From eac309c44a1e8688581c59440da87a5e6b349a54 Mon Sep 17 00:00:00 2001 From: livqiu Date: Thu, 27 Sep 2018 17:29:56 -0400 Subject: [PATCH 1/3] updated banners, added notebook and safety to grids, created final safety and notebook pages --- final/notebook.html | 413 +++++++++++++++++++++++++++++++++++++++++ final/safety.html | 205 ++++++++++++++++++++ notebook.html | 10 +- safety.html | 12 +- styles/grids.css | 30 +++ styles/styles.css | 5 + wetLabDemonstrate.html | 132 +++++++++++++ wetLabFoundations.html | 132 +++++++++++++ wetLabInterLab.html | 132 +++++++++++++ wetLabParts.html | 132 +++++++++++++ 10 files changed, 1192 insertions(+), 11 deletions(-) create mode 100644 final/notebook.html create mode 100644 final/safety.html create mode 100644 wetLabDemonstrate.html create mode 100644 wetLabFoundations.html create mode 100644 wetLabInterLab.html create mode 100644 wetLabParts.html diff --git a/final/notebook.html b/final/notebook.html new file mode 100644 index 0000000..6033d21 --- /dev/null +++ b/final/notebook.html @@ -0,0 +1,413 @@ + + + + + Team:Cornell/Notebook - 2018.igem.org + + + + + + + + + + + + + +
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March 4th to March 10th
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Wet Lab: New members began training by learning about sterile technique, bacterial cultures, and DNA purification. Team practiced miniprep protocols.

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Wiki: Wiki subteam learned the importance of typography during a one-hour long Wiki/Design Training class. Worked on the webpage replication project to practice Adobe Illustrator (due 3/18).

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P & P: On February 27th, P&P worked with YOURS to teach kids about physics and engineering principles by building paper towers to hold up as many books as possible. P&P regrouped to discuss this program and to continue brainstorming for future outreach events. P&P continued brainstorming other outreach events and ideas with the intention of reaching out to the kids at the local Ithaca High school.

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March 11th to March 17th
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Wet Lab: Members split into training groups and performed PCR on gBlocks from last year’s project. Training involved overviews and run-throughs of cloning, transformation, miniprep, gel extraction, and other protocols.

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Wiki: Wiki subteam learned the basics of HTML and CSS during a one-hour long Wiki/Design Training class. Worked on the HTML/CSS project (due 3/26).

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P & P: P&P started planning and finding information for a synthetic biology discussion. Also brainstormed for activities for the annual student outreach event - Splash! at Cornell.

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March 18th to March 24th
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Wiki: Wiki subteam learned the basics of colors, white space, and composition during a one-hour long Wiki/Design Training class. Worked on webpage creation project to practice building information hierarchy (due 4/8).

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P & P: P&P brainstormed applications for two possible projects for the team - incorporating synthetic biology with 3D printing or with fourier transforms/band-pass filters.

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March 25th to March 31st
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Wiki: Wiki subteam learned the basics of JavaScript and jQuery during a one-hour long Wiki/Design Training class. Worked on the JavaScript/jQuery project (due 4/13).

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P & P: P&P started finding research contacts to consult for technical advice on creating a band-pass filter in bacteria. P&P compiled a list of questions for the interviews to inform our biological circuit design.

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April 8th to April 14th
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Wiki: Wiki subteam evaluated past competition winners’ websites and our past competition websites during a one-hour long Wiki/Design Training class. Worked on designing a webpage for our current project (due 4/23).

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P & P: P&P consulted Professor G. Lambert on April 9th regarding our preliminary design of our genetic circuit and any potential issues with the project. On April 10th, P&P interviewed Professor E. Kan about the similar design principles connecting electrical engineering to genetic circuit engineering.

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April 15th to April 21st
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Wiki: Wiki subteam learned the basics of Bootstrap and Git/GitHub during a one-hour long Wiki/Design Training class. Worked on the Bootstrap/Github project (due 4/30).

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P & P: P&P interviewed Professor J. March on April 20th for assistance in choosing specific protein candidates for our genetic circuit. The discussion also addressed control of circuit kinetics via protein degradation and plasmid copy number and potential applications for our project. P&P also continued planning for Splash! and RawExpo, a creative exposition at the architecture school.

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Business: Business held their National Garlic Day fundraiser on 4/19 - earned some money and spread the word about iGEM!

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April 22nd to April 28th
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Wet Lab: Wetlab continued training. Members performed a double digestion and practiced using a NanoDrop Spectrophotometer.

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Wiki: Wiki subteam met up to discuss iGEM wiki rules and go over the general timeline for the summer and fall.

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P & P: The first day of Ithaca High School (IHS) outreach took place on 4/26. P&P introduced Future Problem Solving (FPS) approaches and assigned readings for first topic (spread of infectious diseases).
On April 27th, P&P participated in RawExpo and presented last year’s project, Oxyponics.
P&P hosted an outreach event on April 28th as part of Splash! at Cornell U. We introduced synthetic biology topics including DNA extraction, plasmid transformation, and CRISPR.

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April 29th to May 5th
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Wet Lab: Members practiced double digest and ligation of digested inserts into pSB1C3 vector.

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P & P: P&P continued IHS outreach on 5/3 by going over a practice FPS future scenario about the spread of infectious diseases and introducing the problem-solving process.

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May 6th to May 12th
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P & P: P&P continued reaching out to faculty and experts for consultation on our band-pass filter biological circuit and mapped out the schedule for summer work.

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June 3rd to June 9th
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Wiki: Started discussing possible concepts to consider for the 2018 wiki design, such as going with a dark color scheme (not necessarily black, something more along the lines of a dark color like navy blue) and incorporating geometric aspects. Also went over some brainstorming already done in April.

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June 10th to June 16th
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Wiki: Discussed idea of using templates to make implementation of the wiki easier. Assignment to look up templates that could work for possible wiki designs for 2018 project.

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June 17th to June 23rd
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Wet Lab: We had our first team meeting on Thursday the 21st where we outlined goals for the summer. We also had a group training session on Sunday the 23rd to complete training for new members. In the lab, we attempted to transform stock PSB1C3 into NEB 5-alpha Competent E. coli, however the transformation was not successful.

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Product Development:

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Wiki: Discussed themes we found that represented elements we would like to see in a potential wiki design. Reached out to team lead for more information and clarification on the project and Product Development’s role.

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P & P: P&P outlined the events and goals for the summer while planning for 4-H. One major goal was to finish creating a customizable plasmid kit and to use it for collaboration.

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June 24th to June 30th
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Wet Lab: Wet Lab ran PCR reactions for PhrpL and sigmaF and Confirmed the lengths of each construct by running through a gel. The PCR was cleaned up and nanodropped resulting in high DNA concentration. Wet Lab began a wet culture from NEB 5-alpha E. coli transformed with PSB1c3. The wet culture was miniprepped and then ran through a gel. However, no bands were visible for PSB1C3 indicating an unsuccessful miniprep.

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Product Development:

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P & P: P&P taught a class on synthetic biology during 4-H career explorations on June 27th. Various topics were introduced, including CRISPR, DNA extraction, and phage transduction/plasmid transformation. The first iteration of the plasmid kit was laser cut and used at 4-H. We asked the students about their opinions on its use in pedagogy for feedback to improve our design. P&P began pursuing an educational collaboration with the Greater Ithaca Activities Center nearby.
P&P also began reaching out to professors at Washington University in St. Louis for consultation on our band-pass filter biological circuit.

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July 1st to July 7th
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Wet Lab: We ran PCR on our DNA constructs PhrpL, Sigmaf, and PF2. After several failed attempts, the lengths of each construct was confirmed by running a gel and nanodropping to determine the respective concentrations of each construct.

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Wiki: Called together three of our Wiki subteam members to help design the wiki this summer. Went over the project description to catch up other members of the design team. Assigned each design member to make mock-up(s) of a home page (due 7/12).

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P & P: P&P reflected on 4-H and the feedback about the plasmid kit. Issues included its transparent color, lack of visibility, and difficulty in assembly. A new plasmid kit was designed for laser cutting. P&P also worked on consolidating materials for IHS outreach in the fall and reached out to the NY Affiliate Director.

