Metadata-Version: 2.1
Name: biosimulators-cobrapy
Version: 0.1.4
Summary: BioSimulators-compliant command-line interface to the COBRApy simulation program <https://opencobra.github.io/cobrapy/>.
Home-page: https://github.com/biosimulators/biosimulators_cobrapy
Author: Center for Reproducible Biomedical Modeling
Author-email: info@biosimulators.org
License: MIT
Download-URL: https://github.com/biosimulators/biosimulators_cobrapy
Description: |Latest release| |PyPI| |CI status| |Test coverage|
        
        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>`__.
        
        Contents
        --------
        
        -  `Installation <#installation>`__
        -  `Usage <#usage>`__
        -  `Documentation <#documentation>`__
        -  `License <#license>`__
        -  `Development team <#development-team>`__
        -  `Questions and comments <#questions-and-comments>`__
        
        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://biosimulators.org/standards/simulation-experiments
        for more information.
        
        Local usage
        ~~~~~~~~~~~
        
        ::
        
           usage: 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://biosimulators.github.io/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.
        
        Questions and comments
        ----------------------
        
        Please contact the `BioSimulators
        Team <mailto:info@biosimulators.org>`__ with any questions or comments.
        
        .. |Latest release| image:: https://img.shields.io/github/v/tag/biosimulators/Biosimulators_COBRApy
           :target: https://github.com/biosimulations/Biosimulators_COBRApy/releases
        .. |PyPI| image:: https://img.shields.io/pypi/v/biosimulators_cobrapy
           :target: https://pypi.org/project/biosimulators_cobrapy/
        .. |CI status| image:: https://github.com/biosimulators/Biosimulators_COBRApy/workflows/Continuous%20integration/badge.svg
           :target: https://github.com/biosimulators/Biosimulators_COBRApy/actions?query=workflow%3A%22Continuous+integration%22
        .. |Test coverage| image:: https://codecov.io/gh/biosimulators/Biosimulators_COBRApy/branch/dev/graph/badge.svg
           :target: https://codecov.io/gh/biosimulators/Biosimulators_COBRApy
        
Keywords: systems biology modeling simulation
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Provides-Extra: tests
Provides-Extra: docs
Provides-Extra: all
