Metadata-Version: 2.1
Name: biosimulators-opencor
Version: 0.0.3
Summary: BioSimulators-compliant command-line interface to the OpenCOR simulation program.
Home-page: https://github.com/biosimulators/Biosimulators_OpenCOR
Author: BioSimulators Team
Author-email: info@biosimulators.org
License: MIT
Download-URL: https://github.com/biosimulators/Biosimulators_OpenCOR
Description: |Latest release| |PyPI| |CI status| |Test coverage|
        
        BioSimulators-OpenCOR
        =====================
        
        BioSimulators-compliant command-line interface and Docker image for the
        `OpenCOR <https://opencor.ws/>`__ simulation program.
        
        This command-line interface and Docker image enable users to use OpenCOR
        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 `CellML
        format <https://cellml.org]>`__).
        
        A list of the algorithms and algorithm parameters supported by OpenCOR
        is available at
        `BioSimulators <https://biosimulators.org/simulators/opencor>`__.
        
        A simple web application and web service for using OpenCOR to execute
        COMBINE/OMEX archives is also available at
        `runBioSimulations <https://run.biosimulations.org>`__.
        
        Installation
        ------------
        
        Install Python package and command-line application
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        1. Install the requirements for OpenCOR:
        
           .. code:: sh
        
              apt-get install -y \
                  curl \
                  libpulse-mainloop-glib0 \
                  libx11-6 \
                  libxext6 \
                  libxslt1.1 \
                  sqlite3
        
        2. Install `OpenCOR <https://opencor.ws/downloads/index.html>`__:
        
           .. code:: sh
        
              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:
        
           .. code:: sh
        
              export PATH=/opt/OpenCOR-2021-05-19-Linux:$PATH
        
        4. Install pip for this version of Python:
        
           .. code:: sh
        
              curl https://bootstrap.pypa.io/get-pip.py | OpenCOR -c PythonShell
        
        5. Use pip to install this package:
        
           .. code:: sh
        
              /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://biosimulators.github.io/Biosimulators_OpenCOR/.
        
        License
        -------
        
        This package is released under the `MIT <LICENSE>`__.
        
        Development team
        ----------------
        
        This package was developed by the `Karr Lab <https://www.karrlab.org>`__
        at the Icahn School of Medicine at Mount Sinai and the `Center for
        Reproducible Biomedical
        Modeling <https://reproduciblebiomodels.org/>`__.
        
        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_OpenCOR
           :target: https://github.com/biosimulations/Biosimulators_OpenCOR/releases
        .. |PyPI| image:: https://img.shields.io/pypi/v/biosimulators_opencor
           :target: https://pypi.org/project/biosimulators_opencor/
        .. |CI status| image:: https://github.com/biosimulators/Biosimulators_OpenCOR/workflows/Continuous%20integration/badge.svg
           :target: https://github.com/biosimulators/Biosimulators_OpenCOR/actions?query=workflow%3A%22Continuous+integration%22
        .. |Test coverage| image:: https://codecov.io/gh/biosimulators/Biosimulators_OpenCOR/branch/dev/graph/badge.svg
           :target: https://codecov.io/gh/biosimulators/Biosimulators_OpenCOR
        
Keywords: systems biology,computational biology,CellML,SED-ML,BioSimulators,COMBINE,OMEX,OpenCOR
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: all
Provides-Extra: docs
Provides-Extra: tests
