biosimulators-gillespy2

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

BioSimulators-GillesPy2

BioSimulators-compliant command-line interface and Docker image for the GillesPy2 <https://stochss.github.io/GillesPy2>__ simulation program.

This command-line interface and Docker image enable users to use GillesPy2 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 GillesPy2 is available at BioSimulators <https://biosimulators.org/simulators/gillespy2>__.

A simple web application and web service for using GillesPy2 to execute COMBINE/OMEX archives is also available at runBioSimulations <https://run.biosimulations.org>__.

Installation

Dependencies

-  Python >= 3.7
-  pip
-  build-essential

Install Python package

::

pip install biosimulators-gillespy2

Install Docker image

::

   docker pull ghcr.io/biosimulators/gillespy2

Usage
-----

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

::

   usage: biosimulators-gillespy2 [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

   BioSimulators-compliant command-line interface to the GillesPy2 <https://stochss.github.io/GillesPy2> 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/gillespy2:latest
-i /root/in/modeling-study.omex
-o /root/out

Documentation

Documentation is available at https://docs.biosimulators.org/Biosimulators_GillesPy2/.

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:[e-mail]>__ with any questions or comments.

.. |Latest release| image:: https://img.shields.io/github/v/tag/biosimulators/Biosimulators_GillesPy2 :target: https://github.com/biosimulations/Biosimulators_GillesPy2/releases .. |PyPI| image:: https://img.shields.io/pypi/v/biosimulators_gillespy2 :target: https://pypi.org/project/biosimulators_gillespy2/ .. |CI status| image:: https://github.com/biosimulators/Biosimulators_GillesPy2/workflows/Continuous%20integration/badge.svg :target: https://github.com/biosimulators/Biosimulators_GillesPy2/actions?query=workflow%3A%22Continuous+integration%22 .. |Test coverage| image:: https://codecov.io/gh/biosimulators/Biosimulators_GillesPy2/branch/dev/graph/badge.svg :target: https://codecov.io/gh/biosimulators/Biosimulators_GillesPy2 .. |All Contributors| image:: https://img.shields.io/github/all-contributors/biosimulators/Biosimulators_GillesP2/HEAD :target: #contributors-