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July 8th to July 14th
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Wet Lab: We ran PCR on our DNA constructs PhrpL, Sigmaf, PF2, High pass 1b, Low pass 1b. Confirmed the lengths of each construct by running through a gel. Miniprepped PSB1C3 bacteria with low yields.

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Wiki: Design team went over each member’s home page design. Discussed what we liked/disliked for each person’s design. Picked best design out of the three. Assigned each design member to edit the chosen home page design (due 7/17).

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P & P: On July 9th, P&P interviewed Professor M. DeLisa, who interrogated the circuit design, provided suggestions on the placement different protein degradation tags on different components of the system. P&P also consulted him on the emerging technology and public opinion side of synthetic biology.
On July 10th, P&P interviewed Professor G. Lambert about modelling and testing the biological circuit.
P&P continued brainstorming potential outreach events, including a hackathon and activities for Ithaca High School in the Fall.

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July 15th to July 21st
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Wet Lab: Team ligated Phrpl, mf-lon, High Pass 1b and Low Pass 1b into pSB1C3 vectors. Team unsuccessfully attempted to transform plasmids into competent cells on chloramphenicol plates.

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Wiki: Design team went over each team member’s revised home page design and listed out what features/components to include for the final home page design. Reached out to leads and former members who contributed to design for feedback. Assigned each design member to make mock-up(s) of sub-page (due 7/21).
Design team went over sub-page designs and listed out what features/components to include for final sub-page design. Designated assignments for making team page design, notebook/attributes page design, and looking into incorporating animation into the wiki (due).

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P & P: On July 17th, P&P hosted a workshop at GIAC about synthetic biology teaching 1st graders about parts of a cell by representing different parts with different candies. Additionally, the plasmid kit was painted with methods that did not give a good final aesthetic. P&P contacted NY 4H for outreach opportunities at the upcoming NY State fair.

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July 22nd to July 28th
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Wet Lab: Wet Lab PCRed High Pass 1a, High Pass 1b and Low Pass 1c. We ran the PCR product on a gel, which confirmed a successful PCR. We then cleaned up the PCR product and nanodropped the cleanups. The PCR cleanup was cleaned up, while PSB1c3 was linearized and digested. The digestion were cleaned up and nanodropped. Wet Lab also miniprepped a wet culture that had been started earlier in the week of PSB1C3 transformed bacteria and nanodropped the results.

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P & P: On July 24th, P&P returned to GIAC and made aluminum boats with the kids to learn about engineering principles, buoyancy, and physics. Plasmid kits were designed, cut, and painted for testing for UT-Austin +

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July 29th to August 4th
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Wet Lab: We ligated previously digested High Pass 1a and High Pass 1b into pSB1C3 (to create High Pass 2a) as well as High Pass 1a and High Pass 1c into pSB1C3 (to create high Pass 2b). We performed PCR reactions for some parts we were running low on and then digested and ligated mf-Lon, sigmaF, and PhrpL, High Pass 1a, High Pass 1b, High Pass 1c, Low Pass 1b, and Low Pass 1c individually into pSB1C3 vectors. We heat inactivated and transformed our ligations into NEB 5-alpha Competent E. coli. Since we had been having trouble with transformations, we used SOC instead of LB for our outgrowth steps, with a positive outcome - colonies grew on all plates. We used isolated colonies to inoculate 5 mL liquid cultures which we miniprepped after overnight incubations. We also performed colony PCR reactions on assembled pSB1C3 vectors with High Pass 2a and and mf-lon inserts. We will continue with colony PCRs and run gels for them next week.

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Wiki: Design team discussed and made final decisions for sub-page and team page designs. Went over and made final decisions for animation. Assigned design team members to make these finalized designs.

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P & P: On July 31st, P&P played polymerase tag and made oobleck with the kids at GIAC. P&P interviewed Dr. L. Pierce and Dr. N. Argyres of Washington University in St. Louis in two separate interviews on 8/1 about the potential risks and regulations relevant to our project (see interview notes for specific interview contents).

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August 5th to August 11th
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Wiki: Wiki started setting up the internal structure of the wiki. Wiki set up the wiki repository.

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P & P: P&P interviewed Professor Swingle on August 6th, focusing on understanding methods to test and gather characterization data for modeling of the proteins HrpR and HrpS, which are integral to the biological circuit. New plasmid kits were ready for laser cutting, but the laser cutter was down.

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August 12th to August 18th
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Wiki: Wiki started setting up the layout of the home page and considering what kind of framework to use to set up the layout.

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August 19th to August 25th
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Wiki: Wiki decided to use CSS grid to implement the layout of the wiki. Wiki did more setup of the wiki.

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P & P: P&P had a Skype call interview on 8/22 with Professor M. Baccara from Washington University in St. Louis about the process and ethics of moving a product from science to business.
P&P resumed work on the project, outlining the fall semester outreach events and synthesizing information from various human practices and policies readings and interviews with experts.
P&P met with the IHS teacher on 8/24 to go over lesson plans and how FPS might fit in with the BioBuilder Club activities for the fall semester.

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August 26th to Septmeber 1st
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Wiki: Wiki had its first weekly subteam meeting. Wiki started implementing the nav bar, footer, home page, and standard page template.

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P & P: P&P worked on state fair materials, including a trifold and portable plasmid kits for our outreach efforts on 9/3.

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September 2nd to September 8th
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Wet Lab:

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Product Development:

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Wiki:

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Business:

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September 9th to September 15th
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Wet Lab:

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Business:

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September 16th to September 22nd
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Business:

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September 23rd to September 29th
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Wet Lab:

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Business:

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September 30th to October 6th
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October 7th to October 13th
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October 14th to October 16th
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Business:

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Overview
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At Cornell iGEM, we understand the risks associated with our work and take all necessary precautions to minimize those risks. As a team, we take safety very seriously and a detailed description of our procedures can be found below. Our protocols are guided by the risk matrix, as we try to both minimize the likelihood of an incident as well as the severity of an incident. Our completed safety form can be found here.

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Risk Categories
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Laboratory Safety - Risks in the laboratory include the carcinogenic intercalating agent ethidium bromide and the use of a powerful UV lamp for visualizing the results of gel electrophoresis. Additionally, we use antibiotic resistance - specifically chloramphenicol - as a selection marker. In large doses, chloramphenicol is toxic to humans. Finally, flammable agents such as ethanol and isopropyl alcohol are often used to maintain a sterile work environment. An open flame from an ethanol burner is sometimes used to maintain a sterile environment as well.

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Environmental Safety - If released into nature, our engineered bacteria pose a risk of transferring antibiotic resistance to other organisms.

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Pathogens - Our system was engineered into E. coli K12. E. coli K12 is classified as a Biosafety Level 1 organism and has been used by countless iGEM teams for cloning. Our team has taken parts found in other organisms in nature, notably B. subtilis, M. florum, and P. syringae. All of these organisms are also classified as Biosafety Level 1. While one part was taken from L. monocytogenes, a Biosafety Level 2 organism, the part was an element for control of translation, and not inherently pathogenic.

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Fabrication - Fabrication of the plasmid education kit involved the use of a laser cutter and spray paint. Laser cutters produce significant amounts of heat and the laser itself can cause severe eye damage. Spray paint often contains hazardous propellants.

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Safety Protocol
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Wet Lab - Every member of the lab wears nitrile gloves and closed toed shoes at all times. Gloves are to be replaced after working with ethidium bromide or any hazardous chemical. There are taped-off, designated areas for working with ethidium bromide. When visualizing an agarose gel under a UV lamp, all members are required to use a UV shield, UV-blocking goggles. Alternatively, the gel may be photographed using specific equipment designed for imaging under UV light, and observe the gel on a computer screen. +

+ All biologic material is sterilized and disposed of appropriately. Solid materials are disposed of in biohazard waste, which is collected by Cornell Environmental Health and Safety (EH&S), and is autoclaved and transported to a central facility for our building. It is then disposed of as regulated biological waste. Liquid cultures are disinfected in a 20% bleach solution and then washed down the sink with water. +

+ We maintain two copies of MSDS’s for each chemical we use: one for us, and one for our lab manager and other lab users. Additionally, our lab is equipped with flame-retardant benches, safety showers and eyewash stations, fire extinguishers, laminar flow hoods, biosafety cabinets, and spill kits. It is rated by Cornell EH&S as safe to work with up to Biosafety Level 2 organisms. +

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Fabrication - All members who use the laser cutter must have specific training. To minimize this risk, we asked certified students employed at the Rapid Prototyping Lab (RPL) to laser cut for us. We did not use the machine ourselves. +

+ Spray painting was performed in a well-ventilated composite workspace equipped with vacuums and overhead lighting. Cardboard was placed below the surface that was spray painted to avoid damaging any surfaces. The space was cleaned and nothing obstructed a clear path to the exit that was marked off in tape.

