BioSimulators-compliant command-line interface and Docker image for the BioNetGen simulation program.
This command-line interface and Docker image enable users to use BioNetGen to execute COMBINE/OMEX archives that describe one or more simulation experiments (in SED-ML format) of one or more models (in BNGL format).
A list of the algorithms and algorithm parameters supported by BioNetGen is available at BioSimulators.
A simple web application and web service for using BioNetGen to execute COMBINE/OMEX archives is also available at runBioSimulations.
pip install git+https://github.com/biosimulators/Biosimulators_BioNetGen
docker pull ghcr.io/biosimulators/bionetgen
usage: bionetgen [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]
BioSimulators-compliant command-line interface to the BioNetGen simulation program <https://bionetgen.org>.
optional arguments:
-h, --help show this help message and exit
-d, --debug full application debug mode
-q, --quiet suppress all console output
-i ARCHIVE, --archive ARCHIVE
Path to OMEX file which contains one or more SED-ML-
encoded simulation experiments
-o OUT_DIR, --out-dir OUT_DIR
Directory to save outputs
-v, --version show program's version number and exit
docker run \
--tty \
--rm \
--mount type=bind,source="$(pwd)"/tests/fixtures,target=/root/in,readonly \
--mount type=bind,source="$(pwd)"/tests/results,target=/root/out \
ghcr.io/biosimulators/bionetgen:latest \
-i /root/in/BIOMD0000000297.omex \
-o /root/out
Documentation is available at https://biosimulators.github.io/Biosimulators_BioNetGen/.
This package is released under the MIT license.
This package was developed by Ali Sinan Saglam in the Faeder Lab at the University of Pittsburgh, the Karr Lab at the Icahn School of Medicine at Mount Sinai, and the Center for Reproducible Biomedical Modeling.
Please contact Ali Sinan Saglam or the BioSimulators Team with any questions or comments.