biosimulators-opencor 0.0.13
BioSimulators-compliant command-line interface to the OpenCOR simulation program.
License: MIT
Keywords: systems biology,computational biology,CellML,SED-ML,BioSimulators,COMBINE,OMEX,OpenCOR

|Latest release| |PyPI| |CI status| |Test coverage| |All Contributors|

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://docs.biosimulators.org/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/>`__
with assistance from the contributors listed `here <CONTRIBUTORS.md>`__.

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
.. |All Contributors| image:: https://img.shields.io/github/all-contributors/biosimulators/Biosimulators_OpenCOR/HEAD
   :target: #contributors-