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crnt4sbml-0.0.9
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مشاهده بیشترتوضیحات
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.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | crnt4sbml-0.0.9 |
| نام | crnt4sbml |
| نسخه کتابخانه | 0.0.9 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Brandon Reyes |
| ایمیل نویسنده | reyesb123@gmail.com |
| آدرس صفحه اصلی | https://github.com/PNNL-Comp-Mass-Spec/CRNT4SBML |
| آدرس اینترنتی | https://pypi.org/project/crnt4sbml/ |
| مجوز | Apache Software License 2.0 |
=========
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.
0.0.13 (8-10-2020)
------------------
* Improving usability on Windows machines.
0.0.14 (1-28-2021)
------------------
* Improving the output of plots produced by direct simulation.
0.0.15 (8-25-2021)
------------------
* Updated tolerances for Bayesian stopping rule to 0.1.
نیازمندی
| مقدار | نام |
|---|---|
| ==2.3 | networkx |
| ==5.18.0 | python-libsbml |
| ==1.16.4 | numpy |
| ==1.4 | sympy |
| ==1.4.1 | scipy |
| ==3.1.1 | matplotlib |
| ==0.6.0 | plotnine |
| ==3.0.3) | mpi4py |
| ==2.11.0) | antimony |
| ==1.5.2.1) | libroadrunner |
| ==1.2.2) | rrplugins |
| ==3.0.3) | mpi4py |
| ==2.11.0) | antimony |
| ==1.5.2.1) | libroadrunner |
| ==1.2.2) | rrplugins |
| ==3.0.3) | mpi4py |
| ==2.11.0) | antimony |
| ==1.5.2.1) | libroadrunner |
| ==1.2.2) | rrplugins |
| ==2.11.0) | antimony |
| ==1.5.2.1) | libroadrunner |
| ==1.2.2) | rrplugins |
نحوه نصب
نصب پکیج whl crnt4sbml-0.0.9:
pip install crnt4sbml-0.0.9.whl
نصب پکیج tar.gz crnt4sbml-0.0.9:
pip install crnt4sbml-0.0.9.tar.gz