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Training and Enforcement
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Any team member who works in the lab is required to attend an orientation session with Dr. Shivaun Archer. During this session, Dr. Archer explains all relevant safety features of the lab, as well as how to operate equipment such as the autoclave safely. Additionally, members are required to go through standard training for working in a lab by completing two courses through Cornell EH&S. These courses are about General Lab Safety and Chemical Waste Disposal. Both the orientation session and the EH&S courses are required to be completed before a member is allowed to work in the lab. +

+ When members join our team, they are required to attend a general safety session. This session outlines safety protocols for working in our dry lab space as well as reinforcing the chemical safety lessons learned through the EH&S courses. +

+ Team members who violate safety rules are required to work under the supervision of a team leader for the remainder of the week, or until the leader believes the member is capable of performing the task unsupervised. For multiple infractions or complete disregard to safety protocols, a member may be restricted from laboratory work until he/she undergoes EHS chemical safety online training again, and demonstrates proper performance to a team leader of failed technique(s) in a controlled setting.

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Reporting
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Any incident in which safety protocols failed are to be reported to the team lead. The team lead submits an incident report to Dr. Shivaun Archer, and works with her to determine the appropriate action. Actions include a changing techniques or finding another way to minimize and further reduce the risk involved with a task - whether it be reducing the impact of an incident or its likelihood. The team lead also serves as the liaison between other safety groups and the team, including the Institutional Biosafety Committee and EH&S.

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Overview

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At Cornell iGEM, we understand the risks associated with our work and take all necessary precautions to minimize those risks. As a team, we take safety very seriously and a detailed description of our procedures can be found below. Our protocols are guided by the risk matrix, as we try to both minimize the likelihood of an incident as well as the severity of an incident. Our completed safety form can be found here [LINK TO SAFETY FORM].

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At Cornell iGEM, we understand the risks associated with our work and take all necessary precautions to minimize those risks. As a team, we take safety very seriously and a detailed description of our procedures can be found below. Our protocols are guided by the risk matrix, as we try to both minimize the likelihood of an incident as well as the severity of an incident. Our completed safety form can be found here.

diff --git a/styles/grids.css b/styles/grids.css index ab66f0f..58cae13 100644 --- a/styles/grids.css +++ b/styles/grids.css @@ -215,3 +215,33 @@ footer { grid-area: standardpagecontent; } /******************** STANDARD PAGE END ********************/ +/******************** SAFETY PAGE START ********************/ + .safety-page-wrapper { + display: grid; + grid-template-columns: auto; + grid-template-rows: 100px 550px auto 100px; + grid-template-areas: "navbar" "standardpagebanner" "safetypagecontent" "footer"; +} + .safety-page-content-wrapper { + display: inline-grid; + grid-area: safetypagecontent; + /*grid-template-columns: 7.5% 85% 7.5%;*/ +} + /******************** SAFETY PAGE END ********************/ + /******************** NOTEBOOK PAGE START ********************/ +.notebook-page-wrapper { + display: grid; + grid-template-columns: auto; + grid-template-rows: 100px 550px auto 100px; + grid-template-areas: + "navbar" + "standardpagebanner" + "notebookpagecontent" + "footer"; +} + .notebook-page-content-wrapper { + display: inline-grid; + grid-area: notebookpagecontent; + /*grid-template-columns: 7.5% 85% 7.5%;*/ +} +/******************** NOTEBOOK PAGE END ********************/ diff --git a/styles/styles.css b/styles/styles.css index 11bc9d3..8814942 100644 --- a/styles/styles.css +++ b/styles/styles.css @@ -452,6 +452,7 @@ p .standard-page-content-text { font-family: 'Merriweather', serif; font-size: 24pt; text-align: center; + color: #fff; } .notebook-text-wrapper, .safety-text-wrapper { @@ -463,6 +464,10 @@ p .standard-page-content-text { font-family: 'Open Sans Light', sans-serif; color: white; } + +#safety-hyperlink { + color: #c93843; +} /******************** NOTEBOOK PAGE END ********************/ /******************** TEAM PAGE START ********************/ diff --git a/wetLabDemonstrate.html b/wetLabDemonstrate.html new file mode 100644 index 0000000..ea8bd8b --- /dev/null +++ b/wetLabDemonstrate.html @@ -0,0 +1,132 @@ + + + + Team:Cornell/PageName - 2018.igem.org + + + + + + + + + + +
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+ + + \ No newline at end of file From 179f7a223c75859dc0a2f57c253cecfcd56a2e1e Mon Sep 17 00:00:00 2001 From: zhongat Date: Fri, 28 Sep 2018 22:46:38 -0400 Subject: [PATCH 2/3] Moved class='-page-wrapper' from body to div tag --- final/notebook.html | 722 ++++++++++++++++++++++---------------------- final/safety.html | 294 +++++++++--------- styles/grids.css | 5 +- 3 files changed, 513 insertions(+), 508 deletions(-) diff --git a/final/notebook.html b/final/notebook.html index 6033d21..83a5d81 100644 --- a/final/notebook.html +++ b/final/notebook.html @@ -44,370 +44,372 @@ - - - + + + +
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March 4th to March 10th
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Wet Lab: New members began training by learning about sterile technique, bacterial cultures, and DNA purification. Team practiced miniprep protocols.

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Wiki: Wiki subteam learned the importance of typography during a one-hour long Wiki/Design Training class. Worked on the webpage replication project to practice Adobe Illustrator (due 3/18).

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P & P: On February 27th, P&P worked with YOURS to teach kids about physics and engineering principles by building paper towers to hold up as many books as possible. P&P regrouped to discuss this program and to continue brainstorming for future outreach events. P&P continued brainstorming other outreach events and ideas with the intention of reaching out to the kids at the local Ithaca High school.

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March 4th to March 10th
+
+
+

Wet Lab: New members began training by learning about sterile technique, bacterial cultures, and DNA purification. Team practiced miniprep protocols.

+

Wiki: Wiki subteam learned the importance of typography during a one-hour long Wiki/Design Training class. Worked on the webpage replication project to practice Adobe Illustrator (due 3/18).

+

P & P: On February 27th, P&P worked with YOURS to teach kids about physics and engineering principles by building paper towers to hold up as many books as possible. P&P regrouped to discuss this program and to continue brainstorming for future outreach events. P&P continued brainstorming other outreach events and ideas with the intention of reaching out to the kids at the local Ithaca High school.

+
+
+
+
March 11th to March 17th
+
+
+

Wet Lab: Members split into training groups and performed PCR on gBlocks from last year’s project. Training involved overviews and run-throughs of cloning, transformation, miniprep, gel extraction, and other protocols.

+

Wiki: Wiki subteam learned the basics of HTML and CSS during a one-hour long Wiki/Design Training class. Worked on the HTML/CSS project (due 3/26).

+

P & P: P&P started planning and finding information for a synthetic biology discussion. Also brainstormed for activities for the annual student outreach event - Splash! at Cornell.

+
+
+
March 18th to March 24th
+
+
+

Wiki: Wiki subteam learned the basics of colors, white space, and composition during a one-hour long Wiki/Design Training class. Worked on webpage creation project to practice building information hierarchy (due 4/8).

+

P & P: P&P brainstormed applications for two possible projects for the team - incorporating synthetic biology with 3D printing or with fourier transforms/band-pass filters.

+
+
+
+
March 25th to March 31st
+
+
+

Wiki: Wiki subteam learned the basics of JavaScript and jQuery during a one-hour long Wiki/Design Training class. Worked on the JavaScript/jQuery project (due 4/13).

