You will need both Python (3.7 and above) and Perl (for Windows users) installed.

Once both are available, you can use the following pip command to install PyBioNetGen:

pip install bionetgen

This comes with the latest version of BioNetGen. Please note that, at the moment, PyBioNetGen does not support Atomizer but eventually will.

After installation is complete, you can test to see if PyBioNetGen is properly installed with

bionetgen -h

If this command prints out help, the command line tool is installed.

Basic Usage

PyBioNetGen’s CLI can be used to simply run a BNGL model

bionetgen run -i mymodel.bngl -o output_folder

which will create output_folder and run mymodel.bngl inside that folder. For other subcommands or more information on how to use PyBioNetGen’s CLI, please see Command Line Interface.

PyBioNetGen’s library can also be used to run a BNGL model

import bionetgen
result = bionetgen.run("mymodel.bngl", output="myfolder")

which will create numpy record arrays. For other methods or more information on how to use PyBioNetGen’s library, please see Library.