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. 2024 Apr 24;20(4):e1011800. doi: 10.1371/journal.pcbi.1011800

Fig 11. Example of loading and running BNGL model in MCell4.

Fig 11

Python code for an MCell4 model that will implement loading of the BNGL file shown in Fig 10 (referenced as subsystem.bngl). In this example the entire BNGL file is read. It is also possible to load only specific parts of the BNGL file, for example only reaction rules or only compartment and molecule release information. It is also possible to replace BNGL compartments with actual 3D geometry.