biosimulators-cobrapy

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BioSimulators-COBRApy

BioSimulators-compliant command-line interface and Docker image for the COBRApy <https://opencobra.github.io/cobrapy/>__ simulation program.

This command-line interface and Docker image enable users to use COBRApy to execute COMBINE/OMEX archives <https://combinearchive.org/>__ that describe one or more simulation experiments (in SED-ML format <https://sed-ml.org>) of one or more models (in SBML format <http://sbml.org]>).

A list of the algorithms and algorithm parameters supported by COBRApy is available at BioSimulators <https://biosimulators.org/simulators/cobrapy>__.

A simple web application and web service for using COBRApy to execute COMBINE/OMEX archives is also available at runBioSimulations <https://run.biosimulations.org>__.

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 <LICENSE>__.

Development team

This package was developed by the Center for Reproducible Biomedical Modeling <http://reproduciblebiomodels.org>__ and the Karr Lab <https://www.karrlab.org>__ at the Icahn School of Medicine at Mount Sinai with assistance from the contributors listed here <CONTRIBUTORS.md>__.

Questions and comments

Please contact the BioSimulators Team <mailto:[e-mail]>__ with any questions or comments.

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