Pycellerator

Pycellerator is a Python library that can read Cellerator arrow notation from standard text files, convert them to differential equations, generate Python solvers, and run and plot solutions. The library includes a Python command line interface, an application programming interface, and an iPython notebook interface. The Cellerator reaction arrows, which represent various reactions ranging from mass action, Michales-Menten-Henri (MMH), Gene-Regulation (GRN), to Monod-Wyman-Changeaux (MWC) and user-defined reactions, are now typed as reaction-like commands in ASCII text files and read by Pycellerator.

Topic

Systems biology;Molecular interactions, pathways and networks

Detail

  • Operation: Pathway or network visualisation

  • Software interface: Command-line user interface

  • Language: Python

  • License: GNU General Public License v3.0

  • Cost: Free

  • Version name: v1.0rc2

  • Credit: National Institutes of Health (NIH), the United States Air Force under the DARPA PPAML program.

  • Input: -

  • Output: -

  • Contact: Bruce E Shapiro bruce.e.shapiro@csun.edu

  • Collection: -

  • Maturity: -

Publications

  • Pycellerator: an arrow-based reaction-like modelling language for biological simulations.
  • Shapiro BE and Mjolsness E. Pycellerator: an arrow-based reaction-like modelling language for biological simulations. Pycellerator: an arrow-based reaction-like modelling language for biological simulations. 2016; 32:629-31. doi: 10.1093/bioinformatics/btv596
  • https://doi.org/10.1093/bioinformatics/btv596
  • PMID: 26504142
  • PMC: PMC5963356

Download and documentation

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