BioSimulators-compliant command-line interface to the BioNetGen simulation program <https://bionetgen.org>.
Project description
BioSimulators-BioNetGen
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.
Installation
Install Python package
After installing BioNetGen, use pip to install this package as illustrated below.
pip install biosimulators-bionetgen
Install Docker image
docker pull ghcr.io/biosimulators/bionetgen
Usage
Local usage
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
Usage through Docker container
The entrypoint to the Docker image supports the same command-line interface described above.
For example, the following command could be used to use the Docker image to execute the COMBINE/OMEX archive ./modeling-study.omex and save its outputs to ./.
docker run \
--tty \
--rm \
--mount type=bind,source="$(pwd)",target=/root/in,readonly \
--mount type=bind,source="$(pwd)",target=/root/out \
ghcr.io/biosimulators/bionetgen:latest \
-i /root/in/modeling-study.omex \
-o /root/out
Documentation
Documentation is available at https://docs.biosimulators.org/Biosimulators_BioNetGen/.
License
This package is released under the MIT license.
Development team
This package was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai, Ali Sinan Saglam in the Faeder Lab at the University of Pittsburgh, and the Center for Reproducible Biomedical Modeling with assistance from the contributors listed here.
Questions and comments
Please contact the BioSimulators Team with any questions or comments about the command-line program or Docker image. Please contact Ali Sinan Saglam with any questions or comments about BioNetGen.
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