Biosimulations_BioNetGen

BioSimulations-compliant command-line interface to the BioNetGen simulation program.

Contents

• Installation
• Usage
• License
• Development team
• Questions and comments

Installation

Install Python package

pip install git+https://github.com/reproducible-biomedical-modeling/Biosimulations_BioNetGen

Install Docker image

docker pull crbm/biosimulations_bionetgen

Local usage

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

Usage through Docker container

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

License

This package is released under the MIT license.

Development team

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.

Questions and comments

Please contact Ali Sinan Saglam or the Center for Reproducible Biomedical Modeling with any questions or comments.