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