BioSimulations-compliant command-line interface to the BioNetGen simulation program.
pip install git+https://github.com/reproducible-biomedical-modeling/Biosimulations_BioNetGen
docker pull crbm/biosimulations_bionetgen
usage: bionetgen [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]
BioSimulations-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 \
crbm/biosimulations_bionetgen:latest \
-i /root/in/BIOMD0000000297.omex \
-o /root/out
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 Center for Reproducible Biomedical Modeling with any questions or comments.