+

P & P: P&P started finding research contacts to consult for technical advice on creating a band-pass filter in bacteria. P&P compiled a list of questions for the interviews to inform our biological circuit design.

+
+
+
+
April 8th to April 14th
+
+
+

Wiki: Wiki subteam evaluated past competition winners’ websites and our past competition websites during a one-hour long Wiki/Design Training class. Worked on designing a webpage for our current project (due 4/23).

+

P & P: P&P consulted Professor G. Lambert on April 9th regarding our preliminary design of our genetic circuit and any potential issues with the project. On April 10th, P&P interviewed Professor E. Kan about the similar design principles connecting electrical engineering to genetic circuit engineering.

+
+
+
+
April 15th to April 21st
+
+
+

Wiki: Wiki subteam learned the basics of Bootstrap and Git/GitHub during a one-hour long Wiki/Design Training class. Worked on the Bootstrap/Github project (due 4/30).

+

P & P: P&P interviewed Professor J. March on April 20th for assistance in choosing specific protein candidates for our genetic circuit. The discussion also addressed control of circuit kinetics via protein degradation and plasmid copy number and potential applications for our project. P&P also continued planning for Splash! and RawExpo, a creative exposition at the architecture school.

+

Business: Business held their National Garlic Day fundraiser on 4/19 - earned some money and spread the word about iGEM!

+
+
+
+
April 22nd to April 28th
+
+
+

Wet Lab: Wetlab continued training. Members performed a double digestion and practiced using a NanoDrop Spectrophotometer.

+

Wiki: Wiki subteam met up to discuss iGEM wiki rules and go over the general timeline for the summer and fall.

+

P & P: The first day of Ithaca High School (IHS) outreach took place on 4/26. P&P introduced Future Problem Solving (FPS) approaches and assigned readings for first topic (spread of infectious diseases).
On April 27th, P&P participated in RawExpo and presented last year’s project, Oxyponics.
P&P hosted an outreach event on April 28th as part of Splash! at Cornell U. We introduced synthetic biology topics including DNA extraction, plasmid transformation, and CRISPR.

+
+
+
+
April 29th to May 5th
+
+
+

Wet Lab: Members practiced double digest and ligation of digested inserts into pSB1C3 vector.

+

P & P: P&P continued IHS outreach on 5/3 by going over a practice FPS future scenario about the spread of infectious diseases and introducing the problem-solving process.

+
+
+
+
May 6th to May 12th
+
+
+

P & P: P&P continued reaching out to faculty and experts for consultation on our band-pass filter biological circuit and mapped out the schedule for summer work.

+
+
+
+
June 3rd to June 9th
+
+
+

Wiki: Started discussing possible concepts to consider for the 2018 wiki design, such as going with a dark color scheme (not necessarily black, something more along the lines of a dark color like navy blue) and incorporating geometric aspects. Also went over some brainstorming already done in April.

+
+
+
+
June 10th to June 16th
+
+
+

Wiki: Discussed idea of using templates to make implementation of the wiki easier. Assignment to look up templates that could work for possible wiki designs for 2018 project.

+
+
+
+
June 17th to June 23rd
+
+
+

Wet Lab: We had our first team meeting on Thursday the 21st where we outlined goals for the summer. We also had a group training session on Sunday the 23rd to complete training for new members. In the lab, we attempted to transform stock PSB1C3 into NEB 5-alpha Competent E. coli, however the transformation was not successful.

+

Product Development:

+

Wiki: Discussed themes we found that represented elements we would like to see in a potential wiki design. Reached out to team lead for more information and clarification on the project and Product Development’s role.

+

P & P: P&P outlined the events and goals for the summer while planning for 4-H. One major goal was to finish creating a customizable plasmid kit and to use it for collaboration.

+
+
+
+
June 24th to June 30th
+
+
+

Wet Lab: Wet Lab ran PCR reactions for PhrpL and sigmaF and Confirmed the lengths of each construct by running through a gel. The PCR was cleaned up and nanodropped resulting in high DNA concentration. Wet Lab began a wet culture from NEB 5-alpha E. coli transformed with PSB1c3. The wet culture was miniprepped and then ran through a gel. However, no bands were visible for PSB1C3 indicating an unsuccessful miniprep.

+

Product Development:

+

P & P: P&P taught a class on synthetic biology during 4-H career explorations on June 27th. Various topics were introduced, including CRISPR, DNA extraction, and phage transduction/plasmid transformation. The first iteration of the plasmid kit was laser cut and used at 4-H. We asked the students about their opinions on its use in pedagogy for feedback to improve our design. P&P began pursuing an educational collaboration with the Greater Ithaca Activities Center nearby.
P&P also began reaching out to professors at Washington University in St. Louis for consultation on our band-pass filter biological circuit.

+
+
+
+
July 1st to July 7th
+
+
+

Wet Lab: We ran PCR on our DNA constructs PhrpL, Sigmaf, and PF2. After several failed attempts, the lengths of each construct was confirmed by running a gel and nanodropping to determine the respective concentrations of each construct.

+

Wiki: Called together three of our Wiki subteam members to help design the wiki this summer. Went over the project description to catch up other members of the design team. Assigned each design member to make mock-up(s) of a home page (due 7/12).

+

P & P: P&P reflected on 4-H and the feedback about the plasmid kit. Issues included its transparent color, lack of visibility, and difficulty in assembly. A new plasmid kit was designed for laser cutting. P&P also worked on consolidating materials for IHS outreach in the fall and reached out to the NY Affiliate Director.

+
+
+
+
July 8th to July 14th
+
+
+

Wet Lab: We ran PCR on our DNA constructs PhrpL, Sigmaf, PF2, High pass 1b, Low pass 1b. Confirmed the lengths of each construct by running through a gel. Miniprepped PSB1C3 bacteria with low yields.

+

Wiki: Design team went over each member’s home page design. Discussed what we liked/disliked for each person’s design. Picked best design out of the three. Assigned each design member to edit the chosen home page design (due 7/17).

+

P & P: On July 9th, P&P interviewed Professor M. DeLisa, who interrogated the circuit design, provided suggestions on the placement different protein degradation tags on different components of the system. P&P also consulted him on the emerging technology and public opinion side of synthetic biology.
On July 10th, P&P interviewed Professor G. Lambert about modelling and testing the biological circuit.
P&P continued brainstorming potential outreach events, including a hackathon and activities for Ithaca High School in the Fall.

+
+
+
+
July 15th to July 21st
+
+
+

Wet Lab: Team ligated Phrpl, mf-lon, High Pass 1b and Low Pass 1b into pSB1C3 vectors. Team unsuccessfully attempted to transform plasmids into competent cells on chloramphenicol plates.

+

Wiki: Design team went over each team member’s revised home page design and listed out what features/components to include for the final home page design. Reached out to leads and former members who contributed to design for feedback. Assigned each design member to make mock-up(s) of sub-page (due 7/21).
Design team went over sub-page designs and listed out what features/components to include for final sub-page design. Designated assignments for making team page design, notebook/attributes page design, and looking into incorporating animation into the wiki (due).

+

P & P: On July 17th, P&P hosted a workshop at GIAC about synthetic biology teaching 1st graders about parts of a cell by representing different parts with different candies. Additionally, the plasmid kit was painted with methods that did not give a good final aesthetic. P&P contacted NY 4H for outreach opportunities at the upcoming NY State fair.

+
+
+
+
July 22nd to July 28th
+
+
+

Wet Lab: Wet Lab PCRed High Pass 1a, High Pass 1b and Low Pass 1c. We ran the PCR product on a gel, which confirmed a successful PCR. We then cleaned up the PCR product and nanodropped the cleanups. The PCR cleanup was cleaned up, while PSB1c3 was linearized and digested. The digestion were cleaned up and nanodropped. Wet Lab also miniprepped a wet culture that had been started earlier in the week of PSB1C3 transformed bacteria and nanodropped the results.

