biosimulators-bionetgen 0.1.20
BioSimulators-compliant command-line interface to the BioNetGen simulation program <https://bionetgen.org>.
License: MIT
Keywords: systems biology,rule-based modeling,network-free simulation,kinetic modeling,numerical simulation,BioNetGen,BioSimulators,SED-ML,COMBINE,OMEX

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BioSimulators-BioNetGen
=======================

BioSimulators-compliant command-line interface and Docker image for the
`BioNetGen <https://bionetgen.org/>`__ simulation program.

This command-line interface and Docker image enable users to use
BioNetGen 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 `BNGL format <https://bionetgen.org]>`__).

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

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

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

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

After installing BioNetGen, use pip to install this package as
illustrated below.

::

   pip install biosimulators-bionetgen

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

::

   docker pull ghcr.io/biosimulators/bionetgen

Usage
-----

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

::

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

   BioSimulators-compliant command-line interface to the BioNetGen simulation program <https://bionetgen.org>.

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

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

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

License
-------

This package is released under the `MIT license <LICENSE>`__.

Development team
----------------

This package was developed by the `Karr Lab <https://www.karrlab.org>`__
at the Icahn School of Medicine at Mount Sinai, `Ali Sinan
Saglam <https://scholar.google.com/citations?user=7TM0eekAAAAJ&hl=en>`__
in the Faeder Lab at the University of Pittsburgh, and the `Center for
Reproducible Biomedical Modeling <http://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
about the command-line program or Docker image. Please contact `Ali
Sinan Saglam <mailto:als251@pitt.edu>`__ with any questions or comments
about BioNetGen.

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