Metadata-Version: 2.1
Name: biosimulators-utils
Version: 0.1.128
Summary: Command-line program and library for reading, writing, validating and executing modeling projects (COMBINE/OMEX archives with SED-ML files).
Home-page: https://github.com/biosimulators/Biosimulators_utils
Author: Center for Reproducible Biomedical Modeling
Author-email: info@biosimulators.org
License: MIT
Download-URL: https://github.com/biosimulators/Biosimulators_utils
Keywords: systems biology modeling simulation
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
License-File: LICENSE
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|Latest release| |PyPI| |CI status| |Test coverage| |Binder|

BioSimulators utils
===================

Command-line application and high-level utilities for reading, writing,
validating, and executing `COMBINE/OMEX
format <https://combinearchive.org/>`__ files that contain descriptions
of simulations in `Simulation Experiment Description Markup
Language <https://sed-ml.org/>`__ (SED-ML) format with models in formats
such as the `BioNetGen Language <https://bionetgen.org>`__ (BNGL) and
the `Systems Biology Markup Language <http://sbml.org>`__ (SBML).

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

Requirements
~~~~~~~~~~~~

-  Python >= 3.7
-  pip

Optional requirements
~~~~~~~~~~~~~~~~~~~~~

-  `Docker <https://www.docker.com/>`__: required to execute
   containerized simulation tools
-  `Java <https://www.java.com/>`__: required to parse and validate
   NeuroML/LEMS files
-  `Perl <https://www.perl.org/>`__: required to parse and validate
   BioNetGen files
-  `RBApy <https://sysbioinra.github.io/RBApy/>`__: required to parse
   and validate RBA files
-  `XPP <http://www.math.pitt.edu/~bard/xpp/xpp.html>`__: required to
   parse and validate XPP files

Install latest release from PyPI
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

::

   pip install biosimulators-utils

Install latest revision from GitHub
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

::

   pip install git+https://github.com/biosimulators/Biosimulators_utils.git#biosimulators_utils

Installation optional features
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

To use BioSimulators utils to validate BNGL models, install
BioSimulators utils with the ``bgnl`` option:

::

   pip install biosimulators-utils[bgnl]

To use BioSimulators utils to validate CellML models, install
BioSimulators utils with the ``cellml`` option:

::

   pip install biosimulators-utils[cellml]

To use BioSimulators utils to validate LEMS models, install
`Java <https://www.java.com/>`__ and then install BioSimulators utils
with the ``lems`` option:

::

   pip install biosimulators-utils[lems]

To use BioSimulators utils to validate NeuroML models, install
BioSimulators utils with the ``neuroml`` option:

::

   pip install biosimulators-utils[neuroml]

To use BioSimulators utils to validate SBML models, install
BioSimulators utils with the ``sbml`` option:

::

   pip install biosimulators-utils[sbml]

To use BioSimulators utils to validate SBML models, install
BioSimulators utils with the ``smoldyn`` option:

::

   pip install biosimulators-utils[smoldyn]

To use BioSimulators utils to convert Escher metabolic maps to Vega flux
data visualizations, install BioSimulators utils with the ``escher``
option:

::

   pip install biosimulators-utils[escher]

To use BioSimulators utils to execute containerized simulation tools,
install BioSimulators utils with the ``containers`` option:

::

   pip install biosimulators-utils[containers]

To use BioSimulators utils to log the standard output and error produced
by simulation tools, install BioSimulators utils with the ``logging``
option:

::

   pip install biosimulators-utils[logging]

Dockerfile and Docker image
---------------------------

This package is available in the ``ghcr.io/biosimulators/biosimulators``
Docker image. This image includes all of the optional dependencies and
installation options.

To install and run this image, run the following commands:

::

   docker pull ghcr.io/biosimulators/biosimulators
   docker run -it --rm ghcr.io/biosimulators/biosimulators

This image includes this package, as well as standardized Python APIs
for the simulation tools validated by BioSimulators. Because this image
aims to incorporate as many simulation tools as possible within a single
Python environment, this image may sometimes lag behind the latest
version of this package.

The Dockerfile for this image is available
`here <https://github.com/biosimulators/Biosimulators/blob/dev/Dockerfile>`__.

Tutorials
---------

Command-line interface
~~~~~~~~~~~~~~~~~~~~~~

A tutorial for the command-line interface is available
`here <https://docs.biosimulators.org/Biosimulators_utils/>`__.

Python API
~~~~~~~~~~

Interactive tutorials for using BioSimulators-utils and Python APIs for
simulation tools to execute simulations are available online from Binder
`here <https://mybinder.org/v2/gh/biosimulators/Biosimulators_tutorials/HEAD>`__.
The Jupyter notebooks for these tutorials are also available
`here <https://github.com/biosimulators/Biosimulators_tutorials>`__.

API documentation
-----------------

API documentation is available
`here <https://docs.biosimulators.org/Biosimulators_utils/>`__.

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 in New York and the
`Center for Reproducible Biomedical
Modeling <http://reproduciblebiomodels.org>`__.

Contributing to BioSimulators utils
-----------------------------------

We enthusiastically welcome contributions to BioSimulators utils! Please
see the `guide to contributing <CONTRIBUTING.md>`__ and the `developer's
code of conduct <CODE_OF_CONDUCT.md>`__.

Acknowledgements
----------------

This work was supported by National Institutes of Health award
P41EB023912.

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/release/biosimulators/Biosimulators_utils
   :target: https://github.com/biosimulators/Biosimulators_utils/releases
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   :target: https://pypi.org/project/biosimulators-utils/
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   :target: https://github.com/biosimulators/Biosimulators_utils/actions?query=workflow%3A%22Continuous+integration%22
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.. |Binder| image:: https://mybinder.org/badge_logo.svg
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