+

P & P: On July 24th, P&P returned to GIAC and made aluminum boats with the kids to learn about engineering principles, buoyancy, and physics. Plasmid kits were designed, cut, and painted for testing for UT-Austin +

+
+
+
July 29th to August 4th
+
+
+

Wet Lab: We ligated previously digested High Pass 1a and High Pass 1b into pSB1C3 (to create High Pass 2a) as well as High Pass 1a and High Pass 1c into pSB1C3 (to create high Pass 2b). We performed PCR reactions for some parts we were running low on and then digested and ligated mf-Lon, sigmaF, and PhrpL, High Pass 1a, High Pass 1b, High Pass 1c, Low Pass 1b, and Low Pass 1c individually into pSB1C3 vectors. We heat inactivated and transformed our ligations into NEB 5-alpha Competent E. coli. Since we had been having trouble with transformations, we used SOC instead of LB for our outgrowth steps, with a positive outcome - colonies grew on all plates. We used isolated colonies to inoculate 5 mL liquid cultures which we miniprepped after overnight incubations. We also performed colony PCR reactions on assembled pSB1C3 vectors with High Pass 2a and and mf-lon inserts. We will continue with colony PCRs and run gels for them next week.

+

Wiki: Design team discussed and made final decisions for sub-page and team page designs. Went over and made final decisions for animation. Assigned design team members to make these finalized designs.

+

P & P: On July 31st, P&P played polymerase tag and made oobleck with the kids at GIAC. P&P interviewed Dr. L. Pierce and Dr. N. Argyres of Washington University in St. Louis in two separate interviews on 8/1 about the potential risks and regulations relevant to our project (see interview notes for specific interview contents).

+
+
+
+
August 5th to August 11th
+
+
+

Wiki: Wiki started setting up the internal structure of the wiki. Wiki set up the wiki repository.

+

P & P: P&P interviewed Professor Swingle on August 6th, focusing on understanding methods to test and gather characterization data for modeling of the proteins HrpR and HrpS, which are integral to the biological circuit. New plasmid kits were ready for laser cutting, but the laser cutter was down.

+
+
+
+
August 12th to August 18th
+
+
+

Wiki: Wiki started setting up the layout of the home page and considering what kind of framework to use to set up the layout.

+
+
+
+
August 19th to August 25th
+
+
+

Wiki: Wiki decided to use CSS grid to implement the layout of the wiki. Wiki did more setup of the wiki.

+

P & P: P&P had a Skype call interview on 8/22 with Professor M. Baccara from Washington University in St. Louis about the process and ethics of moving a product from science to business.
P&P resumed work on the project, outlining the fall semester outreach events and synthesizing information from various human practices and policies readings and interviews with experts.
P&P met with the IHS teacher on 8/24 to go over lesson plans and how FPS might fit in with the BioBuilder Club activities for the fall semester.

+
+
+
+
August 26th to Septmeber 1st
+
+
+

Wiki: Wiki had its first weekly subteam meeting. Wiki started implementing the nav bar, footer, home page, and standard page template.

+

P & P: P&P worked on state fair materials, including a trifold and portable plasmid kits for our outreach efforts on 9/3.

+
+
+
+
September 2nd to September 8th
+
+
+

Wet Lab:

+

Product Development:

+

Wiki:

+

P & P:

+

Business:

+
+
+
+
September 9th to September 15th
+
+
+

Wet Lab:

+

Product Development:

+

Wiki:

+

P & P:

+

Business:

+
+
+
+
September 16th to September 22nd
+
+
+

Wet Lab:

+

Product Development:

+

Wiki:

+

P & P:

+

Business:

+
+
+
+
September 23rd to September 29th
+
+
+

Wet Lab:

+

Product Development:

+

Wiki:

+

P & P:

+

Business:

+
+
+
+
September 30th to October 6th
+
+
+

Wet Lab:

+

Product Development:

+

Wiki:

+

P & P:

+

Business:

+
+
+
+
October 7th to October 13th
+
+
+

Wet Lab:

+

Product Development:

+

Wiki:

+

P & P:

+

Business:

+
+
+
+
October 14th to October 16th
+
+
+

Wet Lab:

+

Product Development:

+

Wiki:

+

P & P:

+

Business:

+
-
-
March 11th to March 17th
-
-
-

Wet Lab: Members split into training groups and performed PCR on gBlocks from last year’s project. Training involved overviews and run-throughs of cloning, transformation, miniprep, gel extraction, and other protocols.

-

Wiki: Wiki subteam learned the basics of HTML and CSS during a one-hour long Wiki/Design Training class. Worked on the HTML/CSS project (due 3/26).

-

P & P: P&P started planning and finding information for a synthetic biology discussion. Also brainstormed for activities for the annual student outreach event - Splash! at Cornell.

-
-
-
March 18th to March 24th
-
-
-

Wiki: Wiki subteam learned the basics of colors, white space, and composition during a one-hour long Wiki/Design Training class. Worked on webpage creation project to practice building information hierarchy (due 4/8).

-

P & P: P&P brainstormed applications for two possible projects for the team - incorporating synthetic biology with 3D printing or with fourier transforms/band-pass filters.

-
-
-
-
March 25th to March 31st
-
-
-

Wiki: Wiki subteam learned the basics of JavaScript and jQuery during a one-hour long Wiki/Design Training class. Worked on the JavaScript/jQuery project (due 4/13).

-

P & P: P&P started finding research contacts to consult for technical advice on creating a band-pass filter in bacteria. P&P compiled a list of questions for the interviews to inform our biological circuit design.

-
-
-
-
April 8th to April 14th
-
-
-

Wiki: Wiki subteam evaluated past competition winners’ websites and our past competition websites during a one-hour long Wiki/Design Training class. Worked on designing a webpage for our current project (due 4/23).

-

P & P: P&P consulted Professor G. Lambert on April 9th regarding our preliminary design of our genetic circuit and any potential issues with the project. On April 10th, P&P interviewed Professor E. Kan about the similar design principles connecting electrical engineering to genetic circuit engineering.

-
-
-
-
April 15th to April 21st
-
-
-

Wiki: Wiki subteam learned the basics of Bootstrap and Git/GitHub during a one-hour long Wiki/Design Training class. Worked on the Bootstrap/Github project (due 4/30).

-

P & P: P&P interviewed Professor J. March on April 20th for assistance in choosing specific protein candidates for our genetic circuit. The discussion also addressed control of circuit kinetics via protein degradation and plasmid copy number and potential applications for our project. P&P also continued planning for Splash! and RawExpo, a creative exposition at the architecture school.

-

Business: Business held their National Garlic Day fundraiser on 4/19 - earned some money and spread the word about iGEM!

-
-
-
-
April 22nd to April 28th
-
-
-

Wet Lab: Wetlab continued training. Members performed a double digestion and practiced using a NanoDrop Spectrophotometer.

-

Wiki: Wiki subteam met up to discuss iGEM wiki rules and go over the general timeline for the summer and fall.

-

P & P: The first day of Ithaca High School (IHS) outreach took place on 4/26. P&P introduced Future Problem Solving (FPS) approaches and assigned readings for first topic (spread of infectious diseases).
On April 27th, P&P participated in RawExpo and presented last year’s project, Oxyponics.
P&P hosted an outreach event on April 28th as part of Splash! at Cornell U. We introduced synthetic biology topics including DNA extraction, plasmid transformation, and CRISPR.

-
-
-
-
April 29th to May 5th
-
-
-

Wet Lab: Members practiced double digest and ligation of digested inserts into pSB1C3 vector.

-

P & P: P&P continued IHS outreach on 5/3 by going over a practice FPS future scenario about the spread of infectious diseases and introducing the problem-solving process.

-
-
-
-
May 6th to May 12th
-
-
-

P & P: P&P continued reaching out to faculty and experts for consultation on our band-pass filter biological circuit and mapped out the schedule for summer work.

-
-
-
-
June 3rd to June 9th
-
-
-

Wiki: Started discussing possible concepts to consider for the 2018 wiki design, such as going with a dark color scheme (not necessarily black, something more along the lines of a dark color like navy blue) and incorporating geometric aspects. Also went over some brainstorming already done in April.

-
-
-
-
June 10th to June 16th
-
-
-

Wiki: Discussed idea of using templates to make implementation of the wiki easier. Assignment to look up templates that could work for possible wiki designs for 2018 project.

