NEST 0.1 mL 96-Well PCR Plate, Full Skirt](https://shop.opentrons.com/collections/verified-labware/products/nest-0-1-ml-96-well-pcr-plate-full-skirt)\n* [Opentrons 10\u00b5l tipracks](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-10ul-tips)\n\nTo purchase tips, reagents, or pipettes, please visit our [online store](https://shop.opentrons.com/) or contact our sales team at [info@opentrons.com](mailto:info@opentrons.com)\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "pipettes": "* [P10 Single-channel electronic pipette](https://shop.opentrons.com/collections/ot-2-pipettes/products/single-channel-electronic-pipette)\n* [P10 Multi-channel electronic pipette](https://shop.opentrons.com/collections/ot-2-pipettes/products/8-channel-electronic-pipette)\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "reagents": "* [Logix Smart Nasopharyngeal Covid-19 Kit](https://codiagnostics.com/products/diagnostic-solutions/logix-smart-covid19/)\n\n---\n\n", - "title": "Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station C)" - }, - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "pipettes": "\nP10 Single-channel electronic pipette\nP10 Multi-channel electronic pipette\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "reagents": [ - "Logix Smart Nasopharyngeal Covid-19 Kit" - ], - "title": "Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station C)" -} \ No newline at end of file diff --git a/protoBuilds/313086-station-C/generic_station_C.ot2.apiv2.py.json b/protoBuilds/313086-station-C/generic_station_C.ot2.apiv2.py.json deleted file mode 100644 index d46d1195c..000000000 --- a/protoBuilds/313086-station-C/generic_station_C.ot2.apiv2.py.json +++ /dev/null @@ -1,163 +0,0 @@ -{ - "content": "import json\nimport os\nimport math\n\n# metadata\nmetadata = {\n 'protocolName': 'Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep \\\n(Station C)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.10'\n}\n\n\ndef run(ctx):\n\n [sample_type, num_samples, p10_mount, m10_mount,\n tip_track] = get_values( # noqa: F821\n 'sample_type', 'num_samples', 'p10_mount', 'm10_mount', 'tip_track')\n\n # load labware\n source_plate = ctx.load_labware('nest_96_wellplate_2ml_deep', '1',\n '96-deepwell sample plate')\n dest_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n '2', '96-well PCR plate')\n tuberack = ctx.load_labware('opentrons_24_tuberack_nest_2ml_screwcap',\n '4', 'reagent tuberack')\n tipracks10s = [\n ctx.load_labware('opentrons_96_tiprack_10ul', slot,\n '300\u00b5l tiprack')\n for slot in ['7', '8', '10', '11']]\n tipracks10m = [ctx.load_labware('opentrons_96_tiprack_10ul', slot,\n '10\u00b5l tiprack')\n for slot in ['3', '5', '6', '9']]\n\n # load pipette\n p10 = ctx.load_instrument('p10_single', p10_mount, tip_racks=tipracks10s)\n m10 = ctx.load_instrument('p10_multi', m10_mount, tip_racks=tipracks10m)\n\n # setup samples and reagents\n source_multi = source_plate.rows()[0][:math.ceil((num_samples+2)/8)]\n all_dests = dest_plate.wells()[:2+num_samples]\n all_dests_multi = dest_plate.rows()[0][:math.ceil((num_samples+2)/8)]\n mm, pos_control, neg_control = tuberack.wells()[:3]\n\n tip_log = {val: {} for val in ctx.loaded_instruments.values()}\n\n folder_path = '/data/B'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n data = json.load(json_file)\n for pip in tip_log:\n if pip.name in data:\n tip_log[pip]['count'] = data[pip.name]\n else:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n\n for pip in tip_log:\n if pip.type == 'multi':\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.rows()[0]]\n else:\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.wells()]\n tip_log[pip]['max'] = len(tip_log[pip]['tips'])\n\n def _pick_up(pip, loc=None):\n if tip_log[pip]['count'] == tip_log[pip]['max'] and not loc:\n ctx.pause('Replace ' + str(pip.max_volume) + '\u00b5l tipracks before \\\nresuming.')\n pip.reset_tipracks()\n tip_log[pip]['count'] = 0\n if loc:\n pip.pick_up_tip(loc)\n else:\n pip.pick_up_tip(tip_log[pip]['tips'][tip_log[pip]['count']])\n tip_log[pip]['count'] += 1\n\n if sample_type == 'nasopharyngeal':\n vol_mm = 5\n vol_sample = 5\n else:\n vol_mm = 10\n vol_sample = 10\n\n # transfer mastermix\n _pick_up(p10)\n for d in all_dests:\n if vol_mm <= 7:\n p10.air_gap(2)\n p10.aspirate(vol_mm, mm)\n if vol_mm <= 7:\n p10.air_gap(1)\n p10.dispense(p10.current_volume, d.bottom(1))\n p10.drop_tip()\n\n # transfer sample\n for s, d in zip(source_multi, all_dests_multi):\n _pick_up(m10)\n if vol_mm <= 7:\n m10.air_gap(2)\n m10.aspirate(vol_sample, mm)\n if vol_mm <= 7:\n m10.air_gap(1)\n m10.dispense(p10.current_volume, d.bottom(1))\n m10.drop_tip()\n\n # transfer controls\n for s, d in zip([pos_control, neg_control], dest_plate.wells()[:2]):\n _pick_up(p10)\n if vol_mm <= 7:\n p10.air_gap(2)\n p10.aspirate(vol_sample, mm)\n if vol_mm <= 7:\n p10.air_gap(1)\n p10.dispense(p10.current_volume, d.bottom(1))\n p10.drop_tip()\n\n # track final used tip\n if tip_track and not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n data = {pip.name: tip_log[pip]['count'] for pip in tip_log}\n with open(tip_file_path, 'w') as outfile:\n json.dump(data, outfile)\n", - "custom_labware_defs": [], - "fields": [ - { - "label": "sample type", - "name": "sample_type", - "options": [ - { - "label": "nasopharyngeal (5\u00b5l sample, 5\u00b5l mix)", - "value": "nasopharyngeal" - }, - { - "label": "saliva (10\u00b5l sample, 10\u00b5l mix)", - "value": "saliva" - } - ], - "type": "dropDown" - }, - { - "default": 94, - "label": "number of samples (1-94)", - "name": "num_samples", - "type": "int" - }, - { - "label": "P10 single-channel GEN1 mount", - "name": "p10_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - }, - { - "label": "P10 multi-channel GEN2 mount", - "name": "m10_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - }, - { - "label": "track tips across protocol runs", - "name": "tip_track", - "options": [ - { - "label": "no", - "value": false - }, - { - "label": "yes", - "value": true - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p10_multi" - }, - { - "mount": "right", - "name": "p10_single" - } - ], - "labware": [ - { - "name": "96-deepwell sample plate on 1", - "share": false, - "slot": "1", - "type": "nest_96_wellplate_2ml_deep" - }, - { - "name": "96-well PCR plate on 2", - "share": false, - "slot": "2", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "10\u00b5l tiprack on 3", - "share": false, - "slot": "3", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "reagent tuberack on 4", - "share": false, - "slot": "4", - "type": "opentrons_24_tuberack_nest_2ml_screwcap" - }, - { - "name": "10\u00b5l tiprack on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "10\u00b5l tiprack on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 7", - "share": false, - "slot": "7", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 8", - "share": false, - "slot": "8", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "10\u00b5l tiprack on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 10", - "share": false, - "slot": "10", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 11", - "share": false, - "slot": "11", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.10", - "author": "Nick ", - "protocolName": "Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station C)", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/313086-station-C/metadata.json b/protoBuilds/313086-station-C/metadata.json deleted file mode 100644 index 947784f1b..000000000 --- a/protoBuilds/313086-station-C/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "generic_station_C.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": false, - "skip-tests": false - }, - "path": "protocols/313086-station-C", - "slug": "313086-station-C", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/33900b/protein_purification.ot2.apiv2.py.json b/protoBuilds/33900b/protein_purification.ot2.apiv2.py.json index 3455574df..8a062e94f 100644 --- a/protoBuilds/33900b/protein_purification.ot2.apiv2.py.json +++ b/protoBuilds/33900b/protein_purification.ot2.apiv2.py.json @@ -2726,7 +2726,7 @@ ], "labware": [ { - "name": "Greiner Bio-One 96-Deepwell Plate 2ml on Magnetic Module GEN1 on 1", + "name": "Greiner Bio-One 96-Deepwell Plate 2ml on Magnetic Module on 1", "share": false, "slot": "1", "type": "greinerbioone_96_wellplate_2ml_deep" @@ -2804,5 +2804,12 @@ "protocolName": "Promega MagneHis\u2122 Protein Purification System", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 1 lw Greiner Bio-One 96-Deepwell Plate 2ml on Magnetic Module on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/343001/343001.ot2.apiv2.py.json b/protoBuilds/343001/343001.ot2.apiv2.py.json index 27ff5cef5..d189f8c43 100644 --- a/protoBuilds/343001/343001.ot2.apiv2.py.json +++ b/protoBuilds/343001/343001.ot2.apiv2.py.json @@ -2345,7 +2345,7 @@ "type": "opentrons_6_tuberack_falcon_50ml_conical" }, { - "name": "Zymo 96-Well Block on Magnetic Module GEN1 on 4", + "name": "Zymo 96-Well Block on Magnetic Module on 4", "share": false, "slot": "4", "type": "zymo_96_wellblock" @@ -2405,5 +2405,12 @@ "protocolName": "Zymo Extraction Protocol", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 4 lw Zymo 96-Well Block on Magnetic Module on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/35269b/35269b.ot2.apiv2.py.json b/protoBuilds/35269b/35269b.ot2.apiv2.py.json index f9cae7370..2721b9e09 100644 --- a/protoBuilds/35269b/35269b.ot2.apiv2.py.json +++ b/protoBuilds/35269b/35269b.ot2.apiv2.py.json @@ -1328,5 +1328,12 @@ "description": "Custom Protocol Request", "protocolName": "MAI VIRAL ISOLATION" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw Extraction Plate on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/3607d5-3/extraction1.ot2.apiv2.py.json b/protoBuilds/3607d5-3/extraction1.ot2.apiv2.py.json deleted file mode 100644 index 41e2f7ed3..000000000 --- a/protoBuilds/3607d5-3/extraction1.ot2.apiv2.py.json +++ /dev/null @@ -1,4698 +0,0 @@ -{ - "content": "from opentrons.types import Point\nimport json\nimport os\nimport math\n\nmetadata = {\n 'protocolName': 'SPRI 3',\n 'author': 'Opentrons ',\n 'apiLevel': '2.10'\n}\n\n\n# Start protocol\ndef run(ctx):\n [num_samples, m20_mount, m300_mount, mag_height, sample_vol,\n binding_buffer_vol, wash1_vol, wash2_vol, elution_vol,\n settling_time] = get_values( # noqa: F821\n 'num_samples', 'm20_mount', 'm300_mount', 'mag_height', 'sample_vol',\n 'binding_buffer_vol', 'wash1_vol', 'wash2_vol', 'elution_vol',\n 'settling_time')\n\n # num_samples = 96\n # m20_mount = 'left'\n # m300_mount = 'right'\n # mag_height = 10.5\n # sample_vol = 45.0\n # binding_buffer_vol = 45.0\n # wash1_vol = 200.0\n # wash2_vol = 200.0\n # elution_vol = 50.0\n # settling_time = 5.0\n park_tips = False\n tip_track = False\n radial_offset = 0.3\n z_offset = 0.5\n air_gap_vol = 0\n\n \"\"\"\n Here is where you can change the locations of your labware and modules\n (note that this is the recommended configuration)\n \"\"\"\n pcr_plate = ctx.load_labware('eppendorfmetaladapter_96_wellplate_200ul',\n '7', 'sample plate')\n magdeck = ctx.load_module('magnetic module gen2', '10')\n magdeck.disengage()\n magplate = magdeck.load_labware('abgenemidi_96_wellplate_800ul',\n 'deepwell wash plate')\n elutionplate = ctx.load_labware('eppendorfmetaladapter_96_wellplate_200ul',\n '2', 'elution plate')\n waste = ctx.loaded_labwares[12].wells()[0].top()\n res1 = ctx.load_labware('nest_12_reservoir_15ml', '6', 'reagent reservoir')\n num_cols = math.ceil(num_samples/6) # offset\n tips300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot,\n '200ul tiprack')\n for slot in ['4', '9', '11']]\n tips20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', '5',\n '20ul tiprack')]\n if park_tips:\n rack = ctx.load_labware(\n 'opentrons_96_filtertiprack_200ul', '1', '200ul tiprack')\n parking_spots = rack.rows()[0][:num_cols]\n else:\n rack = ctx.load_labware(\n 'opentrons_96_filtertiprack_200ul', '1', '200ul tiprack')\n parking_spots = [None for none in range(12)]\n tips300.insert(0, rack)\n\n # load pipettes\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=tips20)\n m300 = ctx.load_instrument(\n 'p300_multi_gen2', m300_mount, tip_racks=tips300)\n\n m300.default_speed = 180\n m20.default_speed = 180\n\n tip_log = {val: {} for val in ctx.loaded_instruments.values()}\n\n \"\"\"\n Here is where you can define the locations of your reagents.\n \"\"\"\n binding_buffer = res1.rows()[0][:1]\n wash1 = res1.rows()[0][1:4]\n wash2 = res1.rows()[0][4:7]\n elution_solution = res1.rows()[0][-1]\n\n starting_samples = pcr_plate.rows()[0][:num_cols]\n mag_samples_m = magplate.rows()[0][:num_cols]\n elution_samples_m = elutionplate.rows()[0][:num_cols]\n radius = mag_samples_m[0].diameter/2\n\n magdeck.disengage() # just in case\n\n m300.flow_rate.aspirate = 20\n m300.flow_rate.dispense = 50\n m300.flow_rate.blow_out = 150\n\n folder_path = '/data/B'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n data = json.load(json_file)\n for pip in tip_log:\n if pip.name in data:\n tip_log[pip]['count'] = data[pip.name]\n else:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n\n for pip in tip_log:\n if pip.type == 'multi':\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.rows()[2]] # offset\n else:\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.wells()]\n tip_log[pip]['max'] = len(tip_log[pip]['tips'])\n\n def _pick_up(pip, loc=None):\n if tip_log[pip]['count'] == tip_log[pip]['max'] and not loc:\n ctx.pause('Replace ' + str(pip.max_volume) + 'ul tipracks before \\\nresuming.')\n pip.reset_tipracks()\n tip_log[pip]['count'] = 0\n if loc:\n pip.pick_up_tip(loc)\n else:\n pip.pick_up_tip(tip_log[pip]['tips'][tip_log[pip]['count']])\n tip_log[pip]['count'] += 1\n\n switch = True\n drop_count = 0\n # number of tips trash will accommodate before prompting user to empty\n drop_threshold = 120\n\n def _drop(pip):\n nonlocal switch\n nonlocal drop_count\n side = 30 if switch else -18\n drop_loc = ctx.loaded_labwares[12].wells()[0].top().move(\n Point(x=side))\n pip.drop_tip(drop_loc)\n switch = not switch\n if pip.type == 'multi':\n drop_count += 8\n else:\n drop_count += 1\n if drop_count == drop_threshold:\n # Setup for flashing lights notification to empty trash\n ctx.home() # home before continuing with protocol\n drop_count = 0\n\n waste_vol = 0\n waste_threshold = 185000\n\n def remove_supernatant(vol, pip=m300, park=False):\n \"\"\"\n `remove_supernatant` will transfer supernatant from the deepwell\n extraction plate to the liquid waste reservoir.\n :param vol (float): The amount of volume to aspirate from all deepwell\n sample wells and dispense in the liquid waste.\n :param park (boolean): Whether to pick up sample-corresponding tips\n in the 'parking rack' or to pick up new tips.\n \"\"\"\n def _waste_track(vol):\n nonlocal waste_vol\n if waste_vol + vol >= waste_threshold:\n # Setup for flashing lights notification to empty liquid waste\n ctx.home()\n waste_vol = 0\n waste_vol += vol\n\n for i, (m, spot) in enumerate(zip(mag_samples_m, parking_spots)):\n if park:\n _pick_up(pip, spot)\n else:\n _pick_up(pip)\n side = -1 if i % 2 == 0 else 1\n loc = m.bottom(0).move(Point(x=side*radius*radial_offset,\n z=z_offset))\n _waste_track(vol)\n pip.move_to(m.center())\n # if pip == m300:\n # air_gap_vol = 20\n # else:\n # air_gap_vol = pip.max_volume - vol\n pip.transfer(vol, loc, waste, new_tip='never',\n air_gap=(air_gap_vol))\n # pip.blow_out(waste)\n _drop(pip)\n\n def bind(vol, park=True):\n \"\"\"\n `bind` will perform magnetic bead binding on each sample in the\n deepwell plate. Each channel of binding beads will be mixed before\n transfer, and the samples will be mixed with the binding beads after\n the transfer. The magnetic deck activates after the addition to all\n samples, and the supernatant is removed after bead binding.\n :param vol (float): The amount of volume to aspirate from the elution\n buffer source and dispense to each well containing\n beads.\n :param park (boolean): Whether to save sample-corresponding tips\n between adding elution buffer and transferring\n supernatant to the final clean elutions PCR\n plate.\n \"\"\"\n m300.flow_rate.aspirate = 30\n latest_chan = -1\n _pick_up(m300)\n for i, (well, spot) in enumerate(zip(mag_samples_m, parking_spots)):\n num_trans = math.ceil(vol/200)\n vol_per_trans = vol/num_trans\n asp_per_chan = (\n 0.95*res1.rows()[0][0].max_volume)//(vol_per_trans*8)\n for t in range(num_trans):\n chan_ind = int((i*num_trans + t)//asp_per_chan)\n source = binding_buffer[chan_ind]\n if m300.current_volume > 0:\n # void air gap if necessary\n m300.dispense(m300.current_volume, source.top())\n if chan_ind > latest_chan: # mix if accessing new channel\n for _ in range(5):\n m300.aspirate(180, source.bottom(0.1))\n m300.dispense(180, source.bottom(5))\n latest_chan = chan_ind\n m300.transfer(vol_per_trans, source, well.bottom(0.1),\n air_gap=20, new_tip='never')\n m300.blow_out(well.bottom(2))\n m300.air_gap(20)\n # m300.mix(10, 200, well)\n # m300.blow_out(well.top(-2))\n _drop(m300)\n\n m300.flow_rate.aspirate = 80\n\n # transfer samples\n for source, dest, spot in zip(starting_samples, mag_samples_m,\n parking_spots):\n if not m300.has_tip:\n if park:\n _pick_up(m300, spot)\n else:\n _pick_up(m300)\n # _drop(m300)\n # _pick_up(m300)\n m300.transfer(sample_vol, source.bottom(0.1), dest,\n mix_after=(10, sample_vol),\n air_gap=air_gap_vol, new_tip='never')\n m300.air_gap(air_gap_vol)\n if park:\n m300.drop_tip(spot)\n else:\n _drop(m300)\n\n ctx.delay(minutes=5, msg='Incubating off magnet for 5 minutes.')\n magdeck.engage(height=mag_height)\n ctx.delay(minutes=settling_time, msg=f'Incubating on MagDeck for \\\n{settling_time} minutes.')\n\n # remove initial supernatant\n remove_supernatant(150, park=park)\n\n def wash(vol, source, mix_reps=15, park=True, blow_out=False,\n resuspend=False):\n \"\"\"\n `wash` will perform bead washing for the extraction protocol.\n :param vol (float): The amount of volume to aspirate from each\n source and dispense to each well containing beads.\n :param source (List[Well]): A list of wells from where liquid will be\n aspirated. If the length of the source list\n > 1, `wash` automatically calculates\n the index of the source that should be\n accessed.\n :param mix_reps (int): The number of repititions to mix the beads with\n specified wash buffer (ignored if resuspend is\n False).\n :param park (boolean): Whether to save sample-corresponding tips\n between adding wash buffer and removing\n supernatant.\n :param resuspend (boolean): Whether to resuspend beads in wash buffer.\n \"\"\"\n\n if resuspend and magdeck.status == 'engaged':\n magdeck.disengage()\n\n num_trans = math.ceil(vol/200)\n vol_per_trans = vol/num_trans\n for i, (m, spot) in enumerate(zip(mag_samples_m, parking_spots)):\n _pick_up(m300)\n side = 1 if i % 2 == 0 else -1\n loc = m.bottom().move(Point(x=side*radius*radial_offset,\n z=z_offset))\n src = source[int(i//(12/len(source)))]\n for n in range(num_trans):\n if m300.current_volume > 0:\n m300.dispense(m300.current_volume, src.top())\n m300.transfer(vol_per_trans, src, m.top(), air_gap=air_gap_vol,\n new_tip='never')\n if blow_out:\n m300.blow_out(m.top(-1))\n if n < num_trans - 1: # only air_gap if going back to source\n m300.air_gap(air_gap_vol)\n if resuspend:\n m300.mix(mix_reps, 150, loc)\n m300.blow_out(m.top())\n m300.air_gap(air_gap_vol)\n if park:\n m300.drop_tip(spot)\n else:\n _drop(m300)\n\n if magdeck.status == 'disengaged':\n magdeck.engage(height=mag_height)\n\n ctx.delay(seconds=60, msg='Incubating on MagDeck for 60s seconds.')\n remove_supernatant(vol, park=park)\n\n def elute(vol, park=True):\n \"\"\"\n `elute` will perform elution from the deepwell extraciton plate to the\n final clean elutions PCR plate to complete the extraction protocol.\n :param vol (float): The amount of volume to aspirate from the elution\n buffer source and dispense to each well containing\n beads.\n :param park (boolean): Whether to save sample-corresponding tips\n between adding elution buffer and transferring\n supernatant to the final clean elutions PCR\n plate.\n \"\"\"\n\n # resuspend beads in elution\n magdeck.disengage()\n for i, (m, spot) in enumerate(zip(mag_samples_m, parking_spots)):\n _pick_up(m300)\n side = 1 if i % 2 == 0 else -1\n loc = m.bottom().move(Point(x=side*radius*radial_offset,\n z=z_offset))\n m300.aspirate(vol+2.5, elution_solution)\n m300.move_to(m.center())\n m300.dispense(vol, loc)\n m300.mix(10, 0.8*vol, loc)\n m300.blow_out(m.bottom(5))\n m300.air_gap(air_gap_vol)\n if park:\n m300.drop_tip(spot)\n else:\n _drop(m300)\n\n magdeck.engage(height=mag_height)\n ctx.delay(minutes=settling_time, msg=f'Incubating on MagDeck for \\\n{settling_time} minutes.')\n\n for i, (m, e, spot) in enumerate(\n zip(mag_samples_m, elution_samples_m, parking_spots)):\n if park:\n _pick_up(m300, spot)\n else:\n _pick_up(m300)\n side = -1 if i % 2 == 0 else 1\n loc = m.bottom().move(Point(x=side*radius*radial_offset,\n z=z_offset))\n m300.transfer(vol, loc, e.bottom(5), air_gap=air_gap_vol,\n new_tip='never')\n m300.blow_out(e.top(-2))\n m300.air_gap(air_gap_vol)\n m300.drop_tip()\n\n \"\"\"\n Here is where you can call the methods defined above to fit your specific\n protocol. The normal sequence is:\n \"\"\"\n bind(binding_buffer_vol, park=park_tips)\n wash(wash1_vol, wash1, park=park_tips, blow_out=True)\n wash(wash2_vol, wash2, park=park_tips)\n remove_supernatant(18, pip=m20)\n elute(elution_vol, park=park_tips)\n\n # track final used tip\n if tip_track and not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n data = {pip.name: tip_log[pip]['count'] for pip in tip_log}\n with open(tip_file_path, 'w') as outfile:\n json.dump(data, outfile)\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "Axygen", - "brandId": [ - "14-222-327" - ] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.76, - "yDimension": 85.48, - "zDimension": 15.51 - }, - "groups": [ - { - "brand": { - "brand": "Axygen", - "brandId": [ - "14-222-327" - ] - }, - "metadata": { - "displayCategory": "wellPlate", - "displayName": "Axygen 96 Well Plate 200ul", - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8", - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9", - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10", - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11", - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - } - ], - "metadata": { - "displayCategory": "wellPlate", - "displayName": "Axygen 96 Well Plate 200ul", - "displayVolumeUnits": "\u00b5L", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1" - ], - [ - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2" - ], - [ - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3" - ], - [ - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4" - ], - [ - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5" - ], - [ - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6" - ], - [ - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7" - ], - [ - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8" - ], - [ - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9" - ], - [ - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10" - ], - [ - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11" - ], - [ - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - ], - "parameters": { - "format": "irregular", - "isMagneticModuleCompatible": false, - "isTiprack": false, - "loadName": "axygen_96_wellplate_200ul", - "quirks": [] - }, - "schemaVersion": 2, - "version": 1, - "wells": { - "A1": { - "depth": 14.41, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 74.24, - "z": 1.1 - }, - "A10": { - "depth": 14.41, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 95.38, - "y": 74.24, - "z": 1.1 - }, - "A11": { - "depth": 14.41, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 104.38, - "y": 74.24, - "z": 1.1 - }, - "A12": { - "depth": 14.41, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 113.38, - "y": 74.24, - "z": 1.1 - }, - "A2": { - "depth": 14.41, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 23.38, - "y": 74.24, - "z": 1.1 - }, - "A3": { - "depth": 14.41, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 32.38, - "y": 74.24, - "z": 1.1 - }, - "A4": { - "depth": 14.41, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 74.24, - "z": 1.1 - }, - "A5": { - "depth": 14.41, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 50.38, - "y": 74.24, - "z": 1.1 - }, - "A6": { - "depth": 14.41, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 59.38, - "y": 74.24, - "z": 1.1 - }, - "A7": { - "depth": 14.41, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 74.24, - "z": 1.1 - }, - "A8": { - "depth": 14.41, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 74.24, - "z": 1.1 - }, - "A9": { - "depth": 14.41, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 74.24, - "z": 1.1 - }, - "B1": { - "depth": 14.41, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 65.24, - "z": 1.1 - }, - "B10": { - "depth": 14.41, - "diameter": 5.46, - "shape": "circular", - 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"totalLiquidVolume": 200, - "x": 59.38, - "y": 65.24, - "z": 1.1 - }, - "B7": { - "depth": 14.41, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 65.24, - "z": 1.1 - }, - "B8": { - "depth": 14.41, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 65.24, - "z": 1.1 - }, - "B9": { - "depth": 14.41, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 65.24, - "z": 1.1 - }, - "C1": { - "depth": 14.41, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 56.24, - "z": 1.1 - }, - "C10": { - "depth": 14.41, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 95.38, - "y": 56.24, - "z": 1.1 - }, - "C11": { - "depth": 14.41, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 104.38, - "y": 56.24, - "z": 1.1 - }, - "C12": { - "depth": 14.41, - "diameter": 5.46, - "shape": "circular", - 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"share": false, - "slot": "6", - "type": "nest_12_reservoir_15ml" - }, - { - "name": "sample plate on 7", - "share": false, - "slot": "7", - "type": "eppendorfmetaladapter_96_wellplate_200ul" - }, - { - "name": "200ul tiprack on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "deepwell wash plate on Magnetic Module GEN2 on 10", - "share": false, - "slot": "10", - "type": "abgenemidi_96_wellplate_800ul" - }, - { - "name": "200ul tiprack on 11", - "share": false, - "slot": "11", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.10", - "author": "Opentrons ", - "protocolName": "SPRI 3" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/3633ca/3633ca.ot2.apiv2.py.json b/protoBuilds/3633ca/3633ca.ot2.apiv2.py.json index 917d58bb0..f2931972c 100644 --- a/protoBuilds/3633ca/3633ca.ot2.apiv2.py.json +++ b/protoBuilds/3633ca/3633ca.ot2.apiv2.py.json @@ -87,5 +87,12 @@ "protocolName": "Ethanol Transfer", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 4 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN1 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/39b4c7/39b4c7.ot2.apiv2.py.json b/protoBuilds/39b4c7/39b4c7.ot2.apiv2.py.json index 430ebd935..15a6e67c0 100644 --- a/protoBuilds/39b4c7/39b4c7.ot2.apiv2.py.json +++ b/protoBuilds/39b4c7/39b4c7.ot2.apiv2.py.json @@ -5620,5 +5620,12 @@ "description": "Custom Protocol Request", "protocolName": "Reformat 96 Well Plates to 384 Well Plate for qPCR" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 4 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Snapcap on Temperature Module GEN1 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/3a49b6/3a49b6.ot2.apiv2.py.json b/protoBuilds/3a49b6/3a49b6.ot2.apiv2.py.json index a198f04bc..c0c9ab453 100644 --- a/protoBuilds/3a49b6/3a49b6.ot2.apiv2.py.json +++ b/protoBuilds/3a49b6/3a49b6.ot2.apiv2.py.json @@ -105,5 +105,12 @@ "protocolName": "Normalization", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/3b0db0/3b0db0.ot2.apiv2.py.json b/protoBuilds/3b0db0/3b0db0.ot2.apiv2.py.json index 6187da0f6..e9dbfaeb9 100644 --- a/protoBuilds/3b0db0/3b0db0.ot2.apiv2.py.json +++ b/protoBuilds/3b0db0/3b0db0.ot2.apiv2.py.json @@ -1524,5 +1524,12 @@ "protocolName": "Temperature Controlled PCR Prep With Tube Strips", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/3b3d2f/3b3d2f.ot2.apiv2.py.json b/protoBuilds/3b3d2f/3b3d2f.ot2.apiv2.py.json index 52faf03f5..32bfd8ce7 100644 --- a/protoBuilds/3b3d2f/3b3d2f.ot2.apiv2.py.json +++ b/protoBuilds/3b3d2f/3b3d2f.ot2.apiv2.py.json @@ -106,5 +106,12 @@ "protocolName": "Plate Loading for ddPCR", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw 4 Degree Tube Block on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/3cf31f/3cf31f.ot2.apiv2.py.json b/protoBuilds/3cf31f/3cf31f.ot2.apiv2.py.json index 933d9e8fd..25d8654dd 100644 --- a/protoBuilds/3cf31f/3cf31f.ot2.apiv2.py.json +++ b/protoBuilds/3cf31f/3cf31f.ot2.apiv2.py.json @@ -2295,5 +2295,12 @@ "description": "Custom Protocol Request", "protocolName": "BioFluid Mix and Transfer - Part 1/2 - APIv2" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 10 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Snapcap on Temperature Module GEN1 on 10", + "share": false, + "slot": "10", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/3fad82-part-2/3fad82-part-2.ot2.apiv2.py.json b/protoBuilds/3fad82-part-2/3fad82-part-2.ot2.apiv2.py.json index 2832a981b..3b0f38e82 100644 --- a/protoBuilds/3fad82-part-2/3fad82-part-2.ot2.apiv2.py.json +++ b/protoBuilds/3fad82-part-2/3fad82-part-2.ot2.apiv2.py.json @@ -163,5 +163,18 @@ "author": "Steve Plonk ", "protocolName": "Quarter Volume NEBNext Ultra II DNA Library Prep Kit\n for Illumina: part 2 - purification of samples and PCR" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 4 lw Sample Plate on Magnetic Module GEN1 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw Sample Plate on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/3fad82-part-3/3fad82-part-3.ot2.apiv2.py.json b/protoBuilds/3fad82-part-3/3fad82-part-3.ot2.apiv2.py.json index 1c4429371..44e57aae6 100644 --- a/protoBuilds/3fad82-part-3/3fad82-part-3.ot2.apiv2.py.json +++ b/protoBuilds/3fad82-part-3/3fad82-part-3.ot2.apiv2.py.json @@ -157,5 +157,18 @@ "author": "Steve Plonk ", "protocolName": "Quarter Volume NEBNext Ultra II DNA Library Prep Kit\n for Illumina: part 3 - final purification" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 4 lw Sample Plate on Magnetic Module GEN1 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw None", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/3fad82/3fad82.ot2.apiv2.py.json b/protoBuilds/3fad82/3fad82.ot2.apiv2.py.json index f45a8a4e1..7744372fd 100644 --- a/protoBuilds/3fad82/3fad82.ot2.apiv2.py.json +++ b/protoBuilds/3fad82/3fad82.ot2.apiv2.py.json @@ -114,5 +114,12 @@ "author": "Steve Plonk ", "protocolName": "Quarter Volume NEBNext Ultra II DNA Library Prep Kit for\n Illumina: part 1" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw Sample Plate on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/407d5e/407d5e.ot2.apiv2.py.json b/protoBuilds/407d5e/407d5e.ot2.apiv2.py.json index ea811d088..eb3a40a61 100644 --- a/protoBuilds/407d5e/407d5e.ot2.apiv2.py.json +++ b/protoBuilds/407d5e/407d5e.ot2.apiv2.py.json @@ -162,5 +162,12 @@ "protocolName": "Protein Labeling with Incubation", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 4 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN1 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4175de/4175de.ot2.apiv2.py.json b/protoBuilds/4175de/4175de.ot2.apiv2.py.json index ce6d5a432..c25e8b234 100644 --- a/protoBuilds/4175de/4175de.ot2.apiv2.py.json +++ b/protoBuilds/4175de/4175de.ot2.apiv2.py.json @@ -1233,5 +1233,12 @@ "description": "Custom Protocol Request", "protocolName": "Cherrypicking PCR/qPCR prep" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Applied Biosystems 96 Well Plate 100 \u00b5L on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/44b1ac/44b1ac.ot2.apiv2.py.json b/protoBuilds/44b1ac/44b1ac.ot2.apiv2.py.json index 8ce7b7a40..d8e505ee6 100644 --- a/protoBuilds/44b1ac/44b1ac.ot2.apiv2.py.json +++ b/protoBuilds/44b1ac/44b1ac.ot2.apiv2.py.json @@ -185,5 +185,24 @@ "description": "Custom Protocol Request", "protocolName": ": QIAseq Targeted RNAscan Panel for Illumina Instruments" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/453b5a/nuc_acid_pcr_prep.ot2.apiv2.py.json b/protoBuilds/453b5a/nuc_acid_pcr_prep.ot2.apiv2.py.json index 5ec826d1b..56d5484e4 100644 --- a/protoBuilds/453b5a/nuc_acid_pcr_prep.ot2.apiv2.py.json +++ b/protoBuilds/453b5a/nuc_acid_pcr_prep.ot2.apiv2.py.json @@ -1620,7 +1620,7 @@ "type": "opentrons_96_tiprack_300ul" }, { - "name": "PCR plate on Temperature Module GEN1 on 10", + "name": "PCR plate on Temperature Module on 10", "share": false, "slot": "10", "type": "biozym_96_aluminumblock_200ul" @@ -1644,5 +1644,12 @@ "protocolName": "Nucleic Acid Purification and PCR Prep", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module on 10 lw PCR plate on Temperature Module on 10", + "share": false, + "slot": "10", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4568fa-2/fa_workflow.ot2.apiv2.py.json b/protoBuilds/4568fa-2/fa_workflow.ot2.apiv2.py.json index 7d1a5d5b1..975452eeb 100644 --- a/protoBuilds/4568fa-2/fa_workflow.ot2.apiv2.py.json +++ b/protoBuilds/4568fa-2/fa_workflow.ot2.apiv2.py.json @@ -1267,5 +1267,18 @@ "protocolName": "FA Workflow", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw None", + "share": false, + "slot": "1", + "type": "tempdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 10 lw None", + "share": false, + "slot": "10", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4568fa/fa_workflow.ot2.apiv2.py.json b/protoBuilds/4568fa/fa_workflow.ot2.apiv2.py.json index ab9b85a7a..4d059b2ec 100644 --- a/protoBuilds/4568fa/fa_workflow.ot2.apiv2.py.json +++ b/protoBuilds/4568fa/fa_workflow.ot2.apiv2.py.json @@ -2452,5 +2452,18 @@ "protocolName": "FA Workflow", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw None", + "share": false, + "slot": "1", + "type": "tempdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 10 lw None", + "share": false, + "slot": "10", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4568fa/normalization.ot2.apiv2.py.json b/protoBuilds/4568fa/normalization.ot2.apiv2.py.json deleted file mode 100644 index 7dabd038a..000000000 --- a/protoBuilds/4568fa/normalization.ot2.apiv2.py.json +++ /dev/null @@ -1,1271 +0,0 @@ -{ - "content": "metadata = {\n 'protocolName': 'FA Workflow',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\nTEST_MODE = True\n\n\ndef run(ctx):\n\n [dil_csv_1, desired_conc, fill_plate_blank, p300_mount,\n p20_mount] = get_values( # noqa: F821\n 'dil_csv_1', 'desired_conc', 'fill_plate_blank', 'p300_mount',\n 'p20_mount')\n\n if TEST_MODE:\n mix_reps = 1\n else:\n mix_reps = 8\n\n tempdeck1 = ctx.load_module('temperature module gen2', '1')\n tempdeck1.set_temperature(4)\n dil_plate_final = ctx.load_labware(\n 'microampenduraplate_96_aluminumblock_200ul', '3', 'dilution plate 2')\n dil_plate_1 = ctx.load_labware(\n 'microampenduraplate_96_aluminumblock_200ul', '2',\n 'dilution plate 1')\n reservoir = ctx.load_labware('nest_12_reservoir_15ml', '9',\n 'reagent reservoir')\n tempdeck2 = ctx.load_module('temperature module gen2', '10')\n tempdeck2.set_temperature(70)\n tuberacks = [\n ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap', slot,\n f'sample tuberack {i+1}')\n for i, slot in enumerate(['5', '6'])]\n tipracks200 = [\n ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)\n for slot in ['4', '7']]\n tipracks20 = [\n ctx.load_labware('opentrons_96_filtertiprack_20ul', slot)\n for slot in ['8', '11']]\n\n p300 = ctx.load_instrument('p300_single_gen2', p300_mount,\n tip_racks=tipracks200)\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount,\n tip_racks=tipracks20)\n\n sample_sources = [\n well for tuberack in tuberacks for well in tuberack.wells()]\n water = reservoir.wells()[0]\n hs_dil = tuberacks[-1].columns()[-1][1:]\n blank_solution = reservoir.wells()[1]\n\n data = [\n [val.strip() for val in line.split(',')]\n for line in dil_csv_1.splitlines()\n if line and line.split(',')[0].strip()][1:]\n num_samples = len(data)\n\n # dilute 2x to 4\u00b5g/ml\n dils_1 = dil_plate_1.wells()[:num_samples]\n dils_2 = dil_plate_1.wells()[48:48+num_samples] # use half of plate\n\n # pre-allocate water for dilution to 100\u00b5g/ml\n p300.pick_up_tip()\n for dil, line in zip(dils_1, data):\n conc = float(line[2])\n sample_vol = 10/conc\n dil_1_vol = 100 - sample_vol\n p300.transfer(dil_1_vol, water, dil, new_tip='never')\n\n # pre-allocate water for final desired dilution\n for well in dils_2:\n p300.transfer(100-desired_conc, water, well, new_tip='never')\n p300.drop_tip()\n\n # perform dilutions\n for sample, dil1, dil2, line in zip(sample_sources, dils_1, dils_2, data):\n conc = float(line[2])\n sample_vol = 10/conc\n p20.pick_up_tip()\n p20.transfer(sample_vol, sample, dil1,\n new_tip='never')\n p20.drop_tip()\n\n for dil1 in dils_1:\n p300.pick_up_tip()\n p300.mix(mix_reps, 80, dil1)\n p300.drop_tip()\n\n for sample, dil1, dil2, line in zip(sample_sources, dils_1, dils_2, data):\n p20.pick_up_tip()\n p20.transfer(desired_conc, dil1, dil2, new_tip='never')\n p20.drop_tip()\n\n for dil2 in dils_2:\n p300.pick_up_tip()\n p300.mix(mix_reps, 80, dil2)\n p300.drop_tip()\n\n # determine transfer scheme depending on number of samples\n if 1 <= num_samples <= 15:\n dests = dil_plate_final.rows_by_name()['A'] + [\n dil_plate_final.wells_by_name()[well]\n for well in ['D1', 'D4', 'D7']]\n dests = dests[:num_samples]\n triplicates = [col[:3] for col in dil_plate_final.columns()] + [\n dil_plate_final.rows_by_name()['D'][i*3:(i+1)*3] for i in range(3)]\n triplicate_sets = triplicates[:num_samples]\n dils_final = dests[:num_samples]\n final_dest = dil_plate_final.wells_by_name()['D12']\n # final_set = dil_plate_final.rows_by_name()['D'][9:]\n blank_wells = [\n well for well in [\n well for row in dil_plate_final.rows()[:4] for well in row]\n if well not in [\n well for set in [*triplicate_sets, *[[final_dest]]]\n for well in set]]\n\n elif 15 < num_samples <= 31:\n dests = dil_plate_final.rows()['A'] + dil_plate_final.rows()['D'] + [\n dil_plate_final.wells_by_name()[well]\n for well in ['G1', 'G4', 'G7', 'G10', 'H1', 'H4', 'H7']]\n dests = dests[:num_samples]\n triplicates = [col[:3] for col in dil_plate_final.columns()] + [\n col[4:6] for col in dil_plate_final.columns()] + [\n dil_plate_final.rows_by_name()['G'][i*3:(i+1)*3]\n for i in range(4)] + [\n dil_plate_final.rows_by_name()['H'][i*3:(i+1)*3] for i in range(3)]\n triplicate_sets = triplicates[:num_samples]\n dils_final = dests[:num_samples]\n final_dest = dil_plate_final.wells_by_name()['H12']\n # final_set = dil_plate_final.rows_by_name()['H'][9:]\n blank_wells = [\n well for well in dil_plate_final.wells()\n if well not in [\n well for set in [*triplicate_sets, *[[final_dest]]]\n for well in set]]\n else:\n raise Exception(f'Invalid number of samples given ({num_samples}). \\\nMust be 1-31 samples.')\n\n if num_samples > 15 or fill_plate_blank:\n blank_wells = [\n well for well in dil_plate_final.wells()\n if well not in [\n well for set in [*triplicate_sets, *[[final_dest]]]\n for well in set]]\n else:\n blank_wells = [\n well for well in [\n well for row in dil_plate_final.rows()[:4] for well in row]\n if well not in [\n well for set in [*triplicate_sets, *[[final_dest]]]\n for well in set]]\n\n # pre-add HS diluent\n p300.pick_up_tip()\n\n for i, d in enumerate(dests):\n p300.transfer(135, hs_dil[i//11], d, new_tip='never')\n p300.transfer(27, hs_dil[0], final_dest, new_tip='never')\n p300.drop_tip()\n\n # transfer sample\n for s, d in zip(dils_2, dils_final):\n p20.transfer(15, s, d)\n\n # transfer RNA ladder\n # p20.transfer(3, rna_ladder, final_dest)\n final_well_display = final_dest.display_name.split(' ')[0]\n ctx.pause(f'Add 3ul RNA ladder to well {final_well_display}')\n\n # mix all samples with diluent\n for set in triplicate_sets:\n p300.pick_up_tip()\n p300.mix(mix_reps, 120, set[0])\n # transfer triplicates\n p300.transfer(50, set[0], set[1:], new_tip='never')\n p300.drop_tip()\n\n # mix RNA ladder with diluent\n p300.pick_up_tip()\n p300.mix(mix_reps, 20, final_dest)\n p300.drop_tip()\n\n # heat samples\n ctx.pause('Seal the plate in slot 3 and place on the temperature module on \\\nslot 10. Resume when finished.')\n ctx.home()\n if not TEST_MODE:\n ctx.delay(minutes=2)\n ctx.home()\n ctx.pause('Move the plate from temperature module on slot 10 to temperature \\\nmodule on slot 1.')\n if not TEST_MODE:\n ctx.delay(minutes=5)\n ctx.home()\n [td.deactivate() for td in [tempdeck1, tempdeck2]]\n ctx.pause('Centrifuge the plate on temperature module on slot 1. Replace \\\non temperature module on slot 3 when complete.')\n\n # transfer water to blank wells\n p300.transfer(50, blank_solution, blank_wells)\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "MicroAmp EnduraPlate", - "brandId": [ - "4483352" - ] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.75, - "yDimension": 85.5, - "zDimension": 21.2 - }, - "groups": [ - { - "metadata": { - "displayCategory": "wellPlate", - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8", - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9", - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10", - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11", - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - } - ], - "metadata": { - "displayCategory": "aluminumBlock", - "displayName": "MicroAmp EnduraPlate 96 Aluminum Block 200 \u00b5L", - "displayVolumeUnits": "\u00b5L", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1" - ], - [ - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2" - ], - [ - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3" - ], - [ - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4" - ], - [ - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5" - ], - [ - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6" - ], - [ - "A7", - 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"z": 1.1 - }, - "H9": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 11.25, - "z": 1.1 - } - } - } - ], - "fields": [ - { - "default": "sample number,sample name,sample concentration (mg/ml)\n1,007007009-403-1,1.569\n2,007007009-403-2,0.984\n3,007007009-403-3,2.128\n4,007007009-403-4,2.413\n", - "label": "input .csv for normalization", - "name": "dil_csv_1", - "type": "textFile" - }, - { - "default": 4.0, - "label": "desired final concentration (ug/ml)", - "name": "desired_conc", - "type": "float" - }, - { - "label": "fill entire plate with blank if necessary", - "name": "fill_plate_blank", - "options": [ - { - "label": "yes", - "value": true - }, - { - "label": "no", - "value": false - } - ], - "type": "dropDown" - }, - { - "label": "P300 single-channel pipette mount", - "name": "p300_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - }, - { - "label": "P20 single-channel pipette mount", - "name": "p20_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p300_single_gen2" - }, - { - "mount": "right", - "name": "p20_single_gen2" - } - ], - "labware": [ - { - "name": "dilution plate 1 on 2", - "share": false, - "slot": "2", - "type": "microampenduraplate_96_aluminumblock_200ul" - }, - { - "name": "dilution plate 2 on 3", - "share": false, - "slot": "3", - "type": "microampenduraplate_96_aluminumblock_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 4", - "share": false, - "slot": "4", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "sample tuberack 1 on 5", - "share": false, - "slot": "5", - "type": "opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap" - }, - { - "name": "sample tuberack 2 on 6", - "share": false, - "slot": "6", - "type": "opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 7", - "share": false, - "slot": "7", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 8", - "share": false, - "slot": "8", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "reagent reservoir on 9", - "share": false, - "slot": "9", - "type": "nest_12_reservoir_15ml" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 11", - "share": false, - "slot": "11", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Nick ", - "protocolName": "FA Workflow", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/459a55/mass_spec_prep.ot2.apiv2.py.json b/protoBuilds/459a55/mass_spec_prep.ot2.apiv2.py.json index a7421ea83..459b51d29 100644 --- a/protoBuilds/459a55/mass_spec_prep.ot2.apiv2.py.json +++ b/protoBuilds/459a55/mass_spec_prep.ot2.apiv2.py.json @@ -51,7 +51,7 @@ ], "labware": [ { - "name": "Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN1 on 1", + "name": "Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module on 1", "share": false, "slot": "1", "type": "opentrons_96_aluminumblock_nest_wellplate_100ul" @@ -87,5 +87,12 @@ "protocolName": "Mass Spec Sample Prep", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module on 1 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/48648f/48648f.ot2.apiv2.py.json b/protoBuilds/48648f/48648f.ot2.apiv2.py.json index a45fb5de7..8402e8654 100644 --- a/protoBuilds/48648f/48648f.ot2.apiv2.py.json +++ b/protoBuilds/48648f/48648f.ot2.apiv2.py.json @@ -1554,5 +1554,12 @@ "subcategory": "None", "tags": "None" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Extraction Plate on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/49de51-pt2/49de51-pt2.ot2.apiv2.py.json b/protoBuilds/49de51-pt2/49de51-pt2.ot2.apiv2.py.json index 9e778e9ba..d0717bf96 100644 --- a/protoBuilds/49de51-pt2/49de51-pt2.ot2.apiv2.py.json +++ b/protoBuilds/49de51-pt2/49de51-pt2.ot2.apiv2.py.json @@ -1285,5 +1285,12 @@ "protocolName": "MagMAX Plant DNA Isolation Kit [2/2]", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 7 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 7", + "share": false, + "slot": "7", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/49de51/thermo_magmax_plant_isolation.ot2.apiv2.py.json b/protoBuilds/49de51/thermo_magmax_plant_isolation.ot2.apiv2.py.json index 996558100..8b765db8c 100644 --- a/protoBuilds/49de51/thermo_magmax_plant_isolation.ot2.apiv2.py.json +++ b/protoBuilds/49de51/thermo_magmax_plant_isolation.ot2.apiv2.py.json @@ -95,5 +95,18 @@ "protocolName": "ThermoFisher MagMAX Plant DNA Isolation", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw deepwell plate on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 4 lw NEST 96 Deepwell Plate 2mL on Temperature Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4a5f32/4a5f32.ot2.apiv2.py.json b/protoBuilds/4a5f32/4a5f32.ot2.apiv2.py.json index 2a7cc5dc8..4a460a9f4 100644 --- a/protoBuilds/4a5f32/4a5f32.ot2.apiv2.py.json +++ b/protoBuilds/4a5f32/4a5f32.ot2.apiv2.py.json @@ -1785,5 +1785,12 @@ "description": "Custom Protocol Request", "protocolName": "Nucleic Acid Purification with Magnetic Beads" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw 4ti-0960/C 96 Well Full Skirted Plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4b4a80-fragmentation/4b4a80-fragmentation.ot2.apiv2.py.json b/protoBuilds/4b4a80-fragmentation/4b4a80-fragmentation.ot2.apiv2.py.json index 4e067d87c..e93b4db71 100644 --- a/protoBuilds/4b4a80-fragmentation/4b4a80-fragmentation.ot2.apiv2.py.json +++ b/protoBuilds/4b4a80-fragmentation/4b4a80-fragmentation.ot2.apiv2.py.json @@ -1241,5 +1241,18 @@ "author": "Steve Plonk ", "protocolName": "NEBNext Ultra II FS DNA Library Prep Kit for Illumina\n E6177S/L (for 1-24 DNA samples): Step 2: Fragmentation" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 2 lw Opentrons 24-Well Aluminum Block on Temperature Module GEN1 on 2", + "share": false, + "slot": "2", + "type": "tempdeck" + }, + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw Thermo-Fast 96 Well Plate 200 \u00b5L on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4b4a80-pcr_enrichment/4b4a80-pcr_enrichment.ot2.apiv2.py.json b/protoBuilds/4b4a80-pcr_enrichment/4b4a80-pcr_enrichment.ot2.apiv2.py.json index f352831b9..63470fdec 100644 --- a/protoBuilds/4b4a80-pcr_enrichment/4b4a80-pcr_enrichment.ot2.apiv2.py.json +++ b/protoBuilds/4b4a80-pcr_enrichment/4b4a80-pcr_enrichment.ot2.apiv2.py.json @@ -1313,5 +1313,24 @@ "author": "Steve Plonk ", "protocolName": "NEBNext Ultra II FS DNA Library Prep Kit for Illumina\n E6177S/L (for 1-24 DNA samples): Step 5: PCR Enrichment" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 2 lw Opentrons 24-Well Aluminum Block on Temperature Module GEN1 on 2", + "share": false, + "slot": "2", + "type": "tempdeck" + }, + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4b4a80-size_selection/4b4a80-size_selection.ot2.apiv2.py.json b/protoBuilds/4b4a80-size_selection/4b4a80-size_selection.ot2.apiv2.py.json index 2a426bad2..24f0b3726 100644 --- a/protoBuilds/4b4a80-size_selection/4b4a80-size_selection.ot2.apiv2.py.json +++ b/protoBuilds/4b4a80-size_selection/4b4a80-size_selection.ot2.apiv2.py.json @@ -1289,5 +1289,18 @@ "author": "Steve Plonk ", "protocolName": "NEBNext Ultra II FS DNA Library Prep Kit for Illumina\n E6177S/L (for 1-24 DNA samples): Step 4: Size Selection" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 2 lw Opentrons 24-Well Aluminum Block on Temperature Module GEN1 on 2", + "share": false, + "slot": "2", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4b7268/4b7268.ot2.apiv2.py.json b/protoBuilds/4b7268/4b7268.ot2.apiv2.py.json index 92645f8c3..4ff1c570f 100644 --- a/protoBuilds/4b7268/4b7268.ot2.apiv2.py.json +++ b/protoBuilds/4b7268/4b7268.ot2.apiv2.py.json @@ -182,5 +182,12 @@ "author": "Steve Plonk ", "protocolName": "Custom Nucleic Acid Extraction and Bead Clean Up" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 6 lw Deep Well Plate on Magnetic Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4ee4d6-part2/4ee4d6-part2.ot2.apiv2.py.json b/protoBuilds/4ee4d6-part2/4ee4d6-part2.ot2.apiv2.py.json index 820ac4e03..3ff469ed8 100644 --- a/protoBuilds/4ee4d6-part2/4ee4d6-part2.ot2.apiv2.py.json +++ b/protoBuilds/4ee4d6-part2/4ee4d6-part2.ot2.apiv2.py.json @@ -80,5 +80,24 @@ "author": "Steve Plonk ", "protocolName": "Illumina DNA Prep with Enrichment:\n Part 2 - Clean Up and Pool Libraries, Hybridize and Capture Probes,\n Amplify Enriched Library, Clean Up Enriched Library" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 9 lw Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module GEN1 on 9", + "share": false, + "slot": "9", + "type": "tempdeck" + }, + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 6 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4ee4d6/4ee4d6.ot2.apiv2.py.json b/protoBuilds/4ee4d6/4ee4d6.ot2.apiv2.py.json index d805639d0..38d613b26 100644 --- a/protoBuilds/4ee4d6/4ee4d6.ot2.apiv2.py.json +++ b/protoBuilds/4ee4d6/4ee4d6.ot2.apiv2.py.json @@ -98,5 +98,24 @@ "author": "Steve Plonk ", "protocolName": "Illumina DNA Prep with Enrichment:\n Part 1 - Tagmentation, Clean Up, Amplify Tagmented DNA" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 9 lw Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module GEN1 on 9", + "share": false, + "slot": "9", + "type": "tempdeck" + }, + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 6 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4fa62e/4fa62e.ot2.apiv2.py.json b/protoBuilds/4fa62e/4fa62e.ot2.apiv2.py.json index 9df726c06..1db36ca2d 100644 --- a/protoBuilds/4fa62e/4fa62e.ot2.apiv2.py.json +++ b/protoBuilds/4fa62e/4fa62e.ot2.apiv2.py.json @@ -63,5 +63,12 @@ "description": "Custom Protocol Request", "protocolName": "PCR Preparation" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 4 lw Opentrons 96 Well Aluminum Block with Bio-Rad Well Plate 200 \u00b5L on Temperature Module GEN1 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4fc750/extraction.ot2.apiv2.py.json b/protoBuilds/4fc750/extraction.ot2.apiv2.py.json index e6fa34e97..a074cc9b5 100644 --- a/protoBuilds/4fc750/extraction.ot2.apiv2.py.json +++ b/protoBuilds/4fc750/extraction.ot2.apiv2.py.json @@ -302,5 +302,12 @@ "author": "Opentrons ", "protocolName": "Omega Mag-Bind\u00ae Blood & Tissue DNA 96 Kit - 250\u03bcL Blood Protocol" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 1 lw deepwell plate on Magnetic Module GEN1 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/52d238/52d238.ot2.apiv2.py.json b/protoBuilds/52d238/52d238.ot2.apiv2.py.json index f86b25587..c10d2113b 100644 --- a/protoBuilds/52d238/52d238.ot2.apiv2.py.json +++ b/protoBuilds/52d238/52d238.ot2.apiv2.py.json @@ -1285,5 +1285,24 @@ "description": "PCR, Bead Clean up, and Elution", "protocolName": "NEB Ultra II FS DNA Library Prep (Part 2)" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 4 lw Opentrons 96 Well Aluminum Block with Generic PCR Strip 200 \u00b5L on Temperature Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 9 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 9", + "share": false, + "slot": "9", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/53e6bc_mastermix_creation/antibody_mm_creation.ot2.apiv2.py.json b/protoBuilds/53e6bc_mastermix_creation/antibody_mm_creation.ot2.apiv2.py.json index ac8013624..c10d0ff0f 100644 --- a/protoBuilds/53e6bc_mastermix_creation/antibody_mm_creation.ot2.apiv2.py.json +++ b/protoBuilds/53e6bc_mastermix_creation/antibody_mm_creation.ot2.apiv2.py.json @@ -1415,7 +1415,7 @@ ], "labware": [ { - "name": "Eppendorf Twin.tec 96 Well Plate 150 \u00b5L on Temperature Module GEN1 on 1", + "name": "Eppendorf Twin.tec 96 Well Plate 150 \u00b5L on Temperature Module on 1", "share": false, "slot": "1", "type": "eppendorftwin.tec_96_wellplate_150ul" @@ -1457,5 +1457,12 @@ "protocolName": "Mastermix Creation", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module on 1 lw Eppendorf Twin.tec 96 Well Plate 150 \u00b5L on Temperature Module on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/53fec2/omega_pcr_cleanup.ot2.apiv2.py.json b/protoBuilds/53fec2/omega_pcr_cleanup.ot2.apiv2.py.json index c4ea41031..3b28e678d 100644 --- a/protoBuilds/53fec2/omega_pcr_cleanup.ot2.apiv2.py.json +++ b/protoBuilds/53fec2/omega_pcr_cleanup.ot2.apiv2.py.json @@ -2541,5 +2541,12 @@ "author": "Opentrons ", "protocolName": "Beckman Coulter AMPure XP PCR Cleanup and Size Selection" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 7 lw deepwell plate on Magnetic Module GEN2 on 7", + "share": false, + "slot": "7", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/558d02/peptide_enrichment.ot2.apiv2.py.json b/protoBuilds/558d02/peptide_enrichment.ot2.apiv2.py.json index cd58692cc..9587677b6 100644 --- a/protoBuilds/558d02/peptide_enrichment.ot2.apiv2.py.json +++ b/protoBuilds/558d02/peptide_enrichment.ot2.apiv2.py.json @@ -1187,7 +1187,7 @@ ], "labware": [ { - "name": "USA Scientific 96 Deep Well Plate 2.4 mL on Magnetic Module GEN1 on 1", + "name": "USA Scientific 96 Deep Well Plate 2.4 mL on Magnetic Module on 1", "share": false, "slot": "1", "type": "usascientific_96_wellplate_2.4ml_deep" @@ -1265,5 +1265,12 @@ "protocolName": "Magbead-Based Peptide Enrichment", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 1 lw USA Scientific 96 Deep Well Plate 2.4 mL on Magnetic Module on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/5c7384/mass_spec_sample_prep.ot2.apiv2.py.json b/protoBuilds/5c7384/mass_spec_sample_prep.ot2.apiv2.py.json