BioSimulators-OpenCOR

BioSimulators-compliant command-line interface and Docker image for the OpenCOR simulation program.

This command-line interface and Docker image enable users to use OpenCOR to execute COMBINE/OMEX archives that describe one or more simulation experiments (in SED-ML format) of one or more models (in CellML format).

A list of the algorithms and algorithm parameters supported by OpenCOR is available at BioSimulators.

A simple web application and web service for using OpenCOR to execute COMBINE/OMEX archives is also available at runBioSimulations.

Installation

Install Python package and command-line application

1. Install the requirements for OpenCOR:

   apt-get install -y \
       curl \
       libpulse-mainloop-glib0 \
       libx11-6 \
       libxext6 \
       libxslt1.1 \
       sqlite3

2. Install OpenCOR:

   url=https://opencor.ws/downloads/snapshots/2021-05-19/OpenCOR-2021-05-19-Linux.tar.gz
   curl $url | tar -xz --directory=/opt/

3. Add OpenCOR to your system path:

   export PATH=/opt/OpenCOR-2021-05-19-Linux:$PATH

4. Install pip for this version of Python:

   curl https://bootstrap.pypa.io/get-pip.py | OpenCOR -c PythonShell

5. Use pip to install this package:

   /opt/OpenCOR-2021-05-19-Linux/python/bin/python -m pip install biosimulators-opencor

Install Docker image

docker pull ghcr.io/biosimulators/opencor

Usage

Local usage

usage: opencor [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

BioSimulators-compliant command-line interface to the OpenCOR <https://opencor.ws> simulation program.

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/opencor:latest \
    -i /root/in/modeling-study.omex \
    -o /root/out

Documentation

Documentation is available at https://docs.biosimulators.org/Biosimulators_OpenCOR/.

License

This package is released under the MIT.

Development team

This package was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai 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.