CERENA

CERENA is a software toolbox for analyzing stochastic chemical kinetics in various cellular processes, which is important for understanding cell-to-cell variability and its functional implications. The software implements a range of stochastic simulation algorithms and solution statistics, allowing for the selection of appropriate modeling approaches. It is user-friendly, computationally efficient, and provides forward and adjoint sensitivity analyses for further studies. CERENA is completely general and allows for time-dependent propensities and non-mass action kinetics. The MATLAB code implementing CERENA is freely available.

Topic

Computational chemistry;Molecular interactions, pathways and networks;Simulation experiment

Detail

  • Operation: Pathway or network analysis

  • Software interface: Library

  • Language: MATLAB

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: The European Union within the ERC grant, the German Research Foundation (DFG) through the Graduate School of Quantitative Biosciences Munich, Merrimack Pharmaceuticals Inc.

  • Input: -

  • Output: -

  • Contact: -

  • Collection: -

  • Maturity: -

Publications

  • CERENA: ChEmical REaction Network Analyzer--A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics.
  • Kazeroonian A, et al. CERENA: ChEmical REaction Network Analyzer--A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics. CERENA: ChEmical REaction Network Analyzer--A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics. 2016; 11:e0146732. doi: 10.1371/journal.pone.0146732
  • https://doi.org/10.1371/journal.pone.0146732
  • PMID: 26807911
  • PMC: PMC4726759

Download and documentation

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