CERENA: ChEmical REaction Network Analyzer--A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics

PloS One
A KazeroonianJ Hasenauer

Abstract

Gene expression, signal transduction and many other cellular processes are subject to stochastic fluctuations. The analysis of these stochastic chemical kinetics is important for understanding cell-to-cell variability and its functional implications, but it is also challenging. A multitude of exact and approximate descriptions of stochastic chemical kinetics have been developed, however, tools to automatically generate the descriptions and compare their accuracy and computational efficiency are missing. In this manuscript we introduced CERENA, a toolbox for the analysis of stochastic chemical kinetics using Approximations of the Chemical Master Equation solution statistics. CERENA implements stochastic simulation algorithms and the finite state projection for microscopic descriptions of processes, the system size expansion and moment equations for meso- and macroscopic descriptions, as well as the novel conditional moment equations for a hybrid description. This unique collection of descriptions in a single toolbox facilitates the selection of appropriate modeling approaches. Unlike other software packages, the implementation of CERENA is completely general and allows, e.g., for time-dependent propensities and non-mass action k...Continue Reading

References

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Citations

Jul 3, 2017·The Journal of Chemical Physics·Basil S Bayati
Jul 23, 2016·PLoS Computational Biology·Fabian FröhlichJan Hasenauer
Oct 23, 2016·BMC Systems Biology·Alexander Lück, Verena Wolf
Sep 9, 2017·Bioinformatics·Atefeh KazeroonianJan Hasenauer
Jan 8, 2017·Bioinformatics·Corinna MaierJan Hasenauer
Jun 26, 2021·Bioinformatics·Augustinas Sukys, Ramon Grima
Sep 2, 2020·The Journal of Physical Chemistry. a·Giannis D Savva, Michail Stamatakis

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Software Mentioned

EMRE
StochKit
FSP
IDAS
MCM
MATLAB Symbolic Math Toolbox
CERENA ( ChEmical REaction Network Analyzer )
SHAVE
iNA
Data2Dynamics

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