{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,21]],"date-time":"2025-09-21T17:20:03Z","timestamp":1758475203718},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,1,1]]},"abstract":"Abstract<\/jats:title>\n Motivation: Stochasticity is an indispensable aspect of biochemical processes at the cellular level. Studies on how the noise enters and propagates in biochemical systems provided us with non-trivial insights into the origins of stochasticity, in total, however, they constitute a patchwork of different theoretical analyses.<\/jats:p>\n Results: Here we present a flexible and widely applicable noise decomposition tool that allows us to calculate contributions of individual reactions to the total variability of a system\u2019s output. With the package it is, therefore, possible to quantify how the noise enters and propagates in biochemical systems. We also demonstrate and exemplify using the JAK-STAT signalling pathway that the noise contributions resulting from individual reactions can be inferred from data experimental data along with Bayesian parameter inference. The method is based on the linear noise approximation, which is assumed to provide a reasonable representation of analyzed systems.<\/jats:p>\n Availability and implementation: \u00a0http:\/\/sourceforge.net\/p\/stochdecomp\/<\/jats:p>\n Contact: \u00a0mkomor@ippt.gov.pl or m.stumpf@imperial.ac.uk<\/jats:p>\n Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt631","type":"journal-article","created":{"date-parts":[[2013,11,5]],"date-time":"2013-11-05T01:38:58Z","timestamp":1383615538000},"page":"137-138","source":"Crossref","is-referenced-by-count":4,"title":["StochDecomp\u2014Matlab package for noise decomposition in stochastic biochemical systems"],"prefix":"10.1093","volume":"30","author":[{"given":"Tomasz","family":"Jetka","sequence":"first","affiliation":[{"name":"1 Institute of Fundamental Technological Research, 2Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland, 3Faculty of Mathematics Informatics and Mechanics, Institute of Informatics, University of Warsaw, Warsaw, Poland and 4Division of Molecular Biosciences, Imperial College London, London, UK"}]},{"given":"Agata","family":"Charzy\u0144ska","sequence":"additional","affiliation":[{"name":"1 Institute of Fundamental Technological Research, 2Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland, 3Faculty of Mathematics Informatics and Mechanics, Institute of Informatics, University of Warsaw, Warsaw, Poland and 4Division of Molecular Biosciences, Imperial College London, London, UK"}]},{"given":"Anna","family":"Gambin","sequence":"additional","affiliation":[{"name":"1 Institute of Fundamental Technological Research, 2Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland, 3Faculty of Mathematics Informatics and Mechanics, Institute of Informatics, University of Warsaw, Warsaw, Poland and 4Division of Molecular Biosciences, Imperial College London, London, UK"}]},{"given":"Michael P.H.","family":"Stumpf","sequence":"additional","affiliation":[{"name":"1 Institute of Fundamental Technological Research, 2Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland, 3Faculty of Mathematics Informatics and Mechanics, Institute of Informatics, University of Warsaw, Warsaw, Poland and 4Division of Molecular Biosciences, Imperial College London, London, UK"}]},{"given":"Micha\u0142","family":"Komorowski","sequence":"additional","affiliation":[{"name":"1 Institute of Fundamental Technological Research, 2Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland, 3Faculty of Mathematics Informatics and Mechanics, Institute of Informatics, University of Warsaw, Warsaw, Poland and 4Division of Molecular Biosciences, Imperial College London, London, UK"}]}],"member":"286","published-online":{"date-parts":[[2013,11,4]]},"reference":[{"key":"2023012710380224800_btt631-B1","doi-asserted-by":"crossref","first-page":"e1000705","DOI":"10.1371\/journal.pcbi.1000705","article-title":"Detailed simulations of cell biology with smoldyn 2.1","volume":"6","author":"Andrews","year":"2010","journal-title":"PLoS Comput. 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USA"},{"key":"2023012710380224800_btt631-B6","doi-asserted-by":"crossref","first-page":"e38518","DOI":"10.1371\/journal.pone.0038518","article-title":"Intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion","volume":"7","author":"Thomas","year":"2012","journal-title":"PLoS One"},{"key":"2023012710380224800_btt631-B7","volume-title":"Stochastic Processes in Physics and Chemistry","author":"van Kampen","year":"2007"},{"key":"2023012710380224800_btt631-B8","doi-asserted-by":"crossref","first-page":"1130","DOI":"10.1093\/bioinformatics\/bts088","article-title":"An integrated strategy for prediction uncertainty analysis","volume":"28","author":"Vanlier","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012710380224800_btt631-B9","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1049\/iet-syb.2011.0038","article-title":"Linear noise approximation is valid over limited times for any chemical system that is sufficiently large","volume":"6","author":"Wallace","year":"2012","journal-title":"IET Syst. 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