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Tutorial sources and model translations

The MicroSimulator tutorials draw from the maintained CellModeller wiki, bundled CellModeller examples, and SimBOL examples. This page records those relationships for readers who need to compare equations or reproduce an older workflow; the tutorials themselves focus on using the current modeling interface.

Source revisions

  • CellModeller examples: commit 4896f543c6250f053eea2312e628cc3a96bf7408
  • CellModeller wiki: commit 95587c11899677b7cba87c64bc20210fb1f8f6ce
  • SimBOL: commit 54501f9da6f9809588be48b854a6c4f8abd933b5

Tutorial relationships

Source material MicroSimulator model or guide
Wiki Tutorial 1a biophysics.py, basics
Wiki Tutorial 1b biophysics.py, competition
Wiki Tutorial 1c biophysics.py, box
Wiki Tutorial 2a gene_expression.py, constitutive
Wiki Tutorial 2b gene_expression.py, oscillator
Wiki Tutorial 3 signaling.py, mutualism
Old Example 1 and its exercises biophysics.py, basics, two_types, short_cells
Old Example 2 gene_expression.py, legacy_constitutive, dilution, derepression
Old Example 3 signaling.py, single_gene
Old Example 4 signaling.py, communication
Old Example 5 plasmid_segregation.py
Contact graph and conjugation examples conjugation.py and the analysis tutorial
Legacy analysis scripts analysis tutorial and analysis recipes
SimBOL CM_BBa_01–05, CM_BBa_I5200 simbol_circuits.py
SimBOL CM_Danino.py danino_clock.py
SimBOL CellModeller notebook SimBOL tutorial workflow description

Exact equation translations used by the executable compatibility matrix remain under examples/legacy. The models under examples/tutorials are teaching versions: they consolidate related examples, expose parameters consistently, and support exact resume.

Translation conventions

The teaching models preserve the biological question, initial conditions, rate equations, strain roles, division rule, and physical geometry where those are well-defined. They express those ideas through current interfaces:

  • CellInit defines cell state;
  • NativeController or an explicit controller owns regulation and stochastic state;
  • RatePlanBuilder represents biological equations;
  • SignalGridSpec and CoupledRatePlan define transport and cell-grid exchange;
  • plane and sphere constraints define physical boundaries;
  • checkpoints store restart state; and
  • scene and analysis exports provide visualization and quantitative output.

Some source material uses targetVol as a length, treats callback attributes alternately as molecule counts and concentrations, or applies chemical updates once per GUI step without an explicit dt. The current tutorials name the chosen interpretation where it affects scientific meaning.

SimBOL source workflow

At the pinned SimBOL revision, the intended workflow is:

SBOL 3 document
  -> sbol3_to_json_converter
  -> summarized circuit JSON
  -> parameter preparation / UI
  -> CellModeller-specific generated Python

The checked-in notebooks/CellModeller.ipynb stops after environment setup, SBOL upload, JSON conversion, and parameter-form display. The generated test/CM_*.py files and matching JSON fixtures are therefore the concrete sources used for the MicroSimulator examples.

These examples are explicit translations, not a general SBOL-to-rate-plan import path. MicroSimulator does not accept arbitrary SimBOL output without a versioned intermediate schema, declared parameter units, explicit handling of unsupported SBOL semantics, and source provenance.