index 95b6505b2..d43cd0b5c 100644 --- a/protoBuilds/5c7384/mass_spec_sample_prep.ot2.apiv2.py.json +++ b/protoBuilds/5c7384/mass_spec_sample_prep.ot2.apiv2.py.json @@ -117,5 +117,18 @@ "protocolName": "Mass Spec Sample Prep", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw sample plate on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/5dcd88/5dcd88.ot2.apiv2.py.json b/protoBuilds/5dcd88/5dcd88.ot2.apiv2.py.json index f0596a6ca..deeb9d958 100644 --- a/protoBuilds/5dcd88/5dcd88.ot2.apiv2.py.json +++ b/protoBuilds/5dcd88/5dcd88.ot2.apiv2.py.json @@ -193,5 +193,12 @@ "protocolName": "nCoV-2019 Lo Cost protocol", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 10 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN2 on 10", + "share": false, + "slot": "10", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/5f37a2/5fe7a2.ot2.apiv2.py.json b/protoBuilds/5f37a2/5fe7a2.ot2.apiv2.py.json index eb7a5e7b0..dc1810784 100644 --- a/protoBuilds/5f37a2/5fe7a2.ot2.apiv2.py.json +++ b/protoBuilds/5f37a2/5fe7a2.ot2.apiv2.py.json @@ -2423,7 +2423,7 @@ "type": "eppendorf_96_deepwellplate_500ul" }, { - "name": "Eppendorf DWP 2000ul on Magnetic Module GEN1 on 10", + "name": "Eppendorf DWP 2000ul on Magnetic Module on 10", "share": false, "slot": "10", "type": "eppendorf_96_deepwellplate_2000ul" @@ -2447,5 +2447,12 @@ "protocolName": "Nucleic Acid Purification", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 10 lw Eppendorf DWP 2000ul on Magnetic Module on 10", + "share": false, + "slot": "10", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/5f7d18/5f7d18.ot2.apiv2.py.json b/protoBuilds/5f7d18/5f7d18.ot2.apiv2.py.json index 340844c59..4ec7975fb 100644 --- a/protoBuilds/5f7d18/5f7d18.ot2.apiv2.py.json +++ b/protoBuilds/5f7d18/5f7d18.ot2.apiv2.py.json @@ -195,5 +195,12 @@ "protocolName": "Viral Nucleic Acid Isolation from Oral and Nasal swabs", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/5fa647/5fa647.ot2.apiv2.py.json b/protoBuilds/5fa647/5fa647.ot2.apiv2.py.json index d19e37e15..16fa5d801 100644 --- a/protoBuilds/5fa647/5fa647.ot2.apiv2.py.json +++ b/protoBuilds/5fa647/5fa647.ot2.apiv2.py.json @@ -422,5 +422,12 @@ "protocolName": "SuperScript III: qRT-PCR Prep with CSV File", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/640a85/pcr_prep.ot2.apiv2.py.json b/protoBuilds/640a85/pcr_prep.ot2.apiv2.py.json index dbbbb21c6..d4a11ffb7 100644 --- a/protoBuilds/640a85/pcr_prep.ot2.apiv2.py.json +++ b/protoBuilds/640a85/pcr_prep.ot2.apiv2.py.json @@ -1244,5 +1244,12 @@ "protocolName": "PCR Prepation", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw Thermo Scientific 96 Well Plate 300 \u00b5L on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/65ed01/65ed01.ot2.apiv2.py.json b/protoBuilds/65ed01/65ed01.ot2.apiv2.py.json index ad1e4f60f..8589831f0 100644 --- a/protoBuilds/65ed01/65ed01.ot2.apiv2.py.json +++ b/protoBuilds/65ed01/65ed01.ot2.apiv2.py.json @@ -1299,5 +1299,12 @@ "protocolName": "Nucleic Acid Purification with Magnetic Beads", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 6 lw YDP-96-2.2-SC 96_wellplate_2200ul on Magnetic Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/69db93/69db93.ot2.apiv2.py.json b/protoBuilds/69db93/69db93.ot2.apiv2.py.json index 0afcc823b..ad15616c2 100644 --- a/protoBuilds/69db93/69db93.ot2.apiv2.py.json +++ b/protoBuilds/69db93/69db93.ot2.apiv2.py.json @@ -140,5 +140,12 @@ "protocolName": "RNA Extraction With Magnetic Beads (no tip waste)", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6a77d9/ngs_cleanup.ot2.apiv2.py.json b/protoBuilds/6a77d9/ngs_cleanup.ot2.apiv2.py.json deleted file mode 100644 index 84712e00c..000000000 --- a/protoBuilds/6a77d9/ngs_cleanup.ot2.apiv2.py.json +++ /dev/null @@ -1,142 +0,0 @@ -{ - "content": "from opentrons.types import Point\n\nmetadata = {\n 'protocolName': 'Liquid Deposition on Custom Surface',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.9'\n}\n\n\ndef run(ctx):\n\n volume, loc_csv, p20_type, p20_mount = get_values( # noqa: F821\n 'volume', 'loc_csv', 'p20_type', 'p20_mount')\n\n res = ctx.load_labware('usascientific_96_wellplate_2.4ml_deep', '10')\n tiprack20 = [ctx.load_labware('opentrons_96_tiprack_20ul', '11')]\n source = res.rows()[0][0]\n plate = ctx.load_labware('custom_1_other_20ul', '1')\n\n p20 = ctx.load_instrument(p20_type, p20_mount, tip_racks=tiprack20)\n # match mount to axis\n axis_map = {\n 'right': 'A',\n 'left': 'Z'\n }\n\n # parse .csv\n offsets = [\n [float(val) for val in line.split(',')]\n for line in loc_csv.splitlines()[1:]]\n\n # grid creation methods\n x_spaces = [0, 9, 13.5, 22.5]\n y_spaces = [0, -9, -18, -27]\n ref_a1 = plate.wells()[0].top().move(Point(x=0, y=0))\n\n def create_col(ref):\n col = [ref.move(Point(y=y_space)) for y_space in y_spaces]\n return col\n\n def create_grid(x_grid, y_grid):\n grid = []\n for x_start, y_start in zip([0, -4.5], [0, -4.5]):\n for x_space in x_spaces:\n ref = ref_a1.move(Point(x=x_grid+x_space+x_start,\n y=y_grid+y_start))\n grid.append(create_col(ref))\n return grid\n\n # initialize and create grids\n grids = [create_grid(0, 0)]\n for offset in offsets:\n x, y = offset\n grid = create_grid(x, y)\n grids.append(grid)\n\n # setup destinations depending on pipette type\n if p20_type == 'p20_multi_gen2':\n dests = [col[0] for grid in grids for col in grid]\n # update when P20 multi is received\n else:\n for grid in grids:\n dests = [well for col in grid for well in col]\n p20.pick_up_tip()\n for dest in dests:\n print(dest.point)\n p20.aspirate(volume, source)\n p20.move_to(dest.move(Point(z=10)))\n ctx.max_speeds[axis_map[p20_mount]] = 10\n p20.move_to(dest)\n p20.dispense(volume, dest)\n del ctx.max_speeds[axis_map[p20_mount]]\n p20.drop_tip()\n print('\\n\\n\\n\\n')\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "custom", - "brandId": [], - "links": [] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 397.5, - "yDimension": 236, - "zDimension": 100 - }, - "groups": [ - { - "metadata": { - "wellBottomShape": "flat" - }, - "wells": [ - "A1" - ] - } - ], - "metadata": { - "displayCategory": "other", - "displayName": "Custom Surface", - "displayVolumeUnits": "\u00b5L", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1" - ] - ], - "parameters": { - "format": "irregular", - "isMagneticModuleCompatible": false, - "isTiprack": false, - "loadName": "custom_1_other_20ul" - }, - "schemaVersion": 2, - "version": 1, - "wells": { - "A1": { - "depth": 0.5, - "diameter": 4.5, - "shape": "circular", - "totalLiquidVolume": 20, - "x": 14.38, - "y": 224.77, - "z": 99.5 - } - } - } - ], - "fields": [ - { - "default": 10, - "label": "transfer volume (in \u00b5l)", - "name": "volume", - "type": "float" - }, - { - "default": "x offset (in mm),y offset (in mm)\n20, -20", - "label": "location offset .csv", - "name": "loc_csv", - "type": "textFile" - }, - { - "label": "P20 GEN2 type", - "name": "p20_type", - "options": [ - { - "label": "single", - "value": "p20_single_gen2" - } - ], - "type": "dropDown" - }, - { - "label": "P20 GEN2 pipette mount", - "name": "p20_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p20_single_gen2" - } - ], - "labware": [ - { - "name": "Custom Surface on 1", - "share": false, - "slot": "1", - "type": "custom_1_other_20ul" - }, - { - "name": "USA Scientific 96 Deep Well Plate 2.4 mL on 10", - "share": false, - "slot": "10", - "type": "usascientific_96_wellplate_2.4ml_deep" - }, - { - "name": "Opentrons 96 Tip Rack 20 \u00b5L on 11", - "share": false, - "slot": "11", - "type": "opentrons_96_tiprack_20ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.9", - "author": "Nick ", - "protocolName": "Liquid Deposition on Custom Surface", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/6a93a2-part2/6a93a2-part2.ot2.apiv2.py.json b/protoBuilds/6a93a2-part2/6a93a2-part2.ot2.apiv2.py.json index 5af28b39b..f3a68d4d7 100644 --- a/protoBuilds/6a93a2-part2/6a93a2-part2.ot2.apiv2.py.json +++ b/protoBuilds/6a93a2-part2/6a93a2-part2.ot2.apiv2.py.json @@ -148,5 +148,18 @@ "protocolName": "Swift Rapid NGS Part 2 - Adaptase", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with Generic 2 mL Screwcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6a93a2-part3/6a93a2-part3.ot2.apiv2.py.json b/protoBuilds/6a93a2-part3/6a93a2-part3.ot2.apiv2.py.json index a10dea41d..1fcbab0dc 100644 --- a/protoBuilds/6a93a2-part3/6a93a2-part3.ot2.apiv2.py.json +++ b/protoBuilds/6a93a2-part3/6a93a2-part3.ot2.apiv2.py.json @@ -151,5 +151,24 @@ "protocolName": "Swift Rapid NGS Part 3 - Extension, SPRI, and Ligation", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with Generic 2 mL Screwcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6a93a2-part4/6a93a2-part4.ot2.apiv2.py.json b/protoBuilds/6a93a2-part4/6a93a2-part4.ot2.apiv2.py.json index 74ba0c1c9..19f67dbaa 100644 --- a/protoBuilds/6a93a2-part4/6a93a2-part4.ot2.apiv2.py.json +++ b/protoBuilds/6a93a2-part4/6a93a2-part4.ot2.apiv2.py.json @@ -129,5 +129,12 @@ "protocolName": "Swift Rapid NGS Part 4 - SPRI Clean", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6a93a2-part5/6a93a2-part5.ot2.apiv2.py.json b/protoBuilds/6a93a2-part5/6a93a2-part5.ot2.apiv2.py.json index 8b358d0bc..0937a5915 100644 --- a/protoBuilds/6a93a2-part5/6a93a2-part5.ot2.apiv2.py.json +++ b/protoBuilds/6a93a2-part5/6a93a2-part5.ot2.apiv2.py.json @@ -1289,5 +1289,18 @@ "protocolName": "Swift Rapid NGS Part 5 - Indexing and SPRI Clean", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6a93a2/6a93a2.ot2.apiv2.py.json b/protoBuilds/6a93a2/6a93a2.ot2.apiv2.py.json index 31a2c34b3..bb3b3b964 100644 --- a/protoBuilds/6a93a2/6a93a2.ot2.apiv2.py.json +++ b/protoBuilds/6a93a2/6a93a2.ot2.apiv2.py.json @@ -1277,5 +1277,24 @@ "protocolName": "Swift Rapid NGS Part 1 - Reverse Transcription", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with Generic 2 mL Screwcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6a93a3-part2/6a93a2-part2.ot2.apiv2.py.json b/protoBuilds/6a93a3-part2/6a93a2-part2.ot2.apiv2.py.json deleted file mode 100644 index 4d2be8ee3..000000000 --- a/protoBuilds/6a93a3-part2/6a93a2-part2.ot2.apiv2.py.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "content": "import math\n\nmetadata = {\n 'protocolName': 'Swift Rapid NGS Part 2 - Adaptase',\n 'author': 'Rami Farawi ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.7'\n}\n\n\ndef run(ctx):\n\n [num_samp, tip_type, overage_percent,\n p20_mount, p300_mount] = get_values( # noqa: F821\n \"num_samp\", \"tip_type\", \"overage_percent\",\n \"p20_mount\", \"p300_mount\")\n\n # keep user in range\n num_samp = int(num_samp)\n if not 0.0 <= overage_percent <= 10.0:\n raise Exception(\"Enter a an overage percent between 5-10%\")\n overage_percent = 1+overage_percent/100\n num_cols = math.ceil(int(num_samp/8))\n\n # load labware\n thermocycler = ctx.load_module('thermocycler')\n samp_plate = thermocycler.load_labware(\n 'nest_96_wellplate_100ul_pcr_full_skirt')\n temperature_mod = ctx.load_module('temperature module gen2', '3')\n alum_tuberack = temperature_mod.load_labware(\n 'opentrons_24_aluminumblock_nest_1.5ml_screwcap')\n tiprack20 = [ctx.load_labware(tip_type, slot) for slot in ['6', '9']]\n tiprack300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)\n for slot in ['4', '5']]\n\n # load instruments\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount,\n tip_racks=tiprack20)\n m300 = ctx.load_instrument('p300_multi', p300_mount, tip_racks=tiprack300)\n\n # make Adaptase Mastermix\n temperature_mod.set_temperature(4)\n mastermix = alum_tuberack.rows()[1][0]\n reagents = alum_tuberack.rows()[0][:6]\n vols = [math.ceil(num_samp*rxn_vol*overage_percent)\n for rxn_vol in [2, 2, 1.25, 0.5, 0.5, 4.25]]\n num_cols = math.ceil(int(num_samp/8))\n sample_cols = samp_plate.rows()[0][4:4+num_cols]\n\n for reagent, vol in zip(reagents, vols):\n p20.pick_up_tip()\n p20.transfer(vol, reagent, mastermix.top(), new_tip='never')\n p20.drop_tip()\n\n ctx.pause(\"\"\"Vortex mix Adaptase mix tube (tube B1)\n After placing mix tube back, thermocycler will warm up.\"\"\")\n\n # operate thermocycler - denature samples\n if thermocycler.lid_position != 'open':\n thermocycler.open_lid()\n thermocycler.set_lid_temperature(105)\n thermocycler.set_block_temperature(95)\n profile = [{'temperature': 95, 'hold_time_minutes': 2}]\n ctx.pause('''Thermocycler temperature is at 95C.\n Please add the sample plate to the thermocycler.\n Thermocycler will close lid automatically.\n Be ready to take samples and put on ice\n immediately after the 2 minute cycle has completed. ''')\n\n thermocycler.close_lid()\n thermocycler.execute_profile(steps=profile,\n repetitions=1,\n block_max_volume=10.5)\n thermocycler.open_lid()\n ctx.pause('''Immediately remove samples and put on ice for 2 minutes.\n After, put the plate back on the Thermocycler for the Adaptase Mastermix\n to be added.''')\n\n # add adaptase and mix thouroughly\n for well in samp_plate.wells()[32:32+num_samp]:\n p20.pick_up_tip()\n p20.aspirate(10.5*overage_percent, mastermix)\n p20.dispense(10.5*overage_percent, well.top())\n p20.drop_tip()\n\n for col in sample_cols:\n m300.pick_up_tip()\n m300.mix(15, 20, col)\n m300.blow_out()\n m300.drop_tip()\n\n ctx.pause('''Transfer of Adaptase Mastermix is complete -\n Solutions have been pipette-mixed 15 times.\n Spin samples, seal, and place back on thermocycler for another\n thermocycler profile.''')\n\n profile = [\n {'temperature': 37, 'hold_time_minutes': 15},\n {'temperature': 95, 'hold_time_minutes': 2},\n ]\n thermocycler.close_lid()\n thermocycler.execute_profile(steps=profile,\n repetitions=1,\n block_max_volume=20.5)\n thermocycler.set_block_temperature(4, block_max_volume=20.5)\n thermocycler.open_lid()\n ctx.comment('Protocol complete. Samples ready for extension')\n", - "custom_labware_defs": [], - "fields": [ - { - "label": "Number of Samples", - "name": "num_samp", - "options": [ - { - "label": "8", - "value": "8" - }, - { - "label": "16", - "value": "16" - }, - { - "label": "24", - "value": "24" - } - ], - "type": "dropDown" - }, - { - "default": 7.5, - "label": "Adaptase Mastermix Overage Percent (0-10%)", - "name": "overage_percent", - "type": "float" - }, - { - "label": "Opentrons 96 Tip Rack 20ul Tip Type", - "name": "tip_type", - "options": [ - { - "label": "Filtertips", - "value": "opentrons_96_filtertiprack_20ul" - }, - { - "label": "Non-Filtertips", - "value": "opentrons_96_tiprack_20ul" - } - ], - "type": "dropDown" - }, - { - "label": "Opentrons 96 Tip Rack 20ul Tip Type", - "name": "tip_type", - "options": [ - { - "label": "Filtertips", - "value": "opentrons_96_filtertiprack_200ul" - }, - { - "label": "Non-Filtertips", - "value": "opentrons_96_tiprack_20ul" - } - ], - "type": "dropDown" - }, - { - "label": "P300 Multi GEN2 Mount", - "name": "p300_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - }, - { - "label": "P20 Single GEN2 Mount", - "name": "p20_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p300_multi" - }, - { - "mount": "right", - "name": "p20_single_gen2" - } - ], - "labware": [ - { - "name": "Opentrons 24 Well Aluminum Block with NEST 1.5 mL Screwcap on Temperature Module GEN2 on 3", - "share": false, - "slot": "3", - "type": "opentrons_24_aluminumblock_nest_1.5ml_screwcap" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 4", - "share": false, - "slot": "4", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", - "share": false, - "slot": "7", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.7", - "author": "Rami Farawi ", - "protocolName": "Swift Rapid NGS Part 2 - Adaptase", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/6a93a3-part2/README.json b/protoBuilds/6a93a3-part2/README.json deleted file mode 100644 index c032e17c4..000000000 --- a/protoBuilds/6a93a3-part2/README.json +++ /dev/null @@ -1,43 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "NGS Library Prep": [ - "Swift Rapid RNA Library Kit" - ] - }, - "deck-setup": "", - "description": "This protocol is part two of a five-part series to perform Swift Biosciences Rapid NGS Library Prep kit. The protocol is split in such a way so as to allow for the option to run between the Rapid and Standard versions of the kit. Please find all linked parts of the protocol below:\nLinks:\n Swift NGS Part 1 - Reverse Transcription and SPRI Cleanup\n Swift Rapid NGS Part 3 - Extension, SPRI, and Ligation\n Swift Rapid NGS Part 4 - SPRI Clean\n Swift Rapid NGS Part 5 - Indexing and SPRI Clean\nPart two of this protocol is divided into the following methods for 8, 16, or 24 samples:\n\nMake Adaptase Mastermix\nRun Thermocycler Profile\nAdd Adaptase Mastermix\n\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples that will be processed.\n Adaptase Mastermix Overage Percent (0-10%): Specify the percent overage of Reverse Transcription Mastermix to make and ultimately add to samples.\n Opentrons 96 Tip Rack 20ul Tip Type: Specify whether filter or non-filter 20ul tips will be employed.\n P300 Multi GEN2 Mount: Specify which mount (left or right) to load the P300 multi channel pipette.\n* P20 Single GEN2 Mount: Specify which mount (left or right) to load the P20 single channel pipette.\n", - "internal": "6a93a2-part2", - "labware": "\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons 20\u00b5L Tips\nOpentrons 200uL Tips\nOpentrons 24-Tube Aluminum Block\n", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* NGS Library Prep\n\t* Swift Rapid RNA Library Kit\n\n", - "deck-setup": "![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/6a93a2/pt2/Screen+Shot+2021-05-05+at+1.17.41+PM.png)\n\n", - "description": "This protocol is part two of a five-part series to perform Swift Biosciences Rapid NGS Library Prep kit. The protocol is split in such a way so as to allow for the option to run between the Rapid and Standard versions of the kit. Please find all linked parts of the protocol below:\n\nLinks:\n* [Swift NGS Part 1 - Reverse Transcription and SPRI Cleanup](https://protocols.opentrons.com/protocol/6a93a2)\n* [Swift Rapid NGS Part 3 - Extension, SPRI, and Ligation](https://protocols.opentrons.com/protocol/6a93a2-part3)\n* [Swift Rapid NGS Part 4 - SPRI Clean](https://protocols.opentrons.com/protocol/6a93a2-part4)\n* [Swift Rapid NGS Part 5 - Indexing and SPRI Clean](https://protocols.opentrons.com/protocol/6a93a2-part5)\n\nPart two of this protocol is divided into the following methods for 8, 16, or 24 samples:\n\n* Make Adaptase Mastermix\n* Run Thermocycler Profile\n* Add Adaptase Mastermix\n\nExplanation of complex parameters below:\n* `Number of Samples`: Specify the number of samples that will be processed.\n* `Adaptase Mastermix Overage Percent (0-10%)`: Specify the percent overage of Reverse Transcription Mastermix to make and ultimately add to samples.\n* `Opentrons 96 Tip Rack 20ul Tip Type`: Specify whether filter or non-filter 20ul tips will be employed.\n* `P300 Multi GEN2 Mount`: Specify which mount (left or right) to load the P300 multi channel pipette.\n* `P20 Single GEN2 Mount`: Specify which mount (left or right) to load the P20 single channel pipette.\n\n---\n\n", - "internal": "6a93a2-part2\n", - "labware": "* [NEST 0.1 mL 96-Well PCR Plate, Full Skirt](https://shop.opentrons.com/collections/lab-plates/products/nest-0-1-ml-96-well-pcr-plate-full-skirt)\n* [Opentrons 20\u00b5L Tips](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-10ul-tips)\n* [Opentrons 200uL Tips](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-200ul-filter-tips)\n* [Opentrons 24-Tube Aluminum Block](https://shop.opentrons.com/collections/racks-and-adapters/products/aluminum-block-set)\n\n", - "modules": "* [Temperature Module (GEN2)](https://shop.opentrons.com/collections/hardware-modules/products/tempdeck)\n* [Thermocycler Module](https://shop.opentrons.com/collections/hardware-modules/products/thermocycler-module)\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "partner": "[Swift Biosciences](https://swiftbiosci.com/protocols/)\n\n", - "pipettes": "* [P20 GEN2 Single Channel Pipette](https://shop.opentrons.com/collections/ot-2-robot/products/single-channel-electronic-pipette)\n* [P300 GEN2 Multi-Channel Pipette](https://shop.opentrons.com/collections/ot-2-robot/products/8-channel-electronic-pipette)\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "protocol-steps": "1. Adaptase mastermix is made on ice (4C)\n2. User vortexes mix tube\n3. Samples undergo thermocycler profile\n4. User moves samples to ice for 4 minutes\n5. Adaptase mastermix is added to samples\n6. Samples undergo thermocycler profile\n7. Samples are brought back down to 4C, ready for extension.\n\n\n\n\n", - "reagent-setup": "* Aluminum Tube Rack: Slot 3\n\n![reservoir 2](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/6a93a2/pt2/Screen+Shot+2021-05-05+at+1.17.02+PM.png)\n\n---\n\n", - "reagents": "* [Swift Rapid RNA Library Kit](https://swiftbiosci.com/wp-content/uploads/2020/04/PRT-024-Swift-Rapid-RNA-Library-Kit-Protocol-v3.0.pdf)\n\n---\n\n", - "title": "Swift Rapid NGS Part 2 - Adaptase" - }, - "modules": [ - "Temperature Module (GEN2)", - "Thermocycler Module" - ], - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "partner": "Swift Biosciences", - "pipettes": "\nP20 GEN2 Single Channel Pipette\nP300 GEN2 Multi-Channel Pipette\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "protocol-steps": "\nAdaptase mastermix is made on ice (4C)\nUser vortexes mix tube\nSamples undergo thermocycler profile\nUser moves samples to ice for 4 minutes\nAdaptase mastermix is added to samples\nSamples undergo thermocycler profile\nSamples are brought back down to 4C, ready for extension.\n", - "reagent-setup": "\nAluminum Tube Rack: Slot 3\n\n\n", - "reagents": [ - "Swift Rapid RNA Library Kit" - ], - "title": "Swift Rapid NGS Part 2 - Adaptase" -} \ No newline at end of file diff --git a/protoBuilds/6a93a3-part2/metadata.json b/protoBuilds/6a93a3-part2/metadata.json deleted file mode 100644 index 3b4542ce6..000000000 --- a/protoBuilds/6a93a3-part2/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "6a93a2-part2.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": false, - "skip-tests": false - }, - "path": "protocols/6a93a3-part2", - "slug": "6a93a3-part2", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/6cd9d6/6cd9d6.ot2.apiv2.py.json b/protoBuilds/6cd9d6/6cd9d6.ot2.apiv2.py.json index 70e3f3e8d..b0420fb75 100644 --- a/protoBuilds/6cd9d6/6cd9d6.ot2.apiv2.py.json +++ b/protoBuilds/6cd9d6/6cd9d6.ot2.apiv2.py.json @@ -117,5 +117,24 @@ "description": "Custom Protocol Request", "protocolName": "Custom NGS Library Prep" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw NEST 12 Well Reservoir 15 mL on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6d7fc3-part-2/6d7fc3-part-2.ot2.apiv2.py.json b/protoBuilds/6d7fc3-part-2/6d7fc3-part-2.ot2.apiv2.py.json index 44deeff16..25b6e0061 100644 --- a/protoBuilds/6d7fc3-part-2/6d7fc3-part-2.ot2.apiv2.py.json +++ b/protoBuilds/6d7fc3-part-2/6d7fc3-part-2.ot2.apiv2.py.json @@ -93,5 +93,18 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung DNA UMI Panel Kit: Adapter\n Ligation" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6d7fc3-part-3/6d7fc3-part-3.ot2.apiv2.py.json b/protoBuilds/6d7fc3-part-3/6d7fc3-part-3.ot2.apiv2.py.json index bf2acdb10..31fc94e84 100644 --- a/protoBuilds/6d7fc3-part-3/6d7fc3-part-3.ot2.apiv2.py.json +++ b/protoBuilds/6d7fc3-part-3/6d7fc3-part-3.ot2.apiv2.py.json @@ -117,5 +117,24 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung DNA UMI Panel Kit:Cleanup of Adapter-ligated DNA with\n QIAact Beads" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6d7fc3-part-4/6d7fc3-part-4.ot2.apiv2.py.json b/protoBuilds/6d7fc3-part-4/6d7fc3-part-4.ot2.apiv2.py.json index f00b3d96b..108fd5b23 100644 --- a/protoBuilds/6d7fc3-part-4/6d7fc3-part-4.ot2.apiv2.py.json +++ b/protoBuilds/6d7fc3-part-4/6d7fc3-part-4.ot2.apiv2.py.json @@ -93,5 +93,18 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung DNA UMI Panel Kit:\n Target Enrichment PCR" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6d7fc3-part-5/6d7fc3-part-5.ot2.apiv2.py.json b/protoBuilds/6d7fc3-part-5/6d7fc3-part-5.ot2.apiv2.py.json index 4817a30f3..6d4c1737b 100644 --- a/protoBuilds/6d7fc3-part-5/6d7fc3-part-5.ot2.apiv2.py.json +++ b/protoBuilds/6d7fc3-part-5/6d7fc3-part-5.ot2.apiv2.py.json @@ -111,5 +111,24 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung DNA UMI Panel Kit:\n Cleanup of Target Enrichment PCR with\n QIAact Beads" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6d7fc3-part-6/6d7fc3-part-6.ot2.apiv2.py.json b/protoBuilds/6d7fc3-part-6/6d7fc3-part-6.ot2.apiv2.py.json index 1d307c213..5375b569b 100644 --- a/protoBuilds/6d7fc3-part-6/6d7fc3-part-6.ot2.apiv2.py.json +++ b/protoBuilds/6d7fc3-part-6/6d7fc3-part-6.ot2.apiv2.py.json @@ -93,5 +93,18 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung DNA UMI Panel Kit:\n Universal PCR Amplification" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6d7fc3-part-7/6d7fc3-part-7.ot2.apiv2.py.json b/protoBuilds/6d7fc3-part-7/6d7fc3-part-7.ot2.apiv2.py.json index cadb4a959..b81993811 100644 --- a/protoBuilds/6d7fc3-part-7/6d7fc3-part-7.ot2.apiv2.py.json +++ b/protoBuilds/6d7fc3-part-7/6d7fc3-part-7.ot2.apiv2.py.json @@ -111,5 +111,24 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung DNA UMI Panel Kit:\n Cleanup of Universal PCR with QIAact Beads" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6d7fc3/6d7fc3.ot2.apiv2.py.json b/protoBuilds/6d7fc3/6d7fc3.ot2.apiv2.py.json index 128ea300b..960e291bd 100644 --- a/protoBuilds/6d7fc3/6d7fc3.ot2.apiv2.py.json +++ b/protoBuilds/6d7fc3/6d7fc3.ot2.apiv2.py.json @@ -87,5 +87,18 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung DNA UMI Panel Kit: Fragmentation,\n End-repair and A-addition" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6f4e2c/6f4e2c.ot2.apiv2.py.json b/protoBuilds/6f4e2c/6f4e2c.ot2.apiv2.py.json index f50126a06..9a7b4e646 100644 --- a/protoBuilds/6f4e2c/6f4e2c.ot2.apiv2.py.json +++ b/protoBuilds/6f4e2c/6f4e2c.ot2.apiv2.py.json @@ -1203,7 +1203,7 @@ ], "labware": [ { - "name": "Eppendorf 96 Deep Well Plate 1000\u00b5L on Magnetic Module GEN1 on 1", + "name": "Eppendorf 96 Deep Well Plate 1000\u00b5L on Magnetic Module on 1", "share": false, "slot": "1", "type": "eppendorf_96_wellplate_1000ul" @@ -1221,7 +1221,7 @@ "type": "opentrons_96_tiprack_300ul" }, { - "name": "Eppendorf 96 Deep Well Plate 1000\u00b5L on Temperature Module GEN1 on 4", + "name": "Eppendorf 96 Deep Well Plate 1000\u00b5L on Temperature Module on 4", "share": false, "slot": "4", "type": "eppendorf_96_wellplate_1000ul" @@ -1275,5 +1275,18 @@ "protocolName": "DNA Isolation from Whole Blood", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 1 lw Eppendorf 96 Deep Well Plate 1000\u00b5L on Magnetic Module on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module on 4 lw Eppendorf 96 Deep Well Plate 1000\u00b5L on Temperature Module on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6ff9e9/extraction.ot2.apiv2.py.json b/protoBuilds/6ff9e9/extraction.ot2.apiv2.py.json index 0f6343b51..630463423 100644 --- a/protoBuilds/6ff9e9/extraction.ot2.apiv2.py.json +++ b/protoBuilds/6ff9e9/extraction.ot2.apiv2.py.json @@ -1393,5 +1393,12 @@ "author": "Opentrons ", "protocolName": "COVID-19 Station B RNA Extraction" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw deepwell plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/701319/701319.ot2.apiv2.py.json b/protoBuilds/701319/701319.ot2.apiv2.py.json index 63ab19446..365b4c35b 100644 --- a/protoBuilds/701319/701319.ot2.apiv2.py.json +++ b/protoBuilds/701319/701319.ot2.apiv2.py.json @@ -2444,5 +2444,12 @@ "description": "Custom Protocol Request", "protocolName": "Peptide Mass Spec Sample Prep" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/70567f/ngs_cleanup.ot2.apiv2.py.json b/protoBuilds/70567f/ngs_cleanup.ot2.apiv2.py.json index 826545c42..8ff341fb9 100644 --- a/protoBuilds/70567f/ngs_cleanup.ot2.apiv2.py.json +++ b/protoBuilds/70567f/ngs_cleanup.ot2.apiv2.py.json @@ -209,5 +209,12 @@ "protocolName": "NGS Library Cleanup with Ampure XP Beads", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw magnetic plate on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/7062c9-2/extraction.ot2.apiv2.py.json b/protoBuilds/7062c9-2/extraction.ot2.apiv2.py.json index dd50d9b92..98fb7c7ab 100644 --- a/protoBuilds/7062c9-2/extraction.ot2.apiv2.py.json +++ b/protoBuilds/7062c9-2/extraction.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "from opentrons.types import Point\nimport json\nimport os\nimport math\n\nmetadata = {\n 'protocolName': 'Capping Assay: Steps 3-6',\n 'author': 'Nick ',\n 'apiLevel': '2.11'\n}\n\nTEST_MODE = False\n\n\ndef run(ctx):\n [num_samples, tip_track] = get_values( # noqa: F821\n 'num_samples', 'tip_track')\n\n bead_vol = 125.0\n sample_vol = 110.0\n park_tips = True\n sample_incubation_mixing = True\n mag_height = 11.5\n z_offset = 0.0\n radial_offset = 0.3\n wash1_vol = 200.0\n wash2_vol = 200.0\n elution_vol = 100.0\n air_gap_vol = 0.0\n bead_settling_time = 1.0\n temp_time = 3.0\n mix_reps = 10\n sample_mixing_time_minutes = 15.0\n mix_volume_percentage = 0.9\n sample_mixing_blowout_height_from_bottom = 10.0\n\n if TEST_MODE:\n [bead_settling_time, mix_reps, temp_time,\n sample_incubation_mixing] = 0.0, 1, 0.0, False\n\n \"\"\"\n Here is where you can change the locations of your labware and modules\n (note that this is the recommended configuration)\n \"\"\"\n sample_plate = ctx.load_labware(\n 'neptune_96_aluminumblock_200ul',\n '1', 'starting sample plate')\n magdeck = ctx.load_module('magnetic module gen2', '4')\n magplate = magdeck.load_labware('ge_96_wellplate_500ul',\n 'deepwell plate')\n tempdeck = ctx.load_module('Temperature Module Gen2', '7')\n heatingplate = tempdeck.load_labware(\n 'neptune_96_aluminumblock_200ul',\n 'heating plate')\n elutionplate = ctx.load_labware(\n 'neptune_96_aluminumblock_200ul', '2',\n 'final elution plate')\n waste = ctx.load_labware('nest_1_reservoir_195ml', '11',\n 'Liquid Waste').wells()[0].top()\n res = ctx.load_labware('nest_12_reservoir_15ml', '5', 'reagent reservoir')\n num_cols = math.ceil(num_samples/8)\n tips300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot,\n '200\u00b5l filtertiprack')\n for slot in ['3', '6', '9', '10']]\n if park_tips:\n rack = ctx.load_labware(\n 'opentrons_96_filtertiprack_200ul', '8', 'tiprack for parking')\n parking_spots = rack.rows()[0][:num_cols]\n else:\n rack = ctx.load_labware(\n 'opentrons_96_filtertiprack_200ul', '8', '200\u00b5l filtertiprack')\n parking_spots = [None for none in range(12)]\n tips300.insert(0, rack)\n\n # load P300M pipette\n m300 = ctx.load_instrument(\n 'p300_multi_gen2', 'left', tip_racks=tips300)\n\n tip_log = {val: {} for val in ctx.loaded_instruments.values()}\n\n \"\"\"\n Here is where you can define the locations of your reagents.\n \"\"\"\n wash1 = res.wells()[:2]\n wash2 = res.wells()[2:5]\n beads = res.wells()[10]\n elution_solution = res.wells()[-1]\n\n mag_samples_m = magplate.rows()[0][:num_cols]\n starting_samples_m = sample_plate.rows()[0][:num_cols]\n elution_samples_m = elutionplate.rows()[0][:num_cols]\n heating_samples_m = heatingplate.rows()[0][:num_cols]\n if mag_samples_m[0].width:\n radius = mag_samples_m[0].width/2\n else:\n radius = mag_samples_m[0].diameter/2\n\n magdeck.disengage() # just in case\n tempdeck.set_temperature(85)\n\n ctx._implementation._hw_manager.hardware._attached_instruments[\n m300._implementation.get_mount()].update_config_item(\n 'pick_up_current', 0.5)\n\n folder_path = '/data/B'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n data = json.load(json_file)\n for pip in tip_log:\n if pip.name in data:\n tip_log[pip]['count'] = data[pip.name]\n else:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n\n for pip in tip_log:\n if pip.type == 'multi':\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.rows()[0]]\n else:\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.wells()]\n tip_log[pip]['max'] = len(tip_log[pip]['tips'])\n\n def _pick_up(pip=m300, loc=None):\n if tip_log[pip]['count'] == tip_log[pip]['max'] and not loc:\n ctx.pause('Replace ' + str(pip.max_volume) + '\u00b5l tipracks before \\\nresuming.')\n pip.reset_tipracks()\n tip_log[pip]['count'] = 0\n if loc:\n pip.pick_up_tip(loc)\n else:\n pip.pick_up_tip(tip_log[pip]['tips'][tip_log[pip]['count']])\n tip_log[pip]['count'] += 1\n\n switch = True\n drop_count = 0\n # number of tips trash will accommodate before prompting user to empty\n drop_threshold = 120\n\n def _drop(pip=m300):\n nonlocal switch\n nonlocal drop_count\n side = 30 if switch else -18\n drop_loc = ctx.loaded_labwares[12].wells()[0].top().move(\n Point(x=side))\n pip.drop_tip(drop_loc)\n switch = not switch\n if pip.type == 'multi':\n drop_count += 8\n else:\n drop_count += 1\n if drop_count == drop_threshold:\n # Setup for flashing lights notification to empty trash\n ctx.home() # home before continuing with protocol\n drop_count = 0\n\n waste_vol = 0\n waste_threshold = 185000\n\n def remove_supernatant(vol, park=False, drop=True):\n \"\"\"\n `remove_supernatant` will transfer supernatant from the deepwell\n extraction plate to the liquid waste reservoir.\n :param vol (float): The amount of volume to aspirate from all deepwell\n sample wells and dispense in the liquid waste.\n :param park (boolean): Whether to pick up sample-corresponding tips\n in the 'parking rack' or to pick up new tips.\n \"\"\"\n\n def _waste_track(vol):\n nonlocal waste_vol\n if waste_vol + vol >= waste_threshold:\n # Setup for flashing lights notification to empty liquid waste\n ctx.home()\n ctx.pause('Please empty liquid waste (slot 11) before \\\nresuming.')\n\n waste_vol = 0\n waste_vol += vol\n\n num_trans = math.ceil(vol/200)\n vol_per_trans = vol/num_trans\n for i, (m, spot) in enumerate(zip(mag_samples_m, parking_spots)):\n if not m300.has_tip:\n if park:\n _pick_up(m300, spot)\n else:\n _pick_up(m300)\n side = -1 if i % 2 == 0 else 1\n loc = m.bottom(0).move(Point(x=side*radius*radial_offset,\n z=z_offset))\n for _ in range(num_trans):\n _waste_track(vol_per_trans)\n if m300.current_volume > 0:\n # void air gap if necessary\n m300.dispense(m300.current_volume, m.top())\n m300.move_to(m.center())\n m300.transfer(vol_per_trans, loc, waste, new_tip='never',\n air_gap=air_gap_vol)\n m300.blow_out(waste)\n m300.air_gap(20)\n if drop:\n _drop(m300)\n\n def wash(vol, source, change_tips_for_samples=True, mix_reps=mix_reps,\n park=True, resuspend=True, drop=True):\n \"\"\"\n `wash` will perform bead washing for the extraction protocol.\n :param vol (float): The amount of volume to aspirate from each\n source and dispense to each well containing beads.\n :param source (List[Well]): A list of wells from where liquid will be\n aspirated. If the length of the source list\n > 1, `wash` automatically calculates\n the index of the source that should be\n accessed.\n :param mix_reps (int): The number of repititions to mix the beads with\n specified wash buffer (ignored if resuspend is\n False).\n :param park (boolean): Whether to save sample-corresponding tips\n between adding wash buffer and removing\n supernatant.\n :param resuspend (boolean): Whether to resuspend beads in wash buffer.\n \"\"\"\n\n if resuspend and magdeck.status == 'engaged':\n magdeck.disengage()\n\n num_trans = math.ceil(vol/200)\n vol_per_trans = vol/num_trans\n for i, (m, spot) in enumerate(zip(mag_samples_m, parking_spots)):\n if not m300.has_tip:\n _pick_up(m300)\n side = 1 if i % 2 == 0 else -1\n for n in range(num_trans):\n if m300.current_volume > 0:\n m300.dispense(m300.current_volume, source.top())\n m300.transfer(vol_per_trans, source, m.top(),\n air_gap=air_gap_vol, new_tip='never')\n if n < num_trans - 1: # only air_gap if going back to source\n m300.air_gap(20)\n if resuspend:\n for _ in range(mix_reps):\n m300.aspirate(mix_volume_percentage*vol, m.bottom())\n m300.dispense(mix_volume_percentage*vol,\n m.bottom().move(\n Point(x=side*radius*radial_offset, z=3)))\n m300.blow_out(m.top())\n m300.air_gap(20)\n if change_tips_for_samples:\n if park:\n m300.drop_tip(spot)\n else:\n _drop(m300)\n\n if magdeck.status == 'disengaged':\n magdeck.engage(mag_height)\n\n ctx.delay(minutes=bead_settling_time, msg='Incubating on MagDeck for \\\n' + str(bead_settling_time) + ' minutes.')\n\n remove_supernatant(vol, park=park, drop=drop)\n\n def elute(vol, park=True):\n \"\"\"\n `elute` will perform elution from the deepwell extraction plate to the\n final clean elutions PCR plate to complete the extraction protocol.\n :param vol (float): The amount of volume to aspirate from the elution\n buffer source and dispense to each well containing\n beads.\n :param park (boolean): Whether to save sample-corresponding tips\n between adding elution buffer and transferring\n supernatant to the final clean elutions PCR\n plate.\n \"\"\"\n magdeck.disengage()\n\n # pre-heat elution buffer\n _pick_up(m300)\n for h in heating_samples_m:\n m300.transfer(elution_vol*1.2, elution_solution, h,\n new_tip='never')\n m300.home()\n\n ctx.delay(minutes=temp_time, msg=f'Incubating at 85C for {temp_time} \\\nminutes')\n # resuspend beads in elution\n m300.flow_rate.aspirate /= 5\n m300.flow_rate.dispense /= 5\n m300.flow_rate.blow_out /= 5\n for i, (m, h, spot) in enumerate(zip(mag_samples_m, heating_samples_m,\n parking_spots)):\n if not m300.has_tip:\n _pick_up(m300)\n side = 1 if i % 2 == 0 else -1\n loc = m.bottom().move(Point(x=side*radius*radial_offset,\n z=z_offset))\n m300.aspirate(vol*1.2, h)\n m300.move_to(m.center())\n m300.dispense(vol, loc)\n for _ in range(mix_reps):\n m300.aspirate(vol*mix_volume_percentage, m.bottom())\n m300.dispense(vol*mix_volume_percentage, m.bottom().move(Point(\n x=side*radius*radial_offset, z=3)))\n m300.transfer(vol, m.bottom(), h, new_tip='never')\n m300.blow_out(h.bottom(h.depth/2))\n if park:\n m300.drop_tip(spot)\n else:\n _drop(m300)\n\n ctx.delay(minutes=temp_time, msg=f'Incubating at 85C for {temp_time} \\\nminutes')\n\n for m, h, spot in zip(mag_samples_m, heating_samples_m,\n parking_spots):\n if park:\n _pick_up(m300, spot)\n else:\n _pick_up(m300)\n m300.transfer(vol, h, m, mix_before=(5, 0.5*vol),\n new_tip='never')\n m300.blow_out(m.bottom(m.depth/2))\n _drop(m300)\n\n magdeck.engage(mag_height)\n ctx.delay(minutes=bead_settling_time, msg='Incubating on MagDeck for \\\n' + str(bead_settling_time) + ' minutes.')\n\n for i, (m, e, spot) in enumerate(\n zip(mag_samples_m, elution_samples_m, parking_spots)):\n _pick_up(m300)\n side = -1 if i % 2 == 0 else 1\n loc = m.bottom().move(Point(x=side*radius*radial_offset,\n z=z_offset+2))\n m300.move_to(m.center())\n m300.transfer(0.8*vol, loc, e, air_gap=air_gap_vol,\n new_tip='never')\n m300.drop_tip()\n\n \"\"\"\n ACTIONS\n \"\"\"\n # beads\n _pick_up(m300)\n # add beads\n m300.mix(10, 150, beads)\n for m in mag_samples_m:\n m300.transfer(bead_vol, beads, m, new_tip='never')\n m300.home()\n\n # prewash\n magdeck.engage(mag_height)\n ctx.delay(minutes=bead_settling_time, msg=f'Beads separating for \\\n{bead_settling_time} minutes.')\n remove_supernatant(bead_vol, drop=False)\n # keep tips for wash\n\n for w in range(2):\n wash(wash1_vol, wash1[w], park=park_tips, drop=False,\n change_tips_for_samples=False)\n\n # add sample and mix iteratively for ~30 minutes\n magdeck.disengage()\n for s, d, p in zip(starting_samples_m, mag_samples_m, parking_spots):\n if not m300.has_tip:\n _pick_up()\n m300.transfer(sample_vol, s, d, new_tip='never')\n m300.drop_tip(p)\n\n m300.default_speed = 200\n m300.flow_rate.aspirate = 46.43\n m300.flow_rate.dispense = 92.86\n mixes_per_min = 0.5\n num_mix_cycles = int(sample_mixing_time_minutes*mixes_per_min/num_cols)\n if TEST_MODE or not sample_incubation_mixing:\n num_mix_cycles = 5\n for i in range(num_mix_cycles):\n for j, (s, p) in enumerate(zip(mag_samples_m, parking_spots)):\n _pick_up(m300, p)\n side = 1 if j % 2 == 0 else -1\n loc = s.bottom().move(Point(x=side*radius*radial_offset,\n z=z_offset-1))\n for _ in range(mix_reps):\n m300.aspirate(sample_vol*mix_volume_percentage, loc)\n m300.dispense(sample_vol*mix_volume_percentage,\n s.bottom().move(Point(\n x=side*radius*radial_offset, z=7)))\n m300.blow_out(\n s.bottom(sample_mixing_blowout_height_from_bottom))\n m300.drop_tip(p)\n m300.default_speed = 400\n magdeck.engage(mag_height)\n ctx.delay(minutes=bead_settling_time)\n remove_supernatant(sample_vol, park=park_tips)\n\n # sample washes\n for w in range(2):\n wash(wash1_vol, wash1[w], park=park_tips)\n for w in range(3):\n wash(wash2_vol, wash2[w], park=park_tips)\n elute(elution_vol, park=park_tips)\n\n # track final used tip\n if tip_track and not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n data = {pip.name: tip_log[pip]['count'] for pip in tip_log}\n with open(tip_file_path, 'w') as outfile:\n json.dump(data, outfile)\n", + "content": "from opentrons.types import Point\nimport json\nimport os\nimport math\n\nmetadata = {\n 'protocolName': 'Capping Assay: Steps 3-6',\n 'author': 'Nick ',\n 'apiLevel': '2.11'\n}\n\nTEST_MODE = False\n\n\ndef run(ctx):\n [num_samples, tip_track] = get_values( # noqa: F821\n 'num_samples', 'tip_track')\n\n bead_vol = 125.0\n sample_vol = 110.0\n park_tips = True\n sample_incubation_mixing = True\n mag_height = 11.5\n z_offset = 0.0\n radial_offset = 0.3\n wash1_vol = 200.0\n wash2_vol = 200.0\n elution_vol = 100.0\n air_gap_vol = 0.0\n bead_settling_time = 1.0\n temp_time = 3.0\n mix_reps = 10\n sample_mixing_time_minutes = 15.0\n mix_volume_percentage = 0.9\n sample_mixing_blowout_height_from_bottom = 10.0\n\n if TEST_MODE:\n [bead_settling_time, mix_reps, temp_time,\n sample_incubation_mixing] = 0.0, 1, 0.0, False\n\n \"\"\"\n Here is where you can change the locations of your labware and modules\n (note that this is the recommended configuration)\n \"\"\"\n sample_plate = ctx.load_labware(\n 'neptune_96_aluminumblock_200ul',\n '1', 'starting sample plate')\n magdeck = ctx.load_module('magnetic module gen2', '4')\n magplate = magdeck.load_labware('ge_96_wellplate_500ul',\n 'deepwell plate')\n tempdeck = ctx.load_module('Temperature Module Gen2', '7')\n heatingplate = tempdeck.load_labware(\n 'neptune_96_aluminumblock_200ul',\n 'heating plate')\n elutionplate = ctx.load_labware(\n 'neptune_96_aluminumblock_200ul', '2',\n 'final elution plate')\n waste = ctx.load_labware('nest_1_reservoir_195ml', '11',\n 'Liquid Waste').wells()[0].top()\n res = ctx.load_labware('nest_12_reservoir_15ml', '5', 'reagent reservoir')\n num_cols = math.ceil(num_samples/8)\n tips300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot,\n '200\u00b5l filtertiprack')\n for slot in ['3', '6', '9', '10']]\n if park_tips:\n rack = ctx.load_labware(\n 'opentrons_96_filtertiprack_200ul', '8', 'tiprack for parking')\n parking_spots = rack.rows()[0][:num_cols]\n else:\n rack = ctx.load_labware(\n 'opentrons_96_filtertiprack_200ul', '8', '200\u00b5l filtertiprack')\n parking_spots = [None for none in range(12)]\n tips300.insert(0, rack)\n\n # load P300M pipette\n m300 = ctx.load_instrument(\n 'p300_multi_gen2', 'left', tip_racks=tips300)\n\n tip_log = {val: {} for val in ctx.loaded_instruments.values()}\n\n \"\"\"\n Here is where you can define the locations of your reagents.\n \"\"\"\n wash1 = res.wells()[:2]\n wash2 = res.wells()[2:5]\n beads = res.wells()[10]\n elution_solution = res.wells()[-1]\n\n mag_samples_m = magplate.rows()[0][:num_cols]\n starting_samples_m = sample_plate.rows()[0][:num_cols]\n elution_samples_m = elutionplate.rows()[0][:num_cols]\n heating_samples_m = heatingplate.rows()[0][:num_cols]\n if mag_samples_m[0].width:\n radius = mag_samples_m[0].width/2\n else:\n radius = mag_samples_m[0].diameter/2\n\n magdeck.disengage() # just in case\n tempdeck.set_temperature(85)\n\n ctx._hw_manager.hardware._attached_instruments[\n m300._implementation.get_mount()].update_config_item(\n 'pick_up_current', 0.5)\n\n folder_path = '/data/B'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n data = json.load(json_file)\n for pip in tip_log:\n if pip.name in data:\n tip_log[pip]['count'] = data[pip.name]\n else:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n\n for pip in tip_log:\n if pip.type == 'multi':\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.rows()[0]]\n else:\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.wells()]\n tip_log[pip]['max'] = len(tip_log[pip]['tips'])\n\n def _pick_up(pip=m300, loc=None):\n if tip_log[pip]['count'] == tip_log[pip]['max'] and not loc:\n ctx.pause('Replace ' + str(pip.max_volume) + '\u00b5l tipracks before \\\nresuming.')\n pip.reset_tipracks()\n tip_log[pip]['count'] = 0\n if loc:\n pip.pick_up_tip(loc)\n else:\n pip.pick_up_tip(tip_log[pip]['tips'][tip_log[pip]['count']])\n tip_log[pip]['count'] += 1\n\n switch = True\n drop_count = 0\n # number of tips trash will accommodate before prompting user to empty\n drop_threshold = 120\n\n def _drop(pip=m300):\n nonlocal switch\n nonlocal drop_count\n side = 30 if switch else -18\n drop_loc = ctx.loaded_labwares[12].wells()[0].top().move(\n Point(x=side))\n pip.drop_tip(drop_loc)\n switch = not switch\n if pip.type == 'multi':\n drop_count += 8\n else:\n drop_count += 1\n if drop_count == drop_threshold:\n # Setup for flashing lights notification to empty trash\n ctx.home() # home before continuing with protocol\n drop_count = 0\n\n waste_vol = 0\n waste_threshold = 185000\n\n def remove_supernatant(vol, park=False, drop=True):\n \"\"\"\n `remove_supernatant` will transfer supernatant from the deepwell\n extraction plate to the liquid waste reservoir.\n :param vol (float): The amount of volume to aspirate from all deepwell\n sample wells and dispense in the liquid waste.\n :param park (boolean): Whether to pick up sample-corresponding tips\n in the 'parking rack' or to pick up new tips.\n \"\"\"\n\n def _waste_track(vol):\n nonlocal waste_vol\n if waste_vol + vol >= waste_threshold:\n # Setup for flashing lights notification to empty liquid waste\n ctx.home()\n ctx.pause('Please empty liquid waste (slot 11) before \\\nresuming.')\n\n waste_vol = 0\n waste_vol += vol\n\n num_trans = math.ceil(vol/200)\n vol_per_trans = vol/num_trans\n for i, (m, spot) in enumerate(zip(mag_samples_m, parking_spots)):\n if not m300.has_tip:\n if park:\n _pick_up(m300, spot)\n else:\n _pick_up(m300)\n side = -1 if i % 2 == 0 else 1\n loc = m.bottom(0).move(Point(x=side*radius*radial_offset,\n z=z_offset))\n for _ in range(num_trans):\n _waste_track(vol_per_trans)\n if m300.current_volume > 0:\n # void air gap if necessary\n m300.dispense(m300.current_volume, m.top())\n m300.move_to(m.center())\n m300.transfer(vol_per_trans, loc, waste, new_tip='never',\n air_gap=air_gap_vol)\n m300.blow_out(waste)\n m300.air_gap(20)\n if drop:\n _drop(m300)\n\n def wash(vol, source, change_tips_for_samples=True, mix_reps=mix_reps,\n park=True, resuspend=True, drop=True):\n \"\"\"\n `wash` will perform bead washing for the extraction protocol.\n :param vol (float): The amount of volume to aspirate from each\n source and dispense to each well containing beads.\n :param source (List[Well]): A list of wells from where liquid will be\n aspirated. If the length of the source list\n > 1, `wash` automatically calculates\n the index of the source that should be\n accessed.\n :param mix_reps (int): The number of repititions to mix the beads with\n specified wash buffer (ignored if resuspend is\n False).\n :param park (boolean): Whether to save sample-corresponding tips\n between adding wash buffer and removing\n supernatant.\n :param resuspend (boolean): Whether to resuspend beads in wash buffer.\n \"\"\"\n\n if resuspend and magdeck.status == 'engaged':\n magdeck.disengage()\n\n num_trans = math.ceil(vol/200)\n vol_per_trans = vol/num_trans\n for i, (m, spot) in enumerate(zip(mag_samples_m, parking_spots)):\n if not m300.has_tip:\n _pick_up(m300)\n side = 1 if i % 2 == 0 else -1\n for n in range(num_trans):\n if m300.current_volume > 0:\n m300.dispense(m300.current_volume, source.top())\n m300.transfer(vol_per_trans, source, m.top(),\n air_gap=air_gap_vol, new_tip='never')\n if n < num_trans - 1: # only air_gap if going back to source\n m300.air_gap(20)\n if resuspend:\n for _ in range(mix_reps):\n m300.aspirate(mix_volume_percentage*vol, m.bottom())\n m300.dispense(mix_volume_percentage*vol,\n m.bottom().move(\n Point(x=side*radius*radial_offset, z=3)))\n m300.blow_out(m.top())\n m300.air_gap(20)\n if change_tips_for_samples:\n if park:\n m300.drop_tip(spot)\n else:\n _drop(m300)\n\n if magdeck.status == 'disengaged':\n magdeck.engage(mag_height)\n\n ctx.delay(minutes=bead_settling_time, msg='Incubating on MagDeck for \\\n' + str(bead_settling_time) + ' minutes.')\n\n remove_supernatant(vol, park=park, drop=drop)\n\n def elute(vol, park=True):\n \"\"\"\n `elute` will perform elution from the deepwell extraction plate to the\n final clean elutions PCR plate to complete the extraction protocol.\n :param vol (float): The amount of volume to aspirate from the elution\n buffer source and dispense to each well containing\n beads.\n :param park (boolean): Whether to save sample-corresponding tips\n between adding elution buffer and transferring\n supernatant to the final clean elutions PCR\n plate.\n \"\"\"\n magdeck.disengage()\n\n # pre-heat elution buffer\n _pick_up(m300)\n for h in heating_samples_m:\n m300.transfer(elution_vol*1.2, elution_solution, h,\n new_tip='never')\n m300.home()\n\n ctx.delay(minutes=temp_time, msg=f'Incubating at 85C for {temp_time} \\\nminutes')\n # resuspend beads in elution\n m300.flow_rate.aspirate /= 5\n m300.flow_rate.dispense /= 5\n m300.flow_rate.blow_out /= 5\n for i, (m, h, spot) in enumerate(zip(mag_samples_m, heating_samples_m,\n parking_spots)):\n if not m300.has_tip:\n _pick_up(m300)\n side = 1 if i % 2 == 0 else -1\n loc = m.bottom().move(Point(x=side*radius*radial_offset,\n z=z_offset))\n m300.aspirate(vol*1.2, h)\n m300.move_to(m.center())\n m300.dispense(vol, loc)\n for _ in range(mix_reps):\n m300.aspirate(vol*mix_volume_percentage, m.bottom())\n m300.dispense(vol*mix_volume_percentage, m.bottom().move(Point(\n x=side*radius*radial_offset, z=3)))\n m300.transfer(vol, m.bottom(), h, new_tip='never')\n m300.blow_out(h.bottom(h.depth/2))\n if park:\n m300.drop_tip(spot)\n else:\n _drop(m300)\n\n ctx.delay(minutes=temp_time, msg=f'Incubating at 85C for {temp_time} \\\nminutes')\n\n for m, h, spot in zip(mag_samples_m, heating_samples_m,\n parking_spots):\n if park:\n _pick_up(m300, spot)\n else:\n _pick_up(m300)\n m300.transfer(vol, h, m, mix_before=(5, 0.5*vol),\n new_tip='never')\n m300.blow_out(m.bottom(m.depth/2))\n _drop(m300)\n\n magdeck.engage(mag_height)\n ctx.delay(minutes=bead_settling_time, msg='Incubating on MagDeck for \\\n' + str(bead_settling_time) + ' minutes.')\n\n for i, (m, e, spot) in enumerate(\n zip(mag_samples_m, elution_samples_m, parking_spots)):\n _pick_up(m300)\n side = -1 if i % 2 == 0 else 1\n loc = m.bottom().move(Point(x=side*radius*radial_offset,\n z=z_offset+2))\n m300.move_to(m.center())\n m300.transfer(0.8*vol, loc, e, air_gap=air_gap_vol,\n new_tip='never')\n m300.drop_tip()\n\n \"\"\"\n ACTIONS\n \"\"\"\n # beads\n _pick_up(m300)\n # add beads\n m300.mix(10, 150, beads)\n for m in mag_samples_m:\n m300.transfer(bead_vol, beads, m, new_tip='never')\n m300.home()\n\n # prewash\n magdeck.engage(mag_height)\n ctx.delay(minutes=bead_settling_time, msg=f'Beads separating for \\\n{bead_settling_time} minutes.')\n remove_supernatant(bead_vol, drop=False)\n # keep tips for wash\n\n for w in range(2):\n wash(wash1_vol, wash1[w], park=park_tips, drop=False,\n change_tips_for_samples=False)\n\n # add sample and mix iteratively for ~30 minutes\n magdeck.disengage()\n for s, d, p in zip(starting_samples_m, mag_samples_m, parking_spots):\n if not m300.has_tip:\n _pick_up()\n m300.transfer(sample_vol, s, d, new_tip='never')\n m300.drop_tip(p)\n\n m300.default_speed = 200\n m300.flow_rate.aspirate = 46.43\n m300.flow_rate.dispense = 92.86\n mixes_per_min = 0.5\n num_mix_cycles = int(sample_mixing_time_minutes*mixes_per_min/num_cols)\n if TEST_MODE or not sample_incubation_mixing:\n num_mix_cycles = 5\n for i in range(num_mix_cycles):\n for j, (s, p) in enumerate(zip(mag_samples_m, parking_spots)):\n _pick_up(m300, p)\n side = 1 if j % 2 == 0 else -1\n loc = s.bottom().move(Point(x=side*radius*radial_offset,\n z=z_offset-1))\n for _ in range(mix_reps):\n m300.aspirate(sample_vol*mix_volume_percentage, loc)\n m300.dispense(sample_vol*mix_volume_percentage,\n s.bottom().move(Point(\n x=side*radius*radial_offset, z=7)))\n m300.blow_out(\n s.bottom(sample_mixing_blowout_height_from_bottom))\n m300.drop_tip(p)\n m300.default_speed = 400\n magdeck.engage(mag_height)\n ctx.delay(minutes=bead_settling_time)\n remove_supernatant(sample_vol, park=park_tips)\n\n # sample washes\n for w in range(2):\n wash(wash1_vol, wash1[w], park=park_tips)\n for w in range(3):\n wash(wash2_vol, wash2[w], park=park_tips)\n elute(elution_vol, park=park_tips)\n\n # track final used tip\n if tip_track and not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n data = {pip.name: tip_log[pip]['count'] for pip in tip_log}\n with open(tip_file_path, 'w') as outfile:\n json.dump(data, outfile)\n", "custom_labware_defs": [ { "brand": { diff --git a/protoBuilds/7062c9/normalization.ot2.apiv2.py.json b/protoBuilds/7062c9/normalization.ot2.apiv2.py.json index d095ada06..932b560f9 100644 --- a/protoBuilds/7062c9/normalization.ot2.apiv2.py.json +++ b/protoBuilds/7062c9/normalization.