Metadata-Version: 2.1
Name: crnt4sbml
Version: 0.0.12
Summary: CRNT4SBML is an easily installable Python based package available on MacOS and Windows. CRNT4SBML is concentrated on providing a simple workflow for the testing of core CRNT methods directed at detecting bistability in cell signaling pathways endowed with mass action kinetics.
Home-page: https://github.com/PNNL-Comp-Mass-Spec/CRNT4SBML
Author: Brandon Reyes
Author-email: reyesb123@gmail.com
License: Apache Software License 2.0
Keywords: crnt4sbml
Platform: ALL
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.7
Requires-Dist: networkx (==2.3)
Requires-Dist: python-libsbml (==5.18.0)
Requires-Dist: numpy (==1.16.4)
Requires-Dist: sympy (==1.4)
Requires-Dist: scipy (==1.4.1)
Requires-Dist: matplotlib (==3.1.1)
Requires-Dist: plotnine (==0.6.0)
Provides-Extra: linux
Provides-Extra: mpilinux
Requires-Dist: mpi4py (==3.0.3); extra == 'mpilinux'
Provides-Extra: mpimacos
Requires-Dist: antimony (==2.11.0); extra == 'mpimacos'
Requires-Dist: libroadrunner (==1.5.2.1); extra == 'mpimacos'
Requires-Dist: rrplugins (==1.2.2); extra == 'mpimacos'
Requires-Dist: mpi4py (==3.0.3); extra == 'mpimacos'
Provides-Extra: mpiwindows
Requires-Dist: antimony (==2.11.0); extra == 'mpiwindows'
Requires-Dist: libroadrunner (==1.5.2.1); extra == 'mpiwindows'
Requires-Dist: rrplugins (==1.2.2); extra == 'mpiwindows'
Requires-Dist: mpi4py (==3.0.3); extra == 'mpiwindows'
Provides-Extra: macos
Requires-Dist: antimony (==2.11.0); extra == 'macos'
Requires-Dist: libroadrunner (==1.5.2.1); extra == 'macos'
Requires-Dist: rrplugins (==1.2.2); extra == 'macos'
Provides-Extra: windows
Requires-Dist: antimony (==2.11.0); extra == 'windows'
Requires-Dist: libroadrunner (==1.5.2.1); extra == 'windows'
Requires-Dist: rrplugins (==1.2.2); extra == 'windows'

=========
CRNT4SBML
=========


.. image:: https://img.shields.io/pypi/v/crnt4sbml.svg
        :target: https://pypi.python.org/pypi/crnt4sbml

.. image:: https://img.shields.io/travis/PNNL-Comp-Mass-Spec/CRNT4SBML.svg
        :target: https://travis-ci.org/PNNL-Comp-Mass-Spec/CRNT4SBML

.. image:: https://readthedocs.org/projects/crnt4sbml/badge/?version=latest
        :target: https://crnt4sbml.readthedocs.io/en/latest/?badge=latest
        :alt: Documentation Status

CRNT4SBML is an easily installable Python based package available on MacOS and Windows. CRNT4SBML is concentrated on
providing a simple workflow for the testing of core CRNT methods directed at detecting bistability in cell signaling
pathways endowed with mass action kinetics.

* Free software: Apache Software License 2.0
* Documentation: https://crnt4sbml.readthedocs.io.


Features
--------

* Routine for testing of the Deficiency Zero and One Theorems.
* Routine for running the mass conservation approach.
* Routine for running the semi-diffusive approach.

Citing CRNT4SBML
-----------------

If you use CRNT4SBML in your research, we would appreciate it if you use the following citation in any works you publish:

    Brandon C Reyes, Irene Otero-Muras, Michael T Shuen, Alexandre M Tartakovsky, Vladislav A Petyuk,
    `CRNT4SBML: a Python package for the detection of bistability in biochemical reaction networks <https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa241/5820009?searchresult=1>`_,
    Bioinformatics.

Credits
-------

This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage


=======
History
=======

0.0.1 (08-22-2019)
------------------

* First release on PyPI.

0.0.2 (08-23-2019)
------------------

* Addition of Cytoscape functionality.

0.0.3 (08-26-2019)
------------------

* Improvements to the plots produced by the continuity analysis.

0.0.4 (09-5-2019)
------------------

* Addition of safety precautions for numerical continuation.

0.0.5 (09-16-2019)
------------------

* Addition of routines to parse catalysis in SBML.
* Addition of routines to automatically generate physiological bounds.

0.0.6 (09-23-2019)
------------------

* Updating safety wrapper to smoothly work on Windows and Mac.

0.0.7 (10-11-2019)
------------------

* Adding output to continuity routine to make post-processing simpler.

0.0.8 (10-23-2019)
------------------

* Adding functionality to allow use of Jupyter notebooks.

0.0.9 (11-6-2019)
------------------

* Improving stability when creating the equilibrium manifold in the mass conservation approach.

0.0.10 (11-6-2019)
------------------

* Adding routine for an exhaustive equilibrium manifold creation in the mass conservation approach.

0.0.11 (4-23-2020)
------------------

* Adding a general approach for mass conserving systems.

0.0.12 (5-21-2020)
------------------

* Adding a different layout for installation of package.