-
-
-
-
June 17th to June 23rd
-
-
-

Wet Lab: We had our first team meeting on Thursday the 21st where we outlined goals for the summer. We also had a group training session on Sunday the 23rd to complete training for new members. In the lab, we attempted to transform stock PSB1C3 into NEB 5-alpha Competent E. coli, however the transformation was not successful.

-

Product Development:

-

Wiki: Discussed themes we found that represented elements we would like to see in a potential wiki design. Reached out to team lead for more information and clarification on the project and Product Development’s role.

-

P & P: P&P outlined the events and goals for the summer while planning for 4-H. One major goal was to finish creating a customizable plasmid kit and to use it for collaboration.

-
-
-
-
June 24th to June 30th
-
-
-

Wet Lab: Wet Lab ran PCR reactions for PhrpL and sigmaF and Confirmed the lengths of each construct by running through a gel. The PCR was cleaned up and nanodropped resulting in high DNA concentration. Wet Lab began a wet culture from NEB 5-alpha E. coli transformed with PSB1c3. The wet culture was miniprepped and then ran through a gel. However, no bands were visible for PSB1C3 indicating an unsuccessful miniprep.

-

Product Development:

-

P & P: P&P taught a class on synthetic biology during 4-H career explorations on June 27th. Various topics were introduced, including CRISPR, DNA extraction, and phage transduction/plasmid transformation. The first iteration of the plasmid kit was laser cut and used at 4-H. We asked the students about their opinions on its use in pedagogy for feedback to improve our design. P&P began pursuing an educational collaboration with the Greater Ithaca Activities Center nearby.
P&P also began reaching out to professors at Washington University in St. Louis for consultation on our band-pass filter biological circuit.

-
-
-
-
July 1st to July 7th
-
-
-

Wet Lab: We ran PCR on our DNA constructs PhrpL, Sigmaf, and PF2. After several failed attempts, the lengths of each construct was confirmed by running a gel and nanodropping to determine the respective concentrations of each construct.

-

Wiki: Called together three of our Wiki subteam members to help design the wiki this summer. Went over the project description to catch up other members of the design team. Assigned each design member to make mock-up(s) of a home page (due 7/12).

-

P & P: P&P reflected on 4-H and the feedback about the plasmid kit. Issues included its transparent color, lack of visibility, and difficulty in assembly. A new plasmid kit was designed for laser cutting. P&P also worked on consolidating materials for IHS outreach in the fall and reached out to the NY Affiliate Director.

-
-
-
-
July 8th to July 14th
-
-
-

Wet Lab: We ran PCR on our DNA constructs PhrpL, Sigmaf, PF2, High pass 1b, Low pass 1b. Confirmed the lengths of each construct by running through a gel. Miniprepped PSB1C3 bacteria with low yields.

-

Wiki: Design team went over each member’s home page design. Discussed what we liked/disliked for each person’s design. Picked best design out of the three. Assigned each design member to edit the chosen home page design (due 7/17).

-

P & P: On July 9th, P&P interviewed Professor M. DeLisa, who interrogated the circuit design, provided suggestions on the placement different protein degradation tags on different components of the system. P&P also consulted him on the emerging technology and public opinion side of synthetic biology.
On July 10th, P&P interviewed Professor G. Lambert about modelling and testing the biological circuit.
P&P continued brainstorming potential outreach events, including a hackathon and activities for Ithaca High School in the Fall.

-
-
-
-
July 15th to July 21st
-
-
-

Wet Lab: Team ligated Phrpl, mf-lon, High Pass 1b and Low Pass 1b into pSB1C3 vectors. Team unsuccessfully attempted to transform plasmids into competent cells on chloramphenicol plates.

-

Wiki: Design team went over each team member’s revised home page design and listed out what features/components to include for the final home page design. Reached out to leads and former members who contributed to design for feedback. Assigned each design member to make mock-up(s) of sub-page (due 7/21).
Design team went over sub-page designs and listed out what features/components to include for final sub-page design. Designated assignments for making team page design, notebook/attributes page design, and looking into incorporating animation into the wiki (due).

-

P & P: On July 17th, P&P hosted a workshop at GIAC about synthetic biology teaching 1st graders about parts of a cell by representing different parts with different candies. Additionally, the plasmid kit was painted with methods that did not give a good final aesthetic. P&P contacted NY 4H for outreach opportunities at the upcoming NY State fair.

-
-
-
-
July 22nd to July 28th
-
-
-

Wet Lab: Wet Lab PCRed High Pass 1a, High Pass 1b and Low Pass 1c. We ran the PCR product on a gel, which confirmed a successful PCR. We then cleaned up the PCR product and nanodropped the cleanups. The PCR cleanup was cleaned up, while PSB1c3 was linearized and digested. The digestion were cleaned up and nanodropped. Wet Lab also miniprepped a wet culture that had been started earlier in the week of PSB1C3 transformed bacteria and nanodropped the results.

-

P & P: On July 24th, P&P returned to GIAC and made aluminum boats with the kids to learn about engineering principles, buoyancy, and physics. Plasmid kits were designed, cut, and painted for testing for UT-Austin -

-
-
-
July 29th to August 4th
-
-
-

Wet Lab: We ligated previously digested High Pass 1a and High Pass 1b into pSB1C3 (to create High Pass 2a) as well as High Pass 1a and High Pass 1c into pSB1C3 (to create high Pass 2b). We performed PCR reactions for some parts we were running low on and then digested and ligated mf-Lon, sigmaF, and PhrpL, High Pass 1a, High Pass 1b, High Pass 1c, Low Pass 1b, and Low Pass 1c individually into pSB1C3 vectors. We heat inactivated and transformed our ligations into NEB 5-alpha Competent E. coli. Since we had been having trouble with transformations, we used SOC instead of LB for our outgrowth steps, with a positive outcome - colonies grew on all plates. We used isolated colonies to inoculate 5 mL liquid cultures which we miniprepped after overnight incubations. We also performed colony PCR reactions on assembled pSB1C3 vectors with High Pass 2a and and mf-lon inserts. We will continue with colony PCRs and run gels for them next week.

-

Wiki: Design team discussed and made final decisions for sub-page and team page designs. Went over and made final decisions for animation. Assigned design team members to make these finalized designs.

-

P & P: On July 31st, P&P played polymerase tag and made oobleck with the kids at GIAC. P&P interviewed Dr. L. Pierce and Dr. N. Argyres of Washington University in St. Louis in two separate interviews on 8/1 about the potential risks and regulations relevant to our project (see interview notes for specific interview contents).

-
-
-
-
August 5th to August 11th
-
-
-

Wiki: Wiki started setting up the internal structure of the wiki. Wiki set up the wiki repository.

-

P & P: P&P interviewed Professor Swingle on August 6th, focusing on understanding methods to test and gather characterization data for modeling of the proteins HrpR and HrpS, which are integral to the biological circuit. New plasmid kits were ready for laser cutting, but the laser cutter was down.

-
-
-
-
August 12th to August 18th
-
-
-

Wiki: Wiki started setting up the layout of the home page and considering what kind of framework to use to set up the layout.

-
-
-
-
August 19th to August 25th
-
-
-

Wiki: Wiki decided to use CSS grid to implement the layout of the wiki. Wiki did more setup of the wiki.

-

P & P: P&P had a Skype call interview on 8/22 with Professor M. Baccara from Washington University in St. Louis about the process and ethics of moving a product from science to business.
P&P resumed work on the project, outlining the fall semester outreach events and synthesizing information from various human practices and policies readings and interviews with experts.
P&P met with the IHS teacher on 8/24 to go over lesson plans and how FPS might fit in with the BioBuilder Club activities for the fall semester.

-
-
-
-
August 26th to Septmeber 1st
-
-
-

Wiki: Wiki had its first weekly subteam meeting. Wiki started implementing the nav bar, footer, home page, and standard page template.

-

P & P: P&P worked on state fair materials, including a trifold and portable plasmid kits for our outreach efforts on 9/3.