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "metadata = {\n 'protocolName': 'Capping Assay: Steps 1-2',\n 'author': 'Nick ',\n 'source': 'Protocol Library',\n 'apiLevel': '2.11'\n }\n\n\ndef run(ctx):\n [input_csv, p300_mount, p20_mount] = get_values( # noqa: F821\n 'input_csv', 'p300_mount', 'p20_mount')\n\n # labware\n sample_rack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '7',\n 'sample rack')\n final_plate = ctx.load_labware('neptune_96_aluminumblock_200ul',\n '5', 'normalized plate')\n tuberack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '8',\n 'buffer + probe tuberack')\n tipracks20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', '3')]\n tipracks200 = ctx.load_labware('opentrons_96_filtertiprack_200ul', '9')\n\n # pipettes\n p300 = ctx.load_instrument('p300_multi_gen2', p300_mount,\n tip_racks=[tipracks200])\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount,\n tip_racks=tipracks20)\n\n ctx._implementation._hw_manager.hardware._attached_instruments[\n p300._implementation.get_mount()].update_config_item(\n 'pick_up_current', 0.1)\n\n p300.flow_rate.dispense /= 5\n\n # reagents\n water = tuberack.wells()[0]\n buffer = tuberack.wells()[1]\n protease = tuberack.wells()[2]\n\n def drop_all_tips():\n for pipette in ctx.loaded_instruments.values():\n if pipette.has_tip:\n pipette.drop_tip()\n\n tip_data = {\n 'single': {\n 'count': 0,\n 'tips': [\n well for col in tipracks200.columns()\n for well in col[::-1]]\n },\n 'multi': {\n 'count': 0,\n 'tips': [tipracks200.rows()[0][::-1]]\n }\n }\n\n def pickup_p300(mode='single'):\n p300.pick_up_tip(tip_data[mode]['tips'][tip_data[mode]['count']])\n tip_data[mode]['count'] += 1\n\n # parse csv\n data = [\n [val for val in line.split(',')]\n for line in input_csv.splitlines()][1:]\n\n # prealocate water,\n for i, line in enumerate(data):\n water_vol = float(line[2])\n pip = p20 if water_vol <= 20 else p300\n dest_well = final_plate.wells()[i]\n if not pip.has_tip:\n if pip == p20:\n pip.pick_up_tip()\n else:\n pickup_p300('single')\n pip.aspirate(water_vol, water)\n pip.dispense(water_vol, dest_well)\n drop_all_tips()\n\n # prealocate buffer\n for i, line in enumerate(data):\n buffer_vol = float(line[3])\n pip = p20 if buffer_vol <= 20 else p300\n dest_well = final_plate.wells()[i]\n if not pip.has_tip:\n if pip == p20:\n pip.pick_up_tip()\n else:\n pickup_p300('single')\n pip.aspirate(buffer_vol, buffer)\n pip.dispense(buffer_vol, dest_well)\n drop_all_tips()\n\n last_probe = None\n for i, line in enumerate(data):\n probe_vol = float(line[4])\n probe = tuberack.wells_by_name()[line[5].upper().strip()]\n pip = p20 if probe_vol <= 20 else p300\n dest_well = final_plate.wells()[i]\n if not probe == last_probe:\n if pip.has_tip:\n pip.drop_tip()\n if pip == p20:\n pip.pick_up_tip()\n else:\n pickup_p300('single')\n pip.aspirate(probe_vol, probe)\n pip.dispense(probe_vol, dest_well)\n drop_all_tips()\n\n # transfer sample and mix\n for i, line in enumerate(data):\n sample_vol = float(line[1])\n total_vol = float(line[6])\n pip = p20 if sample_vol <= 20 else p300\n sample_well, dest_well = [\n sample_rack.wells()[i], final_plate.wells()[i]]\n if 0.8*total_vol < pip.max_volume:\n mix_vol = 0.8*total_vol\n else:\n mix_vol = 0.8*pip.max_volume\n if pip == p20:\n pip.pick_up_tip()\n else:\n pickup_p300('single')\n pip.aspirate(sample_vol, sample_well)\n pip.dispense(sample_vol, dest_well)\n pip.mix(3, mix_vol, dest_well)\n drop_all_tips()\n\n ctx.pause('Put sample plate in the thermal cycler for 30min')\n\n # transfer protease\n for i, line in enumerate(data):\n dest_well = final_plate.wells()[i]\n p20.transfer(5, protease, dest_well, mix_after=(3, 20))\n", + "content": "metadata = {\n 'protocolName': 'Capping Assay: Steps 1-2',\n 'author': 'Nick ',\n 'source': 'Protocol Library',\n 'apiLevel': '2.11'\n }\n\n\ndef run(ctx):\n [input_csv, p300_mount, p20_mount] = get_values( # noqa: F821\n 'input_csv', 'p300_mount', 'p20_mount')\n\n # labware\n sample_rack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '7',\n 'sample rack')\n final_plate = ctx.load_labware('neptune_96_aluminumblock_200ul',\n '5', 'normalized plate')\n tuberack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '8',\n 'buffer + probe tuberack')\n tipracks20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', '3')]\n tipracks200 = ctx.load_labware('opentrons_96_filtertiprack_200ul', '9')\n\n # pipettes\n p300 = ctx.load_instrument('p300_multi_gen2', p300_mount,\n tip_racks=[tipracks200])\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount,\n tip_racks=tipracks20)\n\n ctx._hw_manager.hardware._attached_instruments[\n p300._implementation.get_mount()].update_config_item(\n 'pick_up_current', 0.1)\n\n p300.flow_rate.dispense /= 5\n\n # reagents\n water = tuberack.wells()[0]\n buffer = tuberack.wells()[1]\n protease = tuberack.wells()[2]\n\n def drop_all_tips():\n for pipette in ctx.loaded_instruments.values():\n if pipette.has_tip:\n pipette.drop_tip()\n\n tip_data = {\n 'single': {\n 'count': 0,\n 'tips': [\n well for col in tipracks200.columns()\n for well in col[::-1]]\n },\n 'multi': {\n 'count': 0,\n 'tips': [tipracks200.rows()[0][::-1]]\n }\n }\n\n def pickup_p300(mode='single'):\n p300.pick_up_tip(tip_data[mode]['tips'][tip_data[mode]['count']])\n tip_data[mode]['count'] += 1\n\n # parse csv\n data = [\n [val for val in line.split(',')]\n for line in input_csv.splitlines()][1:]\n\n # prealocate water,\n for i, line in enumerate(data):\n water_vol = float(line[2])\n pip = p20 if water_vol <= 20 else p300\n dest_well = final_plate.wells()[i]\n if not pip.has_tip:\n if pip == p20:\n pip.pick_up_tip()\n else:\n pickup_p300('single')\n pip.aspirate(water_vol, water)\n pip.dispense(water_vol, dest_well)\n drop_all_tips()\n\n # prealocate buffer\n for i, line in enumerate(data):\n buffer_vol = float(line[3])\n pip = p20 if buffer_vol <= 20 else p300\n dest_well = final_plate.wells()[i]\n if not pip.has_tip:\n if pip == p20:\n pip.pick_up_tip()\n else:\n pickup_p300('single')\n pip.aspirate(buffer_vol, buffer)\n pip.dispense(buffer_vol, dest_well)\n drop_all_tips()\n\n last_probe = None\n for i, line in enumerate(data):\n probe_vol = float(line[4])\n probe = tuberack.wells_by_name()[line[5].upper().strip()]\n pip = p20 if probe_vol <= 20 else p300\n dest_well = final_plate.wells()[i]\n if not probe == last_probe:\n if pip.has_tip:\n pip.drop_tip()\n if pip == p20:\n pip.pick_up_tip()\n else:\n pickup_p300('single')\n pip.aspirate(probe_vol, probe)\n pip.dispense(probe_vol, dest_well)\n drop_all_tips()\n\n # transfer sample and mix\n for i, line in enumerate(data):\n sample_vol = float(line[1])\n total_vol = float(line[6])\n pip = p20 if sample_vol <= 20 else p300\n sample_well, dest_well = [\n sample_rack.wells()[i], final_plate.wells()[i]]\n if 0.8*total_vol < pip.max_volume:\n mix_vol = 0.8*total_vol\n else:\n mix_vol = 0.8*pip.max_volume\n if pip == p20:\n pip.pick_up_tip()\n else:\n pickup_p300('single')\n pip.aspirate(sample_vol, sample_well)\n pip.dispense(sample_vol, dest_well)\n pip.mix(3, mix_vol, dest_well)\n drop_all_tips()\n\n ctx.pause('Put sample plate in the thermal cycler for 30min')\n\n # transfer protease\n for i, line in enumerate(data):\n dest_well = final_plate.wells()[i]\n p20.transfer(5, protease, dest_well, mix_after=(3, 20))\n", "custom_labware_defs": [ { "brand": { diff --git a/protoBuilds/71381b/71381b.ot2.apiv2.py.json b/protoBuilds/71381b/71381b.ot2.apiv2.py.json index 22e371c47..5508f32eb 100644 --- a/protoBuilds/71381b/71381b.ot2.apiv2.py.json +++ b/protoBuilds/71381b/71381b.ot2.apiv2.py.json @@ -147,5 +147,18 @@ "protocolName": "Zymo Quick DNA HMW + Labelling", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw Opentrons 96 Well Aluminum Block with Bio-Rad Well Plate 200 \u00b5L on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/747d99-assay-1/assay1.ot2.apiv2.py.json b/protoBuilds/747d99-assay-1/assay1.ot2.apiv2.py.json index 4137c4bd1..dfb86c5a3 100644 --- a/protoBuilds/747d99-assay-1/assay1.ot2.apiv2.py.json +++ b/protoBuilds/747d99-assay-1/assay1.ot2.apiv2.py.json @@ -714,5 +714,18 @@ "author": "Opentrons ", "protocolName": "HP COVID-19 Assay 1 V1" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw deepwell plate on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw reaction tubeblock on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/747d99-assay-2/assay2.ot2.apiv2.py.json b/protoBuilds/747d99-assay-2/assay2.ot2.apiv2.py.json index fd845d8c6..3ef43deca 100644 --- a/protoBuilds/747d99-assay-2/assay2.ot2.apiv2.py.json +++ b/protoBuilds/747d99-assay-2/assay2.ot2.apiv2.py.json @@ -693,5 +693,18 @@ "author": "Opentrons ", "protocolName": "HP COVID-19 Assay 2 V1" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw deepwell plate on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw reaction plate on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/74841a-2/extraction.ot2.apiv2.py.json b/protoBuilds/74841a-2/extraction.ot2.apiv2.py.json index 668807087..360d69e9e 100644 --- a/protoBuilds/74841a-2/extraction.ot2.apiv2.py.json +++ b/protoBuilds/74841a-2/extraction.ot2.apiv2.py.json @@ -191,5 +191,12 @@ "author": "Opentrons ", "protocolName": "Swift NormalaseTM Amplicon Panels (SNAP): Size Selection and Cleanup Part 2/2" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw PCR plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/74841a/extraction.ot2.apiv2.py.json b/protoBuilds/74841a/extraction.ot2.apiv2.py.json index 27e660cec..34bee7f1f 100644 --- a/protoBuilds/74841a/extraction.ot2.apiv2.py.json +++ b/protoBuilds/74841a/extraction.ot2.apiv2.py.json @@ -197,5 +197,12 @@ "author": "Opentrons ", "protocolName": "Swift NormalaseTM Amplicon Panels (SNAP): Size Selection and Cleanup Part 1/2" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw PCR plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/75cfa6/generic_station_C.ot2.apiv2.py.json b/protoBuilds/75cfa6/generic_station_C.ot2.apiv2.py.json deleted file mode 100644 index 7e1908240..000000000 --- a/protoBuilds/75cfa6/generic_station_C.ot2.apiv2.py.json +++ /dev/null @@ -1,1233 +0,0 @@ -{ - "content": "import math\n\nmetadata = {\n 'protocolName': 'PCR Prep',\n 'author': 'Nick ',\n 'source': 'Protocol Library',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n num_samples, p10_mount, m10_mount = get_values( # noqa: F821\n 'num_samples', 'p10_mount', 'm10_mount')\n\n tuberack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '2',\n 'mastermix tuberack (column 1)')\n tiprack10s = [ctx.load_labware('opentrons_96_tiprack_10ul', '3')]\n tiprack10m = [ctx.load_labware('opentrons_96_tiprack_10ul', '6')]\n tempdeck1 = ctx.load_module('tempdeck', '4')\n pcr_plate = tempdeck1.load_labware(\n 'opentrons_96_aluminumblock_biorad_wellplate_200ul', 'PCR plate')\n tempdeck2 = ctx.load_module('tempdeck', '7')\n sample_plate = tempdeck2.load_labware(\n 'opentrons_96_aluminumblock_biorad_wellplate_200ul', 'sample plate')\n\n p10 = ctx.load_instrument('p10_single', p10_mount, tip_racks=tiprack10s)\n m10 = ctx.load_instrument('p10_single', m10_mount, tip_racks=tiprack10m)\n\n mms = tuberack.columns()[0]\n num_cols = math.ceil(num_samples/8)\n samples = sample_plate.rows()[0][:num_cols]\n\n # set temperature module temperature\n [tempdeck.set_temperature(6) for tempdeck in [tempdeck1, tempdeck2]]\n p10.home()\n ctx.pause(\"Temperature has reached 6\u00b0C. Place your reagents on the \\\n Temperature Module(s) before resuming.\")\n\n # transfer master mix\n wells_row_order = [well for row in pcr_plate.rows() for well in row]\n mm_sets = [wells_row_order[i::4] for i in range(4)]\n for mm, dest_set in zip(mms, mm_sets):\n p10.pick_up_tip()\n for d in dest_set:\n p10.transfer(8, mm, d, new_tip='never')\n p10.blow_out(d.bottom(5))\n p10.drop_tip()\n\n sample_sets = [pcr_plate.rows()[0][i*4:(i+1)*4] for i in range(num_cols)]\n for s, dest_set in zip(samples, sample_sets):\n for d in dest_set:\n m10.transfer(2, s, d, mix_after=(5, 5))\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "Applied Biosystems", - "brandId": [ - "4483354" - ] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.75, - "yDimension": 85.5, - "zDimension": 26.5 - }, - "groups": [ - { - "brand": { - "brand": "Applied Biosystems", - "brandId": [ - "4483354" - ] - }, - "metadata": { - "displayCategory": "aluminumBlock", - "displayName": "Applied Biosystems 96 Aluminum Block 200 \u00b5L", - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8", - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9", - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10", - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11", - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - } - ], - "metadata": { - "displayCategory": "aluminumBlock", - "displayName": "Applied Biosystems 96 Aluminum Block 200 \u00b5L", - "displayVolumeUnits": "\u00b5L", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1" - ], - [ - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2" - ], - [ - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3" - ], - [ - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4" - ], - [ - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5" - ], - [ - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6" - ], - [ - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7" - ], - [ - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8" - ], - [ - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9" - ], - [ - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10" - ], - [ - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11" - ], - [ - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - ], - "parameters": { - "format": "irregular", - "isMagneticModuleCompatible": false, - "isTiprack": false, - "loadName": "ab_96_aluminumblock", - "quirks": [] - }, - "schemaVersion": 2, - "version": 1, - "wells": { - "A1": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 74.25, - "z": 6.4 - }, - "A10": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 95.38, - "y": 74.25, - "z": 6.4 - }, - "A11": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 104.38, - "y": 74.25, - "z": 6.4 - }, - "A12": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 113.38, - "y": 74.25, - "z": 6.4 - }, - "A2": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 23.38, - "y": 74.25, - "z": 6.4 - }, - "A3": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 32.38, - "y": 74.25, - "z": 6.4 - }, - "A4": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 74.25, - "z": 6.4 - }, - "A5": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 50.38, - "y": 74.25, - "z": 6.4 - }, - "A6": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 59.38, - "y": 74.25, - "z": 6.4 - }, - "A7": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 74.25, - "z": 6.4 - }, - "A8": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 74.25, - "z": 6.4 - }, - "A9": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 74.25, - "z": 6.4 - }, - "B1": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 65.25, - "z": 6.4 - }, - "B10": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 95.38, - "y": 65.25, - "z": 6.4 - }, - "B11": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 104.38, - "y": 65.25, - "z": 6.4 - }, - "B12": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 113.38, - "y": 65.25, - "z": 6.4 - }, - "B2": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 23.38, - "y": 65.25, - "z": 6.4 - }, - "B3": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 32.38, - "y": 65.25, - "z": 6.4 - }, - "B4": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 65.25, - "z": 6.4 - }, - "B5": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 50.38, - "y": 65.25, - "z": 6.4 - }, - "B6": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 59.38, - "y": 65.25, - "z": 6.4 - }, - "B7": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 65.25, - "z": 6.4 - }, - "B8": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 65.25, - "z": 6.4 - }, - "B9": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 65.25, - "z": 6.4 - }, - "C1": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 56.25, - "z": 6.4 - }, - "C10": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 95.38, - "y": 56.25, - "z": 6.4 - }, - "C11": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 104.38, - "y": 56.25, - "z": 6.4 - }, - "C12": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 113.38, - "y": 56.25, - "z": 6.4 - }, - "C2": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 23.38, - "y": 56.25, - "z": 6.4 - }, - "C3": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 32.38, - "y": 56.25, - "z": 6.4 - }, - "C4": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 56.25, - "z": 6.4 - }, - "C5": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 50.38, - "y": 56.25, - "z": 6.4 - }, - "C6": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 59.38, - "y": 56.25, - "z": 6.4 - }, - "C7": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 56.25, - "z": 6.4 - }, - "C8": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 56.25, - "z": 6.4 - }, - "C9": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 56.25, - "z": 6.4 - }, - "D1": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 47.25, - "z": 6.4 - }, - "D10": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 95.38, - "y": 47.25, - "z": 6.4 - }, - "D11": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 104.38, - "y": 47.25, - "z": 6.4 - }, - "D12": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 113.38, - "y": 47.25, - "z": 6.4 - }, - "D2": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 23.38, - "y": 47.25, - "z": 6.4 - }, - "D3": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 32.38, - "y": 47.25, - "z": 6.4 - }, - "D4": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 47.25, - "z": 6.4 - }, - "D5": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 50.38, - "y": 47.25, - "z": 6.4 - }, - "D6": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 59.38, - "y": 47.25, - "z": 6.4 - }, - "D7": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 47.25, - "z": 6.4 - }, - "D8": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 47.25, - "z": 6.4 - }, - "D9": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 47.25, - "z": 6.4 - }, - "E1": { - "depth": 20.1, - 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"value": "right" - } - ], - "type": "dropDown" - }, - { - "label": "P10 multi-channel GEN1 mount", - "name": "m10_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p10_single" - }, - { - "mount": "right", - "name": "p10_single" - } - ], - "labware": [ - { - "name": "mastermix tuberack (column 1) on 2", - "share": false, - "slot": "2", - "type": "opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap" - }, - { - "name": "Opentrons 96 Tip Rack 10 \u00b5L on 3", - "share": false, - "slot": "3", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "PCR plate on Temperature Module GEN1 on 4", - "share": false, - "slot": "4", - "type": "opentrons_96_aluminumblock_biorad_wellplate_200ul" - }, - { - "name": "Opentrons 96 Tip Rack 10 \u00b5L on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "sample plate on Temperature Module GEN1 on 7", - "share": false, - "slot": "7", - "type": "opentrons_96_aluminumblock_biorad_wellplate_200ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Nick ", - "protocolName": "PCR Prep", - "source": "Protocol Library" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/75cfa6/pcr_prep.ot2.apiv2.py.json b/protoBuilds/75cfa6/pcr_prep.ot2.apiv2.py.json index 7e1908240..cb777f1ee 100644 --- a/protoBuilds/75cfa6/pcr_prep.ot2.apiv2.py.json +++ b/protoBuilds/75cfa6/pcr_prep.ot2.apiv2.py.json @@ -1229,5 +1229,18 @@ "protocolName": "PCR Prep", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 4 lw PCR plate on Temperature Module GEN1 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 7 lw sample plate on Temperature Module GEN1 on 7", + "share": false, + "slot": "7", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/76ba23-bisulfite_conversion/76ba23-bisulfite_conversion.ot2.apiv2.py.json b/protoBuilds/76ba23-bisulfite_conversion/76ba23-bisulfite_conversion.ot2.apiv2.py.json index b305006f4..85abbbf69 100644 --- a/protoBuilds/76ba23-bisulfite_conversion/76ba23-bisulfite_conversion.ot2.apiv2.py.json +++ b/protoBuilds/76ba23-bisulfite_conversion/76ba23-bisulfite_conversion.ot2.apiv2.py.json @@ -167,5 +167,12 @@ "protocolName": "Bisulfite Conversion", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 7 lw Collection Plate on Magnetic Module GEN1 on 7", + "share": false, + "slot": "7", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/76ba23-pcr1/76ba23-pcr1.ot2.apiv2.py.json b/protoBuilds/76ba23-pcr1/76ba23-pcr1.ot2.apiv2.py.json index 1cde6430a..79b1d9106 100644 --- a/protoBuilds/76ba23-pcr1/76ba23-pcr1.ot2.apiv2.py.json +++ b/protoBuilds/76ba23-pcr1/76ba23-pcr1.ot2.apiv2.py.json @@ -104,5 +104,12 @@ "protocolName": "PCR 1", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/76ba23-pooling/76ba23-pooling.ot2.apiv2.py.json b/protoBuilds/76ba23-pooling/76ba23-pooling.ot2.apiv2.py.json index e6ffa6d3f..55ec38cdd 100644 --- a/protoBuilds/76ba23-pooling/76ba23-pooling.ot2.apiv2.py.json +++ b/protoBuilds/76ba23-pooling/76ba23-pooling.ot2.apiv2.py.json @@ -126,5 +126,12 @@ "protocolName": "Pooling and Clean Up", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw USA Scientific 96 Deep Well Plate 2.4 mL on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/76ba23/76ba23.ot2.apiv2.py.json b/protoBuilds/76ba23/76ba23.ot2.apiv2.py.json index 320d8e041..7a1b7499a 100644 --- a/protoBuilds/76ba23/76ba23.ot2.apiv2.py.json +++ b/protoBuilds/76ba23/76ba23.ot2.apiv2.py.json @@ -137,5 +137,12 @@ "protocolName": "DNA extraction", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 7 lw USA Scientific 96 Deep Well Plate 2.4 mL on Magnetic Module GEN1 on 7", + "share": false, + "slot": "7", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/7805de-part-2/7805de-part-2.ot2.apiv2.py.json b/protoBuilds/7805de-part-2/7805de-part-2.ot2.apiv2.py.json index 2e494261a..83f237db8 100644 --- a/protoBuilds/7805de-part-2/7805de-part-2.ot2.apiv2.py.json +++ b/protoBuilds/7805de-part-2/7805de-part-2.ot2.apiv2.py.json @@ -179,5 +179,18 @@ "author": "Steve Plonk ", "protocolName": "NEBNext Ultra II Directional RNA Library Prep Kit\n for Illumina with poly(A) selection: part 2 -\n First and Second Strand cDNA Synthesis and Bead Clean Up" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw Mag Plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw 4 Degree Block on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/7805de-part-3/7805de-part-3.ot2.apiv2.py.json b/protoBuilds/7805de-part-3/7805de-part-3.ot2.apiv2.py.json index 693bd6b48..75ab874ba 100644 --- a/protoBuilds/7805de-part-3/7805de-part-3.ot2.apiv2.py.json +++ b/protoBuilds/7805de-part-3/7805de-part-3.ot2.apiv2.py.json @@ -179,5 +179,18 @@ "author": "Steve Plonk ", "protocolName": "NEBNext Ultra II Directional RNA Library Prep Kit\n for Illumina with poly(A) selection: part 3 -\n End Prep, Adapter Ligation and Bead Clean Up" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw Mag Plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw 4 Degree Block on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/7805de-part-4/7805de-part-4.ot2.apiv2.py.json b/protoBuilds/7805de-part-4/7805de-part-4.ot2.apiv2.py.json index 653fb1e91..28d8a3dc5 100644 --- a/protoBuilds/7805de-part-4/7805de-part-4.ot2.apiv2.py.json +++ b/protoBuilds/7805de-part-4/7805de-part-4.ot2.apiv2.py.json @@ -173,5 +173,18 @@ "author": "Steve Plonk ", "protocolName": "NEBNext Ultra II Directional RNA Library Prep Kit\n for Illumina with poly(A) selection: part 4 -\n PCR Enrichment and Bead Clean Up" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw Mag Plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw 4 Degree Block on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/7805de/7805de.ot2.apiv2.py.json b/protoBuilds/7805de/7805de.ot2.apiv2.py.json index 79de28d20..df0b0a30d 100644 --- a/protoBuilds/7805de/7805de.ot2.apiv2.py.json +++ b/protoBuilds/7805de/7805de.ot2.apiv2.py.json @@ -161,5 +161,18 @@ "author": "Steve Plonk ", "protocolName": "NEBNext Ultra II Directional RNA Library Prep Kit\n for Illumina with poly(A) selection: part 1 -\n RNA Isolation, Fragmentation and Priming" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw Mag Plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw 4 Degree Block on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/7855ef-plate-part4/7855ef-plate-part4.ot2.apiv2.py.json b/protoBuilds/7855ef-plate-part4/7855ef-plate-part4.ot2.apiv2.py.json index f467ed097..d88f18f2c 100644 --- a/protoBuilds/7855ef-plate-part4/7855ef-plate-part4.ot2.apiv2.py.json +++ b/protoBuilds/7855ef-plate-part4/7855ef-plate-part4.ot2.apiv2.py.json @@ -261,868 +261,868 @@ "version": 1, "wells": { "A1": { - 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"z": 5.3 + "z": 4.8 }, "H1": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 14.38, "y": 11.24, - "z": 5.3 + "z": 4.8 }, "H10": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 95.38, "y": 11.24, - "z": 5.3 + "z": 4.8 }, "H11": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 104.38, "y": 11.24, - "z": 5.3 + "z": 4.8 }, "H12": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 113.38, "y": 11.24, - "z": 5.3 + "z": 4.8 }, "H2": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 23.38, "y": 11.24, - "z": 5.3 + "z": 4.8 }, "H3": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 32.38, "y": 11.24, - "z": 5.3 + "z": 4.8 }, "H4": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 41.38, "y": 11.24, - "z": 5.3 + "z": 4.8 }, "H5": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 50.38, "y": 11.24, - "z": 5.3 + "z": 4.8 }, "H6": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 59.38, "y": 11.24, - "z": 5.3 + "z": 4.8 }, "H7": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 68.38, "y": 11.24, - "z": 5.3 + "z": 4.8 }, "H8": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 77.38, "y": 11.24, - "z": 5.3 + "z": 4.8 }, "H9": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 86.38, "y": 11.24, - "z": 5.3 + "z": 4.8 } } }, diff --git a/protoBuilds/796af8/796af8.ot2.apiv2.py.json b/protoBuilds/796af8/796af8.ot2.apiv2.py.json index 4d3a95617..a1993b64f 100644 --- a/protoBuilds/796af8/796af8.ot2.apiv2.py.json +++ b/protoBuilds/796af8/796af8.ot2.apiv2.py.json @@ -156,5 +156,24 @@ "description": "Custom Protocol Request", "protocolName": "NEB Ultra II FS DNA Library Prep" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 4 lw Opentrons 96 Well Aluminum Block with Generic PCR Strip 200 \u00b5L on Temperature Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 9 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 9", + "share": false, + "slot": "9", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/7a1ae8/7a1ae8.ot2.apiv2.py.json b/protoBuilds/7a1ae8/7a1ae8.ot2.apiv2.py.json index 038255060..987e577e6 100644 --- a/protoBuilds/7a1ae8/7a1ae8.ot2.apiv2.py.json +++ b/protoBuilds/7a1ae8/7a1ae8.ot2.apiv2.py.json @@ -150,5 +150,18 @@ "protocolName": "Zymobiomics Magbead Nucleic Acid Purification", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 1 lw deepwell plate (on magdeck) on Magnetic Module GEN1 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 7 lw spot for drying mid-protocol on Temperature Module GEN1 on 7", + "share": false, + "slot": "7", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/7aa3fd-library-pooling/lib_pooling.ot2.apiv2.py.json b/protoBuilds/7aa3fd-library-pooling/lib_pooling.ot2.apiv2.py.json index 99911453f..a45d54298 100644 --- a/protoBuilds/7aa3fd-library-pooling/lib_pooling.ot2.apiv2.py.json +++ b/protoBuilds/7aa3fd-library-pooling/lib_pooling.ot2.apiv2.py.json @@ -1201,7 +1201,7 @@ "type": "opentrons_96_filtertiprack_10ul" }, { - "name": "Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module GEN1 on 4", + "name": "Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module on 4", "share": false, "slot": "4", "type": "opentrons_24_aluminumblock_nest_2ml_snapcap" @@ -1231,5 +1231,18 @@ "protocolName": "NGS Prep Part 3/3: Library Pooling", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 1 lw None", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module on 4 lw Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/7aa3fd-library-quantification/lib_quant.ot2.apiv2.py.json b/protoBuilds/7aa3fd-library-quantification/lib_quant.ot2.apiv2.py.json index 88b666b44..a9970224f 100644 --- a/protoBuilds/7aa3fd-library-quantification/lib_quant.ot2.apiv2.py.json +++ b/protoBuilds/7aa3fd-library-quantification/lib_quant.ot2.apiv2.py.json @@ -1189,7 +1189,7 @@ "type": "opentrons_96_filtertiprack_10ul" }, { - "name": "Eppendorf Twin.tec 96 Well Plate 150 \u00b5L on Temperature Module GEN1 on 4", + "name": "Eppendorf Twin.tec 96 Well Plate 150 \u00b5L on Temperature Module on 4", "share": false, "slot": "4", "type": "eppendorftwin.tec_96_wellplate_150ul" @@ -1227,13 +1227,13 @@ }, "modules": [ { - "name": "MagneticModuleContext at Magnetic Module GEN1 on 1 lw None", + "name": "MagneticModuleContext at Magnetic Module on 1 lw None", "share": false, "slot": "1", "type": "magdeck" }, { - "name": "TemperatureModuleContext at Temperature Module GEN1 on 4 lw Eppendorf Twin.tec 96 Well Plate 150 \u00b5L on Temperature Module GEN1 on 4", + "name": "TemperatureModuleContext at Temperature Module on 4 lw Eppendorf Twin.tec 96 Well Plate 150 \u00b5L on Temperature Module on 4", "share": false, "slot": "4", "type": "tempdeck" diff --git a/protoBuilds/7aa3fd-size-selection/size_selection.ot2.apiv2.py.json b/protoBuilds/7aa3fd-size-selection/size_selection.ot2.apiv2.py.json index d4b6ba2ff..2a67c2460 100644 --- a/protoBuilds/7aa3fd-size-selection/size_selection.ot2.apiv2.py.json +++ b/protoBuilds/7aa3fd-size-selection/size_selection.ot2.apiv2.py.json @@ -1210,7 +1210,7 @@ ], "labware": [ { - "name": "Eppendorf Twin.tec 96 Well Plate 150 \u00b5L on Magnetic Module GEN1 on 1", + "name": "Eppendorf Twin.tec 96 Well Plate 150 \u00b5L on Magnetic Module on 1", "share": false, "slot": "1", "type": "eppendorftwin.tec_96_wellplate_150ul" @@ -1258,5 +1258,12 @@ "protocolName": "NGS Prep Part 1/3: Size Selection", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 1 lw Eppendorf Twin.tec 96 Well Plate 150 \u00b5L on Magnetic Module on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/7cfbde/7cfbde.ot2.apiv2.py.json b/protoBuilds/7cfbde/7cfbde.ot2.apiv2.py.json index 965491357..871c4cb8b 100644 --- a/protoBuilds/7cfbde/7cfbde.ot2.apiv2.py.json +++ b/protoBuilds/7cfbde/7cfbde.ot2.apiv2.py.json @@ -109,5 +109,12 @@ "author": "Chaz ", "protocolName": "3D Black Bio RNA Extraction" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 7 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 7", + "share": false, + "slot": "7", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/925d07-v2/README.json b/protoBuilds/925d07-v2/README.json deleted file mode 100644 index e751d5bb0..000000000 --- a/protoBuilds/925d07-v2/README.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "PCR": [ - "PCR Prep" - ] - }, - "deck-setup": "\n", - "description": "This protocol performs a custom PCR prep from 4 source 96-well RNA plate to a single 384-well destination plate. The transfer scheme is shown below.\n", - "internal": "9250d7", - "labware": "\nOpentrons 20ul tips\nCorning 96 Well Plate 360 ul Flat\nCustom 384 Well Plate 100 ul\nGeneric PCR Strips in 96-well aluminum block\n", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* PCR\n\t* PCR Prep\n\n", - "deck-setup": "![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/925d07/deck.png)\n\n---\n\n", - "description": "\nThis protocol performs a custom PCR prep from 4 source 96-well RNA plate to a single 384-well destination plate. The transfer scheme is shown below.\n\n---\n\n", - "internal": "9250d7\n", - "labware": "* [Opentrons 20ul tips](https://shop.opentrons.com/collections/opentrons-tips)\n* Corning 96 Well Plate 360 ul Flat\n* Custom 384 Well Plate 100 ul\n* Generic PCR Strips in [96-well aluminum block](https://shop.opentrons.com/collections/hardware-modules/products/aluminum-block-set)\n\n", - "modules": "* [Temperature Module GEN2](https://shop.opentrons.com/collections/hardware-modules/products/tempdeck)\n\n---\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "pipettes": "* [P20 Multi Channel Pipette](https://shop.opentrons.com/collections/ot-2-robot/products/8-channel-electronic-pipette)\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "title": "PCR Prep" - }, - "modules": [ - "Temperature Module GEN2" - ], - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "pipettes": "\nP20 Multi Channel Pipette\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "title": "PCR Prep" -} \ No newline at end of file diff --git a/protoBuilds/925d07-v2/metadata.json b/protoBuilds/925d07-v2/metadata.json deleted file mode 100644 index 0f18dc2cc..000000000 --- a/protoBuilds/925d07-v2/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "pcr_prep.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": false, - "skip-tests": false - }, - "path": "protocols/925d07-v2", - "slug": "925d07-v2", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/925d07-v2/pcr_prep.ot2.apiv2.py.json b/protoBuilds/925d07-v2/pcr_prep.ot2.apiv2.py.json deleted file mode 100644 index 5a6d87219..000000000 --- a/protoBuilds/925d07-v2/pcr_prep.ot2.apiv2.py.json +++ /dev/null @@ -1,5604 +0,0 @@ -{ - "content": "from opentrons.types import Point\nimport math\n\nmetadata = {\n 'protocolName': 'PCR Prep',\n 'author': 'Nick Diehl ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n \"\"\"Protocol.\"\"\"\n [rna_plate_type, sample_vol, mm_vol, num_samples_1, num_samples_2,\n num_samples_3, num_samples_4, m20_mount] = get_values( # noqa: F821\n 'rna_plate_type', 'sample_vol', 'mm_vol', 'num_samples_1',\n 'num_samples_2', 'num_samples_3', 'num_samples_4', 'm20_mount')\n\n # load labware\n rna_source_plates = [\n ctx.load_labware(rna_plate_type, slot, f'RNA source plate {i+1}')\n for i, slot in enumerate(['2', '3', '5', '6'])]\n tempdeck = ctx.load_module('temperature module gen2', '4')\n tempdeck.set_temperature(4)\n mm_strips = tempdeck.load_labware(\n 'opentrons_96_aluminumblock_generic_pcr_strip_200ul',\n 'mastermix strips (1-3)').rows()[0][:3]\n dest_plate = ctx.load_labware('custom_384_wellplate_100ul', '1',\n 'destination plate')\n tipracks = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['7', '8', '9', '10', '11']]\n\n # load instrument\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=tipracks)\n pick_up_current = 0.7\n ctx._implementation._hw_manager.hardware._attached_instruments[\n m20._implementation.get_mount()].update_config_item(\n 'pick_up_current', pick_up_current)\n\n num_cols_all = [\n math.ceil(num_samples/8)\n for num_samples in [\n num_samples_1, num_samples_2, num_samples_3, num_samples_4]]\n samples_sources_sets = [\n plate.rows()[0][:num_samples]\n for plate, num_samples in zip(rna_source_plates, num_cols_all)]\n destination_sets = [\n dest_plate.rows()[i][j*12:j*12+num_cols_all[i*2+j]]\n for i in range(2) for j in range(2)]\n mm_destinations = [\n well for set in destination_sets for well in set]\n\n # pre-add mastermix\n cols_per_mm_strip = 16\n m20.pick_up_tip()\n r_384 = dest_plate.wells()[0].diameter/2\n for i, d in enumerate(mm_destinations):\n mm_source = mm_strips[i//cols_per_mm_strip]\n m20.aspirate(2, mm_source.top()) # pre-air gap\n m20.aspirate(mm_vol, mm_source)\n m20.dispense(m20.current_volume, d.bottom(2))\n m20.move_to(d.bottom().move(Point(x=r_384*0.5, z=2)))\n m20.drop_tip()\n\n # add samples\n for i, (s_set, d_set) in enumerate(\n zip(samples_sources_sets, destination_sets)):\n ctx.pause(f'Ensure plate {i+1} is on deck before resuming.')\n for s, d in zip(s_set, d_set):\n m20.pick_up_tip()\n m20.aspirate(sample_vol, s.bottom(1))\n m20.aspirate(2, d.bottom(2))\n m20.dispense(m20.current_volume, d.bottom(2))\n m20.drop_tip()\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "custom", - "brandId": [] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.76, - "yDimension": 85.48, - "zDimension": 11 - }, - "groups": [ - { - "metadata": { - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "I1", - "J1", - "K1", - "L1", - "M1", - "N1", - "O1", - "P1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "I2", - "J2", - "K2", - "L2", - "M2", - "N2", - "O2", - "P2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "I3", - "J3", - "K3", - "L3", - "M3", - "N3", - "O3", - "P3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "I4", - "J4", - "K4", - "L4", - "M4", - "N4", - "O4", - "P4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "I5", - "J5", - "K5", - "L5", - "M5", - "N5", - "O5", - "P5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "I6", - "J6", - "K6", - "L6", - "M6", - "N6", - "O6", - "P6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "I7", - "J7", - "K7", - "L7", - "M7", - "N7", - "O7", - "P7", - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8", - "I8", - "J8", - "K8", - "L8", - "M8", - "N8", - "O8", - "P8", - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9", - "I9", - "J9", - "K9", - "L9", - "M9", - "N9", - "O9", - "P9", - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10", - "I10", - "J10", - "K10", - "L10", - "M10", - "N10", - "O10", - "P10", - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11", - "I11", - "J11", - "K11", - "L11", - "M11", - "N11", - "O11", - "P11", - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12", - "I12", - "J12", - "K12", - "L12", - "M12", - "N12", - "O12", - "P12", - "A13", - "B13", - "C13", - "D13", - "E13", - "F13", - "G13", - "H13", - "I13", - "J13", - "K13", - "L13", - 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"diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 32.4, - "y": 11.2, - "z": 1.7 - }, - "H4": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 41.4, - "y": 11.2, - "z": 1.7 - }, - "H5": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 50.4, - "y": 11.2, - "z": 1.7 - }, - "H6": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 59.4, - "y": 11.2, - "z": 1.7 - }, - "H7": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 68.4, - "y": 11.2, - "z": 1.7 - }, - "H8": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 77.4, - "y": 11.2, - "z": 1.7 - }, - "H9": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 86.4, - "y": 11.2, - "z": 1.7 - } - } - } - ], - "fields": [ - { - "label": "RNA source plate type", - "name": "rna_plate_type", - "options": [ - { - "label": "Corning plate", - "value": "corning_96_wellplate_360ul_flat" - }, - { - "label": "KingFisher 96 Deep Well Plate", - "value": "kingfisher_96_deepwell_plate_2ml" - } - ], - "type": "dropDown" - }, - { - "default": 1.0, - "label": "sample volume (ul)", - "name": "sample_vol", - "type": "float" - }, - { - "default": 9.0, - "label": "mastermix volume (ul)", - "name": "mm_vol", - "type": "float" - }, - { - "default": 96, - "label": "number of plate 1 samples (0-96)", - "name": "num_samples_1", - "type": "int" - }, - { - "default": 96, - "label": "number of plate 2 samples (0-96)", - "name": "num_samples_2", - "type": "int" - }, - { - "default": 96, - "label": "number of plate 3 samples (0-96)", - "name": "num_samples_3", - "type": "int" - }, - { - "default": 96, - "label": "number of plate 4 samples (0-96)", - "name": "num_samples_4", - "type": "int" - }, - { - "label": "P20 Multi GEN2 Mount", - "name": "m20_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p20_multi_gen2" - } - ], - "labware": [ - { - "name": "destination plate on 1", - "share": false, - "slot": "1", - "type": "custom_384_wellplate_100ul" - }, - { - "name": "RNA source plate 1 on 2", - "share": false, - "slot": "2", - "type": "corning_96_wellplate_360ul_flat" - }, - { - "name": "RNA source plate 2 on 3", - "share": false, - "slot": "3", - "type": "corning_96_wellplate_360ul_flat" - }, - { - "name": "mastermix strips (1-3) on Temperature Module GEN2 on 4", - "share": false, - "slot": "4", - "type": "opentrons_96_aluminumblock_generic_pcr_strip_200ul" - }, - { - "name": "RNA source plate 3 on 5", - "share": false, - "slot": "5", - "type": "corning_96_wellplate_360ul_flat" - }, - { - "name": "RNA source plate 4 on 6", - "share": false, - "slot": "6", - "type": "corning_96_wellplate_360ul_flat" - }, - { - "name": "Opentrons 96 Tip Rack 20 \u00b5L on 7", - "share": false, - "slot": "7", - "type": "opentrons_96_tiprack_20ul" - }, - { - "name": "Opentrons 96 Tip Rack 20 \u00b5L on 8", - "share": false, - "slot": "8", - "type": "opentrons_96_tiprack_20ul" - }, - { - "name": "Opentrons 96 Tip Rack 20 \u00b5L on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_tiprack_20ul" - }, - { - "name": "Opentrons 96 Tip Rack 20 \u00b5L on 10", - "share": false, - "slot": "10", - "type": "opentrons_96_tiprack_20ul" - }, - { - "name": "Opentrons 96 Tip Rack 20 \u00b5L on 11", - "share": false, - "slot": "11", - "type": "opentrons_96_tiprack_20ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Nick Diehl ", - "protocolName": "PCR Prep", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/9778eb_mass_norm/9778eb_mass_norm.ot2.apiv2.py.json b/protoBuilds/9778eb_mass_norm/9778eb_mass_norm.ot2.apiv2.py.json deleted file mode 100644 index 7579d8211..000000000 --- a/protoBuilds/9778eb_mass_norm/9778eb_mass_norm.ot2.apiv2.py.json +++ /dev/null @@ -1,125 +0,0 @@ -{ - "content": "\"\"\"OPENTRONS.\"\"\"\nimport math\n\nmetadata = {\n 'protocolName': 'Normalization with CSV',\n 'author': 'Opentrons ',\n 'apiLevel': '2.12'\n}\n\n\ndef run(ctx):\n \"\"\"PROTOCOL.\"\"\"\n [vol_water, src_plate, dst_plate,\n p20_mount, file_input] = get_values( # noqa: F821\n 'vol_water', 'src_plate', 'dst_plate', 'p20_mount', 'file_input')\n\n if p20_mount == 'right':\n p300_mount = 'left'\n else:\n p300_mount = 'right'\n source_plate = ctx.load_labware(src_plate, '1')\n dest_plate = ctx.load_labware(dst_plate, '2')\n reagent_tubes = ctx.load_labware('opentrons_6_tuberack_'\n 'falcon_50ml_conical', '4')\n\n # parse\n csv_rows = [val.strip() for val in file_input.split(',')]\n header_removed = csv_rows[6:]\n well_list = header_removed[::5]\n sample_mass = [eval(i) for i in header_removed[1::5]]\n sample_vol = [eval(i) for i in header_removed[2::5]]\n final_mass = [eval(i) for i in header_removed[3::5]]\n final_vol = [eval(i) for i in header_removed[4::5]]\n start_conc = []\n final_conc = []\n bad_wells = []\n\n for mass, vol in zip(sample_mass, sample_vol):\n start_conc.append(mass/vol)\n\n for mass, vol in zip(final_mass, final_vol):\n final_conc.append(mass/vol)\n\n transfer_vol = []\n nfw_vol = []\n for final, start, vol in zip(final_conc, start_conc, final_vol):\n transfer_vol.append(vol*round(final/start, 1))\n for s_vol, f_vol in zip(transfer_vol, final_vol):\n nfw_vol.append(f_vol-s_vol)\n lists = [well_list, sample_mass, sample_vol, final_mass, final_vol,\n start_conc, final_conc, transfer_vol, nfw_vol]\n # clean up bad wells from lists\n for i, (start, final) in enumerate(zip(start_conc, final_conc)):\n if start < final:\n bad_wells.append(well_list[i])\n for list in lists:\n del list[i]\n\n # Reagents and Well Lists\n\n nfw_source = reagent_tubes.wells()[0]\n\n tips20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', slot)\n for slot in ['3', '6'][:math.ceil(len(well_list)/48)]]\n tips300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)\n for slot in ['5', '7'][:math.ceil(len(well_list)/48)]]\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=tips20)\n p300 = ctx.load_instrument('p300_single_gen2', p300_mount,\n tip_racks=tips300)\n\n # liquid height tracking\n v_naught_dil = vol_water*1000\n radius = reagent_tubes.wells()[0].diameter/2\n h_naught_water = 0.85*v_naught_dil/(math.pi*radius**2)\n h = h_naught_water\n\n def adjust_height(vol):\n nonlocal h\n dh = vol/(math.pi*radius**2)\n h -= dh\n if h < 12:\n h = 1\n\n # do NFW addition first to save tips, mix after sample addition\n p20.pick_up_tip()\n p300.pick_up_tip()\n for nfw, d in zip(nfw_vol, well_list):\n if nfw >= 20:\n pip = p300\n else:\n pip = p20\n pip.transfer(nfw, nfw_source.bottom(h), dest_plate[d],\n new_tip='never')\n adjust_height(nfw)\n p20.drop_tip()\n p300.drop_tip()\n\n for t_vol, well in zip(transfer_vol, well_list):\n if t_vol >= 20:\n pip = p300\n else:\n pip = p20\n pip.pick_up_tip()\n pip.transfer(t_vol, source_plate.wells_by_name()[well],\n dest_plate.wells_by_name()[well], new_tip='never')\n pip.mix(4, f_vol/2, dest_plate.wells_by_name()[well])\n pip.drop_tip()\n\n # bad_list = [well.display_name.split(' ')[0] for well in bad_wells]\n # print(lists)\n\n if len(bad_wells) > 0:\n bad_msg = '\\n\\n'.join(bad_wells)\n ctx.comment(f'The following sample wells failed: \\n\\n{bad_msg}')\n\n for c in ctx.commands():\n print(c)\n", - "custom_labware_defs": [], - "fields": [ - { - "default": 50, - "label": "Volume of Water in Falcon Tube (mL)", - "name": "vol_water", - "type": "int" - }, - { - "label": "Source Plate Type", - "name": "src_plate", - "options": [ - { - "label": "NEST 100uL 96 Well Plate", - "value": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "label": "NEST 96 Deepwell Plate 2mL", - "value": "nest_96_wellplate_2ml_deep" - }, - { - "label": "Thermofisher Semi-Skirted on Adapter 96 Well Plate", - "value": "customadapter_96_wellplate_200ul" - } - ], - "type": "dropDown" - }, - { - "label": "Destination Plate Type", - "name": "dst_plate", - "options": [ - { - "label": "NEST 100uL 96 Well Plate", - "value": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "label": "NEST 96 Deepwell Plate 2mL", - "value": "nest_96_wellplate_2ml_deep" - }, - { - "label": "Thermofisher Semi-Skirted on Adapter 96 Well Plate", - "value": "customadapter_96_wellplate_200ul" - } - ], - "type": "dropDown" - }, - { - "label": "P20 Single GEN2 Mount", - "name": "p20_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - }, - { - "default": ",Well,nanograms,sample volume,goal concentration,normalized volume,A1,20,30,30,30,B1,6,30,5,30,C1,7,30,6,30", - "label": "Transfer .csv File", - "name": "file_input", - "type": "textFile" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p300_single_gen2" - }, - { - "mount": "right", - "name": "p20_single_gen2" - } - ], - "labware": [ - { - "name": "NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on 1", - "share": false, - "slot": "1", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on 2", - "share": false, - "slot": "2", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 3", - "share": false, - "slot": "3", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 6 Tube Rack with Falcon 50 mL Conical on 4", - "share": false, - "slot": "4", - "type": "opentrons_6_tuberack_falcon_50ml_conical" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.12", - "author": "Opentrons ", - "protocolName": "Normalization with CSV" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/9778eb_spri/spri_size.ot2.apiv2.py.json b/protoBuilds/9778eb_spri/spri_size.ot2.apiv2.py.json deleted file mode 100644 index 5dc6a38b9..000000000 --- a/protoBuilds/9778eb_spri/spri_size.ot2.apiv2.py.json +++ /dev/null @@ -1,1327 +0,0 @@ -{ - "content": "\"\"\"OPENTRONS.\"\"\"\nimport math\nimport threading\nfrom time import sleep\nfrom opentrons import types\nfrom opentrons import protocol_api\n\n\nmetadata = {\n 'protocolName': 'SPRI Bead Purification, Size Selection',\n 'author': 'Opentrons ',\n 'apiLevel': '2.11'\n}\n\n\n\"\"\"\nHere is where you can modify the magnetic module engage height:\n\"\"\"\nTEST_MODE = False\nflash = True\nmag_height = 10 # for custom labware sitting on mag modules\n# Definitions for deck light flashing\n\n\nclass CancellationToken:\n \"\"\"FLASH SETUP.\"\"\"\n\n def __init__(self):\n \"\"\"FLASH SETUP.\"\"\"\n self.is_continued = False\n\n def set_true(self):\n \"\"\"FLASH SETUP.\"\"\"\n self.is_continued = True\n\n def set_false(self):\n \"\"\"FLASH SETUP.\"\"\"\n self.is_continued = False\n\n\ndef turn_on_blinking_notification(hardware, pause):\n \"\"\"FLASH SETUP.\"\"\"\n while pause.is_continued:\n hardware.set_lights(rails=True)\n sleep(1)\n hardware.set_lights(rails=False)\n sleep(1)\n\n\ndef create_thread(ctx, cancel_token):\n \"\"\"FLASH SETUP.\"\"\"\n t1 = threading.Thread(target=turn_on_blinking_notification,\n args=(ctx._hw_manager.hardware, cancel_token))\n t1.start()\n return t1\n\n\n# Start protocol\ndef run(ctx):\n \"\"\"PROTOCOL.\"\"\"\n # Setup for flashing lights notification to empty trash\n cancellationToken = CancellationToken()\n\n [num_samples, vol_start, bead_ratio_1, bead_ratio_2,\n vol_trans, air_dry_time, incubation_delay_time, bead_delay_time,\n elution_vol, elution_time, vol_final_plate,\n flash, p300_mount, size_select] = get_values( # noqa: F821\n 'num_samples', 'vol_start', 'bead_ratio_1',\n 'bead_ratio_2', 'vol_trans', 'air_dry_time', 'incubation_delay_time',\n 'bead_delay_time', 'elution_vol', 'elution_time', 'vol_final_plate',\n 'flash', 'p300_mount', 'size_select')\n\n # Drop Down Variables for Testing\n # num_samples = 96\n # vol_start = 50 # volume of starting well\n # bead_ratio_1 = 0.6 # ratio of SPRI by volume\n # bead_ratio_2 = 0.8\n # vol_trans = 75\n # air_dry_time = 10\n # incubation_delay_time = 5\n # bead_delay_time = 5 # minutes real run, seconds for test run\n # elution_vol = 50\n # elution_time = 10\n # vol_final_plate = 50\n # flash = True\n # p300_mount = 'left'\n\n # Math and Calculations\n num_cols = math.ceil(num_samples/8)\n vol_bead_add_1 = vol_start*bead_ratio_1\n vol_post_add_1 = vol_bead_add_1+vol_start\n vol_bead_add_2 = (bead_ratio_2*vol_start*(vol_trans/vol_post_add_1))\\\n - vol_bead_add_1\n\n \"\"\"Above vol_bead_add_2 equation came from Illumina website. Source here:\n https://support.illumina.com/bulletins/2020/07/library-size-selection-\n using-sample-purification-beads.html\"\"\"\n\n # Deprecated calculations below\n # PEG_conc_correction = (vol_trans_post_SPRI_1/vol_total)*bead_ratio\n # PEG_vol_correction = round(PEG_conc_correction*vol_total, 1)\n\n supernatant_headspeed_modulator = 10\n flow_mod = 0.25\n if p300_mount == 'right':\n p20_mount = 'left'\n else:\n p20_mount = 'right'\n \"\"\"\n Here is where you can change the locations of your labware and modules\n (note that this is the recommended configuration)\n \"\"\"\n magdeck_1 = ctx.load_module('magnetic module gen2', '7')\n if size_select:\n magdeck_2 = ctx.load_module('magnetic module gen2', '6')\n magdeck_2.disengage()\n magplate_2 = magdeck_2.load_labware('customadapter_96_wellplate_200ul')\n magdeck_1.disengage()\n magplate_1 = magdeck_1.load_labware('customadapter_96_wellplate_200ul',\n 'sample plate')\n elutionplate = ctx.load_labware(\n 'customadapter_96_wellplate_200ul',\n '3')\n waste = ctx.load_labware('nest_1_reservoir_195ml', '4',\n 'Liquid Waste').wells()[0].top()\n res1 = ctx.load_labware('nest_12_reservoir_15ml', '5',\n 'reagent reservoir 1')\n tips300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot,\n '200\u00b5l filtertiprack')\n for slot in ['2', '9', '11']]\n tips20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', slot,\n '20\u00b5l filtertiprack')\n for slot in ['1', '8', '10']]\n\n parking_spots = [column for column in tips300[0].rows()[0][:num_cols]]\n parking_spots_2 = [column for column in tips300[0].rows()[0][:num_cols]]\n \"\"\"\n Above are the same location purely for clerical reasons to help track open\n tip rack parking spots\n \"\"\"\n\n sample_loc_1 = magplate_1.rows()[0][:num_cols]\n if size_select: # where samples start\n sample_dest_1 = magplate_2.rows()[0][:num_cols] # first super dest\n sample_dest_2 = elutionplate.rows()[0][:num_cols] # where final samples go\n\n bead_well = res1.wells()[0]\n # PEG = res1.wells()[1]\n etoh_1_wells = res1.wells()[1:3] # 10mL in each, 6 columns each\n etoh_2_wells = res1.wells()[3:5] # 10mL in each, 6 columns each\n elution_solution = res1.wells()[-1]\n # load pipettes\n m300 = ctx.load_instrument(\n 'p300_multi_gen2', p300_mount, tip_racks=tips300)\n m20 = ctx.load_instrument('p20_multi_gen2', p20_mount, tip_racks=tips20)\n\n # Custom Functions\n def bead_mixing(well, pip, mvol, asp_speed_mod, disp_speed_mod, reps=10):\n \"\"\"bead_mixing.\"\"\"\n \"\"\"\n 'bead_mixing' will mix liquid that contains beads. This will be done by\n aspirating from the middle of the well & dispensing from the bottom to\n mix the beads with the other liquids as much as possible. Aspiration &\n dispensing will also be reversed to ensure proper mixing.\n param well: The current well that the mixing will occur in.\n param pip: The pipet that is currently attached/ being used.\n param mvol: The volume that is transferred before the mixing steps.\n param reps: The number of mix repetitions that should occur. Note~\n During each mix rep, there are 2 cycles of aspirating from bottom,\n dispensing at the top and 2 cycles of aspirating from middle,\n dispensing at the bottom\n \"\"\"\n vol = mvol * .9\n\n pip.move_to(well.center())\n pip.flow_rate.aspirate *= asp_speed_mod\n pip.flow_rate.dispense *= disp_speed_mod\n for _ in range(reps):\n pip.aspirate(vol, well.bottom(1))\n pip.dispense(vol, well.bottom(5))\n pip.aspirate(vol, well.bottom(5))\n pip.dispense(vol, well.bottom(1))\n pip.flow_rate.aspirate /= asp_speed_mod\n pip.flow_rate.dispense /= disp_speed_mod\n\n def pick_up(pip):\n try:\n pip.pick_up_tip()\n except protocol_api.labware.OutOfTipsError:\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n pip.home()\n ctx.pause('\\n\\n~~~~~~~~~~~~~~PLEASE REPLACE TIPRACKS~~~~~~~~~~~~~~~\\n') # noqa: E501\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n pip.reset_tipracks()\n pick_up(pip)\n\n tips_dropped = 0\n\n def drop_tip(pip, home=True):\n nonlocal tips_dropped\n pip.drop_tip(home_after=home)\n if pip == m300:\n tips_dropped += 8\n else:\n tips_dropped += 4\n if tips_dropped >= 288:\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n pip.home()\n ctx.pause('\\n\\n~~~~~~~~~~~~~~PLEASE EMPTY TRASH~~~~~~~~~~~~~~~\\n')\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n tips_dropped = 0\n\n # Default Values\n ctx.max_speeds['Z'] = 400\n ctx.max_speeds['A'] = 400\n m300.flow_rate.aspirate = 94\n m300.flow_rate.dispense = 94\n m20.flow_rate.aspirate = 7.6\n m20.flow_rate.dispense = 7.6\n\n # Begin Protocol\n if size_select:\n # bead addition 1\n ctx.comment('\\n\\n~~~~~~~~~~~~~~BEAD ADDITION 1~~~~~~~~~~~~~~~\\n')\n for i, dest in enumerate(sample_loc_1):\n if vol_bead_add_1 > 15:\n pip = m300\n speed_mod = 2.5\n else:\n pip = m20\n speed_mod = 2\n pick_up(pip)\n pip.flow_rate.aspirate *= flow_mod\n pip.flow_rate.dispense *= flow_mod\n if i == 0:\n bead_mixing(bead_well, pip, 20, flow_mod, flow_mod, reps=5)\n pip.aspirate(5, bead_well.top())\n pip.aspirate(vol_bead_add_1, bead_well)\n # pip.move_to(dest.top())\n pip.dispense(pip.current_volume, dest)\n pip.flow_rate.aspirate /= flow_mod\n pip.flow_rate.dispense /= flow_mod\n bead_mixing(dest, pip, vol_bead_add_1, speed_mod, speed_mod, reps=5)\n pip.aspirate(5, dest.top())\n drop_tip(pip)\n\n # 5 Minute Incubation\n ctx.comment('\\n\\n~~~~~~~~~~~~~~INCUBATING BEADS~~~~~~~~~~~~~~~\\n')\n if TEST_MODE:\n ctx.delay(seconds=incubation_delay_time)\n else:\n ctx.delay(minutes=incubation_delay_time)\n\n # Magnet engage\n ctx.comment('\\n\\n~~~~~~~~~~~~~~SEPARATING BEADS~~~~~~~~~~~~~~~\\n')\n magdeck_1.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(seconds=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n # Move supernatant to new plate (this is everything under a certain size)\n ctx.comment('\\n\\n~~~~~~~~~~~~MOVING SUPERNATANT TO SLOT 6~~~~~~~~~~~~~\\n')\n for src, dest in zip(sample_loc_1, sample_dest_1):\n side = -1 if i % 2 == 0 else 1\n pick_up(m300)\n m300.aspirate(10, src.top()) # extra air for full liquid dispense\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(vol_trans, src.bottom().move(types.Point(x=side,\n y=0, z=0.2)))\n m300.aspirate(10, src.top())\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(10, dest.top())\n m300.dispense(m300.current_volume, dest)\n m300.aspirate(20, dest.top()) # suck in droplets before drop_tip\n drop_tip(m300)\n\n magdeck_1.disengage()\n # samples are now in slot 6's mag plate, aka magdeck_2\n # Add second bead volume (this binds things above a certain size but\n # lower than the previous sizes selected!)\n # bead addition 2\n ctx.comment('\\n\\n~~~~~~~~~~~~~~BEAD ADDITION 2~~~~~~~~~~~~~~~\\n')\n for i, dest in enumerate(sample_dest_1):\n if vol_bead_add_2 > 15:\n pip = m300\n speed_mod = 2.5\n else:\n pip = m20\n speed_mod = 2\n pick_up(pip)\n pip.flow_rate.aspirate *= flow_mod\n pip.flow_rate.dispense *= flow_mod\n if i == 0:\n bead_mixing(bead_well, pip, 20, flow_mod, flow_mod, reps=5)\n pip.aspirate(5, bead_well.top(1))\n pip.aspirate(vol_bead_add_2, bead_well)\n pip.dispense(pip.current_volume, dest)\n pip.flow_rate.aspirate /= flow_mod\n pip.flow_rate.dispense /= flow_mod\n bead_mixing(dest, pip, vol_bead_add_2, speed_mod, speed_mod, reps=5)\n pip.aspirate(5, dest.top())\n drop_tip(pip)\n\n # 5 minute incubation for the new beads to help out\n ctx.comment('\\n\\n~~~~~~~~~~~~~~INCUBATING BEADS~~~~~~~~~~~~~~~\\n')\n if TEST_MODE:\n ctx.delay(seconds=incubation_delay_time)\n else:\n ctx.delay(minutes=incubation_delay_time)\n\n # Engage magnet 2\n ctx.comment('\\n\\n~~~~~~~~~~~~~~SEPARATING BEADS~~~~~~~~~~~~~~~\\n')\n magdeck_2.