BioSimulators-COBRApy

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

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

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

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

Installation

Install Python package

pip install biosimulators-cobrapy

Install Docker image

docker pull ghcr.io/biosimulators/cobrapy

Usage

SED-ML targets for simulation predictions

BioSimulators-COBRApy recognizes the following targets for simulation predictions:

• FBA (KISAO_0000437), parsimonious FBA (KISAO_0000528), geometric FBA (KISAO_0000527):
  • Objective: fbc:objective/@value
  • Reaction flux: sbml:reaction/@flux
  • Reaction reduced cost: sbml:reaction/@reducedCost
  • Species shadow price: sbml:species/@shadowPrice
• FVA (KISAO_0000526):
  • Minimum reaction flux: sbml:reaction/@minFlux
  • Maximum reaction flux: sbml:reaction/@maxFlux

Please see https://docs.biosimulations.org for more information.

Local usage

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

BioSimulators-compliant command-line interface to the COBRApy simulation program <https://opencobra.github.io/cobrapy/>.

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

Documentation

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

License

This package is released under the MIT license.

Development team

This package was developed by the Center for Reproducible Biomedical Modeling and the Karr Lab at the Icahn School of Medicine at Mount Sinai with assistance from the contributors listed here.

Questions and comments

Please contact the BioSimulators Team with any questions or comments.