├── CellModeller ├── Biophysics │ ├── BacterialModels │ │ ├── CLBacterium.cl │ │ ├── CLBacterium.py │ │ └── __init__.py │ ├── GeneralModels │ │ ├── CLFixedPosition.py │ │ └── __init__.py │ └── __init__.py ├── CellState.py ├── GUI │ ├── PyGLCMViewer.py │ ├── PyGLGUI.ui │ ├── PyGLWidget.py │ ├── Renderers.py │ └── __init__.py ├── Integration │ ├── CLCrankNicIntegrator.cl │ ├── CLCrankNicIntegrator.py │ ├── CLEulerIntegrator.cl │ ├── CLEulerIntegrator.py │ ├── CLEulerSigIntegrator.cl │ ├── CLEulerSigIntegrator.py │ └── __init__.py ├── Regulation │ ├── ModuleRegulator.py │ ├── SBMLImport.py │ └── __init__.py ├── Signalling │ ├── GridDiffusion.py │ ├── NeighbourDiffusion.py │ └── __init__.py ├── Simulator.py └── __init__.py ├── Community ├── code_of_conduct.md └── contributing.md ├── CondaRecipes ├── appdirs │ ├── bld.bat │ ├── build.sh │ └── meta.yaml ├── cellmodeller │ ├── bld.bat │ ├── build.sh │ └── meta.yaml ├── cellmodeller_dev │ ├── bld.bat │ ├── build.sh │ └── meta.yaml ├── mako │ ├── bld.bat │ ├── build.sh │ └── meta.yaml ├── pyopencl │ ├── bld.bat │ ├── build.sh │ └── meta.yaml ├── pyopengl │ ├── bld.bat │ ├── build.sh │ ├── meta.yaml │ └── post-link.sh └── pytools │ ├── bld.bat │ ├── build.sh │ └── meta.yaml ├── Doc ├── BacterialBiophysics │ ├── BacterialBiophysics.pdf │ └── BacterialBiophysics.tex ├── Maths │ ├── cellforces.pdf │ ├── celloverlap.ai │ ├── celloverlap.pdf │ ├── cellvel.pdf │ ├── math.pdf │ └── math.tex ├── modules.pdf └── modules.png ├── DoxygenConfig ├── Examples ├── ACS2012 │ └── EdgeDetectorChamber.py ├── Conjugation.py ├── TimRudgeThesis │ └── Meristem.py ├── Tutorial_1 │ ├── Tutorial_1a.py │ ├── Tutorial_1b.py │ └── Tutorial_1c.py ├── Tutorial_2 │ ├── .DS_Store │ ├── Tutorial_2a.py │ └── Tutorial_2b.py ├── Tutorial_3 │ └── Tutorial_3.py ├── colorWalk_planes_3d.py ├── ex1_simpleGrowth.py ├── ex1_simpleGrowth2D.py ├── ex1a_simpleGrowth2D.py ├── ex1a_simpleGrowth2Types.py ├── ex1b_simpleGrowth2D.py ├── ex1b_simpleGrowthRoundCell.py ├── 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