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(seconds=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n # Trash Super, leaves the bead-bound base pairs for specific size range\n ctx.comment('\\n\\n~~~~~~~~~~~~MOVING SUPERNATANT TO TRASH~~~~~~~~~~~~~\\n')\n for src in sample_dest_1:\n side = -1 if i % 2 == 0 else 1\n pick_up(m300)\n m300.aspirate(10, src.top()) # extra air for full dispense\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(vol_trans+vol_bead_add_2,\n src.bottom().move(types.Point(x=side,\n y=0, z=0.2)))\n m300.aspirate(10, src.top()) # air gap\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(10, waste)\n m300.dispense(m300.current_volume, dest)\n m300.aspirate(20, waste) # suck in droplets before drop_tip\n drop_tip(m300)\n magdeck_2.disengage()\n\n # EtOH Wash 1\n ctx.comment('\\n\\n~~~~~~~~~~~~ETHANOL WASH 1~~~~~~~~~~~~~\\n')\n for i, (dest, park_loc) in enumerate(zip(sample_dest_1,\n parking_spots)):\n pick_up(m300)\n m300.aspirate(200, etoh_1_wells[i//6])\n m300.dispense(200, dest.top(-1))\n m300.drop_tip(park_loc)\n\n # Mag 2 Engage\n ctx.comment('\\n\\n~~~~~~~~~~~~SEPARATING BEADS~~~~~~~~~~~~~\\n')\n magdeck_2.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(seconds=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n # Remove EtOH wash 1\n ctx.comment('\\n\\n~~~~~~~~~~~~REMOVING ETHANOL~~~~~~~~~~~~~\\n')\n for src, park_loc in zip(sample_dest_1, parking_spots):\n side = -1 if i % 2 == 0 else 1\n m300.pick_up_tip(park_loc)\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(200,\n src.bottom().move(types.Point(x=side,\n y=0, z=0.2)))\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(200, waste)\n m300.aspirate(20, waste) # suck in droplets before drop_tip\n m300.drop_tip(park_loc)\n\n magdeck_2.disengage()\n\n # EtOH wash 2\n ctx.comment('\\n\\n~~~~~~~~~~~~ETHANOL WASH 2~~~~~~~~~~~~~\\n')\n for i, (dest, park_loc) in enumerate(zip(sample_dest_1,\n parking_spots)):\n m300.pick_up_tip(park_loc)\n m300.aspirate(200, etoh_2_wells[i//6])\n m300.dispense(200, dest.top(-1))\n m300.drop_tip(park_loc)\n\n ctx.comment('\\n\\n~~~~~~~~~~~~SEPARATING BEADS~~~~~~~~~~~~~\\n')\n magdeck_2.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(seconds=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n # Remove EtOH wash 2\n ctx.comment('\\n\\n~~~~~~~~~~~~REMOVING ETHANOL~~~~~~~~~~~~~\\n')\n for src, park_loc in zip(sample_dest_1, parking_spots):\n side = -1 if i % 2 == 0 else 1\n m300.pick_up_tip(park_loc)\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(200,\n src.bottom().move(types.Point(x=side,\n y=0, z=0.2)))\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(200, waste)\n m300.aspirate(20, waste) # suck in droplets before drop_tip\n drop_tip(m300)\n\n magdeck_2.disengage()\n # Air dry\n ctx.comment('\\n\\n~~~~~~~~~~~~AIR DRYING BEADS~~~~~~~~~~~~~\\n')\n if TEST_MODE:\n ctx.delay(seconds=air_dry_time)\n else:\n ctx.delay(minutes=air_dry_time)\n\n # Elute from beads!\n ctx.comment('\\n\\n~~~~~~~~~~~~ADDING ELUTION SOLUTION~~~~~~~~~~~~~\\n')\n for dest, park_loc in zip(sample_dest_1, parking_spots_2):\n pick_up(m300)\n m300.aspirate(elution_vol, elution_solution)\n m300.dispense(m300.current_volume, dest)\n bead_mixing(dest, m300, 50, 2.5, 2.5, reps=5)\n m300.aspirate(20, dest.top())\n m300.drop_tip(park_loc)\n ctx.comment('\\n\\n~~~~~~~~~~INCUBATING WITH ELUTION SOLUTION~~~~~~~~~~~\\n')\n if TEST_MODE:\n ctx.delay(seconds=elution_time)\n else:\n ctx.delay(minutes=elution_time)\n\n # Mag deck 2 engage\n magdeck_2.engage(height_from_base=mag_height)\n ctx.comment('\\n\\n~~~~~~~~~~~~SEPARATING BEADS~~~~~~~~~~~~~\\n')\n if TEST_MODE:\n ctx.delay(seconds=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n # move elution solution to new, final plate\n ctx.comment('\\n\\n~~~~~~~~~~~~MOVING ELUTIONS TO SLOT 3~~~~~~~~~~~~~\\n')\n for src, dest, park_loc in zip(sample_dest_1, sample_dest_2,\n parking_spots_2):\n side = -1 if i % 2 == 0 else 1\n m300.pick_up_tip(park_loc)\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(vol_final_plate,\n src.bottom().move(types.Point(x=side,\n y=0, z=0.2)))\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(m300.current_volume, dest)\n m300.aspirate(20, dest) # suck in droplets before drop_tip\n drop_tip(m300)\n\n else:\n # single purification\n # bead addition\n ctx.comment('\\n\\n~~~~~~~~~~~~~~BEAD ADDITION~~~~~~~~~~~~~~~\\n')\n for i, dest in enumerate(sample_loc_1):\n if vol_bead_add_1 > 15:\n pip = m300\n speed_mod = 2.5\n else:\n pip = m20\n speed_mod = 2\n pick_up(pip)\n pip.flow_rate.aspirate *= flow_mod\n pip.flow_rate.dispense *= flow_mod\n if i == 0:\n bead_mixing(bead_well, pip, 20, flow_mod, flow_mod, reps=5)\n pip.aspirate(5, bead_well.top())\n pip.aspirate(vol_bead_add_1, bead_well)\n # pip.move_to(dest.top())\n pip.dispense(pip.current_volume, dest)\n pip.flow_rate.aspirate /= flow_mod\n pip.flow_rate.dispense /= flow_mod\n bead_mixing(dest, pip, vol_bead_add_1, speed_mod,\n speed_mod, reps=5)\n pip.aspirate(5, dest.top())\n drop_tip(pip)\n\n # 5 Minute Incubation\n ctx.comment('\\n\\n~~~~~~~~~~~~~~INCUBATING BEADS~~~~~~~~~~~~~~~\\n')\n if TEST_MODE:\n ctx.delay(seconds=incubation_delay_time)\n else:\n ctx.delay(minutes=incubation_delay_time)\n\n # Magnet engage\n ctx.comment('\\n\\n~~~~~~~~~~~~~~SEPARATING BEADS~~~~~~~~~~~~~~~\\n')\n magdeck_1.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(seconds=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n # Move supernatant to trash\n ctx.comment('\\n\\n~~~~~~~~~~~~REMOVING SUPERNATANT~~~~~~~~~~~~~\\n')\n for src in sample_loc_1:\n side = -1 if i % 2 == 0 else 1\n pick_up(m300)\n m300.aspirate(10, src.top()) # extra air for full liquid dispense\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(vol_trans,\n src.bottom().move(types.Point(x=side,\n y=0, z=0.2)))\n m300.aspirate(10, src.top())\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(10, waste)\n m300.dispense(m300.current_volume, dest)\n m300.aspirate(20, dest.top()) # suck in droplets before drop_tip\n drop_tip(m300)\n\n # EtOH Wash 1\n ctx.comment('\\n\\n~~~~~~~~~~~~ETHANOL WASH 1~~~~~~~~~~~~~\\n')\n for i, (dest, park_loc) in enumerate(zip(sample_loc_1,\n parking_spots)):\n pick_up(m300)\n m300.aspirate(200, etoh_1_wells[i//6])\n m300.dispense(200, dest.top(-1))\n m300.drop_tip(park_loc)\n\n # Mag 2 Engage\n ctx.comment('\\n\\n~~~~~~~~~~~~SEPARATING BEADS~~~~~~~~~~~~~\\n')\n magdeck_1.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(seconds=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n # Remove EtOH wash 1\n ctx.comment('\\n\\n~~~~~~~~~~~~REMOVING ETHANOL~~~~~~~~~~~~~\\n')\n for src, park_loc in zip(sample_loc_1, parking_spots):\n side = -1 if i % 2 == 0 else 1\n m300.pick_up_tip(park_loc)\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(200,\n src.bottom().move(types.Point(x=side,\n y=0, z=0.2)))\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(200, waste)\n m300.aspirate(20, waste) # suck in droplets before drop_tip\n m300.drop_tip(park_loc)\n\n magdeck_1.disengage()\n\n # EtOH wash 2\n ctx.comment('\\n\\n~~~~~~~~~~~~ETHANOL WASH 2~~~~~~~~~~~~~\\n')\n for i, (dest, park_loc) in enumerate(zip(sample_loc_1,\n parking_spots)):\n m300.pick_up_tip(park_loc)\n m300.aspirate(200, etoh_2_wells[i//6])\n m300.dispense(200, dest.top(-1))\n m300.drop_tip(park_loc)\n\n ctx.comment('\\n\\n~~~~~~~~~~~~SEPARATING BEADS~~~~~~~~~~~~~\\n')\n magdeck_1.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(seconds=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n # Remove EtOH wash 2\n ctx.comment('\\n\\n~~~~~~~~~~~~REMOVING ETHANOL~~~~~~~~~~~~~\\n')\n for src, park_loc in zip(sample_loc_1, parking_spots):\n side = -1 if i % 2 == 0 else 1\n m300.pick_up_tip(park_loc)\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(200,\n src.bottom().move(types.Point(x=side,\n y=0, z=0.2)))\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(200, waste)\n m300.aspirate(20, waste) # suck in droplets before drop_tip\n drop_tip(m300)\n\n magdeck_1.disengage()\n # Air dry\n ctx.comment('\\n\\n~~~~~~~~~~~~AIR DRYING BEADS~~~~~~~~~~~~~\\n')\n if TEST_MODE:\n ctx.delay(seconds=air_dry_time)\n else:\n ctx.delay(minutes=air_dry_time)\n\n # move elution solution to new, final plate\n ctx.comment('\\n\\n~~~~~~~~~~~~MOVING ELUTIONS TO SLOT 3~~~~~~~~~~~~~\\n')\n for src, dest, park_loc in zip(sample_loc_1, sample_dest_2,\n parking_spots_2):\n side = -1 if i % 2 == 0 else 1\n m300.pick_up_tip(park_loc)\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(vol_final_plate,\n src.bottom().move(types.Point(x=side,\n y=0, z=0.2)))\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(m300.current_volume, dest)\n m300.aspirate(20, dest) # suck in droplets before drop_tip\n drop_tip(m300)\n\n for c in ctx.commands():\n print(c)\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "custom_adapter", - "brandId": [] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 128.21, - "yDimension": 85.85, - "zDimension": 22.05 - }, - "groups": [ - { - "metadata": { - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8", - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9", - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10", - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11", - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - } - ], - "metadata": { - "displayCategory": "wellPlate", - "displayName": "Custom_adapter 96 Well Plate 200 \u00b5L", - "displayVolumeUnits": "\u00b5L", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1" - ], - [ - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2" - ], - [ - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3" - ], - [ - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4" - ], - [ - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5" - ], - [ - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6" - ], - [ - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7" - ], - [ - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8" - ], - [ - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9" - ], - [ - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10" - ], - [ - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11" - ], - [ - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - ], - "parameters": { - "format": "irregular", - "isMagneticModuleCompatible": false, - "isTiprack": false, - "loadName": "customadapter_96_wellplate_200ul", - "quirks": [] - }, - "schemaVersion": 2, - "version": 1, - "wells": { - "A1": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 13.63, - "y": 74.36, - "z": 1.85 - }, - "A10": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 94.63, - "y": 74.36, - "z": 1.85 - }, - "A11": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 103.63, - "y": 74.36, - "z": 1.85 - }, - "A12": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 112.63, - "y": 74.36, - "z": 1.85 - }, - "A2": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 22.63, - "y": 74.36, - "z": 1.85 - }, - "A3": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 31.63, - "y": 74.36, - "z": 1.85 - }, - "A4": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 40.63, - "y": 74.36, - "z": 1.85 - }, - "A5": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 49.63, - "y": 74.36, - "z": 1.85 - }, - "A6": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 58.63, - "y": 74.36, - "z": 1.85 - }, - "A7": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 67.63, - "y": 74.36, - "z": 1.85 - }, - "A8": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 76.63, - "y": 74.36, - "z": 1.85 - }, - "A9": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 85.63, - "y": 74.36, - "z": 1.85 - }, - "B1": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 13.63, - "y": 65.36, - "z": 1.85 - }, - "B10": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 94.63, - "y": 65.36, - "z": 1.85 - }, - "B11": { - "depth": 20.2, - 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"diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 49.63, - "y": 11.36, - "z": 1.85 - }, - "H6": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 58.63, - "y": 11.36, - "z": 1.85 - }, - "H7": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 67.63, - "y": 11.36, - "z": 1.85 - }, - "H8": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 76.63, - "y": 11.36, - "z": 1.85 - }, - "H9": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 85.63, - "y": 11.36, - "z": 1.85 - } - } - } - ], - "fields": [ - { - "default": 96, - "label": "Number of Samples, 1-96", - "name": "num_samples", - "type": "int" - }, - { - "default": 50, - "label": "Initial Sample Volume (uL)", - "name": "vol_start", - "type": "int" - }, - { - "default": 0.6, - "label": "Bead Ratio 1", - "name": "bead_ratio_1", - "type": "float" - }, - { - "default": 0.8, - "label": "Bead Ratio 2", - "name": "bead_ratio_2", - "type": "float" - }, - { - "default": 75, - "label": "Transfer Volume Post-Bead Addition (uL)", - "name": "vol_trans", - "type": "int" - }, - { - "default": 10, - "label": "Bead Air Dry Time (Minutes)", - "name": "air_dry_time", - "type": "int" - }, - { - "default": 5, - "label": "Bead Incubation Time (Minutes)", - "name": "incubation_delay_time", - "type": "int" - }, - { - "default": 5, - "label": "Bead Separation Time (Minutes)", - "name": "bead_delay_time", - "type": "int" - }, - { - "default": 50, - "label": "Elution Solution Volume (uL)", - "name": "elution_vol", - "type": "int" - }, - { - "default": 10, - "label": "Elution Time (Minutes)", - "name": "elution_time", - "type": "int" - }, - { - "default": 50, - "label": "Final Plate Volume", - "name": "vol_final_plate", - "type": "int" - }, - { - "label": "Flash Robot on Pause", - "name": "flash", - "options": [ - { - "label": "yes", - "value": true - }, - { - "label": "no", - "value": false - } - ], - "type": "dropDown" - }, - { - "label": "P300 Multi Channel Pipette Mount", - "name": "p300_mount", - "options": [ - { - "label": "Left", - "value": "left" - }, - { - "label": "Right", - "value": "right" - } - ], - "type": "dropDown" - }, - { - "label": "Size Selection or Single Purification?", - "name": "size_select", - "options": [ - { - "label": "Size Selection", - "value": false - }, - { - "label": "Single Purification", - "value": false - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p300_multi_gen2" - }, - { - "mount": "right", - "name": "p20_multi_gen2" - } - ], - "labware": [ - { - "name": "20\u00b5l filtertiprack on 1", - "share": false, - "slot": "1", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "200\u00b5l filtertiprack on 2", - "share": false, - "slot": "2", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Custom_adapter 96 Well Plate 200 \u00b5L on 3", - "share": false, - "slot": "3", - "type": "customadapter_96_wellplate_200ul" - }, - { - "name": "Liquid Waste on 4", - "share": false, - "slot": "4", - "type": "nest_1_reservoir_195ml" - }, - { - "name": "reagent reservoir 1 on 5", - "share": false, - "slot": "5", - "type": "nest_12_reservoir_15ml" - }, - { - "name": "sample plate on Magnetic Module GEN2 on 7", - "share": false, - "slot": "7", - "type": "customadapter_96_wellplate_200ul" - }, - { - "name": "20\u00b5l filtertiprack on 8", - "share": false, - "slot": "8", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "200\u00b5l filtertiprack on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "20\u00b5l filtertiprack on 10", - "share": false, - "slot": "10", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "200\u00b5l filtertiprack on 11", - "share": false, - "slot": "11", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Opentrons ", - "protocolName": "SPRI Bead Purification, Size Selection" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/979d28-pcr/normalization.ot2.apiv2.py.json b/protoBuilds/979d28-pcr/normalization.ot2.apiv2.py.json deleted file mode 100644 index 19b68005e..000000000 --- a/protoBuilds/979d28-pcr/normalization.ot2.apiv2.py.json +++ /dev/null @@ -1,2449 +0,0 @@ -{ - "content": "import math\nfrom opentrons.types import Point\n\nmetadata = {\n 'protocolName': 'qPCR Prep',\n 'author': 'Opentrons ',\n 'apiLevel': '2.12'\n}\n\ndilution_factor = 10.0\ndilution_total_volume = 50.0\n\n\ndef run(ctx):\n\n num_samples, vol_mm, vol_dna, lw_384 = get_values( # noqa: F821\n 'num_samples', 'vol_mm', 'vol_dna', 'lw_384')\n\n source_plate = ctx.load_labware('vwr_96_aluminumblock_200ul', '11',\n 'source cDNA plate')\n dil_plate = ctx.load_labware('vwr_96_aluminumblock_200ul', '8',\n 'dilution plate')\n res = ctx.load_labware('nest_12_reservoir_15ml', '2')\n tips20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', slot)\n for slot in ['7']]\n tips200 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)\n for slot in ['10']]\n plate384 = ctx.load_labware(lw_384, '5', '384-wellplate')\n\n water = res.wells()[0]\n mm = res.wells()[1]\n\n m20 = ctx.load_instrument('p20_multi_gen2', 'left', tip_racks=tips20)\n m300 = ctx.load_instrument('p300_multi_gen2', 'right', tip_racks=tips200)\n\n num_cols = math.ceil(num_samples/8)\n sources = source_plate.rows()[0][:num_cols]\n dil_locs = dil_plate.rows()[0][:num_cols]\n\n dest_sets_384 = [\n row[i*3:(i+1)*3]\n for row in plate384.rows()[:2] for i in range(8)][:num_cols+1]\n all_dests_384 = [well for set in dest_sets_384 for well in set]\n\n # add mastermix\n m20.pick_up_tip()\n for dest in all_dests_384:\n m20.aspirate(vol_mm, mm)\n m20.dispense(vol_mm, dest)\n m20.move_to(dest.bottom().move(Point(x=-1, z=5)))\n m20.drop_tip()\n\n # dilute and transfer to 384-well plate\n water_vol = dilution_total_volume*(dilution_factor-1)/dilution_factor\n vol_dna_dilution = dilution_total_volume/dilution_factor\n m300.pick_up_tip()\n for dest in dil_locs:\n m300.aspirate(water_vol, water)\n m300.dispense(water_vol, dest.bottom(1))\n m300.move_to(dest.bottom().move(Point(x=-2, z=5)))\n m300.drop_tip()\n\n for source, dest, dest_set in zip(sources, dil_locs,\n dest_sets_384[:num_cols]):\n if not m20.has_tip:\n m20.pick_up_tip()\n m20.aspirate(vol_dna_dilution, source)\n m20.dispense(vol_dna_dilution, dest)\n m20.mix(5, 10, dest)\n for final_well in dest_set:\n m20.aspirate(vol_dna, dest)\n m20.move_to(dest.bottom().move(Point(x=-1, z=5)))\n m20.dispense(vol_dna, final_well)\n m20.mix(5, 10, final_well)\n m20.move_to(final_well.bottom().move(Point(x=-1, z=5)))\n m20.drop_tip()\n\n # add blank\n for dest in dest_sets_384[-1]:\n m20.pick_up_tip()\n m20.aspirate(vol_dna, water)\n m20.dispense(vol_dna_dilution, dest)\n m20.mix(5, 10, dest)\n m20.move_to(dest.bottom().move(Point(x=-1, z=5)))\n m20.drop_tip()\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "NEST Bioshake", - "brandId": [] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.86, - "yDimension": 85.8, - "zDimension": 104.13 - }, - "groups": [ - { - "metadata": { - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "A8", - "B8", - "C8", 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(1-96)", - "name": "num_samples", - "type": "int" - }, - { - "default": 18.0, - "label": "volume of mastermix (in ul)", - "name": "vol_mm", - "type": "float" - }, - { - "default": 2.0, - "label": "volume of diluted cDNA (in ul)", - "name": "vol_dna", - "type": "float" - }, - { - "label": "384-wellplate type", - "name": "lw_384", - "options": [ - { - "label": "Applied Biosystems MicroAmp 384 Well Plate 40 \u00b5L", - "value": "corning_384_wellplate_112ul_flat" - }, - { - "label": "Axygen 384 Well Plate", - "value": "axygen_384_wellplate_50ul" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p20_multi_gen2" - }, - { - "mount": "right", - "name": "p300_multi_gen2" - } - ], - "labware": [ - { - "name": "NEST 12 Well Reservoir 15 mL on 2", - "share": false, - "slot": "2", - "type": "nest_12_reservoir_15ml" - }, - { - "name": "384-wellplate on 5", - "share": false, - "slot": "5", - "type": "corning_384_wellplate_112ul_flat" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 7", - "share": false, - "slot": "7", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "dilution plate on 8", - "share": false, - "slot": "8", - "type": "vwr_96_aluminumblock_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 10", - "share": false, - "slot": "10", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "source cDNA plate on 11", - "share": false, - "slot": "11", - "type": "vwr_96_aluminumblock_200ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.12", - "author": "Opentrons ", - "protocolName": "qPCR Prep" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/bc-rnadvance-viral-feat/beckman_viral.ot2.apiv2.py.json b/protoBuilds/bc-rnadvance-viral-feat/beckman_viral.ot2.apiv2.py.json index a596dd860..fe17d7754 100644 --- a/protoBuilds/bc-rnadvance-viral-feat/beckman_viral.ot2.apiv2.py.json +++ b/protoBuilds/bc-rnadvance-viral-feat/beckman_viral.ot2.apiv2.py.json @@ -106,5 +106,18 @@ "author": "Opentrons ", "protocolName": "Beckman Coulter RNAdvance Viral RNA Isolation" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 6 lw deepwell plate on Magnetic Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw elution plate on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/bc-rnadvance-viral/beckman_viral.ot2.apiv2.py.json b/protoBuilds/bc-rnadvance-viral/beckman_viral.ot2.apiv2.py.json index a596dd860..fe17d7754 100644 --- a/protoBuilds/bc-rnadvance-viral/beckman_viral.ot2.apiv2.py.json +++ b/protoBuilds/bc-rnadvance-viral/beckman_viral.ot2.apiv2.py.json @@ -106,5 +106,18 @@ "author": "Opentrons ", "protocolName": "Beckman Coulter RNAdvance Viral RNA Isolation" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 6 lw deepwell plate on Magnetic Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw elution plate on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/bpg-rna-extraction/bpg-rna-extraction.ot2.apiv2.py.json b/protoBuilds/bpg-rna-extraction/bpg-rna-extraction.ot2.apiv2.py.json index 34c821bf1..0276b5bdb 100644 --- a/protoBuilds/bpg-rna-extraction/bpg-rna-extraction.ot2.apiv2.py.json +++ b/protoBuilds/bpg-rna-extraction/bpg-rna-extraction.ot2.apiv2.py.json @@ -1216,7 +1216,7 @@ "type": "opentrons_96_tiprack_20ul" }, { - "name": "NEST 1mL Deep Well Plate on Magnetic Module GEN1 on 4", + "name": "NEST 1mL Deep Well Plate on Magnetic Module on 4", "share": false, "slot": "4", "type": "nest_96_wellplate_1000ul" @@ -1248,7 +1248,7 @@ }, "modules": [ { - "name": "MagneticModuleContext at Magnetic Module GEN1 on 4 lw NEST 1mL Deep Well Plate on Magnetic Module GEN1 on 4", + "name": "MagneticModuleContext at Magnetic Module on 4 lw NEST 1mL Deep Well Plate on Magnetic Module on 4", "share": false, "slot": "4", "type": "magdeck" diff --git a/protoBuilds/complete-pcr/complete_pcr.ot2.apiv2.py.json b/protoBuilds/complete-pcr/complete_pcr.ot2.apiv2.py.json index ead4d5836..5d0986102 100644 --- a/protoBuilds/complete-pcr/complete_pcr.ot2.apiv2.py.json +++ b/protoBuilds/complete-pcr/complete_pcr.ot2.apiv2.py.json @@ -338,5 +338,12 @@ "protocolName": "Complete PCR Workflow with Thermocycler", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw thermocycler plate on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/covid19-rna-extraction/extraction.ot2.apiv2.py.json b/protoBuilds/covid19-rna-extraction/extraction.ot2.apiv2.py.json index 1ca276603..6ced65163 100644 --- a/protoBuilds/covid19-rna-extraction/extraction.ot2.apiv2.py.json +++ b/protoBuilds/covid19-rna-extraction/extraction.ot2.apiv2.py.json @@ -235,5 +235,18 @@ "author": "Opentrons ", "protocolName": "COVID-19 Station B RNA Extraction" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw deepwell plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw elution plate on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/demo/test_drive.ot2.apiv2.py.json b/protoBuilds/demo/test_drive.ot2.apiv2.py.json index d99b3f2ff..c5b6c97ff 100644 --- a/protoBuilds/demo/test_drive.ot2.apiv2.py.json +++ b/protoBuilds/demo/test_drive.ot2.apiv2.py.json @@ -144,5 +144,12 @@ "protocolName": "OT-2 Demo", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 7 lw None", + "share": false, + "slot": "7", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/gna_octea/gna_octea.ot2.apiv2.py.json b/protoBuilds/gna_octea/gna_octea.ot2.apiv2.py.json index fab6b1eb0..c9e7de074 100644 --- a/protoBuilds/gna_octea/gna_octea.ot2.apiv2.py.json +++ b/protoBuilds/gna_octea/gna_octea.ot2.apiv2.py.json @@ -337,5 +337,18 @@ "protocolName": "Automated Sample Prep for GNA Octea", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 6 lw Opentrons 96 Well Aluminum Block with Bio-Rad Well Plate 200 \u00b5L on Temperature Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/gna_octea_v2/gna_octea_v2.ot2.apiv2.py.json b/protoBuilds/gna_octea_v2/gna_octea_v2.ot2.apiv2.py.json index 2a2f14d2a..e267441bc 100644 --- a/protoBuilds/gna_octea_v2/gna_octea_v2.ot2.apiv2.py.json +++ b/protoBuilds/gna_octea_v2/gna_octea_v2.ot2.apiv2.py.json @@ -369,5 +369,18 @@ "protocolName": "Automated Sample Prep for GNA Octea [v2]", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 7 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 7", + "share": false, + "slot": "7", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 4 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Snapcap on Temperature Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/illumina-nextera-XT-library-prep-part2/nexteraXT_dna_library_prep_part2.ot2.apiv2.py.json b/protoBuilds/illumina-nextera-XT-library-prep-part2/nexteraXT_dna_library_prep_part2.ot2.apiv2.py.json index 44fdc1447..3ff332f9e 100644 --- a/protoBuilds/illumina-nextera-XT-library-prep-part2/nexteraXT_dna_library_prep_part2.ot2.apiv2.py.json +++ b/protoBuilds/illumina-nextera-XT-library-prep-part2/nexteraXT_dna_library_prep_part2.ot2.apiv2.py.json @@ -116,7 +116,7 @@ "type": "usascientific_12_reservoir_22ml" }, { - "name": "Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN1 on 4", + "name": "Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module on 4", "share": false, "slot": "4", "type": "biorad_96_wellplate_200ul_pcr" @@ -158,5 +158,12 @@ "protocolName": "Illumina Nextera XT NGS Prep 2: Clean-Up Libraries", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 4 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/illumina-nextera-XT-library-prep-part3/nexteraXT_dna_library_prep_part3.ot2.apiv2.py.json b/protoBuilds/illumina-nextera-XT-library-prep-part3/nexteraXT_dna_library_prep_part3.ot2.apiv2.py.json index ce0e8c8fe..a47243d29 100644 --- a/protoBuilds/illumina-nextera-XT-library-prep-part3/nexteraXT_dna_library_prep_part3.ot2.apiv2.py.json +++ b/protoBuilds/illumina-nextera-XT-library-prep-part3/nexteraXT_dna_library_prep_part3.ot2.apiv2.py.json @@ -86,7 +86,7 @@ "type": "usascientific_12_reservoir_22ml" }, { - "name": "Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN1 on 4", + "name": "Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module on 4", "share": false, "slot": "4", "type": "biorad_96_wellplate_200ul_pcr" @@ -128,5 +128,12 @@ "protocolName": "Illumina Nextera XT NGS Prep 3: Normalize Libraries", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 4 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/nextera-flex-library-prep-amplify-tagmented-dna/nextera_flex_amplify_tagmented_dna.ot2.apiv2.py.json b/protoBuilds/nextera-flex-library-prep-amplify-tagmented-dna/nextera_flex_amplify_tagmented_dna.ot2.apiv2.py.json index 5a21453ed..f0d050875 100644 --- a/protoBuilds/nextera-flex-library-prep-amplify-tagmented-dna/nextera_flex_amplify_tagmented_dna.ot2.apiv2.py.json +++ b/protoBuilds/nextera-flex-library-prep-amplify-tagmented-dna/nextera_flex_amplify_tagmented_dna.ot2.apiv2.py.json @@ -66,13 +66,13 @@ ], "labware": [ { - "name": "1 on Magnetic Module GEN1 on 1", + "name": "1 on Magnetic Module on 1", "share": false, "slot": "1", "type": "biorad_96_wellplate_200ul_pcr" }, { - "name": "4 on Temperature Module GEN1 on 4", + "name": "4 on Temperature Module on 4", "share": false, "slot": "4", "type": "opentrons_24_aluminumblock_nest_1.5ml_snapcap" @@ -120,5 +120,18 @@ "protocolName": "Nextera DNA Flex NGS Library Prep: Amplify Tagmented DNA", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 1 lw 1 on Magnetic Module on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module on 4 lw 4 on Temperature Module on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/nextera-flex-library-prep-cleanup-libraries/nextera_flex_cleanup_libraries.ot2.apiv2.py.json b/protoBuilds/nextera-flex-library-prep-cleanup-libraries/nextera_flex_cleanup_libraries.ot2.apiv2.py.json index 56cd45900..678b2be0f 100644 --- a/protoBuilds/nextera-flex-library-prep-cleanup-libraries/nextera_flex_cleanup_libraries.ot2.apiv2.py.json +++ b/protoBuilds/nextera-flex-library-prep-cleanup-libraries/nextera_flex_cleanup_libraries.ot2.apiv2.py.json @@ -81,7 +81,7 @@ ], "labware": [ { - "name": "Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN1 on 1", + "name": "Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module on 1", "share": false, "slot": "1", "type": "biorad_96_wellplate_200ul_pcr" @@ -159,5 +159,12 @@ "protocolName": "Nextera DNA Flex NGS Library Prep: Cleanup Libraries", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 1 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/nextera-flex-library-prep-post-tag-cleanup/nextera_flex_post_tag_cleanup.ot2.apiv2.py.json b/protoBuilds/nextera-flex-library-prep-post-tag-cleanup/nextera_flex_post_tag_cleanup.ot2.apiv2.py.json index 515d2edd1..2090a10f5 100644 --- a/protoBuilds/nextera-flex-library-prep-post-tag-cleanup/nextera_flex_post_tag_cleanup.ot2.apiv2.py.json +++ b/protoBuilds/nextera-flex-library-prep-post-tag-cleanup/nextera_flex_post_tag_cleanup.ot2.apiv2.py.json @@ -47,7 +47,7 @@ ], "labware": [ { - "name": "1 on Magnetic Module GEN1 on 1", + "name": "1 on Magnetic Module on 1", "share": false, "slot": "1", "type": "biorad_96_wellplate_200ul_pcr" @@ -107,5 +107,12 @@ "protocolName": "Nextera DNA Flex NGS Library Prep: Post Tagmentation Cleanup", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 1 lw 1 on Magnetic Module on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/nucleic_acid_purification_with_magnetic_beads/dna_purification.ot2.apiv2.py.json b/protoBuilds/nucleic_acid_purification_with_magnetic_beads/dna_purification.ot2.apiv2.py.json index 015ea4072..f82e7b161 100644 --- a/protoBuilds/nucleic_acid_purification_with_magnetic_beads/dna_purification.ot2.apiv2.py.json +++ b/protoBuilds/nucleic_acid_purification_with_magnetic_beads/dna_purification.ot2.apiv2.py.json @@ -180,5 +180,12 @@ "protocolName": "DNA Purification", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 1 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN1 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/omega-biotek-xpress/omega-biotek-xpress.ot2.apiv2.py.json b/protoBuilds/omega-biotek-xpress/omega-biotek-xpress.ot2.apiv2.py.json index e270645f1..3d8d9af89 100644 --- a/protoBuilds/omega-biotek-xpress/omega-biotek-xpress.ot2.apiv2.py.json +++ b/protoBuilds/omega-biotek-xpress/omega-biotek-xpress.ot2.apiv2.py.json @@ -179,5 +179,18 @@ "author": "Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11' # CHECK IF YOUR API LEVEL HERE IS UP TO DATE\n # IN SECTION 5.2 OF THE APIV2 \"VERSIONING\"\n}\n\n\ndef run(ctx):\n \"\"\"PROTOCOL.\"\"\"\n [\n num_samples, m20_mount\n ] = get_values( # noqa: F821 (<--- DO NOT REMOVE!)\n \"num_samples\", \"m20_mount\")\n\n # define all custom variables above here with descriptions:\n\n num_cols = math.ceil(num_samples/8)\n m20_speed_mod = 4\n airgap_library = 5\n # load modules\n mag_module = ctx.load_module('magnetic module gen2', '1')\n\n # load labware\n sample_plate = mag_module.load_labware('nest_96_wellplate'\n '_100ul_pcr_full_skirt')\n reagent_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n '2')\n # load tipracks\n tiprack20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul',\n str(slot))\n for slot in [3, 5, 6]]\n\n # load instrument\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=tiprack20)\n\n # pipette functions # INCLUDE ANY BINDING TO CLASS\n\n # helper functions\n\n # reagents\n library_mix = reagent_plate.rows()[0][0]\n pcr_forward = reagent_plate.rows()[0][1]\n pcr_reverse = reagent_plate.rows()[0][2]\n # plate, tube rack maps\n sample_dest = sample_plate.rows()[0][:num_cols]\n # protocol\n\n # add library mix, 5 uL\n for dest in sample_dest:\n m20.flow_rate.aspirate /= m20_speed_mod\n m20.flow_rate.dispense /= m20_speed_mod\n m20.pick_up_tip()\n m20.aspirate(5, library_mix)\n m20.move_to(library_mix.top(-2))\n ctx.delay(seconds=2)\n m20.touch_tip(v_offset=-2)\n m20.move_to(library_mix.top(-2))\n m20.aspirate(airgap_library, library_mix.top())\n m20.dispense(airgap_library, dest.top())\n m20.dispense(5, dest)\n m20.drop_tip()\n m20.flow_rate.aspirate *= m20_speed_mod\n m20.flow_rate.dispense *= m20_speed_mod\n # add forward, reverse primers, 2 uL each\n for reagent_source in [pcr_forward, pcr_reverse]:\n for dest in sample_dest:\n m20.flow_rate.aspirate /= m20_speed_mod\n m20.flow_rate.dispense /= m20_speed_mod\n m20.pick_up_tip()\n m20.aspirate(2, reagent_source)\n m20.move_to(reagent_source.top(-2))\n ctx.delay(seconds=2)\n m20.touch_tip(v_offset=-2)\n m20.move_to(reagent_source.top(-2))\n m20.aspirate(airgap_library, reagent_source.top())\n m20.dispense(airgap_library, dest.top())\n m20.dispense(5, dest)\n m20.drop_tip()\n m20.flow_rate.aspirate *= m20_speed_mod\n m20.flow_rate.dispense *= m20_speed_mod\n\n for c in ctx.commands():\n print(c)\n", - "custom_labware_defs": [], - "fields": [ - { - "default": 96, - "label": "Number of Samples", - "name": "num_samples", - "type": "int" - }, - { - "label": "P20 Multi GEN2 mount", - "name": "m20_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "right", - "name": "p20_multi_gen2" - } - ], - "labware": [ - { - "name": "NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 1", - "share": false, - "slot": "1", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on 2", - "share": false, - "slot": "2", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 3", - "share": false, - "slot": "3", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Opentrons ", - "protocolName": "rhAmpSeq Library Prep Part 1 - PCR 1", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/onsite-ganda-2/part2.ot2.apiv2.py.json b/protoBuilds/onsite-ganda-2/part2.ot2.apiv2.py.json deleted file mode 100644 index 45d3a7267..000000000 --- a/protoBuilds/onsite-ganda-2/part2.ot2.apiv2.py.json +++ /dev/null @@ -1,124 +0,0 @@ -{ - "content": "\"\"\"OPENTRONS.\"\"\"\nimport math\nfrom opentrons import types\n\nmetadata = {\n 'protocolName': 'rhAmpSeq Library Prep Part 1 - PCR 1',\n 'author': 'Opentrons ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11' # CHECK IF YOUR API LEVEL HERE IS UP TO DATE\n # IN SECTION 5.2 OF THE APIV2 \"VERSIONING\"\n}\n\n\ndef run(ctx):\n \"\"\"PROTOCOL.\"\"\"\n [\n num_samples, m20_mount\n ] = get_values( # noqa: F821 (<--- DO NOT REMOVE!)\n \"num_samples\", \"m20_mount\")\n\n # define all custom variables above here with descriptions:\n if m20_mount == 'right':\n m300_mount = 'left'\n else:\n m300_mount = 'right'\n num_cols = math.ceil(num_samples/8)\n num_etoh_wells = math.ceil((0.4*num_samples)/15)\n m20_speed_mod = 4\n airgap_library = 5\n etoh_res_vol = 15000\n # load modules\n mag_module = ctx.load_module('magnetic module gen2', '1')\n\n # load labware\n sample_plate = mag_module.load_labware('nest_96_wellplate'\n '_100ul_pcr_full_skirt')\n reagent_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n '2')\n reagent_resv = ctx.load_labware('nest_12_reservoir_15ml', '3')\n # load tipracks\n tiprack20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul',\n str(slot))\n for slot in [4, 5]]\n tiprack300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul',\n str(slot))\n for slot in [6, 7, 8, 9, 10, 11]]\n # load instrument\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=tiprack20)\n m300 = ctx.load_instrument('p300_multi_gen2', m300_mount,\n tip_racks=tiprack300)\n # reagents\n sample_plate_dest = sample_plate.rows()[0][:num_cols]\n library_mix = reagent_plate.rows()[0][0]\n pcr_forward = reagent_plate.rows()[0][1]\n pcr_reverse = reagent_plate.rows()[0][2]\n beads_1 = reagent_plate.rows()[0][3]\n beads_2 = reagent_plate.rows()[0][4]\n idte = reagent_plate.rows()[0][5]\n # well volume tracking is better solution for this\n etoh_1 = reagent_resv.wells()[0]\n etoh_2 = reagent_resv.wells()[1]\n etoh_3 = reagent_resv.wells()[2]\n etoh_4 = reagent_resv.wells()[3]\n liquid_trash_1 = reagent_resv.wells()[8]\n liquid_trash_2 = reagent_resv.wells()[9]\n liquid_trash_3 = reagent_resv.wells()[10]\n liquid_trash_4 = reagent_resv.wells()[11]\n\n etoh_total = [etoh_1, etoh_2, etoh_3, etoh_4]\n trash_total = [liquid_trash_1, liquid_trash_2, liquid_trash_3,\n liquid_trash_4]\n # Volume and Height Tracking\n # class VolHeightTracker:\n # def __init__(self, labware, well_vol, start=0, end=12,\n # min_height=1, comp_coeff=0.9, msg='Reset Labware'):\n # try:\n # self.labware_wells = dict.fromkeys(\n # labware.wells()[start:end], 0)\n # except Exception:\n # self.labware_wells = dict.fromkeys(\n # labware, 0)\n # self.labware_wells_backup = self.labware_wells.copy()\n # self.well_vol = well_vol\n # self.start = start\n # self.end = end\n # self.min_height = min_height\n # self.comp_coeff = comp_coeff\n # self.width = labware.wells()[0].xDimension\n # self.length = labware.wells()[0].yDimension\n # self.area = self.width*self.length\n # self.msg = msg\n #\n # def tracker(self, vol):\n # '''tracker() will track how much liquid\n # was used up per well. If the volume of\n # a given well is greater than self.well_vol\n # it will remove it from the dictionary and iterate\n # to the next well which will act as the reservoir.'''\n # well = next(iter(self.labware_wells))\n # if self.labware_wells[well] + vol >= self.well_vol:\n # del self.labware_wells[well]\n # if len(self.labware_wells) < 1:\n # ctx.pause(self.msg)\n # self.labware_wells = self.labware_wells_backup.copy()\n # well = next(iter(self.labware_wells))\n # dh = (self.well_vol - self.labware_wells[well]) / self.area \\\n # * self.comp_coeff\n # height = self.min_height if dh < 1 else round(dh, 2)\n # self.labware_wells[well] = self.labware_wells[well] + vol\n # ctx.comment(f'''{int(self.labware_wells[well])} uL of liquid\n # used from {well}''')\n # ctx.comment(f'Current Liquid Height of {well}: {height}mm')\n # return well.bottom(height)\n #\n # def trash_tracker(self, vol):\n # '''WIP trash_tracker() will track how much liquid\n # was added per well. If the volume of\n # a given well is greater than self.well_vol\n # it will remove it from the dictionary and iterate\n # to the next well which will act as the new trash.'''\n # cutoff_vol = self.well_vol*0.75\n # well = next(iter(self.labware_wells))\n # if self.labware_wells[well] + vol >= cutoff_vol:\n # del self.labware_wells[well]\n # if len(self.labware_wells) < 1:\n # ctx.pause(self.msg)\n # self.labware_wells = self.labware_wells_backup.copy()\n # well = next(iter(self.labware_wells))\n # dh = (self.well_vol - self.labware_wells[well]) / self.area \\\n # * self.comp_coeff\n # height = self.min_height if dh < 1 else round(dh, 2)\n # self.labware_wells[well] = self.labware_wells[well] + vol\n # ctx.comment(f'''{int(self.labware_wells[well])} uL of liquid\n # used from {well}''')\n # ctx.comment(f'Current Liquid Height of {well}: {height}mm')\n # return well.bottom(height)\n\n # etohTrack = VolHeightTracker(etoh_total, well_vol=etoh_res_vol, start=0,\n # end=96)\n etoh_volumes = dict.fromkeys(reagent_resv.wells()[:4], 0)\n supernatant_headspeed_modulator = 5\n\n def liquid_tracker(vol):\n '''liquid_tracker() will track how much liquid\n was used up per well. If the volume of\n a given well is greater than 'liquid'_res_vol\n it will remove it from the dictionary and iterate\n to the next well which will act as the reservoir.'''\n well = next(iter(etoh_volumes))\n if etoh_volumes[well] > etoh_res_vol:\n del etoh_volumes[well]\n well = next(iter(etoh_volumes))\n etoh_volumes[well] = etoh_volumes[well] + vol\n ctx.comment(f'{int(etoh_volumes[well])} uL of water used from {well}')\n return well\n\n def bead_mixing(well, pip, mvol, reps=8):\n\n \"\"\"\n 'bead_mixing' will mix liquid that contains beads. This will be done by\n aspirating from the bottom of the well and dispensing from the top as to\n mix the beads with the other liquids as much as possible. Aspiration and\n dispensing will also be reversed for a short to to ensure maximal mixing.\n param well: The current well that the mixing will occur in.\n param pip: The pipet that is currently attached/ being used.\n param mvol: The volume that is transferred before the mixing steps.\n param reps: The number of mix repetitions that should occur. Note~\n During each mix rep, there are 2 cycles of aspirating from bottom,\n dispensing at the top and 2 cycles of aspirating from middle,\n dispensing at the bottom\n \"\"\"\n center = well.top().move(types.Point(x=0, y=0, z=5))\n aspbot = well.bottom(1)\n asptop = well.bottom(10)\n disbot = well.bottom(3)\n distop = well.top()\n\n vol = mvol * .9\n\n pip.move_to(center)\n for _ in range(reps):\n pip.aspirate(vol, aspbot)\n pip.dispense(vol, distop)\n pip.aspirate(vol, asptop)\n pip.dispense(vol, disbot)\n # PROTOCOL\n etoh_wash_vol = 200\n for dest in sample_plate_dest:\n m300.flow_rate.aspirate /= 4\n m300.flow_rate.dispense /= 4\n m300.pick_up_tip()\n m300.aspirate(30, beads_1)\n m300.dispense(30, dest)\n m300.flow_rate.aspirate *= 2\n m300.flow_rate.dispense *= 2\n bead_mixing(dest, m300, 30, reps=10)\n m300.flow_rate.aspirate *= 2\n m300.flow_rate.dispense *= 2\n m300.drop_tip()\n\n ctx.delay(minutes=10)\n mag_module.engage()\n ctx.delay(minutes=5)\n\n ctx.comment('''discarding supernatant''')\n ctx.max_speeds['Z'] = 50\n ctx.max_speeds['A'] = 50\n num_times = 1\n mag_module.engage()\n ctx.delay(minutes=3)\n for source in sample_plate_dest:\n side = 1 if num_times % 2 == 0 else -1\n m300.pick_up_tip()\n m300.flow_rate.aspirate /= 5\n m300.move_to(source.top())\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(\n 50, source.bottom().move(types.Point(x=side,\n y=0, z=0.5)))\n m300.move_to(source.top())\n m300.flow_rate.aspirate *= 5\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(50, liquid_trash_1)\n m300.drop_tip()\n num_times += 1\n print(side)\n\n # etoh wash needs the multi-source well function to work!\n ctx.comment(\"Ethanol Wash\")\n for _ in range(2):\n for dest in sample_plate_dest:\n m300.pick_up_tip()\n m300.aspirate(200, etoh_1)\n m300.dispense(200, dest)\n m300.drop_tip()\n ctx.delay(minutes=1)\n for source in sample_plate_dest:\n side = 1 if num_times % 2 == 0 else -1\n m300.pick_up_tip()\n m300.flow_rate.aspirate /= 5\n m300.move_to(source.top())\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(\n 50, source.bottom().move(types.Point(x=side,\n y=0, z=0.5)))\n m300.move_to(source.top())\n m300.flow_rate.aspirate *= 5\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(50, liquid_trash_1)\n m300.drop_tip()\n num_times += 1\n print(side)\n\n ctx.delay(minutes=3)\n mag_module.disengage()\n ctx.comment('Adding IDTE')\n for dest in sample_plate_dest:\n m20.pick_up_tip()\n m20.aspirate(15, idte)\n m20.dispense(15, idte)\n m20.drop_tip()\n\n ctx.pause(\"Please vortex and centrifuge sample plate, return to slot 1\")\n\n ctx.delay(minutes=3)\n", - "custom_labware_defs": [], - "fields": [ - { - "default": 96, - "label": "Number of Samples (max 288)", - "name": "num_samples", - "type": "int" - }, - { - "label": "P20 Multi GEN2 mount", - "name": "m20_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - }, - { - "default": 15, - "label": "Overage Percent", - "name": "overage_percent", - "type": "float" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p300_multi_gen2" - }, - { - "mount": "right", - "name": "p20_multi_gen2" - } - ], - "labware": [ - { - "name": "NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 1", - "share": false, - "slot": "1", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on 2", - "share": false, - "slot": "2", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "NEST 12 Well Reservoir 15 mL on 3", - "share": false, - "slot": "3", - "type": "nest_12_reservoir_15ml" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 4", - "share": false, - "slot": "4", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 7", - "share": false, - "slot": "7", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 8", - "share": false, - "slot": "8", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 10", - "share": false, - "slot": "10", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 11", - "share": false, - "slot": "11", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Opentrons ", - "protocolName": "rhAmpSeq Library Prep Part 1 - PCR 1", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/onsite-ganda-3/part3.ot2.apiv2.py.json b/protoBuilds/onsite-ganda-3/part3.ot2.apiv2.py.json deleted file mode 100644 index a275a7ac8..000000000 --- a/protoBuilds/onsite-ganda-3/part3.ot2.apiv2.py.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "content": "\"\"\"OPENTRONS.\"\"\"\nimport math\n\nmetadata = {\n 'protocolName': 'rhAmpSeq Library Prep Part 3 - PCR 2',\n 'author': 'Opentrons ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11' # CHECK IF YOUR API LEVEL HERE IS UP TO DATE\n # IN SECTION 5.2 OF THE APIV2 \"VERSIONING\"\n}\n\n\ndef run(ctx):\n \"\"\"PROTOCOL.\"\"\"\n [\n num_samples, m20_mount\n ] = get_values( # noqa: F821 (<--- DO NOT REMOVE!)\n \"num_samples\", \"m20_mount\")\n\n # define all custom variables above here with descriptions:\n\n num_cols = math.ceil(num_samples/8)\n m20_speed_mod = 4\n airgap_library = 5\n # load modules\n mag_module = ctx.load_module('magnetic module gen2', '1')\n\n # load labware\n sample_plate = mag_module.load_labware('nest_96_wellplate'\n '_100ul_pcr_full_skirt')\n reagent_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n '2')\n # load tipracks\n tiprack20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul',\n str(slot))\n for slot in [3, 5, 6]]\n\n # load instrument\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=tiprack20)\n\n # pipette functions # INCLUDE ANY BINDING TO CLASS\n\n # helper functions\n\n # reagents\n library_mix = reagent_plate.rows()[0][3]\n index_i5 = reagent_plate.rows()[0][4]\n index_i7 = reagent_plate.rows()[0][5]\n # plate, tube rack maps\n sample_dest = sample_plate.rows()[0][:num_cols]\n # protocol\n\n # add library mix, 5 uL\n for dest in sample_dest:\n m20.flow_rate.aspirate /= m20_speed_mod\n m20.flow_rate.dispense /= m20_speed_mod\n m20.pick_up_tip()\n m20.aspirate(5, library_mix)\n m20.move_to(library_mix.top(-2))\n ctx.delay(seconds=2)\n m20.touch_tip(v_offset=-2)\n m20.move_to(library_mix.top(-2))\n m20.aspirate(airgap_library, library_mix.top())\n m20.dispense(airgap_library, dest.top())\n m20.dispense(5, dest)\n m20.drop_tip()\n m20.flow_rate.aspirate *= m20_speed_mod\n m20.flow_rate.dispense *= m20_speed_mod\n # add indexing primers, 2 uL each\n for reagent_source in [index_i5, index_i7]:\n for dest in sample_dest:\n m20.flow_rate.aspirate /= m20_speed_mod\n m20.flow_rate.dispense /= m20_speed_mod\n m20.pick_up_tip()\n m20.aspirate(2, reagent_source)\n m20.move_to(reagent_source.top(-2))\n ctx.delay(seconds=2)\n m20.touch_tip(v_offset=-2)\n m20.move_to(reagent_source.top(-2))\n m20.aspirate(airgap_library, reagent_source.top())\n m20.dispense(airgap_library, dest.top())\n m20.dispense(5, dest)\n m20.drop_tip()\n m20.flow_rate.aspirate *= m20_speed_mod\n m20.flow_rate.dispense *= m20_speed_mod\n\n for c in ctx.commands():\n print(c)\n", - "custom_labware_defs": [], - "fields": [ - { - "default": 96, - "label": "Number of Samples (max 96)", - "name": "num_samples", - "type": "int" - }, - { - "label": "P20 Multi GEN2 mount", - "name": "m20_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "right", - "name": "p20_multi_gen2" - } - ], - "labware": [ - { - "name": "NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 1", - "share": false, - "slot": "1", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on 2", - "share": false, - "slot": "2", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 3", - "share": false, - "slot": "3", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Opentrons ", - "protocolName": "rhAmpSeq Library Prep Part 3 - PCR 2", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/pcr_test_plan/pcr_test_plan.ot2.apiv2.py.json b/protoBuilds/pcr_test_plan/pcr_test_plan.ot2.apiv2.py.json index d6b05f1a9..99390641b 100644 --- a/protoBuilds/pcr_test_plan/pcr_test_plan.ot2.apiv2.py.json +++ b/protoBuilds/pcr_test_plan/pcr_test_plan.ot2.apiv2.py.json @@ -108,5 +108,12 @@ "protocolName": "PCR Prep", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/promega-maxwell/promega-maxwell.ot2.apiv2.py.json b/protoBuilds/promega-maxwell/promega-maxwell.ot2.apiv2.py.json index 52b0cdc48..b7ae7ed57 100644 --- a/protoBuilds/promega-maxwell/promega-maxwell.ot2.apiv2.py.json +++ b/protoBuilds/promega-maxwell/promega-maxwell.ot2.apiv2.py.json @@ -136,5 +136,18 @@ "author": "Nick Diehl", "protocolName": "Promega Maxwell\u00ae HT Viral TNA Kit" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 6 lw deepwell plate on Magnetic Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw elution plate on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/sci-illumina-dna-prep/README.json b/protoBuilds/sci-illumina-dna-prep/README.json deleted file mode 100644 index 34007e21c..000000000 --- a/protoBuilds/sci-illumina-dna-prep/README.json +++ /dev/null @@ -1,44 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "NGS Library Prep": [ - "Illumina DNA Prep" - ] - }, - "deck-setup": "\nInital slot layout:\n1. Magnetic module for the sample plate (Nest 96 well plate full skirt).\n2. Reservoir: NEST 12-well reservoir 15 mL. This is substituted for a NEST 2 mL deep well plate if tip-reuse is on in order to minimize cross-contamination. See Reagent Setup section for information about the location of the reagents\n3. Reagent plate 2: Temperature module with Bio-rad 200 \u00b5L plate on aluminum block. See Reagent Setup section for information about the location of the reagents\n4. 20 \u00b5L filter tiprack\n5. 200 \u00b5L filter tiprack\n6. 200 \u00b5L filter tiprack\n7. Sample plate on Thermocycler module with NEST 96 well plate full skirt 100 \u00b5L\n8. Empty\n9. 200 \u00b5L filter tiprack\n10. Sample plate on Thermocycler module with NEST 96 well plate full (thermocycler uses two slots)\n11. Empty", - "description": "This protocol automates the Illumina DNA prep protocol. Illumina DNA prep offers a fast, integrated workflow for a wide range of applications, from human whole-genome sequencing to amplicons, plasmids, and microbial species\nThe protocol allows you to set the number of samples to 8, 16 or 24 (i.e. 8 samples per column, up to 3 columns). Samples are prepared in the wells as shown in the table and figure below, with 30 \u00b5L of 100 ng:s of sample DNA in each well. See the Illumina DNA Prep protocol for more information about sample input requirements.\n\n\nThe user can choose which steps of the protocol they want to run, or skip - see explanation of parameters below.\nPlate Moving\nThe Protocol requires manually transferring the sample plate between the Thermocycler and Magnet 3 times. It starts on the Thermocycler and needs to be moved to the Magnet for the post-Tagmentation washes, and then moved to the Thermocycler for PCR and then back to the Magnet for the post-PCR cleanup. In the script the two positions are handled as sample_plate_mag and sample_plate_thermo; during calibration use an empty plate of the same labware as the sample plate on the magnet position to allow calibration.\nExplanation of parameters below:\n Number of samples: 8 (column 1), 16 (column 1, 3), or 24 (column 1, 3, 5) samples (see above).\n Do a dry run?: Sets the Use modules? parameter to No (see below). Tips will be returned, incubation steps skipped, and mixes shortened. This parameter is for testing purposes.\n Use modules?: Runs the protocol without module steps (e.g. thermocycle steps such as incubation and PCR cycles, or the steps using the magbetic module). Will be automatically set to Yes if the Do a dry run? parameter is set to Yes\n Tip reuse?: Reuses tips for washing steps so that no tip refill is neccesary during the run. Recommended only for a 24x samples run.\n Use tip offsets?: Whether to use specific offsets for each tip type\n Include tagmentation step in protocol run?: Run the tagmentation step or skip it.\n Run tagmentation incubation on the deck thermocycler?: Run the tagmentation incubation step on the deck thermocycler or on an off-deck external thermocycler.\n Run TSB step?: Run the TSB/adapter ligation step or not\n Run TSB incubation step on the deck thermocycler: Whether to do the incubation on the on-deck thermocycler or off-deck on an external thermocycler\n Run tagmentation wash with TWB step: Run the bead washing steps with TWB\n Run PCR cycle step: Whether to run the PCR amplification step\n Run PCR step on deck thermocycler?: Run the PCR amplification on the on-deck thermocycler or on an external thermocycler\n* Run post PCR cleanup step: Run or skip the post-PCR bead cleanup using AMPure beads\n", - "internal": "illumina-dna-prep", - "labware": "\nNest 96 well plate full skirt 100 \u00b5L\nNEST 2 mL 96-Well Deep Well Plate\nNEST 12-Well Reservoirs, 15 mL\nOpentrons aluminum block set\n", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* NGS Library Prep\n\t* Illumina DNA Prep\n\n", - "deck-setup": "![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-illumina-dna-prep/v3/deck.jpg)\n\nInital slot layout:\n1. Magnetic module for the sample plate (Nest 96 well plate full skirt).\n2. Reservoir: NEST 12-well reservoir 15 mL. This is substituted for a NEST 2 mL deep well plate if tip-reuse is on in order to minimize cross-contamination. See Reagent Setup section for information about the location of the reagents\n3. Reagent plate 2: Temperature module with Bio-rad 200 \u00b5L plate on aluminum block. See Reagent Setup section for information about the location of the reagents\n4. 20 \u00b5L filter tiprack\n5. 200 \u00b5L filter tiprack\n6. 200 \u00b5L filter tiprack\n7. Sample plate on Thermocycler module with NEST 96 well plate full skirt 100 \u00b5L\n8. Empty\n9. 200 \u00b5L filter tiprack\n10. Sample plate on Thermocycler module with NEST 96 well plate full (thermocycler uses two slots)\n11. Empty\n\n", - "description": "This protocol automates the [Illumina DNA prep protocol](https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/illumina_prep/illumina-dna-prep-reference-guide-1000000025416-09.pdf). Illumina DNA prep offers a fast, integrated workflow for a wide range of applications, from human whole-genome sequencing to amplicons, plasmids, and microbial species\n\nThe protocol allows you to set the number of samples to 8, 16 or 24 (i.e. 8 samples per column, up to 3 columns). Samples are prepared in the wells as shown in the table and figure below, with 30 \u00b5L of 100 ng:s of sample DNA in each well. See the [Illumina DNA Prep protocol](https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/illumina_prep/illumina-dna-prep-reference-guide-1000000025416-09.pdf) for more information about sample input requirements.