biosimulators-ginsim 0.0.9
BioSimulators-compliant command-line interface to the GINsim simulation program.
License: MIT
Keywords: systems biology,computational biology,logical model,numerical simulation,BioSimulators,SBML,SED-ML,COMBINE,OMEX,GINsim

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BioSimulators-GINsim
====================

BioSimulators-compliant command-line interface to the
`GINsim <http://ginsim.org/>`__ simulation program.

This command-line interface and Docker image enable users to use GINsim
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 logical models (in
`SBML-qual <http://sbml.org]>`__ or GINsim's formats).

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

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

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

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

1. Install Java, Python, and pip
2. Install the `GINsim Python
   package <https://github.com/GINsim/GINsim-python>`__
3. Install this package
   ::

      pip install biosimulators-ginsim

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

::

   docker pull ghcr.io/biosimulators/ginsim

Usage
-----

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

::

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

   BioSimulators-compliant command-line interface to the GINsim simulation program <http://ginsim.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/ginsim:latest \
       -i /root/in/modeling-study.omex \
       -o /root/out

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

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

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_GINsim
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   :target: https://github.com/biosimulators/Biosimulators_GINsim/actions?query=workflow%3A%22Continuous+integration%22
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   :target: https://codecov.io/gh/biosimulators/Biosimulators_GINsim
.. |All Contributors| image:: https://img.shields.io/github/all-contributors/biosimulators/Biosimulators_GINsim/HEAD
   :target: #contributors-