-
-
-
-
September 2nd to September 8th
-
-
-

Wet Lab:

-

Product Development:

-

Wiki:

-

P & P:

-

Business:

-
-
-
-
September 9th to September 15th
-
-
-

Wet Lab:

-

Product Development:

-

Wiki:

-

P & P:

-

Business:

-
-
-
-
September 16th to September 22nd
-
-
-

Wet Lab:

-

Product Development:

-

Wiki:

-

P & P:

-

Business:

-
-
-
-
September 23rd to September 29th
-
-
-

Wet Lab:

-

Product Development:

-

Wiki:

-

P & P:

-

Business:

-
-
-
-
September 30th to October 6th
-
-
-

Wet Lab:

-

Product Development:

-

Wiki:

-

P & P:

-

Business:

-
-
-
-
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October 14th to October 16th
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\ No newline at end of file diff --git a/final/safety.html b/final/safety.html index 99c2292..28cb480 100644 --- a/final/safety.html +++ b/final/safety.html @@ -44,162 +44,164 @@ - - - + + + +
+ + + Safety + +
+ - -
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Overview
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At Cornell iGEM, we understand the risks associated with our work and take all necessary precautions to minimize those risks. As a team, we take safety very seriously and a detailed description of our procedures can be found below. Our protocols are guided by the risk matrix, as we try to both minimize the likelihood of an incident as well as the severity of an incident. Our completed safety form can be found here.

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- -
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Risk Categories
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Laboratory Safety - Risks in the laboratory include the carcinogenic intercalating agent ethidium bromide and the use of a powerful UV lamp for visualizing the results of gel electrophoresis. Additionally, we use antibiotic resistance - specifically chloramphenicol - as a selection marker. In large doses, chloramphenicol is toxic to humans. Finally, flammable agents such as ethanol and isopropyl alcohol are often used to maintain a sterile work environment. An open flame from an ethanol burner is sometimes used to maintain a sterile environment as well.

-

Environmental Safety - If released into nature, our engineered bacteria pose a risk of transferring antibiotic resistance to other organisms.

-

Pathogens - Our system was engineered into E. coli K12. E. coli K12 is classified as a Biosafety Level 1 organism and has been used by countless iGEM teams for cloning. Our team has taken parts found in other organisms in nature, notably B. subtilis, M. florum, and P. syringae. All of these organisms are also classified as Biosafety Level 1. While one part was taken from L. monocytogenes, a Biosafety Level 2 organism, the part was an element for control of translation, and not inherently pathogenic.

-

Fabrication - Fabrication of the plasmid education kit involved the use of a laser cutter and spray paint. Laser cutters produce significant amounts of heat and the laser itself can cause severe eye damage. Spray paint often contains hazardous propellants.

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Safety Protocol
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Wet Lab - Every member of the lab wears nitrile gloves and closed toed shoes at all times. Gloves are to be replaced after working with ethidium bromide or any hazardous chemical. There are taped-off, designated areas for working with ethidium bromide. When visualizing an agarose gel under a UV lamp, all members are required to use a UV shield, UV-blocking goggles. Alternatively, the gel may be photographed using specific equipment designed for imaging under UV light, and observe the gel on a computer screen. -

- All biologic material is sterilized and disposed of appropriately. Solid materials are disposed of in biohazard waste, which is collected by Cornell Environmental Health and Safety (EH&S), and is autoclaved and transported to a central facility for our building. It is then disposed of as regulated biological waste. Liquid cultures are disinfected in a 20% bleach solution and then washed down the sink with water. -

- We maintain two copies of MSDS’s for each chemical we use: one for us, and one for our lab manager and other lab users. Additionally, our lab is equipped with flame-retardant benches, safety showers and eyewash stations, fire extinguishers, laminar flow hoods, biosafety cabinets, and spill kits. It is rated by Cornell EH&S as safe to work with up to Biosafety Level 2 organisms. -

-

Fabrication - All members who use the laser cutter must have specific training. To minimize this risk, we asked certified students employed at the Rapid Prototyping Lab (RPL) to laser cut for us. We did not use the machine ourselves. -

- Spray painting was performed in a well-ventilated composite workspace equipped with vacuums and overhead lighting. Cardboard was placed below the surface that was spray painted to avoid damaging any surfaces. The space was cleaned and nothing obstructed a clear path to the exit that was marked off in tape.

-
-
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Training and Enforcement
-
-
-

Any team member who works in the lab is required to attend an orientation session with Dr. Shivaun Archer. During this session, Dr. Archer explains all relevant safety features of the lab, as well as how to operate equipment such as the autoclave safely. Additionally, members are required to go through standard training for working in a lab by completing two courses through Cornell EH&S. These courses are about General Lab Safety and Chemical Waste Disposal. Both the orientation session and the EH&S courses are required to be completed before a member is allowed to work in the lab. -

- When members join our team, they are required to attend a general safety session. This session outlines safety protocols for working in our dry lab space as well as reinforcing the chemical safety lessons learned through the EH&S courses. -

- Team members who violate safety rules are required to work under the supervision of a team leader for the remainder of the week, or until the leader believes the member is capable of performing the task unsupervised. For multiple infractions or complete disregard to safety protocols, a member may be restricted from laboratory work until he/she undergoes EHS chemical safety online training again, and demonstrates proper performance to a team leader of failed technique(s) in a controlled setting.

-
-
-
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Reporting
-
-
-

Any incident in which safety protocols failed are to be reported to the team lead. The team lead submits an incident report to Dr. Shivaun Archer, and works with her to determine the appropriate action. Actions include a changing techniques or finding another way to minimize and further reduce the risk involved with a task - whether it be reducing the impact of an incident or its likelihood. The team lead also serves as the liaison between other safety groups and the team, including the Institutional Biosafety Committee and EH&S.

-
-
-
- + +
+
+
Overview
+
+
+

At Cornell iGEM, we understand the risks associated with our work and take all necessary precautions to minimize those risks. As a team, we take safety very seriously and a detailed description of our procedures can be found below. Our protocols are guided by the risk matrix, as we try to both minimize the likelihood of an incident as well as the severity of an incident. Our completed safety form can be found here.

+
+ +
+
+
Risk Categories
+
+
+

Laboratory Safety - Risks in the laboratory include the carcinogenic intercalating agent ethidium bromide and the use of a powerful UV lamp for visualizing the results of gel electrophoresis. Additionally, we use antibiotic resistance - specifically chloramphenicol - as a selection marker. In large doses, chloramphenicol is toxic to humans. Finally, flammable agents such as ethanol and isopropyl alcohol are often used to maintain a sterile work environment. An open flame from an ethanol burner is sometimes used to maintain a sterile environment as well.

+

Environmental Safety - If released into nature, our engineered bacteria pose a risk of transferring antibiotic resistance to other organisms.

+

Pathogens - Our system was engineered into E. coli K12. E. coli K12 is classified as a Biosafety Level 1 organism and has been used by countless iGEM teams for cloning. Our team has taken parts found in other organisms in nature, notably B. subtilis, M. florum, and P. syringae. All of these organisms are also classified as Biosafety Level 1. While one part was taken from L. monocytogenes, a Biosafety Level 2 organism, the part was an element for control of translation, and not inherently pathogenic.

+

Fabrication - Fabrication of the plasmid education kit involved the use of a laser cutter and spray paint. Laser cutters produce significant amounts of heat and the laser itself can cause severe eye damage. Spray paint often contains hazardous propellants.

+
+
+
+
Safety Protocol
+
+
+

Wet Lab - Every member of the lab wears nitrile gloves and closed toed shoes at all times. Gloves are to be replaced after working with ethidium bromide or any hazardous chemical. There are taped-off, designated areas for working with ethidium bromide. When visualizing an agarose gel under a UV lamp, all members are required to use a UV shield, UV-blocking goggles. Alternatively, the gel may be photographed using specific equipment designed for imaging under UV light, and observe the gel on a computer screen. +

+ All biologic material is sterilized and disposed of appropriately. Solid materials are disposed of in biohazard waste, which is collected by Cornell Environmental Health and Safety (EH&S), and is autoclaved and transported to a central facility for our building. It is then disposed of as regulated biological waste. Liquid cultures are disinfected in a 20% bleach solution and then washed down the sink with water. +

+ We maintain two copies of MSDS’s for each chemical we use: one for us, and one for our lab manager and other lab users. Additionally, our lab is equipped with flame-retardant benches, safety showers and eyewash stations, fire extinguishers, laminar flow hoods, biosafety cabinets, and spill kits. It is rated by Cornell EH&S as safe to work with up to Biosafety Level 2 organisms. +

+

Fabrication - All members who use the laser cutter must have specific training. To minimize this risk, we asked certified students employed at the Rapid Prototyping Lab (RPL) to laser cut for us. We did not use the machine ourselves. +

+ Spray painting was performed in a well-ventilated composite workspace equipped with vacuums and overhead lighting. Cardboard was placed below the surface that was spray painted to avoid damaging any surfaces. The space was cleaned and nothing obstructed a clear path to the exit that was marked off in tape.