\n\n![Sample input and output columns](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-illumina-dna-prep/v3/samples_output.jpg)\n\n![Sample columns](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-illumina-dna-prep/v3/sample_setup.jpg)\n\nThe user can choose which steps of the protocol they want to run, or skip - see explanation of parameters below.\n\n**Plate Moving**\nThe Protocol requires manually transferring the sample plate between the Thermocycler and Magnet 3 times. It starts on the Thermocycler and needs to be moved to the Magnet for the post-Tagmentation washes, and then moved to the Thermocycler for PCR and then back to the Magnet for the post-PCR cleanup. In the script the two positions are handled as sample_plate_mag and sample_plate_thermo; during calibration use an empty plate of the same labware as the sample plate on the magnet position to allow calibration.\n\nExplanation of parameters below:\n* `Number of samples`: 8 (column 1), 16 (column 1, 3), or 24 (column 1, 3, 5) samples (see above).\n* `Do a dry run?`: Sets the `Use modules?` parameter to `No` (see below). Tips will be returned, incubation steps skipped, and mixes shortened. This parameter is for testing purposes.\n* `Use modules?`: Runs the protocol without module steps (e.g. thermocycle steps such as incubation and PCR cycles, or the steps using the magbetic module). Will be automatically set to `Yes` if the `Do a dry run?` parameter is set to `Yes`\n* `Tip reuse?`: Reuses tips for washing steps so that no tip refill is neccesary during the run. Recommended only for a 24x samples run.\n* `Use tip offsets?`: Whether to use specific offsets for each tip type\n* `Include tagmentation step in protocol run?`: Run the tagmentation step or skip it.\n* `Run tagmentation incubation on the deck thermocycler?`: Run the tagmentation incubation step on the deck thermocycler or on an off-deck external thermocycler.\n* `Run TSB step?`: Run the TSB/adapter ligation step or not\n* `Run TSB incubation step on the deck thermocycler`: Whether to do the incubation on the on-deck thermocycler or off-deck on an external thermocycler\n* `Run tagmentation wash with TWB step`: Run the bead washing steps with TWB\n* `Run PCR cycle step`: Whether to run the PCR amplification step\n* `Run PCR step on deck thermocycler?`: Run the PCR amplification on the on-deck thermocycler or on an external thermocycler\n* `Run post PCR cleanup step`: Run or skip the post-PCR bead cleanup using AMPure beads\n---\n\n", - "internal": "illumina-dna-prep\n", - "labware": "* [Nest 96 well plate full skirt 100 \u00b5L](https://shop.opentrons.com/nest-0-1-ml-96-well-pcr-plate-full-skirt/)\n* [NEST 2 mL 96-Well Deep Well Plate](https://shop.opentrons.com/nest-2-ml-96-well-deep-well-plate-v-bottom/)\n* [NEST 12-Well Reservoirs, 15 mL](https://shop.opentrons.com/nest-12-well-reservoirs-15-ml/)\n* [Opentrons aluminum block set](https://shop.opentrons.com/aluminum-block-set/)\n\n", - "modules": "* [Temperature Module (GEN2)](https://shop.opentrons.com/collections/hardware-modules/products/tempdeck)\n* [Magnetic Module (GEN2)](https://shop.opentrons.com/collections/hardware-modules/products/magdeck)\n* [Thermocycler Module](https://shop.opentrons.com/collections/hardware-modules/products/thermocycler-module)\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "partner": "[Illumina](https://www.illumina.com/)\n\n", - "pipettes": "* [P300 multi-Channel (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/)\n* [P20 multi-Channel (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/)\n* [P10 multi-Channel](https://shop.opentrons.com/8-channel-electronic-pipette/)\n**Tips**\n* [Opentrons 20 \u00b5L filter tiprack](https://shop.opentrons.com/opentrons-20ul-filter-tips/)\n* [Opentrons 200 \u00b5L filter tiprack](https://shop.opentrons.com/opentrons-200ul-filter-tips/)\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "protocol-steps": "1. Prepare the thermocycler by setting the block temperature to 4 degrees, and the lid to 100 degrees.\n2. Add tagmentation mix to the samples\n3. User seals the plate and the protocol incubates the samples with the mix in the thermocycler, 55 degrees for 15 minutes.\n4. The thermocycler opens, and the user removes the seal.\n5. Add Tagmentation Stop Buffer to the samples.\n6. Seal and incubate the mix at 37 degrees for 15 minutes.\n7. User removes seal; remove the supernatant and wash the beads three times with Tagmentation Wash Buffer.\n8. Amplification of DNA: Addition of PCR mix and addition of barcodes.\n9. The protocol runs PCR protocol for 5 cycles. This takes 25 minutes to complete. The supernatant is transferred to columns 7, 9 and 11 depending on how many sample columns there are.\n10. Post-PCR cleanup using AMPure beads.\n11. The protocol performs two ethanol washes.\n12. RSB (resuspension buffer) is added to the bead wells and the supernatant is transferred to the output columns (8, 10, and 12).\n\n", - "reagent-setup": "* Reservoir, slot 2:\n![Reagent plate 1](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-illumina-dna-prep/v3/reagent_plate1.jpg)\n* Reagent plate on temperature module, slot 3:\n![Reagent plate 2](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-illumina-dna-prep/v3/reagent_plate2.jpg)\n\n---\n\n", - "reagents": "* [Illumina DNA Prep](https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/nextera-dna-flex.html)\n\n---\n\n", - "title": "Illumina DNA Prep - Opentrons v3" - }, - "modules": [ - "Temperature Module (GEN2)", - "Magnetic Module (GEN2)", - "Thermocycler Module" - ], - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "partner": "Illumina", - "pipettes": "\nP300 multi-Channel (GEN2)\nP20 multi-Channel (GEN2)\nP10 multi-Channel\nTips\nOpentrons 20 \u00b5L filter tiprack\nOpentrons 200 \u00b5L filter tiprack\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "protocol-steps": "\nPrepare the thermocycler by setting the block temperature to 4 degrees, and the lid to 100 degrees.\nAdd tagmentation mix to the samples\nUser seals the plate and the protocol incubates the samples with the mix in the thermocycler, 55 degrees for 15 minutes.\nThe thermocycler opens, and the user removes the seal.\nAdd Tagmentation Stop Buffer to the samples.\nSeal and incubate the mix at 37 degrees for 15 minutes.\nUser removes seal; remove the supernatant and wash the beads three times with Tagmentation Wash Buffer.\nAmplification of DNA: Addition of PCR mix and addition of barcodes.\nThe protocol runs PCR protocol for 5 cycles. This takes 25 minutes to complete. The supernatant is transferred to columns 7, 9 and 11 depending on how many sample columns there are.\nPost-PCR cleanup using AMPure beads.\nThe protocol performs two ethanol washes.\nRSB (resuspension buffer) is added to the bead wells and the supernatant is transferred to the output columns (8, 10, and 12).\n", - "reagent-setup": "\nReservoir, slot 2:\n\nReagent plate on temperature module, slot 3:\n\n\n", - "reagents": [ - "Illumina DNA Prep" - ], - "title": "Illumina DNA Prep - Opentrons v3" -} \ No newline at end of file diff --git a/protoBuilds/sci-illumina-dna-prep/metadata.json b/protoBuilds/sci-illumina-dna-prep/metadata.json deleted file mode 100644 index d75df21c2..000000000 --- a/protoBuilds/sci-illumina-dna-prep/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "sci-illumina-dna-prep.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": true, - "skip-tests": false - }, - "path": "protocols/sci-illumina-dna-prep", - "slug": "sci-illumina-dna-prep", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/sci-illumina-dna-prep/sci-illumina-dna-prep.ot2.apiv2.py.json b/protoBuilds/sci-illumina-dna-prep/sci-illumina-dna-prep.ot2.apiv2.py.json deleted file mode 100644 index 3cca7dd7e..000000000 --- a/protoBuilds/sci-illumina-dna-prep/sci-illumina-dna-prep.ot2.apiv2.py.json +++ /dev/null @@ -1,278 +0,0 @@ -{ - "content": "from opentrons import protocol_api\n\nfrom opentrons import types\n\nimport inspect\n\nmetadata = {\n 'protocolName': 'Illumina DNA Prep',\n 'author': 'Opentrons ',\n 'source': 'Protocol Library',\n 'apiLevel': '2.9'\n}\n# I removed the right() function because it is never used\n# settings\n# SAMPLES = '24x' # 8x, 16x, or 24x\n# YES or NO, DRYRUN = 'YES' will return tips, skip incubation times,\n# shorten mix, for testing purposes\n# DRYRUN = 'NO'\n# YES or NO, NOMODULES = 'YES' will not require modules on the deck and will\n# skip module steps, for testing purposes, if DRYRUN = 'YES', then NOMODULES\n# will automatically set itself to 'NO'\n# NOMODULES = 'NO'\n# TIPREUSE = 'NO'\n# YES or NO, Reusing tips on wash steps reduces tips needed, no tip refill\n# needed, suggested only for 24x run with all steps\n\n# YES or NO, Sets whether to use protocol specific z offsets for each tip and\n# labware or no offsets aside from defaults\n# OFFSET = 'YES'\n\n# sections\n# STEP_TAG = 1 # 1 is include, 0 is skip, steps with \"DECK\" are\n# for reaction\n# to take place with the on deck Thermocycler module\n# This arrangement makes it possibly to set up and run only the first\n# half, or to skips steps and resume if there is an Error.\n# STEP_TAGDECK = 1\n# If non \"DECK\" steps are skipped, then TIPREUSE will automatically set\n# itself to 'NO' in order to keep tip order correct.\n# STEP_TSB = 1\n# STEP_TSBDECK = 1\n# STEP_WASH = 1\n# STEP_PCR = 1\n# STEP_PCRDECK = 1\n# STEP_POSTPCR = 1\n\n\ndef run(protocol: protocol_api.ProtocolContext):\n\n global TIPREUSE\n\n [SAMPLES,\n DRYRUN,\n NOMODULES,\n TIPREUSE,\n OFFSET,\n STEP_TAG,\n STEP_TAGDECK,\n STEP_TSB,\n STEP_TSBDECK,\n STEP_WASH,\n STEP_PCR,\n STEP_PCRDECK,\n STEP_POSTPCR] = get_values( # noqa: F821\n \"SAMPLES\",\n \"DRYRUN\",\n \"NOMODULES\",\n \"TIPREUSE\",\n \"OFFSET\",\n \"STEP_TAG\",\n \"STEP_TAGDECK\",\n \"STEP_TSB\",\n \"STEP_TSBDECK\",\n \"STEP_WASH\",\n \"STEP_PCR\",\n \"STEP_PCRDECK\",\n \"STEP_POSTPCR\")\n\n STEPS = {STEP_TAG, STEP_TSB, STEP_WASH, STEP_PCR, STEP_POSTPCR}\n\n if DRYRUN == 'YES':\n protocol.comment(\"THIS IS A DRY RUN\")\n else:\n protocol.comment(\"THIS IS A REACTION RUN\")\n NOMODULES = 'NO'\n\n if all(STEPS) is True:\n if TIPREUSE == 'YES':\n TIPREUSE = 'YES'\n protocol.comment(\"TIP REUSING\")\n else:\n TIPREUSE = 'NO'\n protocol.comment(\"NO TIP REUSING\")\n\n # labware\n if NOMODULES == 'YES':\n protocol.comment(\"THIS IS A NO MODULE RUN\")\n # <--- Actually an Eppendorf 96 well, same dimensions\n sample_plate_mag = protocol.load_labware(\n 'nest_96_wellplate_100ul_pcr_full_skirt', '1')\n if TIPREUSE == 'NO':\n reservoir = protocol.load_labware('nest_12_reservoir_15ml', '2')\n else:\n reservoir = protocol.load_labware(\n 'nest_96_wellplate_2ml_deep', '2')\n reagent_plate = protocol.load_labware(\n 'opentrons_96_aluminumblock_biorad_wellplate_200ul', '3')\n tiprack_20 = protocol.load_labware(\n 'opentrons_96_filtertiprack_20ul', '4')\n tiprack_200_1 = protocol.load_labware(\n 'opentrons_96_filtertiprack_200ul', '5')\n tiprack_200_2 = protocol.load_labware(\n 'opentrons_96_filtertiprack_200ul', '6')\n sample_plate_thermo = protocol.load_labware(\n 'nest_96_wellplate_100ul_pcr_full_skirt', '7')\n tiprack_200_3 = protocol.load_labware(\n 'opentrons_96_filtertiprack_200ul', '9')\n else:\n protocol.comment(\"THIS IS A MODULE RUN\")\n mag_block = protocol.load_module('magnetic module gen2', '1')\n # <--- Actually an Eppendorf 96 well, same dimensions\n sample_plate_mag = mag_block.load_labware(\n 'nest_96_wellplate_100ul_pcr_full_skirt')\n if TIPREUSE == 'NO':\n reservoir = protocol.load_labware('nest_12_reservoir_15ml', '2')\n else:\n reservoir = protocol.load_labware(\n 'nest_96_wellplate_2ml_deep', '2')\n temp_block = protocol.load_module('temperature module gen2', '3')\n reagent_plate = temp_block.load_labware(\n 'opentrons_96_aluminumblock_biorad_wellplate_200ul')\n tiprack_20 = protocol.load_labware(\n 'opentrons_96_filtertiprack_20ul', '4')\n tiprack_200_1 = protocol.load_labware(\n 'opentrons_96_filtertiprack_200ul', '5')\n tiprack_200_2 = protocol.load_labware(\n 'opentrons_96_filtertiprack_200ul', '6')\n thermocycler = protocol.load_module('thermocycler module')\n sample_plate_thermo = thermocycler.load_labware(\n 'nest_96_wellplate_100ul_pcr_full_skirt')\n tiprack_200_3 = protocol.load_labware(\n 'opentrons_96_filtertiprack_200ul', '9')\n\n if TIPREUSE == 'YES':\n protocol.comment(\"THIS PROTOCOL WILL REUSE TIPS FOR WASHES\")\n\n # reagent - plate\n TAG = reagent_plate.wells_by_name()['A1']\n TSB = reagent_plate.wells_by_name()['A2']\n PCR = reagent_plate.wells_by_name()['A3']\n Barcodes1 = reagent_plate.wells_by_name()['A7']\n Barcodes2 = reagent_plate.wells_by_name()['A8']\n Barcodes3 = reagent_plate.wells_by_name()['A9']\n\n # reagent - deepwell\n if TIPREUSE == 'NO':\n AMPure = reservoir['A1']\n EtOH_1 = reservoir['A4']\n EtOH_2 = reservoir['A4']\n EtOH_3 = reservoir['A4']\n RSB = reservoir['A6']\n TWB_1 = reservoir['A8']\n TWB_2 = reservoir['A8']\n TWB_3 = reservoir['A8']\n Liquid_trash = reservoir['A12']\n else:\n AMPure = reservoir['A1']\n EtOH_1 = reservoir['A4']\n EtOH_2 = reservoir['A3']\n EtOH_3 = reservoir['A2']\n RSB = reservoir['A6']\n TWB_1 = reservoir['A8']\n TWB_2 = reservoir['A9']\n TWB_3 = reservoir['A10']\n Liquid_trash = reservoir['A12']\n\n # pipette\n if NOMODULES == 'NO':\n p300 = protocol.load_instrument('p300_multi_gen2', 'left', tip_racks=[\n tiprack_200_1, tiprack_200_2,\n tiprack_200_3])\n p20 = protocol.load_instrument(\n 'p20_multi_gen2', 'right', tip_racks=[tiprack_20])\n else:\n p300 = protocol.load_instrument('p300_multi', 'left', tip_racks=[\n tiprack_200_1, tiprack_200_2,\n tiprack_200_3])\n p20 = protocol.load_instrument(\n 'p10_multi', 'right', tip_racks=[tiprack_20])\n\n # samples\n # FIXME: This does not seem to be used\n src_file_path = inspect.getfile(lambda: None)\n protocol.comment(src_file_path)\n\n # tip and sample tracking\n if SAMPLES == '8x':\n protocol.comment(\"There are 8 Samples\")\n samplecolumns = 1\n TWB_washtip_1 = tiprack_200_1['A3']\n TWB_removetip_1 = tiprack_200_1['A4']\n W1_ETOH_washtip_1 = tiprack_200_1['A10']\n W1_ETOH_removetip_1 = tiprack_200_1['A11']\n elif SAMPLES == '16x':\n protocol.comment(\"There are 16 Samples\")\n samplecolumns = 2\n TWB_washtip_1 = tiprack_200_1['A5']\n TWB_washtip_2 = tiprack_200_1['A6']\n TWB_removetip_1 = tiprack_200_1['A7']\n TWB_removetip_2 = tiprack_200_1['A8']\n W1_ETOH_washtip_1 = tiprack_200_2['A7']\n W1_ETOH_washtip_2 = tiprack_200_2['A8']\n W1_ETOH_removetip_1 = tiprack_200_2['A9']\n W1_ETOH_removetip_2 = tiprack_200_2['A10']\n elif SAMPLES == '24x':\n protocol.comment(\"There are 24 Samples\")\n samplecolumns = 3\n TWB_washtip_1 = tiprack_200_1['A7']\n TWB_washtip_2 = tiprack_200_1['A8']\n TWB_washtip_3 = tiprack_200_1['A9']\n TWB_removetip_1 = tiprack_200_1['A10']\n TWB_removetip_2 = tiprack_200_1['A11']\n TWB_removetip_3 = tiprack_200_1['A12']\n W1_ETOH_washtip_1 = tiprack_200_3['A4']\n W1_ETOH_washtip_2 = tiprack_200_3['A5']\n W1_ETOH_washtip_3 = tiprack_200_3['A6']\n W1_ETOH_removetip_1 = tiprack_200_3['A7']\n W1_ETOH_removetip_2 = tiprack_200_3['A8']\n W1_ETOH_removetip_3 = tiprack_200_3['A9']\n else:\n protocol.pause(\"ERROR?\")\n\n # FIXME: commented out variables are never used in the protocol\n p300_offset_Res = 0\n p300_offset_Thermo = 0\n p300_offset_Mag = 0\n # p300_offset_Deck = 0\n p300_offset_Temp = 0\n # p300_offset_Tube = 0\n # p20_offset_Res = 0\n p20_offset_Thermo = 0\n p20_offset_Mag = 0\n # p20_offset_Deck = 0\n p20_offset_Temp = 0\n # p20_offset_Tube = 0\n\n # offset\n if OFFSET == 'YES':\n if TIPREUSE == 'NO':\n p300_offset_Res = 2\n else:\n p300_offset_Res = 2\n p300_offset_Thermo = 1\n p300_offset_Mag = 0.70\n # p300_offset_Deck = 0.3\n p300_offset_Temp = 0.65\n # p300_offset_Tube = 0\n # if TIPREUSE == 'NO':\n # p20_offset_Res = 2\n # else:\n # p20_offset_Res = 2\n p20_offset_Thermo = 1\n p20_offset_Mag = 0.75\n # p20_offset_Deck = 0.3\n p20_offset_Temp = 0.85\n # p20_offset_Tube = 0\n\n # FIXME: Commented out variables are never used in the protocol\n # positions\n ##########################################################################\n # sample_plate_thermo on the Thermocycler\n # A1_p20_bead_side = sample_plate_thermo['A1'].center().move(types.Point(\n # x=-1.8 * 0.50, y=0, z=p20_offset_Thermo - 5)) # Beads to the Right\n # A1_p20_bead_top = sample_plate_thermo['A1'].center().move(types.Point(\n # x=1.5, y=0, z=p20_offset_Thermo + 2)) # Beads to the Right\n # A1_p20_bead_mid = sample_plate_thermo['A1'].center().move(types.Point(\n # x=1, y=0, z=p20_offset_Thermo - 2)) # Beads to the Right\n A1_p300_bead_side = sample_plate_thermo['A1'].center().move(types.Point(\n x=-0.50, y=0, z=p300_offset_Thermo - 7.2)) # Beads to the Right\n A1_p300_bead_top = sample_plate_thermo['A1'].center().move(types.Point(\n x=1.30, y=0, z=p300_offset_Thermo - 1)) # Beads to the Right\n A1_p300_bead_mid = sample_plate_thermo['A1'].center().move(types.Point(\n x=0.80, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right\n A1_p300_loc1 = sample_plate_thermo['A1'].center().move(types.Point(\n x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Thermo - 4))\n # Beads to the Right\n A1_p300_loc2 = sample_plate_thermo['A1'].center().move(types.Point(\n x=1.3, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right\n A1_p300_loc3 = sample_plate_thermo['A1'].center().move(types.Point(\n x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Thermo - 4))\n # Beads to the Right\n # A3_p20_bead_side = sample_plate_thermo['A3'].center().move(types.Point(\n # x=-1.8 * 0.50, y=0, z=p20_offset_Thermo - 5)) # Beads to the Right\n # A3_p20_bead_top = sample_plate_thermo['A3'].center().move(types.Point(\n # x=1.5, y=0, z=p20_offset_Thermo + 2)) # Beads to the Right\n # A3_p20_bead_mid = sample_plate_thermo['A3'].center().move(types.Point(\n # x=1, y=0, z=p20_offset_Thermo - 2)) # Beads to the Right\n A3_p300_bead_side = sample_plate_thermo['A3'].center().move(types.Point(\n x=-0.50, y=0, z=p300_offset_Thermo - 7.2)) # Beads to the Right\n A3_p300_bead_top = sample_plate_thermo['A3'].center().move(types.Point(\n x=1.30, y=0, z=p300_offset_Thermo - 1)) # Beads to the Right\n A3_p300_bead_mid = sample_plate_thermo['A3'].center().move(types.Point(\n x=0.80, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right\n A3_p300_loc1 = sample_plate_thermo['A3'].center().move(types.Point(\n x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Thermo - 4))\n # Beads to the Right\n A3_p300_loc2 = sample_plate_thermo['A3'].center().move(types.Point(\n x=1.3, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right\n A3_p300_loc3 = sample_plate_thermo['A3'].center().move(types.Point(\n x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Thermo - 4))\n # Beads to the Right\n # A5_p20_bead_side = sample_plate_thermo['A5'].center().move(types.Point(\n # x=-1.8 * 0.50, y=0, z=p20_offset_Thermo - 5)) # Beads to the Right\n # A5_p20_bead_top = sample_plate_thermo['A5'].center().move(types.Point(\n # x=1.5, y=0, z=p20_offset_Thermo + 2)) # Beads to the Right\n # A5_p20_bead_mid = sample_plate_thermo['A5'].center().move(types.Point(\n # x=1, y=0, z=p20_offset_Thermo - 2)) # Beads to the Right\n A5_p300_bead_side = sample_plate_thermo['A5'].center().move(types.Point(\n x=-0.50, y=0, z=p300_offset_Thermo - 7.2)) # Beads to the Right\n A5_p300_bead_top = sample_plate_thermo['A5'].center().move(types.Point(\n x=1.30, y=0, z=p300_offset_Thermo - 1)) # Beads to the Right\n A5_p300_bead_mid = sample_plate_thermo['A5'].center().move(types.Point(\n x=0.80, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right\n A5_p300_loc1 = sample_plate_thermo['A5'].center().move(types.Point(\n x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Thermo - 4))\n # Beads to the Right\n A5_p300_loc2 = sample_plate_thermo['A5'].center().move(types.Point(\n x=1.3, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right\n A5_p300_loc3 = sample_plate_thermo['A5'].center().move(types.Point(\n x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Thermo - 4))\n # Beads to the Right\n ##########################################################################\n\n bypass = protocol.deck.position_for(\n '11').move(types.Point(x=70, y=80, z=130))\n\n # commands\n if DRYRUN == 'NO':\n protocol.comment(\"SETTING THERMO and TEMP BLOCK Temperature\")\n thermocycler.set_block_temperature(4)\n thermocycler.set_lid_temperature(100)\n# temp_block.set_temperature(4)\n thermocycler.open_lid()\n protocol.pause(\"Ready\")\n\n if STEP_TAG == 1:\n protocol.comment('==============================================')\n protocol.comment('--> TAGMENTATION')\n protocol.comment('==============================================')\n\n protocol.comment('--> Adding Tagmentation Mix ')\n if DRYRUN == 'NO':\n TagVol = 20\n TagMixRep = 10\n TagMixVol = 40\n if DRYRUN == 'YES':\n TagVol = 20\n TagMixRep = 1\n TagMixVol = 40\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A1'\n p300.pick_up_tip()\n p300.mix(3, 20, TAG.bottom(z=p300_offset_Temp), rate=0.5)\n p300.aspirate(TagVol, TAG.bottom(z=p300_offset_Temp), rate=0.25)\n p300.dispense(TagVol, sample_plate_thermo[X].bottom(\n z=p300_offset_Thermo), rate=0.25)\n p300.mix(TagMixRep, TagMixVol)\n p300.blow_out(sample_plate_thermo[X].top(z=-5))\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A3'\n p300.pick_up_tip()\n p300.mix(3, 20, TAG.bottom(z=p300_offset_Temp), rate=0.5)\n p300.aspirate(TagVol, TAG.bottom(z=p300_offset_Temp), rate=0.25)\n p300.dispense(TagVol, sample_plate_thermo[X].bottom(\n z=p300_offset_Thermo), rate=0.25)\n p300.mix(TagMixRep, TagMixVol)\n p300.blow_out(sample_plate_thermo[X].top(z=-5))\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A5'\n p300.pick_up_tip()\n p300.mix(3, 20, TAG.bottom(z=p300_offset_Temp), rate=0.5)\n p300.aspirate(TagVol, TAG.bottom(z=p300_offset_Temp), rate=0.25)\n p300.dispense(TagVol, sample_plate_thermo[X].bottom(\n z=p300_offset_Thermo), rate=0.25)\n p300.mix(TagMixRep, TagMixVol)\n p300.blow_out(sample_plate_thermo[X].top(z=-5))\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n\n if STEP_TAGDECK == 1:\n if DRYRUN == 'NO':\n ###################################################################\n protocol.pause('Seal, Run TAG (15min)')\n\n thermocycler.close_lid()\n profile_TAG = [\n {'temperature': 55, 'hold_time_minutes': 15}\n ]\n thermocycler.execute_profile(\n steps=profile_TAG, repetitions=1, block_max_volume=50)\n thermocycler.set_block_temperature(10)\n #######################################################################\n thermocycler.open_lid()\n protocol.pause(\"Remove Seal\")\n else:\n protocol.pause('Seal, Run ERAT (60min)')\n\n if STEP_TSB == 1:\n protocol.pause(\"Add TSB to Reagent Wells\")\n protocol.comment('==============================================')\n protocol.comment('--> Adapter Ligation')\n protocol.comment('==============================================')\n\n protocol.comment('--> Adding Tagmentation Stop Buffer')\n if DRYRUN == 'NO':\n if NOMODULES == 'NO':\n TSBVol = 10\n TSBMixRep = 10\n TSBMixVol = 20\n else:\n TSBVol = 10\n TSBMixRep = 10\n TSBMixVol = 10\n if DRYRUN == 'YES':\n if NOMODULES == 'NO':\n TSBVol = 10\n TSBMixRep = 1\n TSBMixVol = 20\n else:\n TSBVol = 10\n TSBMixRep = 1\n TSBMixVol = 10\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A1'\n p20.pick_up_tip()\n p20.aspirate(TSBVol, TSB.bottom(z=p20_offset_Temp))\n p20.dispense(TSBVol, sample_plate_thermo[X].bottom(\n z=p20_offset_Thermo))\n p20.mix(TSBMixRep, TSBMixVol)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A3'\n p20.pick_up_tip()\n p20.aspirate(TSBVol, TSB.bottom(z=p20_offset_Temp))\n p20.dispense(TSBVol, sample_plate_thermo[X].bottom(\n z=p20_offset_Thermo))\n p20.mix(TSBMixRep, TSBMixVol)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A5'\n p20.pick_up_tip()\n p20.aspirate(TSBVol, TSB.bottom(z=p20_offset_Temp))\n p20.dispense(TSBVol, sample_plate_thermo[X].bottom(\n z=p20_offset_Thermo))\n p20.mix(TSBMixRep, TSBMixVol)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n\n if STEP_TSBDECK == 1:\n if DRYRUN == 'NO':\n ###################################################################\n protocol.pause('Seal, Run PTC (15min)')\n\n thermocycler.close_lid()\n profile_PTC = [\n {'temperature': 37, 'hold_time_minutes': 15}\n ]\n thermocycler.execute_profile(\n steps=profile_PTC, repetitions=1, block_max_volume=60)\n thermocycler.set_block_temperature(10)\n ###################################################################\n thermocycler.open_lid()\n protocol.pause(\"Remove Seal\")\n else:\n protocol.pause('Seal, Run PTC (15min)')\n\n # FIXME: Commented out variables are never used in the protocol\n # positions\n ##########################################################################\n # sample_plate_mag on the Mag Block\n # A1_p20_bead_side = sample_plate_mag['A1'].center().move(types.Point(\n # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right\n # A1_p20_bead_top = sample_plate_mag['A1'].center().move(types.Point(\n # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right\n # A1_p20_bead_mid = sample_plate_mag['A1'].center().move(types.Point(\n # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right\n A1_p300_bead_side = sample_plate_mag['A1'].center().move(types.Point(\n x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right\n A1_p300_bead_top = sample_plate_mag['A1'].center().move(types.Point(\n x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right\n A1_p300_bead_mid = sample_plate_mag['A1'].center().move(types.Point(\n x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A1_p300_loc1 = sample_plate_mag['A1'].center().move(types.Point(\n x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right\n A1_p300_loc2 = sample_plate_mag['A1'].center().move(types.Point(\n x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A1_p300_loc3 = sample_plate_mag['A1'].center().move(types.Point(\n x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4))\n # Beads to the Right\n # A3_p20_bead_side = sample_plate_mag['A3'].center().move(types.Point(\n # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right\n # A3_p20_bead_top = sample_plate_mag['A3'].center().move(types.Point(\n # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right\n # A3_p20_bead_mid = sample_plate_mag['A3'].center().move(types.Point(\n # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right\n A3_p300_bead_side = sample_plate_mag['A3'].center().move(types.Point(\n x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right\n A3_p300_bead_top = sample_plate_mag['A3'].center().move(types.Point(\n x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right\n A3_p300_bead_mid = sample_plate_mag['A3'].center().move(types.Point(\n x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A3_p300_loc1 = sample_plate_mag['A3'].center().move(types.Point(\n x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right\n A3_p300_loc2 = sample_plate_mag['A3'].center().move(types.Point(\n x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A3_p300_loc3 = sample_plate_mag['A3'].center().move(types.Point(\n x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4))\n # Beads to the Right\n # A5_p20_bead_side = sample_plate_mag['A5'].center().move(types.Point(\n # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right\n # A5_p20_bead_top = sample_plate_mag['A5'].center().move(types.Point(\n # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right\n # A5_p20_bead_mid = sample_plate_mag['A5'].center().move(types.Point(\n # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right\n A5_p300_bead_side = sample_plate_mag['A5'].center().move(types.Point(\n x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right\n A5_p300_bead_top = sample_plate_mag['A5'].center().move(types.Point(\n x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right\n A5_p300_bead_mid = sample_plate_mag['A5'].center().move(types.Point(\n x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A5_p300_loc1 = sample_plate_mag['A5'].center().move(types.Point(\n x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right\n A5_p300_loc2 = sample_plate_mag['A5'].center().move(types.Point(\n x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A5_p300_loc3 = sample_plate_mag['A5'].center().move(types.Point(\n x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4))\n # Beads to the Right\n # A7_p20_bead_side = sample_plate_mag['A7'].center().move(types.Point(\n # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right\n # A7_p20_bead_top = sample_plate_mag['A7'].center().move(types.Point(\n # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right\n # A7_p20_bead_mid = sample_plate_mag['A7'].center().move(types.Point(\n # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right\n A7_p300_bead_side = sample_plate_mag['A7'].center().move(types.Point(\n x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right\n A7_p300_bead_top = sample_plate_mag['A7'].center().move(types.Point(\n x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right\n # A7_p300_bead_mid = sample_plate_mag['A7'].center().move(types.Point(\n # x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A7_p300_loc1 = sample_plate_mag['A7'].center().move(types.Point(\n x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right\n A7_p300_loc2 = sample_plate_mag['A7'].center().move(types.Point(\n x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A7_p300_loc3 = sample_plate_mag['A7'].center().move(types.Point(\n x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4))\n # Beads to the Right\n # A9_p20_bead_side = sample_plate_mag['A9'].center().move(types.Point(\n # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right\n # A9_p20_bead_top = sample_plate_mag['A9'].center().move(types.Point(\n # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right\n # A9_p20_bead_mid = sample_plate_mag['A9'].center().move(types.Point(\n # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right\n A9_p300_bead_side = sample_plate_mag['A9'].center().move(types.Point(\n x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right\n A9_p300_bead_top = sample_plate_mag['A9'].center().move(types.Point(\n x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right\n # A9_p300_bead_mid = sample_plate_mag['A9'].center().move(types.Point(\n # x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A9_p300_loc1 = sample_plate_mag['A9'].center().move(types.Point(\n x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right\n A9_p300_loc2 = sample_plate_mag['A9'].center().move(types.Point(\n x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A9_p300_loc3 = sample_plate_mag['A9'].center().move(types.Point(\n x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4))\n # Beads to the Right\n # A11_p20_bead_side = sample_plate_mag['A11'].center().move(types.Point(\n # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right\n # A11_p20_bead_top = sample_plate_mag['A11'].center().move(types.Point(\n # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right\n # A11_p20_bead_mid = sample_plate_mag['A11'].center().move(types.Point(\n # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right\n A11_p300_bead_side = sample_plate_mag['A11'].center().move(types.Point(\n x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right\n A11_p300_bead_top = sample_plate_mag['A11'].center().move(types.Point(\n x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right\n # A11_p300_bead_mid = sample_plate_mag['A11'].center().move(types.Point(\n # x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A11_p300_loc1 = sample_plate_mag['A11'].center().move(types.Point(\n x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right\n A11_p300_loc2 = sample_plate_mag['A11'].center().move(types.Point(\n x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A11_p300_loc3 = sample_plate_mag['A11'].center().move(types.Point(\n x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4))\n # Beads to the Right\n ##########################################################################\n\n if STEP_WASH == 1:\n protocol.pause(\"PLACE sample_plate on MAGNET\")\n protocol.comment('==============================================')\n protocol.comment('--> TAGMENTATION WASH')\n protocol.comment('==============================================')\n\n if DRYRUN == 'NO':\n protocol.comment('MAGNET ENGAGE')\n mag_block.engage(height_from_base=8.5)\n protocol.delay(minutes=1)\n mag_block.engage(height_from_base=7)\n protocol.delay(minutes=1)\n mag_block.engage(height_from_base=5)\n protocol.delay(minutes=1)\n\n protocol.comment('--> Removing Supernatant')\n RemoveSup = 90\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A1'\n p300.pick_up_tip()\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(RemoveSup - 30, rate=0.25)\n p300.default_speed = 5\n if X == 'A1':\n p300.move_to(A1_p300_bead_side)\n if X == 'A3':\n p300.move_to(A3_p300_bead_side)\n if X == 'A5':\n p300.move_to(A5_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(20, rate=0.2)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n protocol.delay(minutes=0.1)\n p300.aspirate(10, rate=0.2)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A3'\n p300.pick_up_tip()\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(RemoveSup - 30, rate=0.25)\n p300.default_speed = 5\n if X == 'A1':\n p300.move_to(A1_p300_bead_side)\n if X == 'A3':\n p300.move_to(A3_p300_bead_side)\n if X == 'A5':\n p300.move_to(A5_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(20, rate=0.2)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n protocol.delay(minutes=0.1)\n p300.aspirate(10, rate=0.2)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A5'\n p300.pick_up_tip()\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(RemoveSup - 30, rate=0.25)\n p300.default_speed = 5\n if X == 'A1':\n p300.move_to(A1_p300_bead_side)\n if X == 'A3':\n p300.move_to(A3_p300_bead_side)\n if X == 'A5':\n p300.move_to(A5_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(20, rate=0.2)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n protocol.delay(minutes=0.1)\n p300.aspirate(10, rate=0.2)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n\n if DRYRUN == 'NO':\n protocol.comment('MAGNET DISENGAGE')\n mag_block.disengage()\n\n protocol.comment('--> Repeating 3 washes')\n washreps = 3\n for wash in range(washreps):\n protocol.comment('--> TWB Wash #' + str(wash + 1))\n if DRYRUN == 'NO':\n TWBMixRep = 15\n TWBMixVol = 70\n if DRYRUN == 'YES':\n TWBMixRep = 3\n TWBMixVol = 70\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A1'\n p300.pick_up_tip()if TIPREUSE == 'NO' else \\\n p300.pick_up_tip(TWB_washtip_1)\n p300.aspirate(100, TWB_1.bottom(z=p300_offset_Res))\n if X == 'A1':\n p300.move_to(A1_p300_bead_top)\n if X == 'A3':\n p300.move_to(A3_p300_bead_top)\n if X == 'A5':\n p300.move_to(A5_p300_bead_top)\n p300.dispense(100, rate=0.75)\n p300.default_speed = 5\n reps = 4\n for x in range(reps):\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.aspirate(100)\n if X == 'A1':\n p300.move_to(A1_p300_bead_top)\n if X == 'A3':\n p300.move_to(A3_p300_bead_top)\n if X == 'A5':\n p300.move_to(A5_p300_bead_top)\n p300.dispense(100, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_bead_mid)\n if X == 'A3':\n p300.move_to(A3_p300_bead_mid)\n if X == 'A5':\n p300.move_to(A5_p300_bead_mid)\n p300.mix(TWBMixRep, TWBMixVol)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.mix(TWBMixRep, TWBMixVol)\n p300.default_speed = 400\n p300.move_to(bypass)\n if TIPREUSE == 'NO':\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n else:\n p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A3'\n p300.pick_up_tip()if TIPREUSE == 'NO' else \\\n p300.pick_up_tip(TWB_washtip_2)\n p300.aspirate(100, TWB_2.bottom(z=p300_offset_Res))\n if X == 'A1':\n p300.move_to(A1_p300_bead_top)\n if X == 'A3':\n p300.move_to(A3_p300_bead_top)\n if X == 'A5':\n p300.move_to(A5_p300_bead_top)\n p300.dispense(100, rate=0.75)\n p300.default_speed = 5\n reps = 4\n for x in range(reps):\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.aspirate(100)\n if X == 'A1':\n p300.move_to(A1_p300_bead_top)\n if X == 'A3':\n p300.move_to(A3_p300_bead_top)\n if X == 'A5':\n p300.move_to(A5_p300_bead_top)\n p300.dispense(100, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_bead_mid)\n if X == 'A3':\n p300.move_to(A3_p300_bead_mid)\n if X == 'A5':\n p300.move_to(A5_p300_bead_mid)\n p300.mix(TWBMixRep, TWBMixVol)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.mix(TWBMixRep, TWBMixVol)\n p300.default_speed = 400\n p300.move_to(bypass)\n if TIPREUSE == 'NO':\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n else:\n p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A5'\n p300.pick_up_tip()if TIPREUSE == 'NO' else \\\n p300.pick_up_tip(TWB_washtip_3)\n p300.aspirate(100, TWB_3.bottom(z=p300_offset_Res))\n if X == 'A1':\n p300.move_to(A1_p300_bead_top)\n if X == 'A3':\n p300.move_to(A3_p300_bead_top)\n if X == 'A5':\n p300.move_to(A5_p300_bead_top)\n p300.dispense(100, rate=0.75)\n p300.default_speed = 5\n reps = 4\n for x in range(reps):\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.aspirate(100)\n if X == 'A1':\n p300.move_to(A1_p300_bead_top)\n if X == 'A3':\n p300.move_to(A3_p300_bead_top)\n if X == 'A5':\n p300.move_to(A5_p300_bead_top)\n p300.dispense(100, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_bead_mid)\n if X == 'A3':\n p300.move_to(A3_p300_bead_mid)\n if X == 'A5':\n p300.move_to(A5_p300_bead_mid)\n p300.mix(TWBMixRep, TWBMixVol)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.mix(TWBMixRep, TWBMixVol)\n p300.default_speed = 400\n p300.move_to(bypass)\n if TIPREUSE == 'NO':\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n else:\n p300.return_tip()\n\n if DRYRUN == 'NO':\n protocol.comment('MAGNET ENGAGE')\n mag_block.engage(height_from_base=8.5)\n protocol.delay(minutes=1)\n mag_block.engage(height_from_base=7)\n protocol.delay(minutes=1)\n mag_block.engage(height_from_base=5)\n protocol.delay(minutes=1)\n\n protocol.comment('--> Remove TWB Wash #' + str(wash + 1))\n RemoveSup = 110\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A1'\n p300.pick_up_tip()if TIPREUSE == 'NO' else \\\n p300.pick_up_tip(TWB_removetip_1)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(RemoveSup - 30, rate=0.25)\n p300.default_speed = 5\n if X == 'A1':\n p300.move_to(A1_p300_bead_side)\n if X == 'A3':\n p300.move_to(A3_p300_bead_side)\n if X == 'A5':\n p300.move_to(A5_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(20, rate=0.2)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n protocol.delay(minutes=0.1)\n p300.aspirate(10, rate=0.2)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(bypass)\n if TIPREUSE == 'NO':\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n else:\n p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A3'\n p300.pick_up_tip()if TIPREUSE == 'NO' else \\\n p300.pick_up_tip(TWB_removetip_2)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(RemoveSup - 30, rate=0.25)\n p300.default_speed = 5\n if X == 'A1':\n p300.move_to(A1_p300_bead_side)\n if X == 'A3':\n p300.move_to(A3_p300_bead_side)\n if X == 'A5':\n p300.move_to(A5_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(20, rate=0.2)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n protocol.delay(minutes=0.1)\n p300.aspirate(10, rate=0.2)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(bypass)\n if TIPREUSE == 'NO':\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n else:\n p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A5'\n p300.pick_up_tip()if TIPREUSE == 'NO' else \\\n p300.pick_up_tip(TWB_removetip_3)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(RemoveSup - 30, rate=0.25)\n p300.default_speed = 5\n if X == 'A1':\n p300.move_to(A1_p300_bead_side)\n if X == 'A3':\n p300.move_to(A3_p300_bead_side)\n if X == 'A5':\n p300.move_to(A5_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(20, rate=0.2)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n protocol.delay(minutes=0.1)\n p300.aspirate(10, rate=0.2)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(bypass)\n if TIPREUSE == 'NO':\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n else:\n p300.return_tip()\n\n if DRYRUN == 'NO':\n protocol.comment('MAGNET DISENGAGE')\n mag_block.disengage()\n\n wash += 1\n\n if DRYRUN == 'NO':\n protocol.comment('MAGNET ENGAGE')\n mag_block.engage(height_from_base=5)\n\n protocol.comment('--> Removing Residual Supernatant')\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A1'\n p300.pick_up_tip()\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 3))\n p300.aspirate(50, rate=0.25)\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A3'\n p300.pick_up_tip()\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 3))\n p300.aspirate(50, rate=0.25)\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A5'\n p300.pick_up_tip()\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 3))\n p300.aspirate(50, rate=0.25)\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n\n if DRYRUN == 'NO':\n mag_block.engage(height_from_base=3)\n protocol.delay(minutes=0.5)\n\n protocol.comment('MAGNET DISENGAGE')\n mag_block.disengage()\n\n if STEP_PCR == 1:\n protocol.comment('==============================================')\n protocol.comment('--> AMPLIFICATION')\n protocol.comment('==============================================')\n\n protocol.comment('ADDING PCR')\n if DRYRUN == 'NO':\n PCRVol = 40\n PCRMixRep = 5\n PCRMixVol = 30\n if DRYRUN == 'YES':\n PCRVol = 40\n PCRMixRep = 1\n PCRMixVol = 30\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A1'\n p300.pick_up_tip()\n p300.aspirate(PCRVol, PCR.bottom(p300_offset_Temp))\n if X == 'A1':\n p300.move_to(A1_p300_loc1)\n if X == 'A3':\n p300.move_to(A3_p300_loc1)\n if X == 'A5':\n p300.move_to(A5_p300_loc1)\n p300.dispense(PCRVol / 5, rate=0.75)\n p300.default_speed = 5\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.dispense(PCRVol / 5, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_loc3)\n if X == 'A3':\n p300.move_to(A3_p300_loc3)\n if X == 'A5':\n p300.move_to(A5_p300_loc3)\n p300.dispense(PCRVol / 5, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.dispense(PCRVol / 5, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_loc1)\n if X == 'A3':\n p300.move_to(A3_p300_loc1)\n if X == 'A5':\n p300.move_to(A5_p300_loc1)\n p300.dispense(PCRVol / 5, rate=0.75)\n reps = 5\n for x in range(reps):\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.aspirate(PCRVol, rate=0.5)\n if X == 'A1':\n p300.move_to(A1_p300_bead_top)\n if X == 'A3':\n p300.move_to(A3_p300_bead_top)\n if X == 'A5':\n p300.move_to(A5_p300_bead_top)\n p300.dispense(PCRVol, rate=1)\n reps = 3\n for x in range(reps):\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.mix(PCRMixRep, PCRMixVol)\n if X == 'A1':\n p300.move_to(A1_p300_loc1)\n if X == 'A3':\n p300.move_to(A3_p300_loc1)\n if X == 'A5':\n p300.move_to(A5_p300_loc1)\n p300.mix(PCRMixRep, PCRMixVol)\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.mix(PCRMixRep, PCRMixVol)\n if X == 'A1':\n p300.move_to(A1_p300_loc3)\n if X == 'A3':\n p300.move_to(A3_p300_loc3)\n if X == 'A5':\n p300.move_to(A5_p300_loc3)\n p300.mix(PCRMixRep, PCRMixVol)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.mix(PCRMixRep, PCRMixVol)\n p300.move_to(sample_plate_mag[X].top())\n protocol.delay(seconds=0.5)\n p300.move_to(sample_plate_mag[X].center())\n p300.default_speed = 400\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A3'\n p300.pick_up_tip()\n p300.aspirate(PCRVol, PCR.bottom(p300_offset_Temp))\n if X == 'A1':\n p300.move_to(A1_p300_loc1)\n if X == 'A3':\n p300.move_to(A3_p300_loc1)\n if X == 'A5':\n p300.move_to(A5_p300_loc1)\n p300.dispense(PCRVol / 5, rate=0.75)\n p300.default_speed = 5\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.dispense(PCRVol / 5, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_loc3)\n if X == 'A3':\n p300.move_to(A3_p300_loc3)\n if X == 'A5':\n p300.move_to(A5_p300_loc3)\n p300.dispense(PCRVol / 5, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.dispense(PCRVol / 5, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_loc1)\n if X == 'A3':\n p300.move_to(A3_p300_loc1)\n if X == 'A5':\n p300.move_to(A5_p300_loc1)\n p300.dispense(PCRVol / 5, rate=0.75)\n reps = 5\n for x in range(reps):\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.aspirate(PCRVol, rate=0.5)\n if X == 'A1':\n p300.move_to(A1_p300_bead_top)\n if X == 'A3':\n p300.move_to(A3_p300_bead_top)\n if X == 'A5':\n p300.move_to(A5_p300_bead_top)\n p300.dispense(PCRVol, rate=1)\n reps = 3\n for x in range(reps):\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.mix(PCRMixRep, PCRMixVol)\n if X == 'A1':\n p300.move_to(A1_p300_loc1)\n if X == 'A3':\n p300.move_to(A3_p300_loc1)\n if X == 'A5':\n p300.move_to(A5_p300_loc1)\n p300.mix(PCRMixRep, PCRMixVol)\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.mix(PCRMixRep, PCRMixVol)\n if X == 'A1':\n p300.move_to(A1_p300_loc3)\n if X == 'A3':\n p300.move_to(A3_p300_loc3)\n if X == 'A5':\n p300.move_to(A5_p300_loc3)\n p300.mix(PCRMixRep, PCRMixVol)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.mix(PCRMixRep, PCRMixVol)\n p300.move_to(sample_plate_mag[X].top())\n protocol.delay(seconds=0.5)\n p300.move_to(sample_plate_mag[X].center())\n p300.default_speed = 400\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A5'\n p300.pick_up_tip()\n p300.aspirate(PCRVol, PCR.bottom(p300_offset_Temp))\n if X == 'A1':\n p300.move_to(A1_p300_loc1)\n if X == 'A3':\n p300.move_to(A3_p300_loc1)\n if X == 'A5':\n p300.move_to(A5_p300_loc1)\n p300.dispense(PCRVol / 5, rate=0.75)\n p300.default_speed = 5\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.dispense(PCRVol / 5, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_loc3)\n if X == 'A3':\n p300.move_to(A3_p300_loc3)\n if X == 'A5':\n p300.move_to(A5_p300_loc3)\n p300.dispense(PCRVol / 5, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.dispense(PCRVol / 5, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_loc1)\n if X == 'A3':\n p300.move_to(A3_p300_loc1)\n if X == 'A5':\n p300.move_to(A5_p300_loc1)\n p300.dispense(PCRVol / 5, rate=0.75)\n reps = 5\n for x in range(reps):\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.aspirate(PCRVol, rate=0.5)\n if X == 'A1':\n p300.move_to(A1_p300_bead_top)\n if X == 'A3':\n p300.move_to(A3_p300_bead_top)\n if X == 'A5':\n p300.move_to(A5_p300_bead_top)\n p300.dispense(PCRVol, rate=1)\n reps = 3\n for x in range(reps):\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.mix(PCRMixRep, PCRMixVol)\n if X == 'A1':\n p300.move_to(A1_p300_loc1)\n if X == 'A3':\n p300.move_to(A3_p300_loc1)\n if X == 'A5':\n p300.move_to(A5_p300_loc1)\n p300.mix(PCRMixRep, PCRMixVol)\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.mix(PCRMixRep, PCRMixVol)\n if X == 'A1':\n p300.move_to(A1_p300_loc3)\n if X == 'A3':\n p300.move_to(A3_p300_loc3)\n if X == 'A5':\n p300.move_to(A5_p300_loc3)\n p300.mix(PCRMixRep, PCRMixVol)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.mix(PCRMixRep, PCRMixVol)\n p300.move_to(sample_plate_mag[X].top())\n protocol.delay(seconds=0.5)\n p300.move_to(sample_plate_mag[X].center())\n p300.default_speed = 400\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n\n protocol.comment('--> Adding Barcodes')\n BarcodeVol = 10\n BarcodeMixRep = 10\n BarcodeMixVol = 10\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A1'\n p20.pick_up_tip()\n p20.aspirate(BarcodeVol, Barcodes1.bottom(\n z=p20_offset_Temp), rate=0.25)\n p20.dispense(\n BarcodeVol, sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.mix(BarcodeMixRep, BarcodeMixVol)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A3'\n p20.pick_up_tip()\n p20.aspirate(BarcodeVol, Barcodes2.bottom(\n z=p20_offset_Temp), rate=0.25)\n p20.dispense(\n BarcodeVol, sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.mix(BarcodeMixRep, BarcodeMixVol)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A5'\n p20.pick_up_tip()\n p20.aspirate(BarcodeVol, Barcodes3.bottom(\n z=p20_offset_Temp), rate=0.25)\n p20.dispense(\n BarcodeVol, sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.mix(BarcodeMixRep, BarcodeMixVol)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n\n if DRYRUN == 'NO':\n protocol.pause(\"PLACE sample_plate on THERMO\")\n\n if STEP_PCRDECK == 1:\n #######################################################################\n protocol.pause('Seal, Run PCR (25min)')\n\n thermocycler.close_lid()\n profile_PCR_1 = [\n {'temperature': 68, 'hold_time_minutes': 3},\n {'temperature': 98, 'hold_time_minutes': 3}\n ]\n thermocycler.execute_profile(\n steps=profile_PCR_1, repetitions=1, block_max_volume=50)\n profile_PCR_2 = [\n {'temperature': 98, 'hold_time_seconds': 45},\n {'temperature': 62, 'hold_time_seconds': 30},\n {'temperature': 68, 'hold_time_minutes': 2}\n ]\n thermocycler.execute_profile(\n steps=profile_PCR_2, repetitions=5, block_max_volume=50)\n profile_PCR_3 = [\n {'temperature': 68, 'hold_time_minutes': 1}\n ]\n thermocycler.execute_profile(\n steps=profile_PCR_3, repetitions=1, block_max_volume=50)\n thermocycler.set_block_temperature(4)\n #######################################################################\n thermocycler.open_lid()\n protocol.pause(\"Remove Seal\")\n else:\n protocol.pause('Seal, Run PCR (60min)')\n\n Liquid_trash = reservoir['A11']\n\n if STEP_POSTPCR == 1:\n protocol.pause(\"PLACE sample_plate on MAGNET\")\n protocol.comment('==============================================')\n protocol.comment('--> CLEANUP')\n protocol.comment('==============================================')\n\n if DRYRUN == 'NO':\n protocol.comment('MAGNET ENGAGE')\n mag_block.engage(height_from_base=8.5)\n protocol.delay(minutes=1)\n mag_block.engage(height_from_base=7)\n protocol.delay(minutes=1)\n mag_block.engage(height_from_base=5)\n protocol.delay(minutes=1)\n\n protocol.comment('--> Transferring Supernatant')\n TransferSup = 45\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A1'\n Y = 'A7'\n p300.pick_up_tip()\n p300.aspirate(\n TransferSup / 2, sample_plate_mag[X].\n bottom(z=p300_offset_Mag + 1), rate=0.5)\n protocol.delay(seconds=0.1)\n p300.aspirate(\n TransferSup / 2, sample_plate_mag[X].\n bottom(z=p300_offset_Mag), rate=0.5)\n p300.dispense(\n TransferSup + 5, sample_plate_mag[Y].bottom(z=p300_offset_Mag))\n protocol.delay(seconds=0.1)\n p300.blow_out(sample_plate_mag[Y].top(z=-2))\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A3'\n Y = 'A9'\n p300.pick_up_tip()\n p300.aspirate(\n TransferSup / 2, sample_plate_mag[X].\n bottom(z=p300_offset_Mag + 1), rate=0.5)\n protocol.delay(seconds=0.1)\n p300.aspirate(\n TransferSup / 2, sample_plate_mag[X].\n bottom(z=p300_offset_Mag), rate=0.5)\n p300.dispense(\n TransferSup + 5, sample_plate_mag[Y].bottom(z=p300_offset_Mag))\n protocol.delay(seconds=0.1)\n p300.blow_out(sample_plate_mag[Y].top(z=-2))\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A5'\n Y = 'A11'\n p300.pick_up_tip()\n p300.aspirate(\n TransferSup / 2, sample_plate_mag[X].