Fig 5. Recommended structure of a standard MCell4 model.

The main files included in a standard MCell4 model are: 1) parameters.py with all the model parameters, 2) subsystem.py that captures information on species and reactions in a way that is independent of a particular model and can be used as a reusable module, 3) geometry.py with a definition of 3D geometry objects, 4) instantiation.py that usually defines the initial model state, i.e., which geometry objects are created in the simulation and the number and positions of molecules to be released at a given time, 5) observables.py with lists of characteristics to be measured and saved in files during simulation, and 6) model.py in which all the parts of the model are assembled together and in which the the simulation loop with optional interactions with external simulators is defined. This recommended model structure is not enforced by MCell4 itself. However, use of this structure promotes readability, modularity, navigation, and sharing of models with others. The MCell4 Python code generator in CellBlender follows this recommended structure with the addition of a file called customization.py whose purpose is to provide a means to modify/expand the model in the case when the standard files are automatically generated from the CellBlender representation.