+
+
+
+
Training and Enforcement
+
+
+

Any team member who works in the lab is required to attend an orientation session with Dr. Shivaun Archer. During this session, Dr. Archer explains all relevant safety features of the lab, as well as how to operate equipment such as the autoclave safely. Additionally, members are required to go through standard training for working in a lab by completing two courses through Cornell EH&S. These courses are about General Lab Safety and Chemical Waste Disposal. Both the orientation session and the EH&S courses are required to be completed before a member is allowed to work in the lab. +

+ When members join our team, they are required to attend a general safety session. This session outlines safety protocols for working in our dry lab space as well as reinforcing the chemical safety lessons learned through the EH&S courses. +

+ Team members who violate safety rules are required to work under the supervision of a team leader for the remainder of the week, or until the leader believes the member is capable of performing the task unsupervised. For multiple infractions or complete disregard to safety protocols, a member may be restricted from laboratory work until he/she undergoes EHS chemical safety online training again, and demonstrates proper performance to a team leader of failed technique(s) in a controlled setting.

+
+
+
+
Reporting
+
+
+

Any incident in which safety protocols failed are to be reported to the team lead. The team lead submits an incident report to Dr. Shivaun Archer, and works with her to determine the appropriate action. Actions include a changing techniques or finding another way to minimize and further reduce the risk involved with a task - whether it be reducing the impact of an incident or its likelihood. The team lead also serves as the liaison between other safety groups and the team, including the Institutional Biosafety Committee and EH&S.

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\ No newline at end of file diff --git a/styles/grids.css b/styles/grids.css index 58cae13..7a0db7f 100644 --- a/styles/grids.css +++ b/styles/grids.css @@ -235,11 +235,12 @@ footer { grid-template-rows: 100px 550px auto 100px; grid-template-areas: "navbar" - "standardpagebanner" + "nopicbanner" "notebookpagecontent" "footer"; } - .notebook-page-content-wrapper { + +.notebook-page-content-wrapper { display: inline-grid; grid-area: notebookpagecontent; /*grid-template-columns: 7.5% 85% 7.5%;*/ From 8805e988b907e9eecbc4e16ae0fe2472dfa45427 Mon Sep 17 00:00:00 2001 From: livqiu Date: Sat, 29 Sep 2018 10:27:49 -0400 Subject: [PATCH 3/3] updated nav bar for all (existing) pages --- final/notebook.html | 8 +-- final/safety.html | 8 +-- index.html | 120 ++++++++++++++++++------------------ noBannerPage.html | 10 +-- notebook.html | 136 ++++++++++++++++++++--------------------- safety.html | 136 ++++++++++++++++++++--------------------- sponsors.html | 136 ++++++++++++++++++++--------------------- standardPage.html | 10 +-- teamPage.html | 79 ++++++++++++++++++++---- wetLabDemonstrate.html | 10 +-- wetLabFoundations.html | 10 +-- wetLabInterLab.html | 10 +-- wetLabParts.html | 10 +-- 13 files changed, 370 insertions(+), 313 deletions(-) diff --git a/final/notebook.html b/final/notebook.html index 83a5d81..cde4a38 100644 --- a/final/notebook.html +++ b/final/notebook.html @@ -65,15 +65,15 @@
- COLLABORATIONS - PUBLIC ENGAGEMENT + COLLABORATIONS + PUBLIC ENGAGEMENT
- PRACTICES - POLICIES + PRACTICES + POLICIES ENTREPRENEURSHIP
diff --git a/final/safety.html b/final/safety.html index 28cb480..c87f14b 100644 --- a/final/safety.html +++ b/final/safety.html @@ -65,15 +65,15 @@
- COLLABORATIONS - PUBLIC ENGAGEMENT + COLLABORATIONS + PUBLIC ENGAGEMENT
- PRACTICES - POLICIES + PRACTICES + POLICIES ENTREPRENEURSHIP
diff --git a/index.html b/index.html index d849769..006b44f 100644 --- a/index.html +++ b/index.html @@ -12,75 +12,75 @@ + diff --git a/noBannerPage.html b/noBannerPage.html index 619caea..5bb8341 100644 --- a/noBannerPage.html +++ b/noBannerPage.html @@ -12,7 +12,7 @@
@@ -26,15 +26,15 @@
- COLLABORATIONS - PUBLIC ENGAGEMENT + COLLABORATIONS + PUBLIC ENGAGEMENT
- PRACTICES - POLICIES + PRACTICES + POLICIES ENTREPRENEURSHIP
diff --git a/notebook.html b/notebook.html index df1cf3f..bac3466 100644 --- a/notebook.html +++ b/notebook.html @@ -12,75 +12,75 @@ +
+
  • DOCUMENTATION
    • +
  • NOTEBOOK
    • +
  • SAFETY
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    +
  • DOCUMENTATION
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  • NOTEBOOK
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  • SAFETY
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    + + + + diff --git a/sponsors.html b/sponsors.html index 62c0e11..3cbd9ae 100644 --- a/sponsors.html +++ b/sponsors.html @@ -12,75 +12,75 @@ +
    +
  • DOCUMENTATION
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  • NOTEBOOK
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  • SAFETY
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    + + + + diff --git a/standardPage.html b/standardPage.html index ffe6bd6..76bb88b 100644 --- a/standardPage.html +++ b/standardPage.html @@ -12,7 +12,7 @@
    @@ -26,15 +26,15 @@
    - COLLABORATIONS - PUBLIC ENGAGEMENT + COLLABORATIONS + PUBLIC ENGAGEMENT
    - PRACTICES - POLICIES + PRACTICES + POLICIES ENTREPRENEURSHIP
    diff --git a/teamPage.html b/teamPage.html index 4a38779..a966f31 100644 --- a/teamPage.html +++ b/teamPage.html @@ -9,18 +9,75 @@ +
    +
  • DOCUMENTATION
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    + + diff --git a/wetLabDemonstrate.html b/wetLabDemonstrate.html index ea8bd8b..a5e0ceb 100644 --- a/wetLabDemonstrate.html +++ b/wetLabDemonstrate.html @@ -12,7 +12,7 @@
    @@ -26,15 +26,15 @@
    - COLLABORATIONS - PUBLIC ENGAGEMENT + COLLABORATIONS + PUBLIC ENGAGEMENT
    - PRACTICES - POLICIES + PRACTICES + POLICIES ENTREPRENEURSHIP
    diff --git a/wetLabFoundations.html b/wetLabFoundations.html index 5c96d68..d07eaa9 100644 --- a/wetLabFoundations.html +++ b/wetLabFoundations.html @@ -12,7 +12,7 @@
    @@ -26,15 +26,15 @@
    - COLLABORATIONS - PUBLIC ENGAGEMENT + COLLABORATIONS + PUBLIC ENGAGEMENT
    - PRACTICES - POLICIES + PRACTICES + POLICIES ENTREPRENEURSHIP
    diff --git a/wetLabInterLab.html b/wetLabInterLab.html index b3f7818..69eebff 100644 --- a/wetLabInterLab.html +++ b/wetLabInterLab.html @@ -12,7 +12,7 @@
    @@ -26,15 +26,15 @@
    - COLLABORATIONS - PUBLIC ENGAGEMENT + COLLABORATIONS + PUBLIC ENGAGEMENT
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    diff --git a/wetLabParts.html b/wetLabParts.html index 7850c36..0096f94 100644 --- a/wetLabParts.html +++ b/wetLabParts.html @@ -12,7 +12,7 @@
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    - COLLABORATIONS - PUBLIC ENGAGEMENT + COLLABORATIONS + PUBLIC ENGAGEMENT
    - PRACTICES - POLICIES + PRACTICES + POLICIES ENTREPRENEURSHIP