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
- Objective:
- FVA (
KISAO_0000526
):- Minimum reaction flux:
sbml:reaction/@minFlux
- Maximum reaction flux:
sbml:reaction/@maxFlux
- Minimum reaction flux:
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.