biosimulators-xpp 0.0.13
BioSimulators-compliant command-line interface to the XPP simulation program.
License: MIT
Keywords: systems biology,computational biology,numerical simulation,BioSimulators,SBML,SED-ML,COMBINE,OMEX,XPP

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BioSimulators-XPP
=================

BioSimulators-compliant command-line interface to the
`XPP <http://www.math.pitt.edu/~bard/xpp/xpp.html>`__ simulation
program.

This command-line interface and Docker image enable users to use XPP 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 kinetic models in XPP
format.

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

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

Installation
------------

Install Python package
~~~~~~~~~~~~~~~~~~~~~~

1. Install `XPP <http://www.math.pitt.edu/~bard/xpp/xpp.html>`__
2. Install this package
   ::

      pip install biosimulators-xpp

Install Docker image
~~~~~~~~~~~~~~~~~~~~

::

   docker pull ghcr.io/biosimulators/xpp

Usage
-----

Local usage
~~~~~~~~~~~

::

   usage: biosimulators-xpp [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

   BioSimulators-compliant command-line interface to the XPP simulation program <http://www.math.pitt.edu/~bard/xpp/xpp.html>.

   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/xpp:latest \
       -i /root/in/modeling-study.omex \
       -o /root/out

Documentation
-------------

Documentation is available at
https://docs.biosimulators.org/Biosimulators_XPP/.

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 in New York 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_XPP
   :target: https://github.com/biosimulations/Biosimulators_XPP/releases
.. |PyPI| image:: https://img.shields.io/pypi/v/biosimulators_xpp
   :target: https://pypi.org/project/biosimulators_xpp/
.. |CI status| image:: https://github.com/biosimulators/Biosimulators_XPP/workflows/Continuous%20integration/badge.svg
   :target: https://github.com/biosimulators/Biosimulators_XPP/actions?query=workflow%3A%22Continuous+integration%22
.. |Test coverage| image:: https://codecov.io/gh/biosimulators/Biosimulators_XPP/branch/dev/graph/badge.svg
   :target: https://codecov.io/gh/biosimulators/Biosimulators_XPP
.. |All Contributors| image:: https://img.shields.io/github/all-contributors/biosimulators/Biosimulators_XPP/HEAD
   :target: #contributors-