biosimulators-bionetgen 0.1.13

BioSimulators-compliant command-line interface to the BioNetGen simulation program <https://bionetgen.org>.

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.

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.