You will need both python (3.7 and above) and perl installed. Once both are available you can use the following pip command to install PyBioNetGen

pip install bionetgen

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

Basic usage

After installation 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.

You can use PyBioNetGen 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 more information on how to use PyBioNetGen please see Command line Interface and Library.