\n bottom(z=p300_offset_Mag + 1), rate=0.5)\n protocol.delay(seconds=0.1)\n p300.aspirate(\n TransferSup / 2, sample_plate_mag[X].bottom(z=p300_offset_Mag),\n rate=0.5)\n p300.dispense(\n TransferSup + 5, sample_plate_mag[Y].bottom(z=p300_offset_Mag))\n protocol.delay(seconds=0.1)\n p300.blow_out(sample_plate_mag[Y].top(z=-2))\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n\n if DRYRUN == 'NO':\n protocol.comment('MAGNET DISENGAGE')\n mag_block.disengage()\n\n protocol.comment('--> ADDING AMPure (0.8x)')\n AMPureVol = 40\n AMPureMixRep = 50\n AMPureMixVol = 80\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A7'\n p300.pick_up_tip()\n p300.mix(10, AMPureVol + 10, AMPure.bottom(z=p300_offset_Res))\n p300.aspirate(AMPureVol, AMPure.bottom(\n z=p300_offset_Res), rate=0.25)\n p300.dispense(AMPureVol, sample_plate_mag[X].bottom(\n z=p300_offset_Mag), rate=0.25)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.mix(AMPureMixRep, AMPureMixVol)\n p300.blow_out(sample_plate_mag[X].top(z=-5))\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A9'\n p300.pick_up_tip()\n p300.mix(3, AMPureVol + 10, AMPure.bottom(z=p300_offset_Res))\n p300.aspirate(AMPureVol, AMPure.bottom(\n z=p300_offset_Res), rate=0.25)\n p300.dispense(AMPureVol, sample_plate_mag[X].bottom(\n z=p300_offset_Mag), rate=0.25)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.mix(AMPureMixRep, AMPureMixVol)\n p300.blow_out(sample_plate_mag[X].top(z=-5))\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A11'\n p300.pick_up_tip()\n p300.mix(3, AMPureVol + 10, AMPure.bottom(z=p300_offset_Res))\n p300.aspirate(AMPureVol, AMPure.bottom(\n z=p300_offset_Res), rate=0.25)\n p300.dispense(AMPureVol, sample_plate_mag[X].bottom(\n z=p300_offset_Mag), rate=0.25)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.mix(AMPureMixRep, AMPureMixVol)\n p300.blow_out(sample_plate_mag[X].top(z=-5))\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n\n if DRYRUN == 'NO':\n protocol.delay(minutes=5)\n\n protocol.comment('MAGNET ENGAGE')\n mag_block.engage(height_from_base=8.5)\n protocol.delay(minutes=1)\n mag_block.engage(height_from_base=7.5)\n protocol.delay(minutes=1)\n mag_block.engage(height_from_base=7)\n protocol.delay(minutes=1)\n mag_block.engage(height_from_base=6)\n protocol.delay(minutes=1)\n mag_block.engage(height_from_base=5)\n protocol.delay(minutes=1)\n\n if TIPREUSE == 'NO':\n if all(STEPS) is True:\n protocol.pause('RESET TIPS')\n p300.reset_tipracks()\n p20.reset_tipracks()\n\n protocol.comment('--> Removing Supernatant')\n RemoveSup = 100\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A7'\n p300.pick_up_tip()\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(RemoveSup - 30, rate=0.25)\n p300.default_speed = 5\n if X == 'A7':\n p300.move_to(A7_p300_bead_side)\n if X == 'A9':\n p300.move_to(A9_p300_bead_side)\n if X == 'A11':\n p300.move_to(A11_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(20, rate=0.2)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n protocol.delay(minutes=0.1)\n p300.aspirate(10, rate=0.1)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A9'\n p300.pick_up_tip()\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(RemoveSup - 30, rate=0.25)\n p300.default_speed = 5\n if X == 'A7':\n p300.move_to(A7_p300_bead_side)\n if X == 'A9':\n p300.move_to(A9_p300_bead_side)\n if X == 'A11':\n p300.move_to(A11_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(20, rate=0.2)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n protocol.delay(minutes=0.1)\n p300.aspirate(10, rate=0.1)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A11'\n p300.pick_up_tip()\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(RemoveSup - 30, rate=0.25)\n p300.default_speed = 5\n if X == 'A7':\n p300.move_to(A7_p300_bead_side)\n if X == 'A9':\n p300.move_to(A9_p300_bead_side)\n if X == 'A11':\n p300.move_to(A11_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(20, rate=0.2)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n protocol.delay(minutes=0.1)\n p300.aspirate(10, rate=0.1)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n\n protocol.comment('--> Repeating 2 washes')\n washreps = 2\n for wash in range(washreps):\n protocol.comment('--> ETOH Wash #' + str(wash + 1))\n ETOHMaxVol = 150\n WASHNUM = 1\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A7'\n if TIPREUSE == 'NO':\n p300.pick_up_tip()\n elif WASHNUM == 1:\n p300.pick_up_tip(W1_ETOH_washtip_1)\n elif WASHNUM == 2:\n pass # # FIXME: W2_ETOH_washtip_1 is never defined\n # p300.pick_up_tip(W2_ETOH_washtip_1)\n p300.aspirate(ETOHMaxVol, EtOH_1.bottom(z=p300_offset_Res))\n if X == 'A7':\n p300.move_to(A7_p300_bead_side)\n if X == 'A9':\n p300.move_to(A9_p300_bead_side)\n if X == 'A11':\n p300.move_to(A11_p300_bead_side)\n p300.dispense(ETOHMaxVol - 50, rate=0.5)\n p300.move_to(sample_plate_mag[X].center())\n p300.dispense(50, rate=0.5)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 5\n p300.move_to(sample_plate_mag[X].top(z=-2))\n protocol.delay(minutes=0.1)\n p300.blow_out()\n p300.default_speed = 400\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A9'\n if TIPREUSE == 'NO':\n p300.pick_up_tip()\n elif WASHNUM == 1:\n p300.pick_up_tip(W1_ETOH_washtip_2)\n elif WASHNUM == 2:\n pass\n # FIXME: W2_ETOH_washtip_2 is never defined\n # p300.pick_up_tip(W2_ETOH_washtip_2)\n p300.aspirate(ETOHMaxVol, EtOH_2.bottom(z=p300_offset_Res))\n if X == 'A7':\n p300.move_to(A7_p300_bead_side)\n if X == 'A9':\n p300.move_to(A9_p300_bead_side)\n if X == 'A11':\n p300.move_to(A11_p300_bead_side)\n p300.dispense(ETOHMaxVol - 50, rate=0.5)\n p300.move_to(sample_plate_mag[X].center())\n p300.dispense(50, rate=0.5)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 5\n p300.move_to(sample_plate_mag[X].top(z=-2))\n protocol.delay(minutes=0.1)\n p300.blow_out()\n p300.default_speed = 400\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A11'\n if TIPREUSE == 'NO':\n p300.pick_up_tip()\n elif WASHNUM == 1:\n p300.pick_up_tip(W1_ETOH_washtip_3)\n elif WASHNUM == 2:\n pass\n # FIXME: W2_ETOH_washtip_3 is undefined\n # p300.pick_up_tip(W2_ETOH_washtip_3)\n p300.aspirate(ETOHMaxVol, EtOH_3.bottom(z=p300_offset_Res))\n if X == 'A7':\n p300.move_to(A7_p300_bead_side)\n if X == 'A9':\n p300.move_to(A9_p300_bead_side)\n if X == 'A11':\n p300.move_to(A11_p300_bead_side)\n p300.dispense(ETOHMaxVol - 50, rate=0.5)\n p300.move_to(sample_plate_mag[X].center())\n p300.dispense(50, rate=0.5)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 5\n p300.move_to(sample_plate_mag[X].top(z=-2))\n protocol.delay(minutes=0.1)\n p300.blow_out()\n p300.default_speed = 400\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n protocol.delay(minutes=0.5)\n\n protocol.comment('--> Remove ETOH Wash #' + str(wash + 1))\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A7'\n if TIPREUSE == 'NO':\n p300.pick_up_tip()\n elif WASHNUM == 1:\n p300.pick_up_tip(W1_ETOH_removetip_1)\n elif WASHNUM == 2:\n pass\n # FIXME: W2_ETOH_removetip_1 is never defined\n # p300.pick_up_tip(W2_ETOH_removetip_1)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(ETOHMaxVol, rate=0.25)\n p300.default_speed = 5\n if X == 'A7':\n p300.move_to(A7_p300_bead_side)\n if X == 'A9':\n p300.move_to(A9_p300_bead_side)\n if X == 'A11':\n p300.move_to(A11_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(200 - ETOHMaxVol, rate=0.25)\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(Liquid_trash.top(z=5))\n protocol.delay(minutes=0.1)\n p300.blow_out()\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A9'\n if TIPREUSE == 'NO':\n p300.pick_up_tip()\n elif WASHNUM == 1:\n p300.pick_up_tip(W1_ETOH_removetip_2)\n elif WASHNUM == 2:\n pass\n # FIXME: W2_ETOH_removetip_2 is never defined\n # p300.pick_up_tip(W2_ETOH_removetip_2)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(ETOHMaxVol, rate=0.25)\n p300.default_speed = 5\n if X == 'A7':\n p300.move_to(A7_p300_bead_side)\n if X == 'A9':\n p300.move_to(A9_p300_bead_side)\n if X == 'A11':\n p300.move_to(A11_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(200 - ETOHMaxVol, rate=0.25)\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(Liquid_trash.top(z=5))\n protocol.delay(minutes=0.1)\n p300.blow_out()\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A11'\n if TIPREUSE == 'NO':\n p300.pick_up_tip()\n elif WASHNUM == 1:\n p300.pick_up_tip(W1_ETOH_removetip_3)\n elif WASHNUM == 2:\n pass\n # FIXME: W2_ETOH_removetip_3 is never defined\n # p300.pick_up_tip(W2_ETOH_removetip_3)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(ETOHMaxVol, rate=0.25)\n p300.default_speed = 5\n if X == 'A7':\n p300.move_to(A7_p300_bead_side)\n if X == 'A9':\n p300.move_to(A9_p300_bead_side)\n if X == 'A11':\n p300.move_to(A11_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(200 - ETOHMaxVol, rate=0.25)\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(Liquid_trash.top(z=5))\n protocol.delay(minutes=0.1)\n p300.blow_out()\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n wash += 1\n\n if DRYRUN == 'NO':\n protocol.delay(minutes=2)\n\n protocol.comment('--> Removing Residual ETOH')\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A7'\n p20.pick_up_tip()\n p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.aspirate(20, rate=0.25)if NOMODULES == 'NO' else p20.aspirate(\n 10, rate=0.25)\n p20.move_to(bypass)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A9'\n p20.pick_up_tip()\n p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.aspirate(20, rate=0.25)if NOMODULES == 'NO' else p20.aspirate(\n 10, rate=0.25)\n p20.move_to(bypass)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A11'\n p20.pick_up_tip()\n p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.aspirate(20, rate=0.25)if NOMODULES == 'NO' else p20.aspirate(\n 10, rate=0.25)\n p20.move_to(bypass)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n\n if DRYRUN == 'NO':\n mag_block.engage(height_from_base=6)\n protocol.comment('AIR DRY')\n protocol.delay(minutes=0.5)\n\n protocol.comment('MAGNET DISENGAGE')\n mag_block.disengage()\n\n protocol.comment('--> Adding RSB')\n RSBVol = 32\n RSBMixRep = 5\n RSBMixVol = 25\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A7'\n p300.pick_up_tip()\n p300.aspirate(RSBVol, RSB.bottom(p300_offset_Res))\n if X == 'A7':\n p300.move_to(A7_p300_loc1)\n if X == 'A9':\n p300.move_to(A9_p300_loc1)\n if X == 'A11':\n p300.move_to(A11_p300_loc1)\n p300.dispense(RSBVol / 5, rate=0.75)\n p300.default_speed = 5\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.dispense(RSBVol / 5, rate=0.75)\n if X == 'A7':\n p300.move_to(A7_p300_loc3)\n if X == 'A9':\n p300.move_to(A9_p300_loc3)\n if X == 'A11':\n p300.move_to(A11_p300_loc3)\n p300.dispense(RSBVol / 5, rate=0.75)\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.dispense(RSBVol / 5, rate=0.75)\n if X == 'A7':\n p300.move_to(A7_p300_loc1)\n if X == 'A9':\n p300.move_to(A9_p300_loc1)\n if X == 'A11':\n p300.move_to(A11_p300_loc1)\n p300.dispense(RSBVol / 5, rate=0.75)\n reps = 5\n for x in range(reps):\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.aspirate(RSBVol, rate=0.5)\n if X == 'A7':\n p300.move_to(A7_p300_bead_top)\n if X == 'A9':\n p300.move_to(A9_p300_bead_top)\n if X == 'A11':\n p300.move_to(A11_p300_bead_top)\n p300.dispense(RSBVol, rate=1)\n reps = 3\n for x in range(reps):\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.mix(RSBMixRep, RSBMixVol)\n if X == 'A7':\n p300.move_to(A7_p300_loc1)\n if X == 'A9':\n p300.move_to(A9_p300_loc1)\n if X == 'A11':\n p300.move_to(A11_p300_loc1)\n p300.mix(RSBMixRep, RSBMixVol)\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.mix(RSBMixRep, RSBMixVol)\n if X == 'A7':\n p300.move_to(A7_p300_loc3)\n if X == 'A9':\n p300.move_to(A9_p300_loc3)\n if X == 'A11':\n p300.move_to(A11_p300_loc3)\n p300.mix(RSBMixRep, RSBMixVol)\n p300.move_to(sample_plate_mag.wells_by_name()\n [X].bottom(z=p300_offset_Mag))\n p300.mix(RSBMixRep, RSBMixVol)\n p300.move_to(sample_plate_mag.wells_by_name()[X].top())\n protocol.delay(seconds=0.5)\n p300.move_to(sample_plate_mag.wells_by_name()[X].center())\n p300.default_speed = 400\n if TIPREUSE == 'NO':\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n else:\n p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A9'\n p300.pick_up_tip()\n p300.aspirate(RSBVol, RSB.bottom(p300_offset_Res))\n if X == 'A7':\n p300.move_to(A7_p300_loc1)\n if X == 'A9':\n p300.move_to(A9_p300_loc1)\n if X == 'A11':\n p300.move_to(A11_p300_loc1)\n p300.dispense(RSBVol / 5, rate=0.75)\n p300.default_speed = 5\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.dispense(RSBVol / 5, rate=0.75)\n if X == 'A7':\n p300.move_to(A7_p300_loc3)\n if X == 'A9':\n p300.move_to(A9_p300_loc3)\n if X == 'A11':\n p300.move_to(A11_p300_loc3)\n p300.dispense(RSBVol / 5, rate=0.75)\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.dispense(RSBVol / 5, rate=0.75)\n if X == 'A7':\n p300.move_to(A7_p300_loc1)\n if X == 'A9':\n p300.move_to(A9_p300_loc1)\n if X == 'A11':\n p300.move_to(A11_p300_loc1)\n p300.dispense(RSBVol / 5, rate=0.75)\n reps = 5\n for x in range(reps):\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.aspirate(RSBVol, rate=0.5)\n if X == 'A7':\n p300.move_to(A7_p300_bead_top)\n if X == 'A9':\n p300.move_to(A9_p300_bead_top)\n if X == 'A11':\n p300.move_to(A11_p300_bead_top)\n p300.dispense(RSBVol, rate=1)\n reps = 3\n for x in range(reps):\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.mix(RSBMixRep, RSBMixVol)\n if X == 'A7':\n p300.move_to(A7_p300_loc1)\n if X == 'A9':\n p300.move_to(A9_p300_loc1)\n if X == 'A11':\n p300.move_to(A11_p300_loc1)\n p300.mix(RSBMixRep, RSBMixVol)\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.mix(RSBMixRep, RSBMixVol)\n if X == 'A7':\n p300.move_to(A7_p300_loc3)\n if X == 'A9':\n p300.move_to(A9_p300_loc3)\n if X == 'A11':\n p300.move_to(A11_p300_loc3)\n p300.mix(RSBMixRep, RSBMixVol)\n p300.move_to(sample_plate_mag.wells_by_name()\n [X].bottom(z=p300_offset_Mag))\n p300.mix(RSBMixRep, RSBMixVol)\n p300.move_to(sample_plate_mag.wells_by_name()[X].top())\n protocol.delay(seconds=0.5)\n p300.move_to(sample_plate_mag.wells_by_name()[X].center())\n p300.default_speed = 400\n if TIPREUSE == 'NO':\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n else:\n p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A11'\n p300.pick_up_tip()\n p300.aspirate(RSBVol, RSB.bottom(p300_offset_Res))\n if X == 'A7':\n p300.move_to(A7_p300_loc1)\n if X == 'A9':\n p300.move_to(A9_p300_loc1)\n if X == 'A11':\n p300.move_to(A11_p300_loc1)\n p300.dispense(RSBVol / 5, rate=0.75)\n p300.default_speed = 5\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.dispense(RSBVol / 5, rate=0.75)\n if X == 'A7':\n p300.move_to(A7_p300_loc3)\n if X == 'A9':\n p300.move_to(A9_p300_loc3)\n if X == 'A11':\n p300.move_to(A11_p300_loc3)\n p300.dispense(RSBVol / 5, rate=0.75)\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.dispense(RSBVol / 5, rate=0.75)\n if X == 'A7':\n p300.move_to(A7_p300_loc1)\n if X == 'A9':\n p300.move_to(A9_p300_loc1)\n if X == 'A11':\n p300.move_to(A11_p300_loc1)\n p300.dispense(RSBVol / 5, rate=0.75)\n reps = 5\n for x in range(reps):\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.aspirate(RSBVol, rate=0.5)\n if X == 'A7':\n p300.move_to(A7_p300_bead_top)\n if X == 'A9':\n p300.move_to(A9_p300_bead_top)\n if X == 'A11':\n p300.move_to(A11_p300_bead_top)\n p300.dispense(RSBVol, rate=1)\n reps = 3\n for x in range(reps):\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.mix(RSBMixRep, RSBMixVol)\n if X == 'A7':\n p300.move_to(A7_p300_loc1)\n if X == 'A9':\n p300.move_to(A9_p300_loc1)\n if X == 'A11':\n p300.move_to(A11_p300_loc1)\n p300.mix(RSBMixRep, RSBMixVol)\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.mix(RSBMixRep, RSBMixVol)\n if X == 'A7':\n p300.move_to(A7_p300_loc3)\n if X == 'A9':\n p300.move_to(A9_p300_loc3)\n if X == 'A11':\n p300.move_to(A11_p300_loc3)\n p300.mix(RSBMixRep, RSBMixVol)\n p300.move_to(sample_plate_mag.wells_by_name()\n [X].bottom(z=p300_offset_Mag))\n p300.mix(RSBMixRep, RSBMixVol)\n p300.move_to(sample_plate_mag.wells_by_name()[X].top())\n protocol.delay(seconds=0.5)\n p300.move_to(sample_plate_mag.wells_by_name()[X].center())\n p300.default_speed = 400\n if TIPREUSE == 'NO':\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n else:\n p300.return_tip()\n\n if DRYRUN == 'NO':\n protocol.delay(minutes=2)\n\n protocol.comment('MAGNET ENGAGE')\n mag_block.engage(height_from_base=5)\n\n protocol.delay(minutes=4)\n\n protocol.comment('--> Transferring Supernatant')\n\n if NOMODULES == 'NO':\n TransferSup = 30\n else:\n TransferSup = 20\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A7'\n Y = 'A8'\n p20.pick_up_tip()\n p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.aspirate(TransferSup / 2, rate=0.25)\n p20.dispense(\n TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag))\n p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.aspirate(TransferSup / 2, rate=0.25)\n p20.dispense(\n TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag))\n p20.move_to(bypass)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A9'\n Y = 'A10'\n p20.pick_up_tip()\n p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.aspirate(TransferSup / 2, rate=0.25)\n p20.dispense(\n TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag))\n p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.aspirate(TransferSup / 2, rate=0.25)\n p20.dispense(\n TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag))\n p20.move_to(bypass)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A11'\n Y = 'A12'\n p20.pick_up_tip()\n p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.aspirate(TransferSup / 2, rate=0.25)\n p20.dispense(\n TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag))\n p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.aspirate(TransferSup / 2, rate=0.25)\n p20.dispense(\n TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag))\n p20.move_to(bypass)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n\n if DRYRUN == 'NO':\n protocol.comment('MAGNET DISENGAGE')\n mag_block.disengage()\n", - "custom_labware_defs": [], - "fields": [ - { - "label": "Number of samples", - "name": "SAMPLES", - "options": [ - { - "label": "24 samples", - "value": "24x" - }, - { - "label": "16 samples", - "value": "16x" - }, - { - "label": "8 samples", - "value": "8x" - } - ], - "type": "dropDown" - }, - { - "label": "Do a dry run?", - "name": "DRYRUN", - "options": [ - { - "label": "No", - "value": "NO" - }, - { - "label": "Yes", - "value": "YES" - } - ], - "type": "dropDown" - }, - { - "label": "Use modules?", - "name": "NOMODULES", - "options": [ - { - "label": "No", - "value": "NO" - }, - { - "label": "Yes", - "value": "YES" - } - ], - "type": "dropDown" - }, - { - "label": "Tip reuse?", - "name": "TIPREUSE", - "options": [ - { - "label": "No", - "value": "NO" - }, - { - "label": "Yes", - "value": "YES" - } - ], - "type": "dropDown" - }, - { - "label": "Offset?", - "name": "OFFSET", - "options": [ - { - "label": "Yes", - "value": "YES" - }, - { - "label": "No", - "value": "NO" - } - ], - "type": "dropDown" - }, - { - "label": "Include tagmentation step in protocol run?", - "name": "STEP_TAG", - "options": [ - { - "label": "Include", - "value": 1 - }, - { - "label": "Skip", - "value": 0 - } - ], - "type": "dropDown" - }, - { - "label": "Run tagmentation incubation on the deck thermocycler?", - "name": "STEP_TAGDECK", - "options": [ - { - "label": "Yes", - "value": 1 - }, - { - "label": "No", - "value": 0 - } - ], - "type": "dropDown" - }, - { - "label": "Run TSB step?", - "name": "STEP_TSB", - "options": [ - { - "label": "Include", - "value": 1 - }, - { - "label": "Skip", - "value": 0 - } - ], - "type": "dropDown" - }, - { - "label": "Run TSB incubation step on the deck thermocycler", - "name": "STEP_TSBDECK", - "options": [ - { - "label": "Yes", - "value": 1 - }, - { - "label": "No", - "value": 0 - } - ], - "type": "dropDown" - }, - { - "label": "Run tagmentation wash with TWB step", - "name": "STEP_WASH", - "options": [ - { - "label": "Include", - "value": 1 - }, - { - "label": "Skip", - "value": 0 - } - ], - "type": "dropDown" - }, - { - "label": "Run PCR cycle step", - "name": "STEP_PCR", - "options": [ - { - "label": "Include", - "value": 1 - }, - { - "label": "Skip", - "value": 0 - } - ], - "type": "dropDown" - }, - { - "label": "Run PCR step on deck thermocycler?", - "name": "STEP_PCRDECK", - "options": [ - { - "label": "Yes", - "value": 1 - }, - { - "label": "No", - "value": 0 - } - ], - "type": "dropDown" - }, - { - "label": "Run post PCR cleanup step", - "name": "STEP_POSTPCR", - "options": [ - { - "label": "Include", - "value": 1 - }, - { - "label": "Skip", - "value": 0 - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p300_multi_gen2" - }, - { - "mount": "right", - "name": "p20_multi_gen2" - } - ], - "labware": [ - { - "name": "NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 1", - "share": false, - "slot": "1", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "NEST 12 Well Reservoir 15 mL on 2", - "share": false, - "slot": "2", - "type": "nest_12_reservoir_15ml" - }, - { - "name": "Opentrons 96 Well Aluminum Block with Bio-Rad Well Plate 200 \u00b5L on Temperature Module GEN2 on 3", - "share": false, - "slot": "3", - "type": "opentrons_96_aluminumblock_biorad_wellplate_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 4", - "share": false, - "slot": "4", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", - "share": false, - "slot": "7", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.9", - "author": "Opentrons ", - "protocolName": "Illumina DNA Prep", - "source": "Protocol Library" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/sci-macherey-nagel-nucleomag/sci-macherey-nagel-nucleomag.ot2.apiv2.py.json b/protoBuilds/sci-macherey-nagel-nucleomag/sci-macherey-nagel-nucleomag.ot2.apiv2.py.json index b6325090f..06173c226 100644 --- a/protoBuilds/sci-macherey-nagel-nucleomag/sci-macherey-nagel-nucleomag.ot2.apiv2.py.json +++ b/protoBuilds/sci-macherey-nagel-nucleomag/sci-macherey-nagel-nucleomag.ot2.apiv2.py.json @@ -250,5 +250,12 @@ "author": "Opentrons ", "protocolName": "NucleoMag\u00ae Virus Viral DNA/RNA Isolation" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 6 lw deepwell plate on Magnetic Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/sci-mag-bind-blood-tissue-kit/sci-mag-bind-blood-tissue-kit.ot2.apiv2.py.json b/protoBuilds/sci-mag-bind-blood-tissue-kit/sci-mag-bind-blood-tissue-kit.ot2.apiv2.py.json index a86f16694..fe463c127 100644 --- a/protoBuilds/sci-mag-bind-blood-tissue-kit/sci-mag-bind-blood-tissue-kit.ot2.apiv2.py.json +++ b/protoBuilds/sci-mag-bind-blood-tissue-kit/sci-mag-bind-blood-tissue-kit.ot2.apiv2.py.json @@ -232,5 +232,12 @@ "author": "Opentrons ", "protocolName": "Mag-Bind\u00ae Blood & Tissue DNA HDQ 96 Kit" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 6 lw deepwell plate on Magnetic Module GEN1 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/sci-mgi-mgieasy-nucleic-acid-extraction-kit/sci-mgi-mgieasy-nucleic-acid-extraction-kit.ot2.apiv2.py.json b/protoBuilds/sci-mgi-mgieasy-nucleic-acid-extraction-kit/sci-mgi-mgieasy-nucleic-acid-extraction-kit.ot2.apiv2.py.json index 6b2855a5d..ec6355552 100644 --- a/protoBuilds/sci-mgi-mgieasy-nucleic-acid-extraction-kit/sci-mgi-mgieasy-nucleic-acid-extraction-kit.ot2.apiv2.py.json +++ b/protoBuilds/sci-mgi-mgieasy-nucleic-acid-extraction-kit/sci-mgi-mgieasy-nucleic-acid-extraction-kit.ot2.apiv2.py.json @@ -187,5 +187,18 @@ "author": "Opentrons ", "protocolName": "MGIEasy Nucleic Acid Extraction Kit" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 6 lw deepwell plate on Magnetic Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw elution plate on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/sci-omegabiotek-extraction/sci-omegabiotek-extraction.ot2.apiv2.py.json b/protoBuilds/sci-omegabiotek-extraction/sci-omegabiotek-extraction.ot2.apiv2.py.json index 881903d57..64664fd67 100644 --- a/protoBuilds/sci-omegabiotek-extraction/sci-omegabiotek-extraction.ot2.apiv2.py.json +++ b/protoBuilds/sci-omegabiotek-extraction/sci-omegabiotek-extraction.ot2.apiv2.py.json @@ -182,5 +182,12 @@ "protocolName": "Mag-Bind\u00ae Blood & Tissue DNA HDQ 96 Kit", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 6 lw deepwell plate on Magnetic Module GEN1 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/sci-omegabiotek-magbind/sci-omegabiotek-magbind.ot2.apiv2.py.json b/protoBuilds/sci-omegabiotek-magbind/sci-omegabiotek-magbind.ot2.apiv2.py.json index 1ef7ae2ed..ecf6f8a47 100644 --- a/protoBuilds/sci-omegabiotek-magbind/sci-omegabiotek-magbind.ot2.apiv2.py.json +++ b/protoBuilds/sci-omegabiotek-magbind/sci-omegabiotek-magbind.ot2.apiv2.py.json @@ -151,5 +151,18 @@ "author": "Opentrons ", "protocolName": "Mag-Bind\u00ae Viral DNA/RNA 96 Kit" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 3 lw deepwell plate on Magnetic Module GEN1 on 3", + "share": false, + "slot": "3", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw elution plate on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/sci-promega-magazorb-dna-mini-prep-kit/sci-promega-magazorb-dna-mini-prep-kit.ot2.apiv2.py.json b/protoBuilds/sci-promega-magazorb-dna-mini-prep-kit/sci-promega-magazorb-dna-mini-prep-kit.ot2.apiv2.py.json index 00345b692..0a9e19bdd 100644 --- a/protoBuilds/sci-promega-magazorb-dna-mini-prep-kit/sci-promega-magazorb-dna-mini-prep-kit.ot2.apiv2.py.json +++ b/protoBuilds/sci-promega-magazorb-dna-mini-prep-kit/sci-promega-magazorb-dna-mini-prep-kit.ot2.apiv2.py.json @@ -232,5 +232,12 @@ "author": "Opentrons ", "protocolName": "MagaZorb\u00ae DNA Mini-Prep Kit" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 6 lw deepwell plate on Magnetic Module GEN1 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/sci-thermofisher-magmax/extraction.ot2.apiv2.py.json b/protoBuilds/sci-thermofisher-magmax/extraction.ot2.apiv2.py.json index 10d6782c8..6646742bc 100644 --- a/protoBuilds/sci-thermofisher-magmax/extraction.ot2.apiv2.py.json +++ b/protoBuilds/sci-thermofisher-magmax/extraction.ot2.apiv2.py.json @@ -214,5 +214,18 @@ "author": "Opentrons ", "protocolName": "Thermofisher MagMAX Viral/Pathogen Kit" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 6 lw deepwell plate on Magnetic Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw elution plate on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/sci-zymo-directzol-magbead/sci-zymo-directzol-magbead.ot2.apiv2.py.json b/protoBuilds/sci-zymo-directzol-magbead/sci-zymo-directzol-magbead.ot2.apiv2.py.json index 8aa6db59b..42a9760d8 100644 --- a/protoBuilds/sci-zymo-directzol-magbead/sci-zymo-directzol-magbead.ot2.apiv2.py.json +++ b/protoBuilds/sci-zymo-directzol-magbead/sci-zymo-directzol-magbead.ot2.apiv2.py.json @@ -181,5 +181,18 @@ "author": "Opentrons ", "protocolName": "Zymo Research Direct-zol\u2122-96 MagBead RNA Kit" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 6 lw deepwell plate on Magnetic Module GEN1 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/swift-2s-turbo-pt1/swift-2s-turbo-pt1.ot2.apiv2.py.json b/protoBuilds/swift-2s-turbo-pt1/swift-2s-turbo-pt1.ot2.apiv2.py.json index 801f13ee7..94cd12d78 100644 --- a/protoBuilds/swift-2s-turbo-pt1/swift-2s-turbo-pt1.ot2.apiv2.py.json +++ b/protoBuilds/swift-2s-turbo-pt1/swift-2s-turbo-pt1.ot2.apiv2.py.json @@ -87,5 +87,12 @@ "protocolName": "Swift 2S Turbo DNA Library Kit Protocol: Part 1/3 - Enzymatic Prep & Ligation", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 3 lw Opentrons 24-Well Aluminum Block on Temperature Module GEN1 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/thermocycler/thermocycler.ot2.apiv2.py.json b/protoBuilds/thermocycler/thermocycler.ot2.apiv2.py.json index d3a64c665..fb4803c4a 100644 --- a/protoBuilds/thermocycler/thermocycler.ot2.apiv2.py.json +++ b/protoBuilds/thermocycler/thermocycler.ot2.apiv2.py.json @@ -102,5 +102,12 @@ "protocolName": "Thermocycler Example Protocol", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw None", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/zymo-quick-96/zymo-quick-96.ot2.apiv2.py.json b/protoBuilds/zymo-quick-96/zymo-quick-96.ot2.apiv2.py.json index 6e478c31e..7c49c5d4d 100644 --- a/protoBuilds/zymo-quick-96/zymo-quick-96.ot2.apiv2.py.json +++ b/protoBuilds/zymo-quick-96/zymo-quick-96.ot2.apiv2.py.json @@ -1268,5 +1268,12 @@ "protocolName": "Zymo Quick-DNA/RNA Viral Kit [Custom]", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 7 lw VWR 96 Well Plate 1000 \u00b5L on Magnetic Module GEN2 on 7", + "share": false, + "slot": "7", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/zymo-quick-custom/zymo-quick-custom.ot2.apiv2.py.json b/protoBuilds/zymo-quick-custom/zymo-quick-custom.ot2.apiv2.py.json index d1e5fc31d..a7c6457f4 100644 --- a/protoBuilds/zymo-quick-custom/zymo-quick-custom.ot2.apiv2.py.json +++ b/protoBuilds/zymo-quick-custom/zymo-quick-custom.ot2.apiv2.py.json @@ -154,5 +154,12 @@ "protocolName": "Zymo Quick-DNA/RNA Viral Kit with PCR Prep", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/zymo-quick/zymo-quick.ot2.apiv2.py.json b/protoBuilds/zymo-quick/zymo-quick.ot2.apiv2.py.json index 2566963ab..140d0242f 100644 --- a/protoBuilds/zymo-quick/zymo-quick.ot2.apiv2.py.json +++ b/protoBuilds/zymo-quick/zymo-quick.ot2.apiv2.py.json @@ -169,5 +169,12 @@ "protocolName": "Zymo Quick-DNA/RNA Viral Kit", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/zymo-ribofree-cleanup/cleanup.ot2.apiv2.py.json b/protoBuilds/zymo-ribofree-cleanup/cleanup.ot2.apiv2.py.json index 74d449a8f..92c6bd231 100644 --- a/protoBuilds/zymo-ribofree-cleanup/cleanup.ot2.apiv2.py.json +++ b/protoBuilds/zymo-ribofree-cleanup/cleanup.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "import math\nimport json\nimport os\nfrom opentrons.types import Point\n\nmetadata = {\n 'protocolName': 'Zymo-Seq RiboFree\u2122 Total RNA Library Prep Select-a-Size \\\nMagBead Clean-up (robot 2)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.0'\n}\n\n\ndef run(ctx):\n\n [number_of_samples, cleanup_stage, p20_mount,\n p300_mount] = get_values( # noqa: F821\n 'number_of_samples', 'cleanup_stage', 'p20_mount', 'p300_mount')\n\n # load modules and labware\n racks20 = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['1', '4']\n ]\n elution_plate = ctx.load_labware(\n 'nest_96_wellplate_100ul_pcr_full_skirt', '2', 'elution PCR plate')\n reagent_res = ctx.load_labware(\n 'nest_12_reservoir_15ml', '3', 'reagent reservoir')\n magdeck = ctx.load_module('magnetic module gen2', '6')\n mag_plate = magdeck.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')\n racks300 = [\n ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in ['5', '8', '10', '11']\n ]\n waste = ctx.load_labware(\n 'agilent_1_reservoir_290ml', '9', 'waste reservoir').wells()[0].top()\n\n # pipettes\n if p20_mount == p300_mount:\n raise Exception('Pipette mounts cannot match.')\n m20 = ctx.load_instrument('p20_multi_gen2', p20_mount)\n m300 = ctx.load_instrument('p300_multi_gen2', p300_mount)\n\n file_path = '/data/csv/tip_track.json'\n # file_path = 'protocols/tip_track.json'\n if os.path.isfile(file_path):\n with open(file_path) as json_file:\n data = json.load(json_file)\n if 'tips20' in data:\n tip20_count = data['tips20']\n else:\n tip20_count = 0\n if 'tips300' in data:\n tip300_count = data['tips300']\n else:\n tip300_count = 0\n else:\n tip20_count = 0\n tip300_count = 0\n\n all_tips20 = [tip for rack in racks20 for tip in rack.rows()[0]]\n all_tips300 = [tip for rack in racks300 for tip in rack.rows()[0]]\n tip20_max = len(all_tips20)\n tip300_max = len(all_tips300)\n\n def pick_up(pip):\n nonlocal tip20_count\n nonlocal tip300_count\n if pip == m20:\n if tip20_count == tip20_max:\n ctx.pause('Replace 20\u00b5l tipracks before resuming.')\n tip20_count = 0\n [rack.reset() for rack in racks300]\n pip.pick_up_tip(all_tips20[tip20_count])\n tip20_count += 1\n else:\n if tip300_count == tip300_max:\n ctx.pause('Replace tipracks before resuming.')\n tip300_count = 0\n [rack.reset() for rack in racks300]\n pip.pick_up_tip(all_tips300[tip300_count])\n tip300_count += 1\n\n # reagents and sample setup\n if number_of_samples > 96 or number_of_samples < 1:\n raise Exception('Invalid number of samples (must be 1-96).')\n mag_samples = mag_plate.rows()[0][:math.ceil(number_of_samples/8)]\n elution_samples = elution_plate.rows()[0][:math.ceil(number_of_samples/8)]\n beads = reagent_res.wells()[0]\n wash_buffer = reagent_res.wells()[1:4]\n dna_eb = reagent_res.wells()[4]\n # waste = [chan.top() for chan in reagent_res.wells()[6:]]\n\n # setup cleanup parameters\n if cleanup_stage == 'post-first-strand synthesis and universal depletion':\n start_vol = 75\n bead_vol = 150\n elution_vol = 10\n tempdeck = ctx.load_module('temperature module gen2', '7')\n # tempplate = tempdeck.load_labware(\n # 'opentrons_96_aluminumblock_nest_wellplate_100ul')\n inc_temp = 95\n inc_time = 5\n end_msg = 'This is a safe stopping point. Cleaned-up DNA can be safely \\\nstored at \u2264 4\u00b0C overnight or \u2264 \u221220\u00b0C for up to one week.'\n elif cleanup_stage == 'post-P7 adapter ligation':\n start_vol = 40\n bead_vol = 60\n elution_vol = 10\n inc_temp = None\n inc_time = None\n end_msg = 'This is a safe stopping point. Cleaned-up DNA can be safely \\\nstored at \u2264 4\u00b0C overnight or \u2264 \u221220\u00b0C for up to one week.'\n elif cleanup_stage == 'post-P5 adapter ligation':\n start_vol = 100\n bead_vol = 100\n elution_vol = 20\n inc_temp = None\n inc_time = None\n end_msg = 'This is a safe stopping point. Cleaned-up DNA can be safely \\\nstored at \u2264 4\u00b0C overnight or \u2264 \u221220\u00b0C for up to one week.'\n elif cleanup_stage == 'post-library index PCR':\n start_vol = 100\n bead_vol = 85\n elution_vol = 20\n inc_temp = None\n inc_time = None\n end_msg = 'The eluate is your final RNA-Seq library 3. Libraries may be \\\nstored at \u2264 4\u00b0C overnight or \u2264 -20\u00b0C for long-term storage.'\n\n \"\"\" Appendix A: Select-a-Size MagBead Clean-up Protocol \"\"\"\n # mix and transfer beads\n pick_up(m300)\n for _ in range(10):\n m300.aspirate(250, beads.bottom(2))\n m300.dispense(250, beads.bottom(20))\n for m in mag_samples:\n if not m300.hw_pipette['has_tip']:\n pick_up(m300)\n m300.transfer(\n bead_vol,\n beads,\n m,\n air_gap=20,\n mix_after=(5, bead_vol),\n new_tip='never'\n )\n m300.drop_tip()\n\n ctx.delay(minutes=5, msg='Incubating at room temperature for 5 minutes')\n\n # separate beads and remove supernatant\n magdeck.engage()\n ctx.delay(minutes=3, msg='Incubating on magnet for 3 minutes.')\n supernatant_vol = start_vol + bead_vol\n for i, m in enumerate(mag_samples):\n pick_up(m300)\n m300.aspirate(supernatant_vol*1.1, m)\n m300.air_gap(20)\n m300.dispense(supernatant_vol*1.1+30, waste)\n m300.air_gap(20)\n # m300.transfer(\n # supernatant_vol*1.1, m, waste[i//6], air_gap=30, new_tip='never')\n m300.drop_tip()\n\n # 2x washes\n for wash in range(2):\n pick_up(m300)\n for i, m in enumerate(mag_samples):\n chan = (i+wash*12)//8\n m300.transfer(\n 200,\n wash_buffer[chan],\n m.top(),\n air_gap=20,\n new_tip='never'\n )\n for i, m in enumerate(mag_samples):\n if not m300.hw_pipette['has_tip']:\n pick_up(m300)\n chan = (i+wash*12)//8\n side = -1 if i % 2 == 0 else 1\n loc = m.bottom().move(Point(x=side*m.diameter/2*0.9, z=0.5))\n m300.move_to(m.center())\n m300.aspirate(supernatant_vol*1.1, m)\n m300.air_gap(20)\n m300.dispense(supernatant_vol*1.1+30, waste)\n m300.air_gap(20)\n m300.drop_tip()\n\n magdeck.disengage()\n ctx.delay(minutes=3, msg='Airdrying beads for 3 minutes.')\n\n # resuspend in elution buffer\n for i, m in enumerate(mag_samples):\n side = 1 if i % 2 == 0 else -1\n loc = m.bottom().move(Point(x=side*m.diameter/2*0.9, y=0, z=0.5))\n pick_up(m20)\n if elution_vol > 10:\n pre_vol = elution_vol - 10\n m20.transfer(pre_vol, dna_eb, m.top(), new_tip='never')\n m20.blow_out(m.top())\n m20.aspirate(10, dna_eb)\n m20.move_to(m.center())\n m20.dispense(10, loc)\n m20.mix(10, 9, m)\n m20.blow_out(m.top(-2))\n m20.air_gap(5)\n m20.drop_tip()\n\n if inc_temp and inc_time:\n tempdeck.set_temperature(inc_temp)\n # m20.move_to(tempplate.wells()[0].top(10))\n m20.home()\n ctx.pause('Transfer plate from magnetic module to aluminum block on \\\ntemperature module. Once you resume, the plate will incubate for \\\n' + str(inc_temp) + ' minutes.')\n ctx.delay(minutes=inc_time)\n ctx.pause('Transfer plate back to magnetic module from aluminum block \\\non temperature module.')\n\n magdeck.engage()\n ctx.delay(minutes=3, msg='Incubating on magnet for 3 minutes.')\n\n # transfer elution to new plate\n for m, e in zip(mag_samples, elution_samples):\n pick_up(m20)\n side = -1 if i % 2 == 0 else 1\n loc = m.bottom().move(Point(x=side*m.diameter/2*0.9, z=0.5))\n m20.move_to(m.center())\n m20.transfer(elution_vol, loc, e, new_tip='never')\n m20.blow_out(e.top(-2))\n m20.air_gap(5)\n m20.drop_tip()\n\n magdeck.disengage()\n if cleanup_stage == 'post-first-strand synthesis and universal depletion':\n tempdeck.deactivate()\n ctx.comment(end_msg)\n\n # track final used tip\n if not ctx.is_simulating():\n file_path = '/data/csv/tip_track.json'\n # file_path = '/protocols/tip_track.json'\n if cleanup_stage == 'post-library index PCR':\n data = {\n 'tips20': 0,\n 'tips300': 0\n }\n else:\n data = {\n 'tips20': tip20_count,\n 'tips300': tip300_count\n }\n with open(file_path, 'w') as outfile:\n json.dump(data, outfile)\n", + "content": "import math\nimport json\nimport os\nfrom opentrons.types import Point\n\nmetadata = {\n 'protocolName': 'Zymo-Seq RiboFree\u2122 Total RNA Library Prep Select-a-Size \\\nMagBead Clean-up (robot 2)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.3'\n}\n\n\ndef run(ctx):\n\n [number_of_samples, cleanup_stage, p20_mount,\n p300_mount] = get_values( # noqa: F821\n 'number_of_samples', 'cleanup_stage', 'p20_mount', 'p300_mount')\n\n # load modules and labware\n racks20 = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['1', '4']\n ]\n elution_plate = ctx.load_labware(\n 'nest_96_wellplate_100ul_pcr_full_skirt', '2', 'elution PCR plate')\n reagent_res = ctx.load_labware(\n 'nest_12_reservoir_15ml', '3', 'reagent reservoir')\n magdeck = ctx.load_module('magnetic module gen2', '6')\n mag_plate = magdeck.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')\n racks300 = [\n ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in ['5', '8', '10', '11']\n ]\n waste = ctx.load_labware(\n 'agilent_1_reservoir_290ml', '9', 'waste reservoir').wells()[0].top()\n\n # pipettes\n if p20_mount == p300_mount:\n raise Exception('Pipette mounts cannot match.')\n m20 = ctx.load_instrument('p20_multi_gen2', p20_mount)\n m300 = ctx.load_instrument('p300_multi_gen2', p300_mount)\n\n file_path = '/data/csv/tip_track.json'\n # file_path = 'protocols/tip_track.json'\n if os.path.isfile(file_path):\n with open(file_path) as json_file:\n data = json.load(json_file)\n if 'tips20' in data:\n tip20_count = data['tips20']\n else:\n tip20_count = 0\n if 'tips300' in data:\n tip300_count = data['tips300']\n else:\n tip300_count = 0\n else:\n tip20_count = 0\n tip300_count = 0\n\n all_tips20 = [tip for rack in racks20 for tip in rack.rows()[0]]\n all_tips300 = [tip for rack in racks300 for tip in rack.rows()[0]]\n tip20_max = len(all_tips20)\n tip300_max = len(all_tips300)\n\n def pick_up(pip):\n nonlocal tip20_count\n nonlocal tip300_count\n if pip == m20:\n if tip20_count == tip20_max:\n ctx.pause('Replace 20\u00b5l tipracks before resuming.')\n tip20_count = 0\n [rack.reset() for rack in racks300]\n pip.pick_up_tip(all_tips20[tip20_count])\n tip20_count += 1\n else:\n if tip300_count == tip300_max:\n ctx.pause('Replace tipracks before resuming.')\n tip300_count = 0\n [rack.reset() for rack in racks300]\n pip.pick_up_tip(all_tips300[tip300_count])\n tip300_count += 1\n\n # reagents and sample setup\n if number_of_samples > 96 or number_of_samples < 1:\n raise Exception('Invalid number of samples (must be 1-96).')\n mag_samples = mag_plate.rows()[0][:math.ceil(number_of_samples/8)]\n elution_samples = elution_plate.rows()[0][:math.ceil(number_of_samples/8)]\n beads = reagent_res.wells()[0]\n wash_buffer = reagent_res.wells()[1:4]\n dna_eb = reagent_res.wells()[4]\n # waste = [chan.top() for chan in reagent_res.wells()[6:]]\n\n # setup cleanup parameters\n if cleanup_stage == 'post-first-strand synthesis and universal depletion':\n start_vol = 75\n bead_vol = 150\n elution_vol = 10\n tempdeck = ctx.load_module('temperature module gen2', '7')\n # tempplate = tempdeck.load_labware(\n # 'opentrons_96_aluminumblock_nest_wellplate_100ul')\n inc_temp = 95\n inc_time = 5\n end_msg = 'This is a safe stopping point. Cleaned-up DNA can be safely \\\nstored at \u2264 4\u00b0C overnight or \u2264 \u221220\u00b0C for up to one week.'\n elif cleanup_stage == 'post-P7 adapter ligation':\n start_vol = 40\n bead_vol = 60\n elution_vol = 10\n inc_temp = None\n inc_time = None\n end_msg = 'This is a safe stopping point. Cleaned-up DNA can be safely \\\nstored at \u2264 4\u00b0C overnight or \u2264 \u221220\u00b0C for up to one week.'\n elif cleanup_stage == 'post-P5 adapter ligation':\n start_vol = 100\n bead_vol = 100\n elution_vol = 20\n inc_temp = None\n inc_time = None\n end_msg = 'This is a safe stopping point. Cleaned-up DNA can be safely \\\nstored at \u2264 4\u00b0C overnight or \u2264 \u221220\u00b0C for up to one week.'\n elif cleanup_stage == 'post-library index PCR':\n start_vol = 100\n bead_vol = 85\n elution_vol = 20\n inc_temp = None\n inc_time = None\n end_msg = 'The eluate is your final RNA-Seq library 3. Libraries may be \\\nstored at \u2264 4\u00b0C overnight or \u2264 -20\u00b0C for long-term storage.'\n\n \"\"\" Appendix A: Select-a-Size MagBead Clean-up Protocol \"\"\"\n # mix and transfer beads\n pick_up(m300)\n for _ in range(10):\n m300.aspirate(250, beads.bottom(2))\n m300.dispense(250, beads.bottom(20))\n for m in mag_samples:\n if not m300.hw_pipette['has_tip']:\n pick_up(m300)\n m300.transfer(\n bead_vol,\n beads,\n m,\n air_gap=20,\n mix_after=(5, bead_vol),\n new_tip='never'\n )\n m300.drop_tip()\n\n ctx.delay(minutes=5, msg='Incubating at room temperature for 5 minutes')\n\n # separate beads and remove supernatant\n magdeck.engage()\n ctx.delay(minutes=3, msg='Incubating on magnet for 3 minutes.')\n supernatant_vol = start_vol + bead_vol\n for i, m in enumerate(mag_samples):\n pick_up(m300)\n m300.aspirate(supernatant_vol*1.1, m)\n m300.air_gap(20)\n m300.dispense(supernatant_vol*1.1+30, waste)\n m300.air_gap(20)\n # m300.transfer(\n # supernatant_vol*1.1, m, waste[i//6], air_gap=30, new_tip='never')\n m300.drop_tip()\n\n # 2x washes\n for wash in range(2):\n pick_up(m300)\n for i, m in enumerate(mag_samples):\n chan = (i+wash*12)//8\n m300.transfer(\n 200,\n wash_buffer[chan],\n m.top(),\n air_gap=20,\n new_tip='never'\n )\n for i, m in enumerate(mag_samples):\n if not m300.hw_pipette['has_tip']:\n pick_up(m300)\n chan = (i+wash*12)//8\n side = -1 if i % 2 == 0 else 1\n loc = m.bottom().move(Point(x=side*m.diameter/2*0.9, z=0.5))\n m300.move_to(m.center())\n m300.aspirate(supernatant_vol*1.1, m)\n m300.air_gap(20)\n m300.dispense(supernatant_vol*1.1+30, waste)\n m300.air_gap(20)\n m300.drop_tip()\n\n magdeck.disengage()\n ctx.delay(minutes=3, msg='Airdrying beads for 3 minutes.')\n\n # resuspend in elution buffer\n for i, m in enumerate(mag_samples):\n side = 1 if i % 2 == 0 else -1\n loc = m.bottom().move(Point(x=side*m.diameter/2*0.9, y=0, z=0.5))\n pick_up(m20)\n if elution_vol > 10:\n pre_vol = elution_vol - 10\n m20.transfer(pre_vol, dna_eb, m.top(), new_tip='never')\n m20.blow_out(m.top())\n m20.aspirate(10, dna_eb)\n m20.move_to(m.center())\n m20.dispense(10, loc)\n m20.mix(10, 9, m)\n m20.blow_out(m.top(-2))\n m20.air_gap(5)\n m20.drop_tip()\n\n if inc_temp and inc_time:\n tempdeck.set_temperature(inc_temp)\n # m20.move_to(tempplate.wells()[0].top(10))\n m20.home()\n ctx.pause('Transfer plate from magnetic module to aluminum block on \\\ntemperature module. Once you resume, the plate will incubate for \\\n' + str(inc_temp) + ' minutes.')\n ctx.delay(minutes=inc_time)\n ctx.pause('Transfer plate back to magnetic module from aluminum block \\\non temperature module.')\n\n magdeck.engage()\n ctx.delay(minutes=3, msg='Incubating on magnet for 3 minutes.')\n\n # transfer elution to new plate\n for m, e in zip(mag_samples, elution_samples):\n pick_up(m20)\n side = -1 if i % 2 == 0 else 1\n loc = m.bottom().move(Point(x=side*m.diameter/2*0.9, z=0.5))\n m20.move_to(m.center())\n m20.transfer(elution_vol, loc, e, new_tip='never')\n m20.blow_out(e.top(-2))\n m20.air_gap(5)\n m20.drop_tip()\n\n magdeck.disengage()\n if cleanup_stage == 'post-first-strand synthesis and universal depletion':\n tempdeck.deactivate()\n ctx.comment(end_msg)\n\n # track final used tip\n if not ctx.is_simulating():\n file_path = '/data/csv/tip_track.json'\n # file_path = '/protocols/tip_track.json'\n if cleanup_stage == 'post-library index PCR':\n data = {\n 'tips20': 0,\n 'tips300': 0\n }\n else:\n data = {\n 'tips20': tip20_count,\n 'tips300': tip300_count\n }\n with open(file_path, 'w') as outfile:\n json.dump(data, outfile)\n", "custom_labware_defs": [], "fields": [ { @@ -141,10 +141,23 @@ } ], "metadata": { - "apiLevel": "2.0", + "apiLevel": "2.3", "author": "Nick ", "protocolName": "Zymo-Seq RiboFree\u2122 Total RNA Library Prep Select-a-Size MagBead Clean-up (robot 2)", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 6 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 7 lw None", + "share": false, + "slot": "7", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/zymo-ribofree-first-strand-cdna-synth-universal-depletion/1_first_strand_synth_uni_depletion.ot2.apiv2.py.json b/protoBuilds/zymo-ribofree-first-strand-cdna-synth-universal-depletion/1_first_strand_synth_uni_depletion.ot2.apiv2.py.json index 8ca7e5b62..8638d5174 100644 --- a/protoBuilds/zymo-ribofree-first-strand-cdna-synth-universal-depletion/1_first_strand_synth_uni_depletion.ot2.apiv2.py.json +++ b/protoBuilds/zymo-ribofree-first-strand-cdna-synth-universal-depletion/1_first_strand_synth_uni_depletion.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "import math\nimport json\n\nmetadata = {\n 'protocolName': 'Zymo-Seq RiboFree\u2122 Total RNA Library Prep First-Strand \\\ncDNA Synthesis and RiboFreeTM Universal Depletion (robot 1)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.0'\n}\n\n\ndef run(ctx):\n\n [number_of_samples, starting_vol, rna_input, p20_mount,\n m20_mount] = get_values( # noqa: F821\n 'number_of_samples', 'starting_vol', 'rna_input', 'p20_mount',\n 'm20_mount')\n # [number_of_samples, starting_vol, rna_input, p20_mount, p50_mount] = [\n # 96, 5, '> 1\u00b5g', 'right', 'left']\n\n # load modules and labware\n tc = ctx.load_module('thermocycler')\n tc.set_lid_temperature(100)\n tc.set_block_temperature(4)\n tc_plate = tc.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')\n racks20s = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['1', '2', '3']\n ]\n tempdeck = ctx.load_module('temperature module gen2', '4')\n tempdeck.set_temperature(4)\n tempblock = tempdeck.load_labware(\n 'opentrons_24_aluminumblock_nest_1.5ml_screwcap')\n reagent_res = ctx.load_labware(\n 'nest_12_reservoir_15ml', '5', 'reagent reservoir')\n racks20m = [ctx.load_labware('opentrons_96_tiprack_20ul', '6')]\n\n # pipettes\n if p20_mount == m20_mount:\n raise Exception('Pipette mounts cannot match.')\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=racks20s)\n p20.flow_rate.aspirate = 10\n p20.flow_rate.dispense = 20\n p20.flow_rate.blow_out = 30\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=racks20m)\n\n # reagents and sample setup\n if number_of_samples > 96 or number_of_samples < 1:\n raise Exception('Invalid number of samples (must be 1-96).')\n samples = tc_plate.wells()[:number_of_samples]\n samples_multi = tc_plate.rows()[0][:math.ceil(number_of_samples/8)]\n r1, r2, h2o = tempblock.rows()[0][:3]\n d1, d2, d3 = tempblock.rows()[1][:3]\n etoh = reagent_res.wells()[0]\n\n tip20s_count = 0\n all_tips20s = [tip for rack in racks20s for tip in rack.wells()]\n all_tips20m = [tip for rack in racks20m for tip in rack.rows()[0]]\n tip20m_count = 0\n tip20m_max = len(racks20m*12)\n tip20s_max = len(racks20s*96)\n\n def pick_up(pip):\n nonlocal tip20s_count\n nonlocal tip20m_count\n if pip == p20:\n if tip20s_count == tip20s_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20s_count = 0\n [rack.reset() for rack in racks20s]\n pip.pick_up_tip(all_tips20s[tip20s_count])\n tip20s_count += 1\n else:\n if tip20m_count == tip20m_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20m_count = 0\n [rack.reset() for rack in racks20m]\n pip.pick_up_tip(all_tips20m[tip20m_count])\n tip20m_count += 1\n\n \"\"\" Section 1.1: First-Strand cDNA Synthesis (Yellow Caps) \"\"\"\n if tc.lid_position == 'closed':\n tc.open_lid()\n\n # bring samples up to 8\u00b5l with H2O if necessary\n vol_h2o = 9 - starting_vol if rna_input != '< 100ng' else 8 - starting_vol\n for s in samples:\n pick_up(p20)\n p20.transfer(vol_h2o, h2o, s, new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n\n # transfer R1\n vol_r1 = 1 if rna_input != '< 100ng' else 2\n for s in samples:\n pick_up(p20)\n p20.transfer(vol_r1, r1, s, mix_after=(3, 5), new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n ctx.pause('Briefly spin down plate before resuming.')\n\n # execute primer annealing\n profile_1_1 = [\n {'temperature': 98, 'hold_time_minutes': 3},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_1_1, repetitions=1, block_max_volume=10)\n tc.open_lid()\n\n # transfer R2\n for s in samples:\n pick_up(p20)\n p20.transfer(10, r2, s, mix_after=(3, 15), new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n\n # execute reverse transcription\n profile_1_2 = [\n {'temperature': 25, 'hold_time_minutes': 5},\n {'temperature': 48, 'hold_time_minutes': 15},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_1_2, repetitions=1, block_max_volume=20)\n tc.open_lid()\n\n \"\"\" Section 1.2: RiboFreeTM Universal Depletion (Red Caps) \"\"\"\n\n # distribute D reagents to predispesing plate\n if number_of_samples > 24:\n predispense_plate = ctx.load_labware(\n 'nest_96_wellplate_100ul_pcr_full_skirt', '9',\n 'plate to predispense D reagent')\n vol_per_well = 11*math.ceil(number_of_samples/8)\n for d_reagent, col in zip(\n [d1, d2, d3], predispense_plate.columns()[:3]):\n pick_up(p20)\n for well in col:\n p20.transfer(\n vol_per_well, d_reagent, well, air_gap=1, new_tip='never')\n p20.blow_out(well.top(-5))\n p20.touch_tip(well)\n p20.drop_tip()\n d1, d2, d3 = predispense_plate.rows()[0][:3]\n d_pip = m20\n d_samples = samples_multi\n else:\n d_pip = p20\n d_samples = samples\n\n # transfer D1\n for s in d_samples:\n pick_up(d_pip)\n d_pip.transfer(10, d1, s, mix_after=(3, 15), new_tip='never')\n d_pip.blow_out(s.top(-2))\n d_pip.drop_tip()\n ctx.pause('Briefly spin down plate before resuming.')\n\n # execute pre-depletion incubation\n profile_1_3 = [\n {'temperature': 98, 'hold_time_minutes': 3},\n {'temperature': 68, 'hold_time_minutes': 5}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_1_3, repetitions=1, block_max_volume=30)\n tc.open_lid()\n\n # transfer D2\n for s in d_samples:\n pick_up(d_pip)\n d_pip.transfer(10, d2, s, mix_after=(3, 15), new_tip='never')\n d_pip.blow_out(s.top(-2))\n d_pip.drop_tip()\n\n # exeute depletion reaction\n if rna_input == '> 1\u00b5g':\n inc_time = 30\n elif rna_input == '250ng-1\u00b5g':\n inc_time = 60\n else:\n inc_time = 120\n profile_1_4 = [\n {'temperature': 68, 'hold_time_minutes': inc_time}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_1_4, repetitions=1, block_max_volume=40)\n tc.open_lid()\n\n # transfer D3\n for s in d_samples:\n pick_up(d_pip)\n d_pip.transfer(10, d3, s, mix_after=(3, 15), new_tip='never')\n d_pip.blow_out(s.top(-2))\n d_pip.drop_tip()\n\n # execute stop depletion\n profile_1_5 = [\n {'temperature': 98, 'hold_time_minutes': 2},\n {'temperature': 25, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_1_5, repetitions=1, block_max_volume=50)\n tc.open_lid()\n\n # transfer EtOH\n for m in samples_multi:\n pick_up(m20)\n m20.transfer(\n 25, etoh, m.top(-2), air_gap=2, new_tip='never')\n m20.mix(5, 20, m),\n m20.blow_out(m.top(-2))\n m20.air_gap(2)\n m20.drop_tip()\n\n ctx.comment('Carefully remove sample plate from thermocycler and proceed \\\nwith cleanup.')\n\n # track final used tip\n if not ctx.is_simulating():\n file_path = '/data/csv/tip_track.json'\n # file_path = '/protocols/tip_track.json'\n data = {\n 'tips20s': tip20s_count,\n 'tips20m': tip20m_count\n }\n with open(file_path, 'w') as outfile:\n json.dump(data, outfile)\n", + "content": "import math\nimport json\n\nmetadata = {\n 'protocolName': 'Zymo-Seq RiboFree\u2122 Total RNA Library Prep First-Strand \\\ncDNA Synthesis and RiboFreeTM Universal Depletion (robot 1)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.3'\n}\n\n\ndef run(ctx):\n\n [number_of_samples, starting_vol, rna_input, p20_mount,\n m20_mount] = get_values( # noqa: F821\n 'number_of_samples', 'starting_vol', 'rna_input', 'p20_mount',\n 'm20_mount')\n # [number_of_samples, starting_vol, rna_input, p20_mount, p50_mount] = [\n # 96, 5, '> 1\u00b5g', 'right', 'left']\n\n # load modules and labware\n tc = ctx.load_module('thermocycler')\n tc.set_lid_temperature(100)\n tc.set_block_temperature(4)\n tc_plate = tc.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')\n racks20s = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['1', '2', '3']\n ]\n tempdeck = ctx.load_module('temperature module gen2', '4')\n tempdeck.set_temperature(4)\n tempblock = tempdeck.load_labware(\n 'opentrons_24_aluminumblock_nest_1.5ml_screwcap')\n reagent_res = ctx.load_labware(\n 'nest_12_reservoir_15ml', '5', 'reagent reservoir')\n racks20m = [ctx.load_labware('opentrons_96_tiprack_20ul', '6')]\n\n # pipettes\n if p20_mount == m20_mount:\n raise Exception('Pipette mounts cannot match.')\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=racks20s)\n p20.flow_rate.aspirate = 10\n p20.flow_rate.dispense = 20\n p20.flow_rate.blow_out = 30\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=racks20m)\n\n # reagents and sample setup\n if number_of_samples > 96 or number_of_samples < 1:\n raise Exception('Invalid number of samples (must be 1-96).')\n samples = tc_plate.wells()[:number_of_samples]\n samples_multi = tc_plate.rows()[0][:math.ceil(number_of_samples/8)]\n r1, r2, h2o = tempblock.rows()[0][:3]\n d1, d2, d3 = tempblock.rows()[1][:3]\n etoh = reagent_res.wells()[0]\n\n tip20s_count = 0\n all_tips20s = [tip for rack in racks20s for tip in rack.wells()]\n all_tips20m = [tip for rack in racks20m for tip in rack.rows()[0]]\n tip20m_count = 0\n tip20m_max = len(racks20m*12)\n tip20s_max = len(racks20s*96)\n\n def pick_up(pip):\n nonlocal tip20s_count\n nonlocal tip20m_count\n if pip == p20:\n if tip20s_count == tip20s_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20s_count = 0\n [rack.reset() for rack in racks20s]\n pip.pick_up_tip(all_tips20s[tip20s_count])\n tip20s_count += 1\n else:\n if tip20m_count == tip20m_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20m_count = 0\n [rack.reset() for rack in racks20m]\n pip.pick_up_tip(all_tips20m[tip20m_count])\n tip20m_count += 1\n\n \"\"\" Section 1.1: First-Strand cDNA Synthesis (Yellow Caps) \"\"\"\n if tc.lid_position == 'closed':\n tc.open_lid()\n\n # bring samples up to 8\u00b5l with H2O if necessary\n vol_h2o = 9 - starting_vol if rna_input != '< 100ng' else 8 - starting_vol\n for s in samples:\n pick_up(p20)\n p20.transfer(vol_h2o, h2o, s, new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n\n # transfer R1\n vol_r1 = 1 if rna_input != '< 100ng' else 2\n for s in samples:\n pick_up(p20)\n p20.transfer(vol_r1, r1, s, mix_after=(3, 5), new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n ctx.pause('Briefly spin down plate before resuming.')\n\n # execute primer annealing\n profile_1_1 = [\n {'temperature': 98, 'hold_time_minutes': 3},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_1_1, repetitions=1, block_max_volume=10)\n tc.open_lid()\n\n # transfer R2\n for s in samples:\n pick_up(p20)\n p20.transfer(10, r2, s, mix_after=(3, 15), new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n\n # execute reverse transcription\n profile_1_2 = [\n {'temperature': 25, 'hold_time_minutes': 5},\n {'temperature': 48, 'hold_time_minutes': 15},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_1_2, repetitions=1, block_max_volume=20)\n tc.open_lid()\n\n \"\"\" Section 1.2: RiboFreeTM Universal Depletion (Red Caps) \"\"\"\n\n # distribute D reagents to predispesing plate\n if number_of_samples > 24:\n predispense_plate = ctx.load_labware(\n 'nest_96_wellplate_100ul_pcr_full_skirt', '9',\n 'plate to predispense D reagent')\n vol_per_well = 11*math.ceil(number_of_samples/8)\n for d_reagent, col in zip(\n [d1, d2, d3], predispense_plate.columns()[:3]):\n pick_up(p20)\n for well in col:\n p20.transfer(\n vol_per_well, d_reagent, well, air_gap=1, new_tip='never')\n p20.blow_out(well.top(-5))\n p20.touch_tip(well)\n p20.drop_tip()\n d1, d2, d3 = predispense_plate.rows()[0][:3]\n d_pip = m20\n d_samples = samples_multi\n else:\n d_pip = p20\n d_samples = samples\n\n # transfer D1\n for s in d_samples:\n pick_up(d_pip)\n d_pip.transfer(10, d1, s, mix_after=(3, 15), new_tip='never')\n d_pip.blow_out(s.top(-2))\n d_pip.drop_tip()\n ctx.pause('Briefly spin down plate before resuming.')\n\n # execute pre-depletion incubation\n profile_1_3 = [\n {'temperature': 98, 'hold_time_minutes': 3},\n {'temperature': 68, 'hold_time_minutes': 5}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_1_3, repetitions=1, block_max_volume=30)\n tc.open_lid()\n\n # transfer D2\n for s in d_samples:\n pick_up(d_pip)\n d_pip.transfer(10, d2, s, mix_after=(3, 15), new_tip='never')\n d_pip.blow_out(s.top(-2))\n d_pip.drop_tip()\n\n # exeute depletion reaction\n if rna_input == '> 1\u00b5g':\n inc_time = 30\n elif rna_input == '250ng-1\u00b5g':\n inc_time = 60\n else:\n inc_time = 120\n profile_1_4 = [\n {'temperature': 68, 'hold_time_minutes': inc_time}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_1_4, repetitions=1, block_max_volume=40)\n tc.open_lid()\n\n # transfer D3\n for s in d_samples:\n pick_up(d_pip)\n d_pip.transfer(10, d3, s, mix_after=(3, 15), new_tip='never')\n d_pip.blow_out(s.top(-2))\n d_pip.drop_tip()\n\n # execute stop depletion\n profile_1_5 = [\n {'temperature': 98, 'hold_time_minutes': 2},\n {'temperature': 25, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_1_5, repetitions=1, block_max_volume=50)\n tc.open_lid()\n\n # transfer EtOH\n for m in samples_multi:\n pick_up(m20)\n m20.transfer(\n 25, etoh, m.top(-2), air_gap=2, new_tip='never')\n m20.mix(5, 20, m),\n m20.blow_out(m.top(-2))\n m20.air_gap(2)\n m20.drop_tip()\n\n ctx.comment('Carefully remove sample plate from thermocycler and proceed \\\nwith cleanup.')