crnt4sbml 0.0.15

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.

CRNT4SBML

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, Bioinformatics.

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

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.