Skip to main content

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.

Project description

CRNT4SBML

https://img.shields.io/pypi/v/crnt4sbml.svg https://img.shields.io/travis/PNNL-Comp-Mass-Spec/CRNT4SBML.svg 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.

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.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

crnt4sbml-0.0.15.tar.gz (7.3 MB view hashes)

Uploaded source

Built Distribution

crnt4sbml-0.0.15-py2.py3-none-any.whl (71.0 kB view hashes)

Uploaded py2 py3

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page