Intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion.

The accepted stochastic descriptions of biochemical dynamics under well-mixed conditions are given by the Chemical Master Equation and the Stochastic Simulation Algorithm, which are equivalent. The latter is a Monte-Carlo method, which, despite enjoying broad availability in a large number of existi...

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Autores principales:	Philipp Thomas, Hannes Matuschek, Ramon Grima
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/72a7c606284c49478bbc85d24606dc23
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spelling	oai:doaj.org-article:72a7c606284c49478bbc85d24606dc232021-11-18T07:15:41ZIntrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion.1932-620310.1371/journal.pone.0038518https://doaj.org/article/72a7c606284c49478bbc85d24606dc232012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22723865/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203The accepted stochastic descriptions of biochemical dynamics under well-mixed conditions are given by the Chemical Master Equation and the Stochastic Simulation Algorithm, which are equivalent. The latter is a Monte-Carlo method, which, despite enjoying broad availability in a large number of existing software packages, is computationally expensive due to the huge amounts of ensemble averaging required for obtaining accurate statistical information. The former is a set of coupled differential-difference equations for the probability of the system being in any one of the possible mesoscopic states; these equations are typically computationally intractable because of the inherently large state space. Here we introduce the software package intrinsic Noise Analyzer (iNA), which allows for systematic analysis of stochastic biochemical kinetics by means of van Kampen's system size expansion of the Chemical Master Equation. iNA is platform independent and supports the popular SBML format natively. The present implementation is the first to adopt a complementary approach that combines state-of-the-art analysis tools using the computer algebra system Ginac with traditional methods of stochastic simulation. iNA integrates two approximation methods based on the system size expansion, the Linear Noise Approximation and effective mesoscopic rate equations, which to-date have not been available to non-expert users, into an easy-to-use graphical user interface. In particular, the present methods allow for quick approximate analysis of time-dependent mean concentrations, variances, covariances and correlations coefficients, which typically outperforms stochastic simulations. These analytical tools are complemented by automated multi-core stochastic simulations with direct statistical evaluation and visualization. We showcase iNA's performance by using it to explore the stochastic properties of cooperative and non-cooperative enzyme kinetics and a gene network associated with circadian rhythms. The software iNA is freely available as executable binaries for Linux, MacOSX and Microsoft Windows, as well as the full source code under an open source license.Philipp ThomasHannes MatuschekRamon GrimaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 6, p e38518 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Philipp Thomas Hannes Matuschek Ramon Grima Intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion.
description	The accepted stochastic descriptions of biochemical dynamics under well-mixed conditions are given by the Chemical Master Equation and the Stochastic Simulation Algorithm, which are equivalent. The latter is a Monte-Carlo method, which, despite enjoying broad availability in a large number of existing software packages, is computationally expensive due to the huge amounts of ensemble averaging required for obtaining accurate statistical information. The former is a set of coupled differential-difference equations for the probability of the system being in any one of the possible mesoscopic states; these equations are typically computationally intractable because of the inherently large state space. Here we introduce the software package intrinsic Noise Analyzer (iNA), which allows for systematic analysis of stochastic biochemical kinetics by means of van Kampen's system size expansion of the Chemical Master Equation. iNA is platform independent and supports the popular SBML format natively. The present implementation is the first to adopt a complementary approach that combines state-of-the-art analysis tools using the computer algebra system Ginac with traditional methods of stochastic simulation. iNA integrates two approximation methods based on the system size expansion, the Linear Noise Approximation and effective mesoscopic rate equations, which to-date have not been available to non-expert users, into an easy-to-use graphical user interface. In particular, the present methods allow for quick approximate analysis of time-dependent mean concentrations, variances, covariances and correlations coefficients, which typically outperforms stochastic simulations. These analytical tools are complemented by automated multi-core stochastic simulations with direct statistical evaluation and visualization. We showcase iNA's performance by using it to explore the stochastic properties of cooperative and non-cooperative enzyme kinetics and a gene network associated with circadian rhythms. The software iNA is freely available as executable binaries for Linux, MacOSX and Microsoft Windows, as well as the full source code under an open source license.
format	article
author	Philipp Thomas Hannes Matuschek Ramon Grima
author_facet	Philipp Thomas Hannes Matuschek Ramon Grima
author_sort	Philipp Thomas
title	Intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion.
title_short	Intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion.
title_full	Intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion.
title_fullStr	Intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion.
title_full_unstemmed	Intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion.
title_sort	intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/72a7c606284c49478bbc85d24606dc23
work_keys_str_mv	AT philippthomas intrinsicnoiseanalyzerasoftwarepackagefortheexplorationofstochasticbiochemicalkineticsusingthesystemsizeexpansion AT hannesmatuschek intrinsicnoiseanalyzerasoftwarepackagefortheexplorationofstochasticbiochemicalkineticsusingthesystemsizeexpansion AT ramongrima intrinsicnoiseanalyzerasoftwarepackagefortheexplorationofstochasticbiochemicalkineticsusingthesystemsizeexpansion
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Intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion.

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