Model Conversions


This section describes how to create an MCell4 model from an MDL or Data Model representations. MDL is a model definition language used by MCell3 (MDL Quick Reference Guide <>). Data Model is an internal JSON representation used primarily in CellBlender. When converting from MDL to MCell4 Python representation,

The guide below expect that a system variable MCELL_PATH was set as described in

MDL to Data Model

The first step is to convert MDL representation to JSON Data Model. Navigate to the directory where your MDL files reside and run:

$MCELL_PATH/mcell Scene.main.mdl -mdl2datamodel4

MCell loads the MDL files, creates internal representation, and dumps it into a file called data_model.json.

This representation can be then eeither converted to an MCell4 model as described in the following section or imported by CellBlender through File -> Import -> CellBlender Model and Geometry (JSON).

A drawback of this process is that all parameter names and their expressions will be lost because the source for the data model generation is an already processed model with all parameters evaluated. If the parameters and expressions are needed, it is necessary to correct the resulting model manually.

Data Model to MCell4 Python Code

The next step, also used internally by CellBlender is to convert the data model into Python. The optional argument -b tell the converter all parameters, reactions and observables that can be defined with BNGL into a .bngl file. When not using the argument -b, only Python representation of the input model is created.

$MCELL_PATH/bin/data_model_to_pymcell ../data_model.json -b

This step creates several .py files with being the main model file.

Data Model to MDL Code

Models that do not use BNGL compartments and complex BNGL species (species that use components) can also be converted to the Model Description Language (MDL) that is the original model representation used by MCell3.

python $MCELL_PATH/../../mdl/ data_model.json Scene.main.mdl

This step creates several .mdl files with Scene.main.mdl being the main model file.