\n\n # track final used tip\n if not ctx.is_simulating():\n file_path = '/data/csv/tip_track.json'\n # file_path = '/protocols/tip_track.json'\n data = {\n 'tips20s': tip20s_count,\n 'tips20m': tip20m_count\n }\n with open(file_path, 'w') as outfile:\n json.dump(data, outfile)\n", "custom_labware_defs": [], "fields": [ { @@ -135,10 +135,23 @@ } ], "metadata": { - "apiLevel": "2.0", + "apiLevel": "2.3", "author": "Nick ", "protocolName": "Zymo-Seq RiboFree\u2122 Total RNA Library Prep First-Strand cDNA Synthesis and RiboFreeTM Universal Depletion (robot 1)", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 4 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Screwcap on Temperature Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/zymo-ribofree-library-index-pcr/4_library_index_pcr.ot2.apiv2.py.json b/protoBuilds/zymo-ribofree-library-index-pcr/4_library_index_pcr.ot2.apiv2.py.json index d29328c13..f92abdd22 100644 --- a/protoBuilds/zymo-ribofree-library-index-pcr/4_library_index_pcr.ot2.apiv2.py.json +++ b/protoBuilds/zymo-ribofree-library-index-pcr/4_library_index_pcr.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "import math\nimport json\nimport os\n\nmetadata = {\n 'protocolName': 'Zymo-Seq RiboFree\u2122 Total RNA Library Prep Library Index \\\nPCR (robot 1)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.0'\n}\n\n\ndef run(ctx):\n\n [number_of_samples, rna_input, p20_mount,\n m20_mount] = get_values( # noqa: F821\n 'number_of_samples', 'rna_input', 'p20_mount', 'm20_mount')\n # [number_of_samples, rna_input, p20_mount, m20_mount] = [\n # 96, '> 1\u00b5g', 'right', 'left']\n\n # load modules and labware\n tc = ctx.load_module('thermocycler')\n tc.set_lid_temperature(100)\n tc.set_block_temperature(4)\n tc_plate = tc.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')\n racks20s = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['1', '2']\n ]\n tempdeck = ctx.load_module('temperature module gen2', '4')\n tempdeck.set_temperature(4)\n tempblock = tempdeck.load_labware(\n 'opentrons_24_aluminumblock_nest_1.5ml_screwcap')\n reagent_res = ctx.load_labware(\n 'nest_12_reservoir_15ml', '5', 'reagent reservoir')\n index_plate = ctx.load_labware(\n 'opentrons_96_aluminumblock_nest_wellplate_100ul',\n '9', 'UDI primer plate')\n racks20m = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['3', '6']\n ]\n\n # pipettes\n if p20_mount == m20_mount:\n raise Exception('Pipette mounts cannot match.')\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=racks20s)\n p20.flow_rate.aspirate = 10\n p20.flow_rate.dispense = 20\n p20.flow_rate.blow_out = 30\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=racks20m)\n\n # file_path = 'protocols/tip_track.json'\n if not ctx.is_simulating():\n file_path = '/data/csv/tip_track.json'\n if os.path.isfile(file_path):\n with open(file_path) as json_file:\n data = json.load(json_file)\n if 'tips20s' in data:\n tip20s_count = data['tips20s'] % 96\n else:\n tip20s_count = 0\n if 'tips20m' in data:\n tip20m_count = data['tips20m'] % 12\n else:\n tip20m_count = 0\n else:\n tip20s_count = 0\n tip20m_count = 0\n\n all_tips20s = [tip for rack in racks20s for tip in rack.wells()]\n all_tips20m = [tip for rack in racks20m for tip in rack.rows()[0]]\n tip20s_max = len(all_tips20s)\n tip20m_max = len(all_tips20m)\n\n def pick_up(pip):\n nonlocal tip20s_count\n nonlocal tip20m_count\n if pip == p20:\n if tip20s_count == tip20s_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20s_count = 0\n [rack.reset() for rack in racks20s]\n pip.pick_up_tip(all_tips20s[tip20s_count])\n tip20s_count += 1\n else:\n if tip20m_count == tip20m_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20m_count = 0\n [rack.reset() for rack in racks20m]\n pip.pick_up_tip(all_tips20m[tip20m_count])\n tip20m_count += 1\n\n # reagents and sample setup\n if number_of_samples > 96 or number_of_samples < 1:\n raise Exception('Invalid number of samples (must be 1-96).')\n samples = tc_plate.wells()[:number_of_samples]\n udi_primers = index_plate.rows()[0][:math.ceil(number_of_samples/8)]\n samples_multi = tc_plate.rows()[0][:math.ceil(number_of_samples/8)]\n taq_premix = tempblock.rows()[3][0]\n dna_eb = reagent_res.wells()[1]\n\n \"\"\" Section 2.3: Library Index PCR (Green Caps) \"\"\"\n if tc.lid_position == 'closed':\n tc.open_lid()\n\n # transfer UDI primers\n for m in samples_multi:\n pick_up(m20)\n m20.transfer(\n 5, udi_primers, m, mix_after=(3, 15), air_gap=1, new_tip='never')\n m20.blow_out(m.top(-2))\n m20.drop_tip()\n\n # transfer taq premix\n for s in samples:\n for i, vol in enumerate([15, 10]):\n pick_up(p20)\n p20.transfer(vol, taq_premix, s.bottom(1), new_tip='never')\n if i == 0:\n p20.drop_tip()\n p20.mix(3, 15, s)\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n ctx.pause('Briefly spin down sample plate and replace on thermoycler.')\n\n # run first part of profile 1\n tc.close_lid()\n if rna_input == '> 1\u00b5g':\n cycles = 10\n elif rna_input == '250ng-1\u00b5g':\n cycles = 11\n elif rna_input == '100ng-250ng':\n cycles = 12\n elif rna_input == '< 100ng':\n cycles = 13\n profile_2_4 = [{'temperature': 95, 'hold_time_minutes': 10}]\n profile_2_5 = [\n {'temperature': 95, 'hold_time_seconds': 30},\n {'temperature': 60, 'hold_time_seconds': 30},\n {'temperature': 72, 'hold_time_minutes': 1}\n ]\n profile_2_6 = [\n {'temperature': 72, 'hold_time_minutes': 7},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.execute_profile(steps=profile_2_4, repetitions=1, block_max_volume=50)\n tc.execute_profile(\n steps=profile_2_5, repetitions=cycles, block_max_volume=50)\n tc.execute_profile(steps=profile_2_6, repetitions=1, block_max_volume=50)\n tc.open_lid()\n\n # transfer elution buffer\n for m in samples_multi:\n pick_up(m20)\n m20.transfer(50, dna_eb, m.top(-2), new_tip='never')\n m20.mix(5, 15, m)\n m20.blow_out(m.top(-2))\n m20.drop_tip()\n\n ctx.comment('Carefully remove sample plate from thermocycler and proceed \\\nwith cleanup.')\n", + "content": "import math\nimport json\nimport os\n\nmetadata = {\n 'protocolName': 'Zymo-Seq RiboFree\u2122 Total RNA Library Prep Library Index \\\nPCR (robot 1)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.3'\n}\n\n\ndef run(ctx):\n\n [number_of_samples, rna_input, p20_mount,\n m20_mount] = get_values( # noqa: F821\n 'number_of_samples', 'rna_input', 'p20_mount', 'm20_mount')\n # [number_of_samples, rna_input, p20_mount, m20_mount] = [\n # 96, '> 1\u00b5g', 'right', 'left']\n\n # load modules and labware\n tc = ctx.load_module('thermocycler')\n tc.set_lid_temperature(100)\n tc.set_block_temperature(4)\n tc_plate = tc.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')\n racks20s = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['1', '2']\n ]\n tempdeck = ctx.load_module('temperature module gen2', '4')\n tempdeck.set_temperature(4)\n tempblock = tempdeck.load_labware(\n 'opentrons_24_aluminumblock_nest_1.5ml_screwcap')\n reagent_res = ctx.load_labware(\n 'nest_12_reservoir_15ml', '5', 'reagent reservoir')\n index_plate = ctx.load_labware(\n 'opentrons_96_aluminumblock_nest_wellplate_100ul',\n '9', 'UDI primer plate')\n racks20m = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['3', '6']\n ]\n\n # pipettes\n if p20_mount == m20_mount:\n raise Exception('Pipette mounts cannot match.')\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=racks20s)\n p20.flow_rate.aspirate = 10\n p20.flow_rate.dispense = 20\n p20.flow_rate.blow_out = 30\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=racks20m)\n\n # file_path = 'protocols/tip_track.json'\n if not ctx.is_simulating():\n file_path = '/data/csv/tip_track.json'\n if os.path.isfile(file_path):\n with open(file_path) as json_file:\n data = json.load(json_file)\n if 'tips20s' in data:\n tip20s_count = data['tips20s'] % 96\n else:\n tip20s_count = 0\n if 'tips20m' in data:\n tip20m_count = data['tips20m'] % 12\n else:\n tip20m_count = 0\n else:\n tip20s_count = 0\n tip20m_count = 0\n\n all_tips20s = [tip for rack in racks20s for tip in rack.wells()]\n all_tips20m = [tip for rack in racks20m for tip in rack.rows()[0]]\n tip20s_max = len(all_tips20s)\n tip20m_max = len(all_tips20m)\n\n def pick_up(pip):\n nonlocal tip20s_count\n nonlocal tip20m_count\n if pip == p20:\n if tip20s_count == tip20s_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20s_count = 0\n [rack.reset() for rack in racks20s]\n pip.pick_up_tip(all_tips20s[tip20s_count])\n tip20s_count += 1\n else:\n if tip20m_count == tip20m_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20m_count = 0\n [rack.reset() for rack in racks20m]\n pip.pick_up_tip(all_tips20m[tip20m_count])\n tip20m_count += 1\n\n # reagents and sample setup\n if number_of_samples > 96 or number_of_samples < 1:\n raise Exception('Invalid number of samples (must be 1-96).')\n samples = tc_plate.wells()[:number_of_samples]\n udi_primers = index_plate.rows()[0][:math.ceil(number_of_samples/8)]\n samples_multi = tc_plate.rows()[0][:math.ceil(number_of_samples/8)]\n taq_premix = tempblock.rows()[3][0]\n dna_eb = reagent_res.wells()[1]\n\n \"\"\" Section 2.3: Library Index PCR (Green Caps) \"\"\"\n if tc.lid_position == 'closed':\n tc.open_lid()\n\n # transfer UDI primers\n for m in samples_multi:\n pick_up(m20)\n m20.transfer(\n 5, udi_primers, m, mix_after=(3, 15), air_gap=1, new_tip='never')\n m20.blow_out(m.top(-2))\n m20.drop_tip()\n\n # transfer taq premix\n for s in samples:\n for i, vol in enumerate([15, 10]):\n pick_up(p20)\n p20.transfer(vol, taq_premix, s.bottom(1), new_tip='never')\n if i == 0:\n p20.drop_tip()\n p20.mix(3, 15, s)\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n ctx.pause('Briefly spin down sample plate and replace on thermoycler.')\n\n # run first part of profile 1\n tc.close_lid()\n if rna_input == '> 1\u00b5g':\n cycles = 10\n elif rna_input == '250ng-1\u00b5g':\n cycles = 11\n elif rna_input == '100ng-250ng':\n cycles = 12\n elif rna_input == '< 100ng':\n cycles = 13\n profile_2_4 = [{'temperature': 95, 'hold_time_minutes': 10}]\n profile_2_5 = [\n {'temperature': 95, 'hold_time_seconds': 30},\n {'temperature': 60, 'hold_time_seconds': 30},\n {'temperature': 72, 'hold_time_minutes': 1}\n ]\n profile_2_6 = [\n {'temperature': 72, 'hold_time_minutes': 7},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.execute_profile(steps=profile_2_4, repetitions=1, block_max_volume=50)\n tc.execute_profile(\n steps=profile_2_5, repetitions=cycles, block_max_volume=50)\n tc.execute_profile(steps=profile_2_6, repetitions=1, block_max_volume=50)\n tc.open_lid()\n\n # transfer elution buffer\n for m in samples_multi:\n pick_up(m20)\n m20.transfer(50, dna_eb, m.top(-2), new_tip='never')\n m20.mix(5, 15, m)\n m20.blow_out(m.top(-2))\n m20.drop_tip()\n\n ctx.comment('Carefully remove sample plate from thermocycler and proceed \\\nwith cleanup.')\n", "custom_labware_defs": [], "fields": [ { @@ -129,10 +129,23 @@ } ], "metadata": { - "apiLevel": "2.0", + "apiLevel": "2.3", "author": "Nick ", "protocolName": "Zymo-Seq RiboFree\u2122 Total RNA Library Prep Library Index PCR (robot 1)", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 4 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Screwcap on Temperature Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/zymo-ribofree-p5-adapter-ligation/3_p5_adapter_ligation.ot2.apiv2.py.json b/protoBuilds/zymo-ribofree-p5-adapter-ligation/3_p5_adapter_ligation.ot2.apiv2.py.json index cec4ece47..bf04c5e19 100644 --- a/protoBuilds/zymo-ribofree-p5-adapter-ligation/3_p5_adapter_ligation.ot2.apiv2.py.json +++ b/protoBuilds/zymo-ribofree-p5-adapter-ligation/3_p5_adapter_ligation.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "import math\nimport json\nimport os\n\nmetadata = {\n 'protocolName': 'Zymo-Seq RiboFree\u2122 Total RNA Library Prep P5 Adapter \\\nLigation (robot 1)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.0'\n}\n\n\ndef run(ctx):\n\n [number_of_samples, p20_mount, m20_mount] = get_values( # noqa: F821\n 'number_of_samples', 'p20_mount', 'm20_mount')\n # [number_of_samples, p20_mount, m20_mount] = [96, 'right', 'left']\n\n # load modules and labware\n tc = ctx.load_module('thermocycler')\n tc.set_lid_temperature(100)\n tc.set_block_temperature(4)\n tc_plate = tc.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')\n racks20s = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['1', '2', '3', '6']\n ]\n tempdeck = ctx.load_module('temperature module gen2', '4')\n tempdeck.set_temperature(4)\n tempblock = tempdeck.load_labware(\n 'opentrons_24_aluminumblock_nest_1.5ml_screwcap')\n reagent_res = ctx.load_labware(\n 'nest_12_reservoir_15ml', '5', 'reagent reservoir')\n racks20m = [ctx.load_labware('opentrons_96_tiprack_20ul', '9')]\n\n # pipettes\n if p20_mount == m20_mount:\n raise Exception('Pipette mounts cannot match.')\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=racks20s)\n p20.flow_rate.aspirate = 10\n p20.flow_rate.dispense = 20\n p20.flow_rate.blow_out = 30\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=racks20m)\n\n if not ctx.is_simulating():\n file_path = '/data/csv/tip_track.json'\n # file_path = 'protocols/tip_track.json'\n if os.path.isfile(file_path):\n with open(file_path) as json_file:\n data = json.load(json_file)\n if 'tips20s' in data:\n tip20s_count = data['tips20s']\n else:\n tip20s_count = 0\n if 'tips20m' in data:\n tip20m_count = data['tips20m']\n else:\n tip20m_count = 0\n else:\n tip20s_count = 0\n tip20m_count = 0\n\n all_tips20s = [tip for rack in racks20s for tip in rack.wells()]\n all_tips20m = [tip for rack in racks20m for tip in rack.rows()[0]]\n tip20s_max = len(all_tips20s)\n tip20m_max = len(all_tips20m)\n\n def pick_up(pip):\n nonlocal tip20s_count\n nonlocal tip20m_count\n if pip == p20:\n if tip20s_count == tip20s_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20s_count = 0\n [rack.reset() for rack in racks20s]\n pip.pick_up_tip(all_tips20s[tip20s_count])\n tip20s_count += 1\n else:\n if tip20m_count == tip20m_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20m_count = 0\n [rack.reset() for rack in racks20m]\n pip.pick_up_tip(all_tips20m[tip20m_count])\n tip20m_count += 1\n\n # reagents and sample setup\n if number_of_samples > 96 or number_of_samples < 1:\n raise Exception('Invalid number of samples (must be 1-96).')\n samples = tc_plate.wells()[:number_of_samples]\n samples_multi = tc_plate.rows()[0][:math.ceil(number_of_samples/8)]\n l3 = tempblock.rows()[2][2]\n dna_eb = reagent_res.wells()[1]\n\n \"\"\" Section 2.2: P5 Adapter Ligation (Green Caps) \"\"\"\n if tc.lid_position == 'closed':\n tc.open_lid()\n\n # transfer L3\n for s in samples:\n pick_up(p20)\n p20.transfer(10, l3, s, mix_after=(3, 15), new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n ctx.pause('Briefly spin down plate before resuming.')\n\n # execute P5 ligation reaction\n profile_2_3 = [\n {'temperature': 25, 'hold_time_minutes': 15},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_2_3, repetitions=1, block_max_volume=20)\n tc.open_lid()\n\n # transer DNA elution buffer\n ctx.pause('Briefly spin down plate before resuming.')\n for m in samples_multi:\n pick_up(m20)\n m20.transfer(80, dna_eb, m.top(-2), new_tip='never')\n m20.mix(5, 15, m)\n m20.blow_out(m.top(-2))\n m20.drop_tip()\n\n ctx.comment('Carefully remove sample plate from thermocycler and proceed \\\nwith cleanup.')\n\n # track final used tip\n # file_path = '/data/csv/tip_track.json'\n if not ctx.is_simulating():\n data = {\n 'tips20s': tip20s_count,\n 'tips20m': tip20m_count\n }\n with open(file_path, 'w') as outfile:\n json.dump(data, outfile)\n", + "content": "import math\nimport json\nimport os\n\nmetadata = {\n 'protocolName': 'Zymo-Seq RiboFree\u2122 Total RNA Library Prep P5 Adapter \\\nLigation (robot 1)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.3'\n}\n\n\ndef run(ctx):\n\n [number_of_samples, p20_mount, m20_mount] = get_values( # noqa: F821\n 'number_of_samples', 'p20_mount', 'm20_mount')\n # [number_of_samples, p20_mount, m20_mount] = [96, 'right', 'left']\n\n # load modules and labware\n tc = ctx.load_module('thermocycler')\n tc.set_lid_temperature(100)\n tc.set_block_temperature(4)\n tc_plate = tc.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')\n racks20s = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['1', '2', '3', '6']\n ]\n tempdeck = ctx.load_module('temperature module gen2', '4')\n tempdeck.set_temperature(4)\n tempblock = tempdeck.load_labware(\n 'opentrons_24_aluminumblock_nest_1.5ml_screwcap')\n reagent_res = ctx.load_labware(\n 'nest_12_reservoir_15ml', '5', 'reagent reservoir')\n racks20m = [ctx.load_labware('opentrons_96_tiprack_20ul', '9')]\n\n # pipettes\n if p20_mount == m20_mount:\n raise Exception('Pipette mounts cannot match.')\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=racks20s)\n p20.flow_rate.aspirate = 10\n p20.flow_rate.dispense = 20\n p20.flow_rate.blow_out = 30\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=racks20m)\n\n if not ctx.is_simulating():\n file_path = '/data/csv/tip_track.json'\n # file_path = 'protocols/tip_track.json'\n if os.path.isfile(file_path):\n with open(file_path) as json_file:\n data = json.load(json_file)\n if 'tips20s' in data:\n tip20s_count = data['tips20s']\n else:\n tip20s_count = 0\n if 'tips20m' in data:\n tip20m_count = data['tips20m']\n else:\n tip20m_count = 0\n else:\n tip20s_count = 0\n tip20m_count = 0\n\n all_tips20s = [tip for rack in racks20s for tip in rack.wells()]\n all_tips20m = [tip for rack in racks20m for tip in rack.rows()[0]]\n tip20s_max = len(all_tips20s)\n tip20m_max = len(all_tips20m)\n\n def pick_up(pip):\n nonlocal tip20s_count\n nonlocal tip20m_count\n if pip == p20:\n if tip20s_count == tip20s_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20s_count = 0\n [rack.reset() for rack in racks20s]\n pip.pick_up_tip(all_tips20s[tip20s_count])\n tip20s_count += 1\n else:\n if tip20m_count == tip20m_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20m_count = 0\n [rack.reset() for rack in racks20m]\n pip.pick_up_tip(all_tips20m[tip20m_count])\n tip20m_count += 1\n\n # reagents and sample setup\n if number_of_samples > 96 or number_of_samples < 1:\n raise Exception('Invalid number of samples (must be 1-96).')\n samples = tc_plate.wells()[:number_of_samples]\n samples_multi = tc_plate.rows()[0][:math.ceil(number_of_samples/8)]\n l3 = tempblock.rows()[2][2]\n dna_eb = reagent_res.wells()[1]\n\n \"\"\" Section 2.2: P5 Adapter Ligation (Green Caps) \"\"\"\n if tc.lid_position == 'closed':\n tc.open_lid()\n\n # transfer L3\n for s in samples:\n pick_up(p20)\n p20.transfer(10, l3, s, mix_after=(3, 15), new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n ctx.pause('Briefly spin down plate before resuming.')\n\n # execute P5 ligation reaction\n profile_2_3 = [\n {'temperature': 25, 'hold_time_minutes': 15},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_2_3, repetitions=1, block_max_volume=20)\n tc.open_lid()\n\n # transer DNA elution buffer\n ctx.pause('Briefly spin down plate before resuming.')\n for m in samples_multi:\n pick_up(m20)\n m20.transfer(80, dna_eb, m.top(-2), new_tip='never')\n m20.mix(5, 15, m)\n m20.blow_out(m.top(-2))\n m20.drop_tip()\n\n ctx.comment('Carefully remove sample plate from thermocycler and proceed \\\nwith cleanup.')\n\n # track final used tip\n # file_path = '/data/csv/tip_track.json'\n if not ctx.is_simulating():\n data = {\n 'tips20s': tip20s_count,\n 'tips20m': tip20m_count\n }\n with open(file_path, 'w') as outfile:\n json.dump(data, outfile)\n", "custom_labware_defs": [], "fields": [ { @@ -106,10 +106,23 @@ } ], "metadata": { - "apiLevel": "2.0", + "apiLevel": "2.3", "author": "Nick ", "protocolName": "Zymo-Seq RiboFree\u2122 Total RNA Library Prep P5 Adapter Ligation (robot 1)", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 4 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Screwcap on Temperature Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/zymo-ribofree-p7-adapter-ligation/2_p7_adapter_ligation.ot2.apiv2.py.json b/protoBuilds/zymo-ribofree-p7-adapter-ligation/2_p7_adapter_ligation.ot2.apiv2.py.json index 03c6da2e8..944173eaa 100644 --- a/protoBuilds/zymo-ribofree-p7-adapter-ligation/2_p7_adapter_ligation.ot2.apiv2.py.json +++ b/protoBuilds/zymo-ribofree-p7-adapter-ligation/2_p7_adapter_ligation.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "import json\nimport os\n\nmetadata = {\n 'protocolName': 'Zymo-Seq RiboFree\u2122 Total RNA Library Prep P7 Adapter \\\nLigation (robot 1)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.0'\n}\n\n\ndef run(ctx):\n\n [number_of_samples, p20_mount] = get_values( # noqa: F821\n 'number_of_samples', 'p20_mount')\n # [number_of_samples, p20_mount] = [96, 'right']\n\n # load modules and labware\n tc = ctx.load_module('thermocycler')\n tc.set_lid_temperature(100)\n tc.set_block_temperature(4)\n tc_plate = tc.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')\n racks20 = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['1', '2', '3', '6']\n ]\n tempdeck = ctx.load_module('temperature module gen2', '4')\n tempdeck.set_temperature(4)\n tempblock = tempdeck.load_labware(\n 'opentrons_24_aluminumblock_nest_1.5ml_screwcap')\n\n # pipettes\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=racks20)\n p20.flow_rate.aspirate = 10\n p20.flow_rate.dispense = 20\n p20.flow_rate.blow_out = 30\n\n # file_path = 'protocols/tip_track.json'\n if not ctx.is_simulating():\n file_path = '/data/csv/tip_track.json'\n if os.path.isfile(file_path):\n with open(file_path) as json_file:\n data = json.load(json_file)\n if 'tips20' in data:\n tip20_count = data['tips20']\n else:\n tip20_count = 0\n else:\n tip20_count = 0\n\n all_tips20 = [tip for rack in racks20 for tip in rack.wells()]\n tip20_max = len(all_tips20)\n\n def pick_up():\n nonlocal tip20_count\n if tip20_count == tip20_max:\n ctx.pause('Replace 20\u00b5l tipracks before resuming.')\n tip20_count = 0\n [rack.reset() for rack in racks20]\n p20.pick_up_tip(all_tips20[tip20_count])\n tip20_count += 1\n\n # reagents and sample setup\n if number_of_samples > 96 or number_of_samples < 1:\n raise Exception('Invalid number of samples (must be 1-96).')\n samples = tc_plate.wells()[:number_of_samples]\n l1, l2 = tempblock.rows()[2][:2]\n\n \"\"\" Section 2.1: P7 Adapter Ligation (Green Caps) \"\"\"\n if tc.lid_position == 'closed':\n tc.open_lid()\n\n # transfer L1\n for s in samples:\n p20.pick_up_tip()\n p20.transfer(10, l1, s, mix_after=(3, 15), new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n ctx.pause('Briefly spin down plate before resuming.')\n\n # execute P7 ligation reaction\n profile_2_1 = [\n {'temperature': 37, 'hold_time_minutes': 15},\n {'temperature': 98, 'hold_time_minutes': 2},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_2_1, repetitions=1, block_max_volume=20)\n tc.open_lid()\n\n # transfer L2\n for s in samples:\n p20.pick_up_tip()\n p20.transfer(20, l2, s, mix_after=(3, 15), new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n ctx.pause('Briefly spin down plate before resuming.')\n\n # execute second strand synthesis\n profile_2_2 = [\n {'temperature': 95, 'hold_time_minutes': 10},\n {'temperature': 63, 'hold_time_seconds': 30},\n {'temperature': 72, 'hold_time_minutes': 7},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_2_2, repetitions=1, block_max_volume=40)\n tc.open_lid()\n\n ctx.comment('Carefully remove sample plate from thermocycler and proceed \\\nwith cleanup.')\n\n # track final used tip\n # file_path = '/data/csv/tip_track.json'\n if not ctx.is_simulating():\n data = {\n 'tips20': tip20_count\n }\n with open(file_path, 'w') as outfile:\n json.dump(data, outfile)\n", + "content": "import json\nimport os\n\nmetadata = {\n 'protocolName': 'Zymo-Seq RiboFree\u2122 Total RNA Library Prep P7 Adapter \\\nLigation (robot 1)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.3'\n}\n\n\ndef run(ctx):\n\n [number_of_samples, p20_mount] = get_values( # noqa: F821\n 'number_of_samples', 'p20_mount')\n # [number_of_samples, p20_mount] = [96, 'right']\n\n # load modules and labware\n tc = ctx.load_module('thermocycler')\n tc.set_lid_temperature(100)\n tc.set_block_temperature(4)\n tc_plate = tc.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')\n racks20 = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['1', '2', '3', '6']\n ]\n tempdeck = ctx.load_module('temperature module gen2', '4')\n tempdeck.set_temperature(4)\n tempblock = tempdeck.load_labware(\n 'opentrons_24_aluminumblock_nest_1.5ml_screwcap')\n\n # pipettes\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=racks20)\n p20.flow_rate.aspirate = 10\n p20.flow_rate.dispense = 20\n p20.flow_rate.blow_out = 30\n\n # file_path = 'protocols/tip_track.json'\n if not ctx.is_simulating():\n file_path = '/data/csv/tip_track.json'\n if os.path.isfile(file_path):\n with open(file_path) as json_file:\n data = json.load(json_file)\n if 'tips20' in data:\n tip20_count = data['tips20']\n else:\n tip20_count = 0\n else:\n tip20_count = 0\n\n all_tips20 = [tip for rack in racks20 for tip in rack.wells()]\n tip20_max = len(all_tips20)\n\n def pick_up():\n nonlocal tip20_count\n if tip20_count == tip20_max:\n ctx.pause('Replace 20\u00b5l tipracks before resuming.')\n tip20_count = 0\n [rack.reset() for rack in racks20]\n p20.pick_up_tip(all_tips20[tip20_count])\n tip20_count += 1\n\n # reagents and sample setup\n if number_of_samples > 96 or number_of_samples < 1:\n raise Exception('Invalid number of samples (must be 1-96).')\n samples = tc_plate.wells()[:number_of_samples]\n l1, l2 = tempblock.rows()[2][:2]\n\n \"\"\" Section 2.1: P7 Adapter Ligation (Green Caps) \"\"\"\n if tc.lid_position == 'closed':\n tc.open_lid()\n\n # transfer L1\n for s in samples:\n p20.pick_up_tip()\n p20.transfer(10, l1, s, mix_after=(3, 15), new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n ctx.pause('Briefly spin down plate before resuming.')\n\n # execute P7 ligation reaction\n profile_2_1 = [\n {'temperature': 37, 'hold_time_minutes': 15},\n {'temperature': 98, 'hold_time_minutes': 2},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_2_1, repetitions=1, block_max_volume=20)\n tc.open_lid()\n\n # transfer L2\n for s in samples:\n p20.pick_up_tip()\n p20.transfer(20, l2, s, mix_after=(3, 15), new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n ctx.pause('Briefly spin down plate before resuming.')\n\n # execute second strand synthesis\n profile_2_2 = [\n {'temperature': 95, 'hold_time_minutes': 10},\n {'temperature': 63, 'hold_time_seconds': 30},\n {'temperature': 72, 'hold_time_minutes': 7},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_2_2, repetitions=1, block_max_volume=40)\n tc.open_lid()\n\n ctx.comment('Carefully remove sample plate from thermocycler and proceed \\\nwith cleanup.')\n\n # track final used tip\n # file_path = '/data/csv/tip_track.json'\n if not ctx.is_simulating():\n data = {\n 'tips20': tip20_count\n }\n with open(file_path, 'w') as outfile:\n json.dump(data, outfile)\n", "custom_labware_defs": [], "fields": [ { @@ -75,10 +75,23 @@ } ], "metadata": { - "apiLevel": "2.0", + "apiLevel": "2.3", "author": "Nick ", "protocolName": "Zymo-Seq RiboFree\u2122 Total RNA Library Prep P7 Adapter Ligation (robot 1)", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 4 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Screwcap on Temperature Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/zymo-rna-extraction/zymo-rna-extraction.ot2.apiv2.py.json b/protoBuilds/zymo-rna-extraction/zymo-rna-extraction.ot2.apiv2.py.json index d276be662..6f26d9f12 100644 --- a/protoBuilds/zymo-rna-extraction/zymo-rna-extraction.ot2.apiv2.py.json +++ b/protoBuilds/zymo-rna-extraction/zymo-rna-extraction.ot2.apiv2.py.json @@ -79,13 +79,13 @@ "type": "nest_12_reservoir_15ml" }, { - "name": "Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN1 on 3", + "name": "Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module on 3", "share": false, "slot": "3", "type": "opentrons_96_aluminumblock_nest_wellplate_100ul" }, { - "name": "NEST 96 Deepwell Plate 2mL on Magnetic Module GEN1 on 4", + "name": "NEST 96 Deepwell Plate 2mL on Magnetic Module on 4", "share": false, "slot": "4", "type": "nest_96_wellplate_2ml_deep" @@ -145,5 +145,18 @@ "protocolName": "Zymo Quick-DNA/RNA MagBead Station B", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 4 lw NEST 96 Deepwell Plate 2mL on Magnetic Module on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module on 3 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protocols/118e8c/118e8c.ot2.apiv2.py b/protocols/118e8c/118e8c.ot2.apiv2.py index 8dc8a6579..29f4a9c2e 100644 --- a/protocols/118e8c/118e8c.ot2.apiv2.py +++ b/protocols/118e8c/118e8c.ot2.apiv2.py @@ -145,7 +145,7 @@ def height_dec(self, vol): self.current_volume = self.current_volume - vol else: self.current_volume = 0 - return(self.well.bottom(self.height)) + return (self.well.bottom(self.height)) def height_inc(self, vol, top=False): if self.diameter is not None: @@ -161,9 +161,9 @@ def height_inc(self, vol, top=False): self.height = self.depth self.current_volume += vol if top is False: - return(self.well.bottom(self.height)) + return (self.well.bottom(self.height)) else: - return(self.well.top()) + return (self.well.top()) # to track liquid height water = WellH(w, min_height=1, current_volume=water_volume) @@ -194,14 +194,14 @@ def pick_up(pip): p20m.flow_rate.dispense = 3.8 # capture and report original value for p20m pick_up_current - default_current = ctx._implementation._hw_manager.hardware.\ + default_current = ctx._hw_manager.hardware.\ _attached_instruments[p20m._implementation.get_mount()].\ config.pick_up_current ctx.comment("""Tip pick-up current for the p20 multi-channel pipette initially configured to {} mAmp.""".format(str(default_current))) # temporarily reduce p20m pick_up_current for one-channel tip pickup - ctx._implementation._hw_manager.hardware._attached_instruments[ + ctx._hw_manager.hardware._attached_instruments[ p20m._implementation.get_mount()].update_config_item( 'pick_up_current', reduced_pick_up_current) ctx.comment("""Tip pick-up current configuration for the p20 multi-channel @@ -212,12 +212,12 @@ def pick_up(pip): pick_up(p20m) # reset p20m pick_up_current to original value - ctx._implementation._hw_manager.hardware._attached_instruments[ + ctx._hw_manager.hardware._attached_instruments[ p20m._implementation.get_mount()].update_config_item( 'pick_up_current', default_current) ctx.comment("""Tip pick-up current for the p20 multi-channel pipette restored to initial value of {} mAmp for standard 8-tip pickup.""".format( - str(ctx._implementation._hw_manager.hardware._attached_instruments[ + str(ctx._hw_manager.hardware._attached_instruments[ p20m._implementation.get_mount()].config.pick_up_current))) # water then fluomix to last well of 1st col each tray diff --git a/protocols/121d15-4/manual_cleave.ot2.apiv2.py b/protocols/121d15-4/manual_cleave.ot2.apiv2.py index 8a49aa010..cff627f94 100644 --- a/protocols/121d15-4/manual_cleave.ot2.apiv2.py +++ b/protocols/121d15-4/manual_cleave.ot2.apiv2.py @@ -119,7 +119,7 @@ def pick_up(num_tips, reagent_type): if num_tips > 1: pip = m300 pick_up_current = num_tips*per_tip_pickup_current - ctx._implementation._hw_manager.hardware._attached_instruments[ + ctx._hw_manager.hardware._attached_instruments[ pip._implementation.get_mount()].update_config_item( 'pick_up_current', pick_up_current) else: @@ -227,6 +227,6 @@ def return_tip(pip, tip_loc, chunk_len, reagent_type): with open(tip_file_path, 'w') as outfile: json.dump(tip_data, outfile) - ctx._implementation._hw_manager.hardware._attached_instruments[ + ctx._hw_manager.hardware._attached_instruments[ m300._implementation.get_mount()].update_config_item( 'pick_up_current', 1.0) diff --git a/protocols/1bcd67/normalization.ot2.apiv2.py b/protocols/1bcd67/normalization.ot2.apiv2.py index a1c3f41e3..d03c77b00 100644 --- a/protocols/1bcd67/normalization.ot2.apiv2.py +++ b/protocols/1bcd67/normalization.ot2.apiv2.py @@ -56,7 +56,7 @@ def run(ctx): def pickup_p300(mode='single'): current = 0.1 if mode == 'single' else 0.5 - ctx._implementation._hw_manager.hardware._attached_instruments[ + ctx._hw_manager.hardware._attached_instruments[ p300._implementation.get_mount()].update_config_item( 'pick_up_current', current) diff --git a/protocols/2ed4de-2/fluribogreen.ot2.apiv2.py b/protocols/2ed4de-2/fluribogreen.ot2.apiv2.py index c727ddec0..1f0f852f3 100644 --- a/protocols/2ed4de-2/fluribogreen.ot2.apiv2.py +++ b/protocols/2ed4de-2/fluribogreen.ot2.apiv2.py @@ -58,7 +58,7 @@ def run(ctx): def pickup_p300(mode='single'): current = 0.1 if mode == 'single' else 0.5 - ctx._implementation._hw_manager.hardware._attached_instruments[ + ctx._hw_manager.hardware._attached_instruments[ p300._implementation.get_mount()].update_config_item( 'pick_up_current', current) diff --git a/protocols/2ed4de/fluribogreen.ot2.apiv2.py b/protocols/2ed4de/fluribogreen.ot2.apiv2.py index bc5b28b0c..ba87d1737 100644 --- a/protocols/2ed4de/fluribogreen.ot2.apiv2.py +++ b/protocols/2ed4de/fluribogreen.ot2.apiv2.py @@ -57,7 +57,7 @@ def run(ctx): def pickup_p300(mode='single'): current = 0.1 if mode == 'single' else 0.5 - ctx._implementation._hw_manager.hardware._attached_instruments[ + ctx._hw_manager.hardware._attached_instruments[ p300._implementation.get_mount()].update_config_item( 'pick_up_current', current) diff --git a/protocols/7062c9-2/extraction.ot2.apiv2.py b/protocols/7062c9-2/extraction.ot2.apiv2.py index d1a205b1f..ba37ff1ad 100644 --- a/protocols/7062c9-2/extraction.ot2.apiv2.py +++ b/protocols/7062c9-2/extraction.ot2.apiv2.py @@ -98,7 +98,7 @@ def run(ctx): magdeck.disengage() # just in case tempdeck.set_temperature(85) - ctx._implementation._hw_manager.hardware._attached_instruments[ + ctx._hw_manager.hardware._attached_instruments[ m300._implementation.get_mount()].update_config_item( 'pick_up_current', 0.5) diff --git a/protocols/7062c9/normalization.ot2.apiv2.py b/protocols/7062c9/normalization.ot2.apiv2.py index 5f812d768..e0e894f4f 100644 --- a/protocols/7062c9/normalization.ot2.apiv2.py +++ b/protocols/7062c9/normalization.ot2.apiv2.py @@ -28,7 +28,7 @@ def run(ctx): p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=tipracks20) - ctx._implementation._hw_manager.hardware._attached_instruments[ + ctx._hw_manager.hardware._attached_instruments[ p300._implementation.get_mount()].update_config_item( 'pick_up_current', 0.1) diff --git a/protocols/sci-illumina-dna-prep/.hide-from-search b/protocols/sci-illumina-dna-prep/.hide-from-search deleted file mode 100644 index e69de29bb..000000000 diff --git a/protocols/sci-illumina-dna-prep/.ignore b/protocols/sci-illumina-dna-prep/.ignore deleted file mode 100644 index e69de29bb..000000000 diff --git a/protocols/sci-illumina-dna-prep/README.md b/protocols/sci-illumina-dna-prep/README.md deleted file mode 100644 index a4c486e43..000000000 --- a/protocols/sci-illumina-dna-prep/README.md +++ /dev/null @@ -1,117 +0,0 @@ -# Illumina DNA Prep - Opentrons v3 -### Author -[Opentrons](https://opentrons.com/) - -### Partner -[Illumina](https://www.illumina.com/) - -## Categories -* NGS Library Prep - * Illumina DNA Prep - -## Description -This protocol automates the [Illumina DNA prep protocol](https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/illumina_prep/illumina-dna-prep-reference-guide-1000000025416-09.pdf). Illumina DNA prep offers a fast, integrated workflow for a wide range of applications, from human whole-genome sequencing to amplicons, plasmids, and microbial species - -The protocol allows you to set the number of samples to 8, 16 or 24 (i.e. 8 samples per column, up to 3 columns). Samples are prepared in the wells as shown in the table and figure below, with 30 µL of 100 ng:s of sample DNA in each well. See the [Illumina DNA Prep protocol](https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/illumina_prep/illumina-dna-prep-reference-guide-1000000025416-09.pdf) for more information about sample input requirements. - -![Sample input and output columns](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-illumina-dna-prep/v3/samples_output.jpg) - -![Sample columns](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-illumina-dna-prep/v3/sample_setup.jpg) - -The user can choose which steps of the protocol they want to run, or skip - see explanation of parameters below. - -**Plate Moving** -The Protocol requires manually transferring the sample plate between the Thermocycler and Magnet 3 times. It starts on the Thermocycler and needs to be moved to the Magnet for the post-Tagmentation washes, and then moved to the Thermocycler for PCR and then back to the Magnet for the post-PCR cleanup. In the script the two positions are handled as sample_plate_mag and sample_plate_thermo; during calibration use an empty plate of the same labware as the sample plate on the magnet position to allow calibration. - -Explanation of parameters below: -* `Number of samples`: 8 (column 1), 16 (column 1, 3), or 24 (column 1, 3, 5) samples (see above). -* `Do a dry run?`: Sets the `Use modules?` parameter to `No` (see below). Tips will be returned, incubation steps skipped, and mixes shortened. This parameter is for testing purposes. -* `Use modules?`: Runs the protocol without module steps (e.g. thermocycle steps such as incubation and PCR cycles, or the steps using the magbetic module). Will be automatically set to `Yes` if the `Do a dry run?` parameter is set to `Yes` -* `Tip reuse?`: Reuses tips for washing steps so that no tip refill is neccesary during the run. Recommended only for a 24x samples run. -* `Use tip offsets?`: Whether to use specific offsets for each tip type -* `Include tagmentation step in protocol run?`: Run the tagmentation step or skip it. -* `Run tagmentation incubation on the deck thermocycler?`: Run the tagmentation incubation step on the deck thermocycler or on an off-deck external thermocycler. -* `Run TSB step?`: Run the TSB/adapter ligation step or not -* `Run TSB incubation step on the deck thermocycler`: Whether to do the incubation on the on-deck thermocycler or off-deck on an external thermocycler -* `Run tagmentation wash with TWB step`: Run the bead washing steps with TWB -* `Run PCR cycle step`: Whether to run the PCR amplification step -* `Run PCR step on deck thermocycler?`: Run the PCR amplification on the on-deck thermocycler or on an external thermocycler -* `Run post PCR cleanup step`: Run or skip the post-PCR bead cleanup using AMPure beads ---- - -### Modules -* [Temperature Module (GEN2)](https://shop.opentrons.com/collections/hardware-modules/products/tempdeck) -* [Magnetic Module (GEN2)](https://shop.opentrons.com/collections/hardware-modules/products/magdeck) -* [Thermocycler Module](https://shop.opentrons.com/collections/hardware-modules/products/thermocycler-module) - -### Labware -* [Nest 96 well plate full skirt 100 µL](https://shop.opentrons.com/nest-0-1-ml-96-well-pcr-plate-full-skirt/) -* [NEST 2 mL 96-Well Deep Well Plate](https://shop.opentrons.com/nest-2-ml-96-well-deep-well-plate-v-bottom/) -* [NEST 12-Well Reservoirs, 15 mL](https://shop.opentrons.com/nest-12-well-reservoirs-15-ml/) -* [Opentrons aluminum block set](https://shop.opentrons.com/aluminum-block-set/) - -### Pipettes -* [P300 multi-Channel (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/) -* [P20 multi-Channel (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/) -* [P10 multi-Channel](https://shop.opentrons.com/8-channel-electronic-pipette/) -**Tips** -* [Opentrons 20 µL filter tiprack](https://shop.opentrons.com/opentrons-20ul-filter-tips/) -* [Opentrons 200 µL filter tiprack](https://shop.opentrons.com/opentrons-200ul-filter-tips/) - -### Reagents -* [Illumina DNA Prep](https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/nextera-dna-flex.html) - ---- - -### Deck Setup -![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-illumina-dna-prep/v3/deck.jpg) - -Inital slot layout: -1. Magnetic module for the sample plate (Nest 96 well plate full skirt). -2. Reservoir: NEST 12-well reservoir 15 mL. This is substituted for a NEST 2 mL deep well plate if tip-reuse is on in order to minimize cross-contamination. See Reagent Setup section for information about the location of the reagents -3. Reagent plate 2: Temperature module with Bio-rad 200 µL plate on aluminum block. See Reagent Setup section for information about the location of the reagents -4. 20 µL filter tiprack -5. 200 µL filter tiprack -6. 200 µL filter tiprack -7. Sample plate on Thermocycler module with NEST 96 well plate full skirt 100 µL -8. Empty -9. 200 µL filter tiprack -10. Sample plate on Thermocycler module with NEST 96 well plate full (thermocycler uses two slots) -11. Empty - -### Reagent Setup -* Reservoir, slot 2: -![Reagent plate 1](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-illumina-dna-prep/v3/reagent_plate1.jpg) -* Reagent plate on temperature module, slot 3: -![Reagent plate 2](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-illumina-dna-prep/v3/reagent_plate2.jpg) - ---- - -### Protocol Steps -1. Prepare the thermocycler by setting the block temperature to 4 degrees, and the lid to 100 degrees. -2. Add tagmentation mix to the samples -3. User seals the plate and the protocol incubates the samples with the mix in the thermocycler, 55 degrees for 15 minutes. -4. The thermocycler opens, and the user removes the seal. -5. Add Tagmentation Stop Buffer to the samples. -6. Seal and incubate the mix at 37 degrees for 15 minutes. -7. User removes seal; remove the supernatant and wash the beads three times with Tagmentation Wash Buffer. -8. Amplification of DNA: Addition of PCR mix and addition of barcodes. -9. The protocol runs PCR protocol for 5 cycles. This takes 25 minutes to complete. The supernatant is transferred to columns 7, 9 and 11 depending on how many sample columns there are. -10. Post-PCR cleanup using AMPure beads. -11. The protocol performs two ethanol washes. -12. RSB (resuspension buffer) is added to the bead wells and the supernatant is transferred to the output columns (8, 10, and 12). - -### Process -1. Input your protocol parameters above. -2. Download your protocol and unzip if needed. -3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed. -4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab. -5. Set up your deck according to the deck map. -6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2). -7. Hit 'Run'. - -### Additional Notes -If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/). - -###### Internal -illumina-dna-prep diff --git a/protocols/sci-illumina-dna-prep/fields.json b/protocols/sci-illumina-dna-prep/fields.json deleted file mode 100644 index 75e33c7e4..000000000 --- a/protocols/sci-illumina-dna-prep/fields.json +++ /dev/null @@ -1,120 +0,0 @@ -[ - { - "type": "dropDown", - "label": "Number of samples", - "name": "SAMPLES", - "options": [ - {"label": "24 samples", "value": "24x"}, - {"label": "16 samples", "value": "16x"}, - {"label": "8 samples", "value": "8x"} - ] - }, - { - "type": "dropDown", - "label": "Do a dry run?", - "name": "DRYRUN", - "options": [ - {"label": "No", "value": "NO"}, - {"label": "Yes", "value": "YES"} - ] - }, - { - "type": "dropDown", - "label": "Use modules?", - "name": "NOMODULES", - "options": [ - {"label": "No", "value": "NO"}, - {"label": "Yes", "value": "YES"} - ] - }, - { - "type": "dropDown", - "label": "Tip reuse?", - "name": "TIPREUSE", - "options": [ - { "label": "No", "value": "NO"}, - {"label": "Yes", "value": "YES"} - ] - }, - { - "type": "dropDown", - "label": "Offset?", - "name": "OFFSET", - "options": [ - { "label": "Yes", "value": "YES"}, - { "label": "No", "value": "NO"} - ] - }, - { - "type": "dropDown", - "label": "Include tagmentation step in protocol run?", - "name": "STEP_TAG", - "options": [ - { "label": "Include", "value": 1}, - { "label": "Skip", "value": 0} - ] - }, - { - "type": "dropDown", - "label": "Run tagmentation incubation on the deck thermocycler?", - "name": "STEP_TAGDECK", - "options": [ - { "label": "Yes", "value": 1}, - { "label": "No", "value": 0} - ] - }, - { - "type": "dropDown", - "label": "Run TSB step?", - "name": "STEP_TSB", - "options": [ - { "label": "Include", "value": 1}, - { "label": "Skip", "value": 0} - ] - }, - { - "type": "dropDown", - "label": "Run TSB incubation step on the deck thermocycler", - "name": "STEP_TSBDECK", - "options": [ - { "label": "Yes", "value": 1}, - { "label": "No", "value": 0} - ] - }, - { - "type": "dropDown", - "label": "Run tagmentation wash with TWB step", - "name": "STEP_WASH", - "options": [ - { "label": "Include", "value": 1}, - { "label": "Skip", "value": 0} - ] - }, - { - "type": "dropDown", - "label": "Run PCR cycle step", - "name": "STEP_PCR", - "options": [ - { "label": "Include", "value": 1}, - { "label": "Skip", "value": 0} - ] - }, - { - "type": "dropDown", - "label": "Run PCR step on deck thermocycler?", - "name": "STEP_PCRDECK", - "options": [ - { "label": "Yes", "value": 1}, - { "label": "No", "value": 0} - ] - }, - { - "type": "dropDown", - "label": "Run post PCR cleanup step", - "name": "STEP_POSTPCR", - "options": [ - { "label": "Include", "value": 1}, - { "label": "Skip", "value": 0} - ] - } -] diff --git a/protocols/sci-illumina-dna-prep/sci-illumina-dna-prep.ot2.apiv2.py b/protocols/sci-illumina-dna-prep/sci-illumina-dna-prep.ot2.apiv2.py deleted file mode 100644 index c12857b90..000000000 --- a/protocols/sci-illumina-dna-prep/sci-illumina-dna-prep.ot2.apiv2.py +++ /dev/null @@ -1,2048 +0,0 @@ -from opentrons import protocol_api - -from opentrons import types - -import inspect - -metadata = { - 'protocolName': 'Illumina DNA Prep', - 'author': 'Opentrons ', - 'source': 'Protocol Library', - 'apiLevel': '2.9' -} -# I removed the right() function because it is never used -# settings -# SAMPLES = '24x' # 8x, 16x, or 24x -# YES or NO, DRYRUN = 'YES' will return tips, skip incubation times, -# shorten mix, for testing purposes -# DRYRUN = 'NO' -# YES or NO, NOMODULES = 'YES' will not require modules on the deck and will -# skip module steps, for testing purposes, if DRYRUN = 'YES', then NOMODULES -# will automatically set itself to 'NO' -# NOMODULES = 'NO' -# TIPREUSE = 'NO' -# YES or NO, Reusing tips on wash steps reduces tips needed, no tip refill -# needed, suggested only for 24x run with all steps - -# YES or NO, Sets whether to use protocol specific z offsets for each tip and -# labware or no offsets aside from defaults -# OFFSET = 'YES' - -# sections -# STEP_TAG = 1 # 1 is include, 0 is skip, steps with "DECK" are -# for reaction -# to take place with the on deck Thermocycler module -# This arrangement makes it possibly to set up and run only the first -# half, or to skips steps and resume if there is an Error. -# STEP_TAGDECK = 1 -# If non "DECK" steps are skipped, then TIPREUSE will automatically set -# itself to 'NO' in order to keep tip order correct. -# STEP_TSB = 1 -# STEP_TSBDECK = 1 -# STEP_WASH = 1 -# STEP_PCR = 1 -# STEP_PCRDECK = 1 -# STEP_POSTPCR = 1 - - -def run(protocol: protocol_api.ProtocolContext): - - global TIPREUSE - - [SAMPLES, - DRYRUN, - NOMODULES, - TIPREUSE, - OFFSET, - STEP_TAG, - STEP_TAGDECK, - STEP_TSB, - STEP_TSBDECK, - STEP_WASH, - STEP_PCR, - STEP_PCRDECK, - STEP_POSTPCR] = get_values( # noqa: F821 - "SAMPLES", - "DRYRUN", - "NOMODULES", - "TIPREUSE", - "OFFSET", - "STEP_TAG", - "STEP_TAGDECK", - "STEP_TSB", - "STEP_TSBDECK", - "STEP_WASH", - "STEP_PCR", - "STEP_PCRDECK", - "STEP_POSTPCR") - - STEPS = {STEP_TAG, STEP_TSB, STEP_WASH, STEP_PCR, STEP_POSTPCR} - - if DRYRUN == 'YES': - protocol.comment("THIS IS A DRY RUN") - else: - protocol.comment("THIS IS A REACTION RUN") - NOMODULES = 'NO' - - if all(STEPS) is True: - if TIPREUSE == 'YES': - TIPREUSE = 'YES' - protocol.comment("TIP REUSING") - else: - TIPREUSE = 'NO' - protocol.comment("NO TIP REUSING") - - # labware - if NOMODULES == 'YES': - protocol.comment("THIS IS A NO MODULE RUN") - # <--- Actually an Eppendorf 96 well, same dimensions - sample_plate_mag = protocol.load_labware( - 'nest_96_wellplate_100ul_pcr_full_skirt', '1') - if TIPREUSE == 'NO': - reservoir = protocol.load_labware('nest_12_reservoir_15ml', '2') - else: - reservoir = protocol.load_labware( - 'nest_96_wellplate_2ml_deep', '2') - reagent_plate = protocol.load_labware( - 'opentrons_96_aluminumblock_biorad_wellplate_200ul', '3') - tiprack_20 = protocol.load_labware( - 'opentrons_96_filtertiprack_20ul', '4') - tiprack_200_1 = protocol.load_labware( - 'opentrons_96_filtertiprack_200ul', '5') - tiprack_200_2 = protocol.load_labware( - 'opentrons_96_filtertiprack_200ul', '6') - sample_plate_thermo = protocol.load_labware( - 'nest_96_wellplate_100ul_pcr_full_skirt', '7') - tiprack_200_3 = protocol.load_labware( - 'opentrons_96_filtertiprack_200ul', '9') - else: - protocol.comment("THIS IS A MODULE RUN") - mag_block = protocol.load_module('magnetic module gen2', '1') - # <--- Actually an Eppendorf 96 well, same dimensions - sample_plate_mag = mag_block.load_labware( - 'nest_96_wellplate_100ul_pcr_full_skirt') - if TIPREUSE == 'NO': - reservoir = protocol.load_labware('nest_12_reservoir_15ml', '2') - else: - reservoir = protocol.load_labware( - 'nest_96_wellplate_2ml_deep', '2') - temp_block = protocol.load_module('temperature module gen2', '3') - reagent_plate = temp_block.load_labware( - 'opentrons_96_aluminumblock_biorad_wellplate_200ul') - tiprack_20 = protocol.load_labware( - 'opentrons_96_filtertiprack_20ul', '4') - tiprack_200_1 = protocol.load_labware( - 'opentrons_96_filtertiprack_200ul', '5') - tiprack_200_2 = protocol.load_labware( - 'opentrons_96_filtertiprack_200ul', '6') - thermocycler = protocol.load_module('thermocycler module') - sample_plate_thermo = thermocycler.load_labware( - 'nest_96_wellplate_100ul_pcr_full_skirt') - tiprack_200_3 = protocol.load_labware( - 'opentrons_96_filtertiprack_200ul', '9') - - if TIPREUSE == 'YES': - protocol.comment("THIS PROTOCOL WILL REUSE TIPS FOR WASHES") - - # reagent - plate - TAG = reagent_plate.wells_by_name()['A1'] - TSB = reagent_plate.wells_by_name()['A2'] - PCR = reagent_plate.wells_by_name()['A3'] - Barcodes1 = reagent_plate.wells_by_name()['A7'] - Barcodes2 = reagent_plate.wells_by_name()['A8'] - Barcodes3 = reagent_plate.wells_by_name()['A9'] - - # reagent - deepwell - if TIPREUSE == 'NO': - AMPure = reservoir['A1'] - EtOH_1 = reservoir['A4'] - EtOH_2 = reservoir['A4'] - EtOH_3 = reservoir['A4'] - RSB = reservoir['A6'] - TWB_1 = reservoir['A8'] - TWB_2 = reservoir['A8'] - TWB_3 = reservoir['A8'] - Liquid_trash = reservoir['A12'] - else: - AMPure = reservoir['A1'] - EtOH_1 = reservoir['A4'] - EtOH_2 = reservoir['A3'] - EtOH_3 = reservoir['A2'] - RSB = reservoir['A6'] - TWB_1 = reservoir['A8'] - TWB_2 = reservoir['A9'] - TWB_3 = reservoir['A10'] - Liquid_trash = reservoir['A12'] - - # pipette - if NOMODULES == 'NO': - p300 = protocol.load_instrument('p300_multi_gen2', 'left', tip_racks=[ - tiprack_200_1, tiprack_200_2, - tiprack_200_3]) - p20 = protocol.load_instrument( - 'p20_multi_gen2', 'right', tip_racks=[tiprack_20]) - else: - p300 = protocol.load_instrument('p300_multi', 'left', tip_racks=[ - tiprack_200_1, tiprack_200_2, - tiprack_200_3]) - p20 = protocol.load_instrument( - 'p10_multi', 'right', tip_racks=[tiprack_20]) - - # samples - # FIXME: This does not seem to be used - src_file_path = inspect.getfile(lambda: None) - protocol.comment(src_file_path) - - # tip and sample tracking - if SAMPLES == '8x': - protocol.comment("There are 8 Samples") - samplecolumns = 1 - TWB_washtip_1 = tiprack_200_1['A3'] - TWB_removetip_1 = tiprack_200_1['A4'] - W1_ETOH_washtip_1 = tiprack_200_1['A10'] - W1_ETOH_removetip_1 = tiprack_200_1['A11'] - elif SAMPLES == '16x': - protocol.comment("There are 16 Samples") - samplecolumns = 2 - TWB_washtip_1 = tiprack_200_1['A5'] - TWB_washtip_2 = tiprack_200_1['A6'] - TWB_removetip_1 = tiprack_200_1['A7'] - TWB_removetip_2 = tiprack_200_1['A8'] - W1_ETOH_washtip_1 = tiprack_200_2['A7'] - W1_ETOH_washtip_2 = tiprack_200_2['A8'] - W1_ETOH_removetip_1 = tiprack_200_2['A9'] - W1_ETOH_removetip_2 = tiprack_200_2['A10'] - elif SAMPLES == '24x': - protocol.comment("There are 24 Samples") - samplecolumns = 3 - TWB_washtip_1 = tiprack_200_1['A7'] - TWB_washtip_2 = tiprack_200_1['A8'] - TWB_washtip_3 = tiprack_200_1['A9'] - TWB_removetip_1 = tiprack_200_1['A10'] - TWB_removetip_2 = tiprack_200_1['A11'] - TWB_removetip_3 = tiprack_200_1['A12'] - W1_ETOH_washtip_1 = tiprack_200_3['A4'] - W1_ETOH_washtip_2 = tiprack_200_3['A5'] - W1_ETOH_washtip_3 = tiprack_200_3['A6'] - W1_ETOH_removetip_1 = tiprack_200_3['A7'] - W1_ETOH_removetip_2 = tiprack_200_3['A8'] - W1_ETOH_removetip_3 = tiprack_200_3['A9'] - else: - protocol.pause("ERROR?") - - # FIXME: commented out variables are never used in the protocol - p300_offset_Res = 0 - p300_offset_Thermo = 0 - p300_offset_Mag = 0 - # p300_offset_Deck = 0 - p300_offset_Temp = 0 - # p300_offset_Tube = 0 - # p20_offset_Res = 0 - p20_offset_Thermo = 0 - p20_offset_Mag = 0 - # p20_offset_Deck = 0 - p20_offset_Temp = 0 - # p20_offset_Tube = 0 - - # offset - if OFFSET == 'YES': - if TIPREUSE == 'NO': - p300_offset_Res = 2 - else: - p300_offset_Res = 2 - p300_offset_Thermo = 1 - p300_offset_Mag = 0.70 - # p300_offset_Deck = 0.3 - p300_offset_Temp = 0.65 - # p300_offset_Tube = 0 - # if TIPREUSE == 'NO': - # p20_offset_Res = 2 - # else: - # p20_offset_Res = 2 - p20_offset_Thermo = 1 - p20_offset_Mag = 0.75 - # p20_offset_Deck = 0.3 - p20_offset_Temp = 0.85 - # p20_offset_Tube = 0 - - # FIXME: Commented out variables are never used in the protocol - # positions - ########################################################################## - # sample_plate_thermo on the Thermocycler - # A1_p20_bead_side = sample_plate_thermo['A1'].center().move(types.Point( - # x=-1.8 * 0.50, y=0, z=p20_offset_Thermo - 5)) # Beads to the Right - # A1_p20_bead_top = sample_plate_thermo['A1'].center().move(types.Point( - # x=1.5, y=0, z=p20_offset_Thermo + 2)) # Beads to the Right - # A1_p20_bead_mid = sample_plate_thermo['A1'].center().move(types.Point( - # x=1, y=0, z=p20_offset_Thermo - 2)) # Beads to the Right - A1_p300_bead_side = sample_plate_thermo['A1'].center().move(types.Point( - x=-0.50, y=0, z=p300_offset_Thermo - 7.2)) # Beads to the Right - A1_p300_bead_top = sample_plate_thermo['A1'].center().move(types.Point( - x=1.30, y=0, z=p300_offset_Thermo - 1)) # Beads to the Right - A1_p300_bead_mid = sample_plate_thermo['A1'].center().move(types.Point( - x=0.80, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right - A1_p300_loc1 = sample_plate_thermo['A1'].center().move(types.Point( - x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Thermo - 4)) - # Beads to the Right - A1_p300_loc2 = sample_plate_thermo['A1'].center().move(types.Point( - x=1.3, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right - A1_p300_loc3 = sample_plate_thermo['A1'].center().move(types.Point( - x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Thermo - 4)) - # Beads to the Right - # A3_p20_bead_side = sample_plate_thermo['A3'].center().move(types.Point( - # x=-1.8 * 0.50, y=0, z=p20_offset_Thermo - 5)) # Beads to the Right - # A3_p20_bead_top = sample_plate_thermo['A3'].center().move(types.Point( - # x=1.5, y=0, z=p20_offset_Thermo + 2)) # Beads to the Right - # A3_p20_bead_mid = sample_plate_thermo['A3'].center().move(types.Point( - # x=1, y=0, z=p20_offset_Thermo - 2)) # Beads to the Right - A3_p300_bead_side = sample_plate_thermo['A3'].center().move(types.Point( - x=-0.50, y=0, z=p300_offset_Thermo - 7.2)) # Beads to the Right - A3_p300_bead_top = sample_plate_thermo['A3'].center().move(types.Point( - x=1.30, y=0, z=p300_offset_Thermo - 1)) # Beads to the Right - A3_p300_bead_mid = sample_plate_thermo['A3'].center().move(types.Point( - x=0.80, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right - A3_p300_loc1 = sample_plate_thermo['A3'].center().move(types.Point( - x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Thermo - 4)) - # Beads to the Right - A3_p300_loc2 = sample_plate_thermo['A3'].center().move(types.Point( - x=1.3, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right - A3_p300_loc3 = sample_plate_thermo['A3'].center().move(types.Point( - x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Thermo - 4)) - # Beads to the Right - # A5_p20_bead_side = sample_plate_thermo['A5'].center().move(types.Point( - # x=-1.8 * 0.50, y=0, z=p20_offset_Thermo - 5)) # Beads to the Right - # A5_p20_bead_top = sample_plate_thermo['A5'].center().move(types.Point( - # x=1.5, y=0, z=p20_offset_Thermo + 2)) # Beads to the Right - # A5_p20_bead_mid = sample_plate_thermo['A5'].center().move(types.Point( - # x=1, y=0, z=p20_offset_Thermo - 2)) # Beads to the Right - A5_p300_bead_side = sample_plate_thermo['A5'].center().move(types.Point( - x=-0.50, y=0, z=p300_offset_Thermo - 7.2)) # Beads to the Right - A5_p300_bead_top = sample_plate_thermo['A5'].center().move(types.Point( - x=1.30, y=0, z=p300_offset_Thermo - 1)) # Beads to the Right - A5_p300_bead_mid = sample_plate_thermo['A5'].center().move(types.Point( - x=0.80, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right - A5_p300_loc1 = sample_plate_thermo['A5'].center().move(types.Point( - x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Thermo - 4)) - # Beads to the Right - A5_p300_loc2 = sample_plate_thermo['A5'].center().move(types.Point( - x=1.3, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right - A5_p300_loc3 = sample_plate_thermo['A5'].center().move(types.Point( - x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Thermo - 4)) - # Beads to the Right - ########################################################################## - - bypass = protocol.deck.position_for( - '11').move(types.Point(x=70, y=80, z=130)) - - # commands - if DRYRUN == 'NO': - protocol.comment("SETTING THERMO and TEMP BLOCK Temperature") - thermocycler.set_block_temperature(4) - thermocycler.set_lid_temperature(100) -# temp_block.set_temperature(4) - thermocycler.open_lid() - protocol.pause("Ready") - - if STEP_TAG == 1: - protocol.comment('==============================================') - protocol.comment('--> TAGMENTATION') - protocol.comment('==============================================') - - protocol.comment('--> Adding Tagmentation Mix ') - if DRYRUN == 'NO': - TagVol = 20 - TagMixRep = 10 - TagMixVol = 40 - if DRYRUN == 'YES': - TagVol = 20 - TagMixRep = 1 - TagMixVol = 40 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A1' - p300.pick_up_tip() - p300.mix(3, 20, TAG.bottom(z=p300_offset_Temp), rate=0.5) - p300.aspirate(TagVol, TAG.bottom(z=p300_offset_Temp), rate=0.25) - p300.dispense(TagVol, sample_plate_thermo[X].bottom( - z=p300_offset_Thermo), rate=0.25) - p300.mix(TagMixRep, TagMixVol) - p300.blow_out(sample_plate_thermo[X].top(z=-5)) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A3' - p300.pick_up_tip() - p300.mix(3, 20, TAG.bottom(z=p300_offset_Temp), rate=0.5) - p300.aspirate(TagVol, TAG.bottom(z=p300_offset_Temp), rate=0.25) - p300.dispense(TagVol, sample_plate_thermo[X].bottom( - z=p300_offset_Thermo), rate=0.25) - p300.mix(TagMixRep, TagMixVol) - p300.blow_out(sample_plate_thermo[X].top(z=-5)) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A5' - p300.pick_up_tip() - p300.mix(3, 20, TAG.bottom(z=p300_offset_Temp), rate=0.5) - p300.aspirate(TagVol, TAG.bottom(z=p300_offset_Temp), rate=0.25) - p300.dispense(TagVol, sample_plate_thermo[X].bottom( - z=p300_offset_Thermo), rate=0.25) - p300.mix(TagMixRep, TagMixVol) - p300.blow_out(sample_plate_thermo[X].top(z=-5)) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - - if STEP_TAGDECK == 1: - if DRYRUN == 'NO': - ################################################################### - protocol.pause('Seal, Run TAG (15min)') - - thermocycler.close_lid() - profile_TAG = [ - {'temperature': 55, 'hold_time_minutes': 15} - ] - thermocycler.execute_profile( - steps=profile_TAG, repetitions=1, block_max_volume=50) - thermocycler.set_block_temperature(10) - ####################################################################### - thermocycler.open_lid() - protocol.pause("Remove Seal") - else: - protocol.pause('Seal, Run ERAT (60min)') - - if STEP_TSB == 1: - protocol.pause("Add TSB to Reagent Wells") - protocol.comment('==============================================') - protocol.comment('--> Adapter Ligation') - protocol.comment('==============================================') - - protocol.comment('--> Adding Tagmentation Stop Buffer') - if DRYRUN == 'NO': - if NOMODULES == 'NO': - TSBVol = 10 - TSBMixRep = 10 - TSBMixVol = 20 - else: - TSBVol = 10 - TSBMixRep = 10 - TSBMixVol = 10 - if DRYRUN == 'YES': - if NOMODULES == 'NO': - TSBVol = 10 - TSBMixRep = 1 - TSBMixVol = 20 - else: - TSBVol = 10 - TSBMixRep = 1 - TSBMixVol = 10 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A1' - p20.pick_up_tip() - p20.aspirate(TSBVol, TSB.bottom(z=p20_offset_Temp)) - p20.dispense(TSBVol, sample_plate_thermo[X].bottom( - z=p20_offset_Thermo)) - p20.mix(TSBMixRep, TSBMixVol) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A3' - p20.pick_up_tip() - p20.aspirate(TSBVol, TSB.bottom(z=p20_offset_Temp)) - p20.dispense(TSBVol, sample_plate_thermo[X].bottom( - z=p20_offset_Thermo)) - p20.mix(TSBMixRep, TSBMixVol) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A5' - p20.pick_up_tip() - p20.aspirate(TSBVol, TSB.bottom(z=p20_offset_Temp)) - p20.dispense(TSBVol, sample_plate_thermo[X].bottom( - z=p20_offset_Thermo)) - p20.mix(TSBMixRep, TSBMixVol) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - - if STEP_TSBDECK == 1: - if DRYRUN == 'NO': - ################################################################### - protocol.pause('Seal, Run PTC (15min)') - - thermocycler.close_lid() - profile_PTC = [ - {'temperature': 37, 'hold_time_minutes': 15} - ] - thermocycler.execute_profile( - steps=profile_PTC, repetitions=1, block_max_volume=60) - thermocycler.set_block_temperature(10) - ################################################################### - thermocycler.open_lid() - protocol.pause("Remove Seal") - else: - protocol.pause('Seal, Run PTC (15min)') - - # FIXME: Commented out variables are never used in the protocol - # positions - ########################################################################## - # sample_plate_mag on the Mag Block - # A1_p20_bead_side = sample_plate_mag['A1'].center().move(types.Point( - # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right - # A1_p20_bead_top = sample_plate_mag['A1'].center().move(types.Point( - # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right - # A1_p20_bead_mid = sample_plate_mag['A1'].center().move(types.Point( - # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right - A1_p300_bead_side = sample_plate_mag['A1'].center().move(types.Point( - x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right - A1_p300_bead_top = sample_plate_mag['A1'].center().move(types.Point( - x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right - A1_p300_bead_mid = sample_plate_mag['A1'].center().move(types.Point( - x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A1_p300_loc1 = sample_plate_mag['A1'].center().move(types.Point( - x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right - A1_p300_loc2 = sample_plate_mag['A1'].center().move(types.Point( - x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A1_p300_loc3 = sample_plate_mag['A1'].center().move(types.Point( - x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4)) - # Beads to the Right - # A3_p20_bead_side = sample_plate_mag['A3'].center().move(types.Point( - # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right - # A3_p20_bead_top = sample_plate_mag['A3'].center().move(types.Point( - # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right - # A3_p20_bead_mid = sample_plate_mag['A3'].center().move(types.Point( - # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right - A3_p300_bead_side = sample_plate_mag['A3'].center().move(types.Point( - x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right - A3_p300_bead_top = sample_plate_mag['A3'].center().move(types.Point( - x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right - A3_p300_bead_mid = sample_plate_mag['A3'].center().move(types.Point( - x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A3_p300_loc1 = sample_plate_mag['A3'].center().move(types.Point( - x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right - A3_p300_loc2 = sample_plate_mag['A3'].center().move(types.Point( - x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A3_p300_loc3 = sample_plate_mag['A3'].center().move(types.Point( - x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4)) - # Beads to the Right - # A5_p20_bead_side = sample_plate_mag['A5'].center().move(types.Point( - # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right - # A5_p20_bead_top = sample_plate_mag['A5'].center().move(types.Point( - # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right - # A5_p20_bead_mid = sample_plate_mag['A5'].center().move(types.Point( - # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right - A5_p300_bead_side = sample_plate_mag['A5'].center().move(types.Point( - x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right - A5_p300_bead_top = sample_plate_mag['A5'].center().move(types.Point( - x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right - A5_p300_bead_mid = sample_plate_mag['A5'].center().move(types.Point( - x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A5_p300_loc1 = sample_plate_mag['A5'].center().move(types.Point( - x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right - A5_p300_loc2 = sample_plate_mag['A5'].center().move(types.Point( - x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A5_p300_loc3 = sample_plate_mag['A5'].center().move(types.Point( - x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4)) - # Beads to the Right - # A7_p20_bead_side = sample_plate_mag['A7'].center().move(types.Point( - # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right - # A7_p20_bead_top = sample_plate_mag['A7'].center().move(types.Point( - # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right - # A7_p20_bead_mid = sample_plate_mag['A7'].center().move(types.Point( - # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right - A7_p300_bead_side = sample_plate_mag['A7'].center().move(types.Point( - x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right - A7_p300_bead_top = sample_plate_mag['A7'].center().move(types.Point( - x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right - # A7_p300_bead_mid = sample_plate_mag['A7'].center().move(types.Point( - # x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A7_p300_loc1 = sample_plate_mag['A7'].center().move(types.Point( - x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right - A7_p300_loc2 = sample_plate_mag['A7'].center().move(types.Point( - x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A7_p300_loc3 = sample_plate_mag['A7'].center().move(types.Point( - x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4)) - # Beads to the Right - # A9_p20_bead_side = sample_plate_mag['A9'].center().move(types.Point( - # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right - # A9_p20_bead_top = sample_plate_mag['A9'].center().move(types.Point( - # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right - # A9_p20_bead_mid = sample_plate_mag['A9'].center().move(types.Point( - # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right - A9_p300_bead_side = sample_plate_mag['A9'].center().move(types.Point( - x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right - A9_p300_bead_top = sample_plate_mag['A9'].center().move(types.Point( - x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right - # A9_p300_bead_mid = sample_plate_mag['A9'].center().move(types.Point( - # x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A9_p300_loc1 = sample_plate_mag['A9'].center().move(types.Point( - x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right - A9_p300_loc2 = sample_plate_mag['A9'].center().move(types.Point( - x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A9_p300_loc3 = sample_plate_mag['A9'].center().move(types.Point( - x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4)) - # Beads to the Right - # A11_p20_bead_side = sample_plate_mag['A11'].center().move(types.Point( - # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right - # A11_p20_bead_top = sample_plate_mag['A11'].center().move(types.Point( - # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right - # A11_p20_bead_mid = sample_plate_mag['A11'].center().move(types.Point( - # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right - A11_p300_bead_side = sample_plate_mag['A11'].center().move(types.Point( - x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right - A11_p300_bead_top = sample_plate_mag['A11'].center().move(types.Point( - x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right - # A11_p300_bead_mid = sample_plate_mag['A11'].center().move(types.Point( - # x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A11_p300_loc1 = sample_plate_mag['A11'].center().move(types.Point( - x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right - A11_p300_loc2 = sample_plate_mag['A11'].center().move(types.Point( - x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A11_p300_loc3 = sample_plate_mag['A11'].center().move(types.Point( - x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4)) - # Beads to the Right - ########################################################################## - - if STEP_WASH == 1: - protocol.pause("PLACE sample_plate on MAGNET") - protocol.comment('==============================================') - protocol.comment('--> TAGMENTATION WASH') - protocol.comment('==============================================') - - if DRYRUN == 'NO': - protocol.comment('MAGNET ENGAGE') - mag_block.engage(height_from_base=8.5) - protocol.delay(minutes=1) - mag_block.engage(height_from_base=7) - protocol.delay(minutes=1) - mag_block.engage(height_from_base=5) - protocol.delay(minutes=1) - - protocol.comment('--> Removing Supernatant') - RemoveSup = 90 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A1' - p300.pick_up_tip() - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(RemoveSup - 30, rate=0.25) - p300.default_speed = 5 - if X == 'A1': - p300.move_to(A1_p300_bead_side) - if X == 'A3': - p300.move_to(A3_p300_bead_side) - if X == 'A5': - p300.move_to(A5_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(20, rate=0.2) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - protocol.delay(minutes=0.1) - p300.aspirate(10, rate=0.2) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A3' - p300.pick_up_tip() - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(RemoveSup - 30, rate=0.25) - p300.default_speed = 5 - if X == 'A1': - p300.move_to(A1_p300_bead_side) - if X == 'A3': - p300.move_to(A3_p300_bead_side) - if X == 'A5': - p300.move_to(A5_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(20, rate=0.2) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - protocol.delay(minutes=0.1) - p300.aspirate(10, rate=0.2) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A5' - p300.pick_up_tip() - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(RemoveSup - 30, rate=0.25) - p300.default_speed = 5 - if X == 'A1': - p300.move_to(A1_p300_bead_side) - if X == 'A3': - p300.move_to(A3_p300_bead_side) - if X == 'A5': - p300.move_to(A5_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(20, rate=0.2) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - protocol.delay(minutes=0.1) - p300.aspirate(10, rate=0.2) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - - if DRYRUN == 'NO': - protocol.comment('MAGNET DISENGAGE') - mag_block.disengage() - - protocol.comment('--> Repeating 3 washes') - washreps = 3 - for wash in range(washreps): - protocol.comment('--> TWB Wash #' + str(wash + 1)) - if DRYRUN == 'NO': - TWBMixRep = 15 - TWBMixVol = 70 - if DRYRUN == 'YES': - TWBMixRep = 3 - TWBMixVol = 70 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A1' - p300.pick_up_tip()if TIPREUSE == 'NO' else \ - p300.pick_up_tip(TWB_washtip_1) - p300.aspirate(100, TWB_1.bottom(z=p300_offset_Res)) - if X == 'A1': - p300.move_to(A1_p300_bead_top) - if X == 'A3': - p300.move_to(A3_p300_bead_top) - if X == 'A5': - p300.move_to(A5_p300_bead_top) - p300.dispense(100, rate=0.75) - p300.default_speed = 5 - reps = 4 - for x in range(reps): - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.aspirate(100) - if X == 'A1': - p300.move_to(A1_p300_bead_top) - if X == 'A3': - p300.move_to(A3_p300_bead_top) - if X == 'A5': - p300.move_to(A5_p300_bead_top) - p300.dispense(100, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_bead_mid) - if X == 'A3': - p300.move_to(A3_p300_bead_mid) - if X == 'A5': - p300.move_to(A5_p300_bead_mid) - p300.mix(TWBMixRep, TWBMixVol) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.mix(TWBMixRep, TWBMixVol) - p300.default_speed = 400 - p300.move_to(bypass) - if TIPREUSE == 'NO': - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - else: - p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A3' - p300.pick_up_tip()if TIPREUSE == 'NO' else \ - p300.pick_up_tip(TWB_washtip_2) - p300.aspirate(100, TWB_2.bottom(z=p300_offset_Res)) - if X == 'A1': - p300.move_to(A1_p300_bead_top) - if X == 'A3': - p300.move_to(A3_p300_bead_top) - if X == 'A5': - p300.move_to(A5_p300_bead_top) - p300.dispense(100, rate=0.75) - p300.default_speed = 5 - reps = 4 - for x in range(reps): - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.aspirate(100) - if X == 'A1': - p300.move_to(A1_p300_bead_top) - if X == 'A3': - p300.move_to(A3_p300_bead_top) - if X == 'A5': - p300.move_to(A5_p300_bead_top) - p300.dispense(100, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_bead_mid) - if X == 'A3': - p300.move_to(A3_p300_bead_mid) - if X == 'A5': - p300.move_to(A5_p300_bead_mid) - p300.mix(TWBMixRep, TWBMixVol) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.mix(TWBMixRep, TWBMixVol) - p300.default_speed = 400 - p300.move_to(bypass) - if TIPREUSE == 'NO': - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - else: - p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A5' - p300.pick_up_tip()if TIPREUSE == 'NO' else \ - p300.pick_up_tip(TWB_washtip_3) - p300.aspirate(100, TWB_3.bottom(z=p300_offset_Res)) - if X == 'A1': - p300.move_to(A1_p300_bead_top) - if X == 'A3': - p300.move_to(A3_p300_bead_top) - if X == 'A5': - p300.move_to(A5_p300_bead_top) - p300.dispense(100, rate=0.75) - p300.default_speed = 5 - reps = 4 - for x in range(reps): - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.aspirate(100) - if X == 'A1': - p300.move_to(A1_p300_bead_top) - if X == 'A3': - p300.move_to(A3_p300_bead_top) - if X == 'A5': - p300.move_to(A5_p300_bead_top) - p300.dispense(100, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_bead_mid) - if X == 'A3': - p300.move_to(A3_p300_bead_mid) - if X == 'A5': - p300.move_to(A5_p300_bead_mid) - p300.mix(TWBMixRep, TWBMixVol) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.mix(TWBMixRep, TWBMixVol) - p300.default_speed = 400 - p300.move_to(bypass) - if TIPREUSE == 'NO': - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - else: - p300.return_tip() - - if DRYRUN == 'NO': - protocol.comment('MAGNET ENGAGE') - mag_block.engage(height_from_base=8.5) - protocol.delay(minutes=1) - mag_block.engage(height_from_base=7) - protocol.delay(minutes=1) - mag_block.engage(height_from_base=5) - protocol.delay(minutes=1) - - protocol.comment('--> Remove TWB Wash #' + str(wash + 1)) - RemoveSup = 110 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A1' - p300.pick_up_tip()if TIPREUSE == 'NO' else \ - p300.pick_up_tip(TWB_removetip_1) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(RemoveSup - 30, rate=0.25) - p300.default_speed = 5 - if X == 'A1': - p300.move_to(A1_p300_bead_side) - if X == 'A3': - p300.move_to(A3_p300_bead_side) - if X == 'A5': - p300.move_to(A5_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(20, rate=0.2) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - protocol.delay(minutes=0.1) - p300.aspirate(10, rate=0.2) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(bypass) - if TIPREUSE == 'NO': - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - else: - p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A3' - p300.pick_up_tip()if TIPREUSE == 'NO' else \ - p300.pick_up_tip(TWB_removetip_2) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(RemoveSup - 30, rate=0.25) - p300.default_speed = 5 - if X == 'A1': - p300.move_to(A1_p300_bead_side) - if X == 'A3': - p300.move_to(A3_p300_bead_side) - if X == 'A5': - p300.move_to(A5_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(20, rate=0.2) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - protocol.delay(minutes=0.1) - p300.aspirate(10, rate=0.2) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(bypass) - if TIPREUSE == 'NO': - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - else: - p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A5' - p300.pick_up_tip()if TIPREUSE == 'NO' else \ - p300.pick_up_tip(TWB_removetip_3) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(RemoveSup - 30, rate=0.25) - p300.default_speed = 5 - if X == 'A1': - p300.move_to(A1_p300_bead_side) - if X == 'A3': - p300.move_to(A3_p300_bead_side) - if X == 'A5': - p300.move_to(A5_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(20, rate=0.2) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - protocol.delay(minutes=0.1) - p300.aspirate(10, rate=0.2) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(bypass) - if TIPREUSE == 'NO': - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - else: - p300.return_tip() - - if DRYRUN == 'NO': - protocol.comment('MAGNET DISENGAGE') - mag_block.disengage() - - wash += 1 - - if DRYRUN == 'NO': - protocol.comment('MAGNET ENGAGE') - mag_block.engage(height_from_base=5) - - protocol.comment('--> Removing Residual Supernatant') - if samplecolumns >= 1: # ---------------------------------------- - X = 'A1' - p300.pick_up_tip() - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 3)) - p300.aspirate(50, rate=0.25) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A3' - p300.pick_up_tip() - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 3)) - p300.aspirate(50, rate=0.25) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A5' - p300.pick_up_tip() - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 3)) - p300.aspirate(50, rate=0.25) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - - if DRYRUN == 'NO': - mag_block.engage(height_from_base=3) - protocol.delay(minutes=0.5) - - protocol.comment('MAGNET DISENGAGE') - mag_block.disengage() - - if STEP_PCR == 1: - protocol.comment('==============================================') - protocol.comment('--> AMPLIFICATION') - protocol.comment('==============================================') - - protocol.comment('ADDING PCR') - if DRYRUN == 'NO': - PCRVol = 40 - PCRMixRep = 5 - PCRMixVol = 30 - if DRYRUN == 'YES': - PCRVol = 40 - PCRMixRep = 1 - PCRMixVol = 30 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A1' - p300.pick_up_tip() - p300.aspirate(PCRVol, PCR.bottom(p300_offset_Temp)) - if X == 'A1': - p300.move_to(A1_p300_loc1) - if X == 'A3': - p300.move_to(A3_p300_loc1) - if X == 'A5': - p300.move_to(A5_p300_loc1) - p300.dispense(PCRVol / 5, rate=0.75) - p300.default_speed = 5 - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.dispense(PCRVol / 5, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_loc3) - if X == 'A3': - p300.move_to(A3_p300_loc3) - if X == 'A5': - p300.move_to(A5_p300_loc3) - p300.dispense(PCRVol / 5, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.dispense(PCRVol / 5, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_loc1) - if X == 'A3': - p300.move_to(A3_p300_loc1) - if X == 'A5': - p300.move_to(A5_p300_loc1) - p300.dispense(PCRVol / 5, rate=0.75) - reps = 5 - for x in range(reps): - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.aspirate(PCRVol, rate=0.5) - if X == 'A1': - p300.move_to(A1_p300_bead_top) - if X == 'A3': - p300.move_to(A3_p300_bead_top) - if X == 'A5': - p300.move_to(A5_p300_bead_top) - p300.dispense(PCRVol, rate=1) - reps = 3 - for x in range(reps): - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.mix(PCRMixRep, PCRMixVol) - if X == 'A1': - p300.move_to(A1_p300_loc1) - if X == 'A3': - p300.move_to(A3_p300_loc1) - if X == 'A5': - p300.move_to(A5_p300_loc1) - p300.mix(PCRMixRep, PCRMixVol) - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.mix(PCRMixRep, PCRMixVol) - if X == 'A1': - p300.move_to(A1_p300_loc3) - if X == 'A3': - p300.move_to(A3_p300_loc3) - if X == 'A5': - p300.move_to(A5_p300_loc3) - p300.mix(PCRMixRep, PCRMixVol) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.mix(PCRMixRep, PCRMixVol) - p300.move_to(sample_plate_mag[X].top()) - protocol.delay(seconds=0.5) - p300.move_to(sample_plate_mag[X].center()) - p300.default_speed = 400 - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A3' - p300.pick_up_tip() - p300.aspirate(PCRVol, PCR.bottom(p300_offset_Temp)) - if X == 'A1': - p300.move_to(A1_p300_loc1) - if X == 'A3': - p300.move_to(A3_p300_loc1) - if X == 'A5': - p300.move_to(A5_p300_loc1) - p300.dispense(PCRVol / 5, rate=0.75) - p300.default_speed = 5 - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.dispense(PCRVol / 5, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_loc3) - if X == 'A3': - p300.move_to(A3_p300_loc3) - if X == 'A5': - p300.move_to(A5_p300_loc3) - p300.dispense(PCRVol / 5, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.dispense(PCRVol / 5, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_loc1) - if X == 'A3': - p300.move_to(A3_p300_loc1) - if X == 'A5': - p300.move_to(A5_p300_loc1) - p300.dispense(PCRVol / 5, rate=0.75) - reps = 5 - for x in range(reps): - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.aspirate(PCRVol, rate=0.5) - if X == 'A1': - p300.move_to(A1_p300_bead_top) - if X == 'A3': - p300.move_to(A3_p300_bead_top) - if X == 'A5': - p300.move_to(A5_p300_bead_top) - p300.dispense(PCRVol, rate=1) - reps = 3 - for x in range(reps): - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.mix(PCRMixRep, PCRMixVol) - if X == 'A1': - p300.move_to(A1_p300_loc1) - if X == 'A3': - p300.move_to(A3_p300_loc1) - if X == 'A5': - p300.move_to(A5_p300_loc1) - p300.mix(PCRMixRep, PCRMixVol) - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.mix(PCRMixRep, PCRMixVol) - if X == 'A1': - p300.move_to(A1_p300_loc3) - if X == 'A3': - p300.move_to(A3_p300_loc3) - if X == 'A5': - p300.move_to(A5_p300_loc3) - p300.mix(PCRMixRep, PCRMixVol) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.mix(PCRMixRep, PCRMixVol) - p300.move_to(sample_plate_mag[X].top()) - protocol.delay(seconds=0.5) - p300.move_to(sample_plate_mag[X].center()) - p300.default_speed = 400 - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A5' - p300.pick_up_tip() - p300.aspirate(PCRVol, PCR.bottom(p300_offset_Temp)) - if X == 'A1': - p300.move_to(A1_p300_loc1) - if X == 'A3': - p300.move_to(A3_p300_loc1) - if X == 'A5': - p300.move_to(A5_p300_loc1) - p300.dispense(PCRVol / 5, rate=0.75) - p300.default_speed = 5 - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.dispense(PCRVol / 5, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_loc3) - if X == 'A3': - p300.move_to(A3_p300_loc3) - if X == 'A5': - p300.move_to(A5_p300_loc3) - p300.dispense(PCRVol / 5, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.dispense(PCRVol / 5, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_loc1) - if X == 'A3': - p300.move_to(A3_p300_loc1) - if X == 'A5': - p300.move_to(A5_p300_loc1) - p300.dispense(PCRVol / 5, rate=0.75) - reps = 5 - for x in range(reps): - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.aspirate(PCRVol, rate=0.5) - if X == 'A1': - p300.move_to(A1_p300_bead_top) - if X == 'A3': - p300.move_to(A3_p300_bead_top) - if X == 'A5': - p300.move_to(A5_p300_bead_top) - p300.dispense(PCRVol, rate=1) - reps = 3 - for x in range(reps): - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.mix(PCRMixRep, PCRMixVol) - if X == 'A1': - p300.move_to(A1_p300_loc1) - if X == 'A3': - p300.move_to(A3_p300_loc1) - if X == 'A5': - p300.move_to(A5_p300_loc1) - p300.mix(PCRMixRep, PCRMixVol) - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.mix(PCRMixRep, PCRMixVol) - if X == 'A1': - p300.move_to(A1_p300_loc3) - if X == 'A3': - p300.move_to(A3_p300_loc3) - if X == 'A5': - p300.move_to(A5_p300_loc3) - p300.mix(PCRMixRep, PCRMixVol) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.mix(PCRMixRep, PCRMixVol) - p300.move_to(sample_plate_mag[X].top()) - protocol.delay(seconds=0.5) - p300.move_to(sample_plate_mag[X].center()) - p300.default_speed = 400 - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - - protocol.comment('--> Adding Barcodes') - BarcodeVol = 10 - BarcodeMixRep = 10 - BarcodeMixVol = 10 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A1' - p20.pick_up_tip() - p20.aspirate(BarcodeVol, Barcodes1.bottom( - z=p20_offset_Temp), rate=0.25) - p20.dispense( - BarcodeVol, sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.mix(BarcodeMixRep, BarcodeMixVol) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A3' - p20.pick_up_tip() - p20.aspirate(BarcodeVol, Barcodes2.bottom( - z=p20_offset_Temp), rate=0.25) - p20.dispense( - BarcodeVol, sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.mix(BarcodeMixRep, BarcodeMixVol) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A5' - p20.pick_up_tip() - p20.aspirate(BarcodeVol, Barcodes3.bottom( - z=p20_offset_Temp), rate=0.25) - p20.dispense( - BarcodeVol, sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.mix(BarcodeMixRep, BarcodeMixVol) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - - if DRYRUN == 'NO': - protocol.pause("PLACE sample_plate on THERMO") - - if STEP_PCRDECK == 1: - ####################################################################### - protocol.pause('Seal, Run PCR (25min)') - - thermocycler.close_lid() - profile_PCR_1 = [ - {'temperature': 68, 'hold_time_minutes': 3}, - {'temperature': 98, 'hold_time_minutes': 3} - ] - thermocycler.execute_profile( - steps=profile_PCR_1, repetitions=1, block_max_volume=50) - profile_PCR_2 = [ - {'temperature': 98, 'hold_time_seconds': 45}, - {'temperature': 62, 'hold_time_seconds': 30}, - {'temperature': 68, 'hold_time_minutes': 2} - ] - thermocycler.execute_profile( - steps=profile_PCR_2, repetitions=5, block_max_volume=50) - profile_PCR_3 = [ - {'temperature': 68, 'hold_time_minutes': 1} - ] - thermocycler.execute_profile( - steps=profile_PCR_3, repetitions=1, block_max_volume=50) - thermocycler.set_block_temperature(4) - ####################################################################### - thermocycler.open_lid() - protocol.pause("Remove Seal") - else: - protocol.pause('Seal, Run PCR (60min)') - - Liquid_trash = reservoir['A11'] - - if STEP_POSTPCR == 1: - protocol.pause("PLACE sample_plate on MAGNET") - protocol.comment('==============================================') - protocol.comment('--> CLEANUP') - protocol.comment('==============================================') - - if DRYRUN == 'NO': - protocol.comment('MAGNET ENGAGE') - mag_block.engage(height_from_base=8.5) - protocol.delay(minutes=1) - mag_block.engage(height_from_base=7) - protocol.delay(minutes=1) - mag_block.engage(height_from_base=5) - protocol.delay(minutes=1) - - protocol.comment('--> Transferring Supernatant') - TransferSup = 45 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A1' - Y = 'A7' - p300.pick_up_tip() - p300.aspirate( - TransferSup / 2, sample_plate_mag[X]. - bottom(z=p300_offset_Mag + 1), rate=0.5) - protocol.delay(seconds=0.1) - p300.aspirate( - TransferSup / 2, sample_plate_mag[X]. - bottom(z=p300_offset_Mag), rate=0.5) - p300.dispense( - TransferSup + 5, sample_plate_mag[Y].bottom(z=p300_offset_Mag)) - protocol.delay(seconds=0.1) - p300.blow_out(sample_plate_mag[Y].top(z=-2)) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A3' - Y = 'A9' - p300.pick_up_tip() - p300.aspirate( - TransferSup / 2, sample_plate_mag[X]. - bottom(z=p300_offset_Mag + 1), rate=0.5) - protocol.delay(seconds=0.1) - p300.aspirate( - TransferSup / 2, sample_plate_mag[X]. - bottom(z=p300_offset_Mag), rate=0.5) - p300.dispense( - TransferSup + 5, sample_plate_mag[Y].bottom(z=p300_offset_Mag)) - protocol.delay(seconds=0.1) - p300.blow_out(sample_plate_mag[Y].top(z=-2)) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A5' - Y = 'A11' - p300.pick_up_tip() - p300.aspirate( - TransferSup / 2, sample_plate_mag[X]. - bottom(z=p300_offset_Mag + 1), rate=0.5) - protocol.delay(seconds=0.1) - p300.aspirate( - TransferSup / 2, sample_plate_mag[X].bottom(z=p300_offset_Mag), - rate=0.5) - p300.dispense( - TransferSup + 5, sample_plate_mag[Y].bottom(z=p300_offset_Mag)) - protocol.delay(seconds=0.1) - p300.blow_out(sample_plate_mag[Y].top(z=-2)) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - - if DRYRUN == 'NO': - protocol.comment('MAGNET DISENGAGE') - mag_block.disengage() - - protocol.comment('--> ADDING AMPure (0.8x)') - AMPureVol = 40 - AMPureMixRep = 50 - AMPureMixVol = 80 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A7' - p300.pick_up_tip() - p300.mix(10, AMPureVol + 10, AMPure.bottom(z=p300_offset_Res)) - p300.aspirate(AMPureVol, AMPure.bottom( - z=p300_offset_Res), rate=0.25) - p300.dispense(AMPureVol, sample_plate_mag[X].bottom( - z=p300_offset_Mag), rate=0.25) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.mix(AMPureMixRep, AMPureMixVol) - p300.blow_out(sample_plate_mag[X].top(z=-5)) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A9' - p300.pick_up_tip() - p300.mix(3, AMPureVol + 10, AMPure.bottom(z=p300_offset_Res)) - p300.aspirate(AMPureVol, AMPure.bottom( - z=p300_offset_Res), rate=0.25) - p300.dispense(AMPureVol, sample_plate_mag[X].bottom( - z=p300_offset_Mag), rate=0.25) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.mix(AMPureMixRep, AMPureMixVol) - p300.blow_out(sample_plate_mag[X].top(z=-5)) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A11' - p300.pick_up_tip() - p300.mix(3, AMPureVol + 10, AMPure.bottom(z=p300_offset_Res)) - p300.aspirate(AMPureVol, AMPure.bottom( - z=p300_offset_Res), rate=0.25) - p300.dispense(AMPureVol, sample_plate_mag[X].bottom( - z=p300_offset_Mag), rate=0.25) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.mix(AMPureMixRep, AMPureMixVol) - p300.blow_out(sample_plate_mag[X].top(z=-5)) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - - if DRYRUN == 'NO': - protocol.delay(minutes=5) - - protocol.comment('MAGNET ENGAGE') - mag_block.engage(height_from_base=8.5) - protocol.delay(minutes=1) - mag_block.engage(height_from_base=7.5) - protocol.delay(minutes=1) - mag_block.engage(height_from_base=7) - protocol.delay(minutes=1) - mag_block.engage(height_from_base=6) - protocol.delay(minutes=1) - mag_block.engage(height_from_base=5) - protocol.delay(minutes=1) - - if TIPREUSE == 'NO': - if all(STEPS) is True: - protocol.pause('RESET TIPS') - p300.reset_tipracks() - p20.reset_tipracks() - - protocol.comment('--> Removing Supernatant') - RemoveSup = 100 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A7' - p300.pick_up_tip() - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(RemoveSup - 30, rate=0.25) - p300.default_speed = 5 - if X == 'A7': - p300.move_to(A7_p300_bead_side) - if X == 'A9': - p300.move_to(A9_p300_bead_side) - if X == 'A11': - p300.move_to(A11_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(20, rate=0.2) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - protocol.delay(minutes=0.1) - p300.aspirate(10, rate=0.1) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A9' - p300.pick_up_tip() - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(RemoveSup - 30, rate=0.25) - p300.default_speed = 5 - if X == 'A7': - p300.move_to(A7_p300_bead_side) - if X == 'A9': - p300.move_to(A9_p300_bead_side) - if X == 'A11': - p300.move_to(A11_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(20, rate=0.2) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - protocol.delay(minutes=0.1) - p300.aspirate(10, rate=0.1) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A11' - p300.pick_up_tip() - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(RemoveSup - 30, rate=0.25) - p300.default_speed = 5 - if X == 'A7': - p300.move_to(A7_p300_bead_side) - if X == 'A9': - p300.move_to(A9_p300_bead_side) - if X == 'A11': - p300.move_to(A11_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(20, rate=0.2) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - protocol.delay(minutes=0.1) - p300.aspirate(10, rate=0.1) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - - protocol.comment('--> Repeating 2 washes') - washreps = 2 - for wash in range(washreps): - protocol.comment('--> ETOH Wash #' + str(wash + 1)) - ETOHMaxVol = 150 - WASHNUM = 1 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A7' - if TIPREUSE == 'NO': - p300.pick_up_tip() - elif WASHNUM == 1: - p300.pick_up_tip(W1_ETOH_washtip_1) - elif WASHNUM == 2: - pass # # FIXME: W2_ETOH_washtip_1 is never defined - # p300.pick_up_tip(W2_ETOH_washtip_1) - p300.aspirate(ETOHMaxVol, EtOH_1.bottom(z=p300_offset_Res)) - if X == 'A7': - p300.move_to(A7_p300_bead_side) - if X == 'A9': - p300.move_to(A9_p300_bead_side) - if X == 'A11': - p300.move_to(A11_p300_bead_side) - p300.dispense(ETOHMaxVol - 50, rate=0.5) - p300.move_to(sample_plate_mag[X].center()) - p300.dispense(50, rate=0.5) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 5 - p300.move_to(sample_plate_mag[X].top(z=-2)) - protocol.delay(minutes=0.1) - p300.blow_out() - p300.default_speed = 400 - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A9' - if TIPREUSE == 'NO': - p300.pick_up_tip() - elif WASHNUM == 1: - p300.pick_up_tip(W1_ETOH_washtip_2) - elif WASHNUM == 2: - pass - # FIXME: W2_ETOH_washtip_2 is never defined - # p300.pick_up_tip(W2_ETOH_washtip_2) - p300.aspirate(ETOHMaxVol, EtOH_2.bottom(z=p300_offset_Res)) - if X == 'A7': - p300.move_to(A7_p300_bead_side) - if X == 'A9': - p300.move_to(A9_p300_bead_side) - if X == 'A11': - p300.move_to(A11_p300_bead_side) - p300.dispense(ETOHMaxVol - 50, rate=0.5) - p300.move_to(sample_plate_mag[X].center()) - p300.dispense(50, rate=0.5) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 5 - p300.move_to(sample_plate_mag[X].top(z=-2)) - protocol.delay(minutes=0.1) - p300.blow_out() - p300.default_speed = 400 - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A11' - if TIPREUSE == 'NO': - p300.pick_up_tip() - elif WASHNUM == 1: - p300.pick_up_tip(W1_ETOH_washtip_3) - elif WASHNUM == 2: - pass - # FIXME: W2_ETOH_washtip_3 is undefined - # p300.pick_up_tip(W2_ETOH_washtip_3) - p300.aspirate(ETOHMaxVol, EtOH_3.bottom(z=p300_offset_Res)) - if X == 'A7': - p300.move_to(A7_p300_bead_side) - if X == 'A9': - p300.move_to(A9_p300_bead_side) - if X == 'A11': - p300.move_to(A11_p300_bead_side) - p300.dispense(ETOHMaxVol - 50, rate=0.5) - p300.move_to(sample_plate_mag[X].center()) - p300.dispense(50, rate=0.5) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 5 - p300.move_to(sample_plate_mag[X].top(z=-2)) - protocol.delay(minutes=0.1) - p300.blow_out() - p300.default_speed = 400 - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - protocol.delay(minutes=0.5) - - protocol.comment('--> Remove ETOH Wash #' + str(wash + 1)) - if samplecolumns >= 1: # ---------------------------------------- - X = 'A7' - if TIPREUSE == 'NO': - p300.pick_up_tip() - elif WASHNUM == 1: - p300.pick_up_tip(W1_ETOH_removetip_1) - elif WASHNUM == 2: - pass - # FIXME: W2_ETOH_removetip_1 is never defined - # p300.pick_up_tip(W2_ETOH_removetip_1) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(ETOHMaxVol, rate=0.25) - p300.default_speed = 5 - if X == 'A7': - p300.move_to(A7_p300_bead_side) - if X == 'A9': - p300.move_to(A9_p300_bead_side) - if X == 'A11': - p300.move_to(A11_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(200 - ETOHMaxVol, rate=0.25) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(Liquid_trash.top(z=5)) - protocol.delay(minutes=0.1) - p300.blow_out() - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A9' - if TIPREUSE == 'NO': - p300.pick_up_tip() - elif WASHNUM == 1: - p300.pick_up_tip(W1_ETOH_removetip_2) - elif WASHNUM == 2: - pass - # FIXME: W2_ETOH_removetip_2 is never defined - # p300.pick_up_tip(W2_ETOH_removetip_2) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(ETOHMaxVol, rate=0.25) - p300.default_speed = 5 - if X == 'A7': - p300.move_to(A7_p300_bead_side) - if X == 'A9': - p300.move_to(A9_p300_bead_side) - if X == 'A11': - p300.move_to(A11_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(200 - ETOHMaxVol, rate=0.25) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(Liquid_trash.top(z=5)) - protocol.delay(minutes=0.1) - p300.blow_out() - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A11' - if TIPREUSE == 'NO': - p300.pick_up_tip() - elif WASHNUM == 1: - p300.pick_up_tip(W1_ETOH_removetip_3) - elif WASHNUM == 2: - pass - # FIXME: W2_ETOH_removetip_3 is never defined - # p300.pick_up_tip(W2_ETOH_removetip_3) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(ETOHMaxVol, rate=0.25) - p300.default_speed = 5 - if X == 'A7': - p300.move_to(A7_p300_bead_side) - if X == 'A9': - p300.move_to(A9_p300_bead_side) - if X == 'A11': - p300.move_to(A11_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(200 - ETOHMaxVol, rate=0.25) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(Liquid_trash.top(z=5)) - protocol.delay(minutes=0.1) - p300.blow_out() - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - wash += 1 - - if DRYRUN == 'NO': - protocol.delay(minutes=2) - - protocol.comment('--> Removing Residual ETOH') - if samplecolumns >= 1: # ---------------------------------------- - X = 'A7' - p20.pick_up_tip() - p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.aspirate(20, rate=0.25)if NOMODULES == 'NO' else p20.aspirate( - 10, rate=0.25) - p20.move_to(bypass) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A9' - p20.pick_up_tip() - p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.aspirate(20, rate=0.25)if NOMODULES == 'NO' else p20.aspirate( - 10, rate=0.25) - p20.move_to(bypass) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A11' - p20.pick_up_tip() - p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.aspirate(20, rate=0.25)if NOMODULES == 'NO' else p20.aspirate( - 10, rate=0.25) - p20.move_to(bypass) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - - if DRYRUN == 'NO': - mag_block.engage(height_from_base=6) - protocol.comment('AIR DRY') - protocol.delay(minutes=0.5) - - protocol.comment('MAGNET DISENGAGE') - mag_block.disengage() - - protocol.comment('--> Adding RSB') - RSBVol = 32 - RSBMixRep = 5 - RSBMixVol = 25 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A7' - p300.pick_up_tip() - p300.aspirate(RSBVol, RSB.bottom(p300_offset_Res)) - if X == 'A7': - p300.move_to(A7_p300_loc1) - if X == 'A9': - p300.move_to(A9_p300_loc1) - if X == 'A11': - p300.move_to(A11_p300_loc1) - p300.dispense(RSBVol / 5, rate=0.75) - p300.default_speed = 5 - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.dispense(RSBVol / 5, rate=0.75) - if X == 'A7': - p300.move_to(A7_p300_loc3) - if X == 'A9': - p300.move_to(A9_p300_loc3) - if X == 'A11': - p300.move_to(A11_p300_loc3) - p300.dispense(RSBVol / 5, rate=0.75) - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.dispense(RSBVol / 5, rate=0.75) - if X == 'A7': - p300.move_to(A7_p300_loc1) - if X == 'A9': - p300.move_to(A9_p300_loc1) - if X == 'A11': - p300.move_to(A11_p300_loc1) - p300.dispense(RSBVol / 5, rate=0.75) - reps = 5 - for x in range(reps): - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.aspirate(RSBVol, rate=0.5) - if X == 'A7': - p300.move_to(A7_p300_bead_top) - if X == 'A9': - p300.move_to(A9_p300_bead_top) - if X == 'A11': - p300.move_to(A11_p300_bead_top) - p300.dispense(RSBVol, rate=1) - reps = 3 - for x in range(reps): - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.mix(RSBMixRep, RSBMixVol) - if X == 'A7': - p300.move_to(A7_p300_loc1) - if X == 'A9': - p300.move_to(A9_p300_loc1) - if X == 'A11': - p300.move_to(A11_p300_loc1) - p300.mix(RSBMixRep, RSBMixVol) - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.mix(RSBMixRep, RSBMixVol) - if X == 'A7': - p300.move_to(A7_p300_loc3) - if X == 'A9': - p300.move_to(A9_p300_loc3) - if X == 'A11': - p300.move_to(A11_p300_loc3) - p300.mix(RSBMixRep, RSBMixVol) - p300.move_to(sample_plate_mag.wells_by_name() - [X].bottom(z=p300_offset_Mag)) - p300.mix(RSBMixRep, RSBMixVol) - p300.move_to(sample_plate_mag.wells_by_name()[X].top()) - protocol.delay(seconds=0.5) - p300.move_to(sample_plate_mag.wells_by_name()[X].center()) - p300.default_speed = 400 - if TIPREUSE == 'NO': - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - else: - p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A9' - p300.pick_up_tip() - p300.aspirate(RSBVol, RSB.bottom(p300_offset_Res)) - if X == 'A7': - p300.move_to(A7_p300_loc1) - if X == 'A9': - p300.move_to(A9_p300_loc1) - if X == 'A11': - p300.move_to(A11_p300_loc1) - p300.dispense(RSBVol / 5, rate=0.75) - p300.default_speed = 5 - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.dispense(RSBVol / 5, rate=0.75) - if X == 'A7': - p300.move_to(A7_p300_loc3) - if X == 'A9': - p300.move_to(A9_p300_loc3) - if X == 'A11': - p300.move_to(A11_p300_loc3) - p300.dispense(RSBVol / 5, rate=0.75) - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.dispense(RSBVol / 5, rate=0.75) - if X == 'A7': - p300.move_to(A7_p300_loc1) - if X == 'A9': - p300.move_to(A9_p300_loc1) - if X == 'A11': - p300.move_to(A11_p300_loc1) - p300.dispense(RSBVol / 5, rate=0.75) - reps = 5 - for x in range(reps): - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.aspirate(RSBVol, rate=0.5) - if X == 'A7': - p300.move_to(A7_p300_bead_top) - if X == 'A9': - p300.move_to(A9_p300_bead_top) - if X == 'A11': - p300.move_to(A11_p300_bead_top) - p300.dispense(RSBVol, rate=1) - reps = 3 - for x in range(reps): - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.mix(RSBMixRep, RSBMixVol) - if X == 'A7': - p300.move_to(A7_p300_loc1) - if X == 'A9': - p300.move_to(A9_p300_loc1) - if X == 'A11': - p300.move_to(A11_p300_loc1) - p300.mix(RSBMixRep, RSBMixVol) - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.mix(RSBMixRep, RSBMixVol) - if X == 'A7': - p300.move_to(A7_p300_loc3) - if X == 'A9': - p300.move_to(A9_p300_loc3) - if X == 'A11': - p300.move_to(A11_p300_loc3) - p300.mix(RSBMixRep, RSBMixVol) - p300.move_to(sample_plate_mag.wells_by_name() - [X].bottom(z=p300_offset_Mag)) - p300.mix(RSBMixRep, RSBMixVol) - p300.move_to(sample_plate_mag.wells_by_name()[X].top()) - protocol.delay(seconds=0.5) - p300.move_to(sample_plate_mag.wells_by_name()[X].center()) - p300.default_speed = 400 - if TIPREUSE == 'NO': - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - else: - p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A11' - p300.pick_up_tip() - p300.aspirate(RSBVol, RSB.bottom(p300_offset_Res)) - if X == 'A7': - p300.move_to(A7_p300_loc1) - if X == 'A9': - p300.move_to(A9_p300_loc1) - if X == 'A11': - p300.move_to(A11_p300_loc1) - p300.dispense(RSBVol / 5, rate=0.75) - p300.default_speed = 5 - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.dispense(RSBVol / 5, rate=0.75) - if X == 'A7': - p300.move_to(A7_p300_loc3) - if X == 'A9': - p300.move_to(A9_p300_loc3) - if X == 'A11': - p300.move_to(A11_p300_loc3) - p300.dispense(RSBVol / 5, rate=0.75) - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.dispense(RSBVol / 5, rate=0.75) - if X == 'A7': - p300.move_to(A7_p300_loc1) - if X == 'A9': - p300.move_to(A9_p300_loc1) - if X == 'A11': - p300.move_to(A11_p300_loc1) - p300.dispense(RSBVol / 5, rate=0.75) - reps = 5 - for x in range(reps): - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.aspirate(RSBVol, rate=0.5) - if X == 'A7': - p300.move_to(A7_p300_bead_top) - if X == 'A9': - p300.move_to(A9_p300_bead_top) - if X == 'A11': - p300.move_to(A11_p300_bead_top) - p300.dispense(RSBVol, rate=1) - reps = 3 - for x in range(reps): - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.mix(RSBMixRep, RSBMixVol) - if X == 'A7': - p300.move_to(A7_p300_loc1) - if X == 'A9': - p300.move_to(A9_p300_loc1) - if X == 'A11': - p300.move_to(A11_p300_loc1) - p300.mix(RSBMixRep, RSBMixVol) - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.mix(RSBMixRep, RSBMixVol) - if X == 'A7': - p300.move_to(A7_p300_loc3) - if X == 'A9': - p300.move_to(A9_p300_loc3) - if X == 'A11': - p300.move_to(A11_p300_loc3) - p300.mix(RSBMixRep, RSBMixVol) - p300.move_to(sample_plate_mag.wells_by_name() - [X].bottom(z=p300_offset_Mag)) - p300.mix(RSBMixRep, RSBMixVol) - p300.move_to(sample_plate_mag.wells_by_name()[X].top()) - protocol.delay(seconds=0.5) - p300.move_to(sample_plate_mag.wells_by_name()[X].center()) - p300.default_speed = 400 - if TIPREUSE == 'NO': - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - else: - p300.return_tip() - - if DRYRUN == 'NO': - protocol.delay(minutes=2) - - protocol.comment('MAGNET ENGAGE') - mag_block.engage(height_from_base=5) - - protocol.delay(minutes=4) - - protocol.comment('--> Transferring Supernatant') - - if NOMODULES == 'NO': - TransferSup = 30 - else: - TransferSup = 20 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A7' - Y = 'A8' - p20.pick_up_tip() - p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.aspirate(TransferSup / 2, rate=0.25) - p20.dispense( - TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag)) - p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.aspirate(TransferSup / 2, rate=0.25) - p20.dispense( - TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag)) - p20.move_to(bypass) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A9' - Y = 'A10' - p20.pick_up_tip() - p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.aspirate(TransferSup / 2, rate=0.25) - p20.dispense( - TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag)) - p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.aspirate(TransferSup / 2, rate=0.25) - p20.dispense( - TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag)) - p20.move_to(bypass) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A11' - Y = 'A12' - p20.pick_up_tip() - p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.aspirate(TransferSup / 2, rate=0.25) - p20.dispense( - TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag)) - p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.aspirate(TransferSup / 2, rate=0.25) - p20.dispense( - TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag)) - p20.move_to(bypass) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - - if DRYRUN == 'NO': - protocol.comment('MAGNET DISENGAGE') - mag_block.disengage() diff --git a/protocols/zymo-ribofree-cleanup/cleanup.ot2.apiv2.py b/protocols/zymo-ribofree-cleanup/cleanup.ot2.apiv2.py index 57eb9e518..7f5228cfa 100644 --- a/protocols/zymo-ribofree-cleanup/cleanup.ot2.apiv2.py +++ b/protocols/zymo-ribofree-cleanup/cleanup.ot2.apiv2.py @@ -8,7 +8,7 @@ MagBead Clean-up (robot 2)', 'author': 'Nick ', 'source': 'Custom Protocol Request', - 'apiLevel': '2.0' + 'apiLevel': '2.3' } diff --git a/protocols/zymo-ribofree-first-strand-cdna-synth-universal-depletion/1_first_strand_synth_uni_depletion.ot2.apiv2.py b/protocols/zymo-ribofree-first-strand-cdna-synth-universal-depletion/1_first_strand_synth_uni_depletion.ot2.apiv2.py index 66db61083..f3d496ba6 100644 --- a/protocols/zymo-ribofree-first-strand-cdna-synth-universal-depletion/1_first_strand_synth_uni_depletion.ot2.apiv2.py +++ b/protocols/zymo-ribofree-first-strand-cdna-synth-universal-depletion/1_first_strand_synth_uni_depletion.ot2.apiv2.py @@ -6,7 +6,7 @@ cDNA Synthesis and RiboFreeTM Universal Depletion (robot 1)', 'author': 'Nick ', 'source': 'Custom Protocol Request', - 'apiLevel': '2.0' + 'apiLevel': '2.3' } diff --git a/protocols/zymo-ribofree-library-index-pcr/4_library_index_pcr.ot2.apiv2.py b/protocols/zymo-ribofree-library-index-pcr/4_library_index_pcr.ot2.apiv2.py index a2aeff63d..693d01317 100644 --- a/protocols/zymo-ribofree-library-index-pcr/4_library_index_pcr.ot2.apiv2.py +++ b/protocols/zymo-ribofree-library-index-pcr/4_library_index_pcr.ot2.apiv2.py @@ -7,7 +7,7 @@ PCR (robot 1)', 'author': 'Nick ', 'source': 'Custom Protocol Request', - 'apiLevel': '2.0' + 'apiLevel': '2.3' } diff --git a/protocols/zymo-ribofree-p5-adapter-ligation/3_p5_adapter_ligation.ot2.apiv2.py b/protocols/zymo-ribofree-p5-adapter-ligation/3_p5_adapter_ligation.ot2.apiv2.py index 227c59a30..d2f286d3d 100644 --- a/protocols/zymo-ribofree-p5-adapter-ligation/3_p5_adapter_ligation.ot2.apiv2.py +++ b/protocols/zymo-ribofree-p5-adapter-ligation/3_p5_adapter_ligation.ot2.apiv2.py @@ -7,7 +7,7 @@ Ligation (robot 1)', 'author': 'Nick ', 'source': 'Custom Protocol Request', - 'apiLevel': '2.0' + 'apiLevel': '2.3' } diff --git a/protocols/zymo-ribofree-p7-adapter-ligation/2_p7_adapter_ligation.ot2.apiv2.py b/protocols/zymo-ribofree-p7-adapter-ligation/2_p7_adapter_ligation.ot2.apiv2.py index bc7e8c565..1caf96e0c 100644 --- a/protocols/zymo-ribofree-p7-adapter-ligation/2_p7_adapter_ligation.ot2.apiv2.py +++ b/protocols/zymo-ribofree-p7-adapter-ligation/2_p7_adapter_ligation.ot2.apiv2.py @@ -6,7 +6,7 @@ Ligation (robot 1)', 'author': 'Nick ', 'source': 'Custom Protocol Request', - 'apiLevel': '2.0' + 'apiLevel': '2.3' } diff --git a/protolib/parse/parseOT2v2.py b/protolib/parse/parseOT2v2.py index aa01e0d5b..6ee662b42 100644 --- a/protolib/parse/parseOT2v2.py +++ b/protolib/parse/parseOT2v2.py @@ -2,6 +2,10 @@ import sys from pathlib import Path import opentrons +from opentrons.hardware_control import ( + API as HardwareAPI, + ThreadManager, + ) from opentrons.protocols.execution.execute import run_protocol from opentrons.protocols.parse import parse as parse_protocol from opentrons.protocols.context.simulator.protocol_context \ @@ -106,10 +110,14 @@ def parse(protocol_path): assert protocol.api_level >= (2, 0) # Use a simulating protocol context - context_impl = ProtocolContextSimulation() + sh_arg = ThreadManager(HardwareAPI.build_hardware_simulator).sync + + context_impl = ProtocolContextSimulation( + sync_hardware=sh_arg, api_version=protocol.api_level) context = opentrons.protocol_api.contexts.ProtocolContext( implementation=context_impl) + # NOTE:(IL, 2020-05-13)L there’s no deck calibration, and the # identity deck calibration is about 25 mm too high (as of v1.17.1). # Because of this, tall labware can cross the threshold and cause a diff --git a/protolib/parse/readme_map.json b/protolib/parse/readme_map.json index 956dafea5..281282cc1 100644 --- a/protolib/parse/readme_map.json +++ b/protolib/parse/readme_map.json @@ -61,6 +61,10 @@ "thermocycler": { "displayText": "Opentrons Thermocycler Module", "link": "https://shop.opentrons.com/thermocycler-module-1/" + }, + "heatershaker": { + "displayText": "Opentrons Heater-Shaker Module", + "link": "https://shop.opentrons.com/heater-shaker-module/" } } }