BiPSim: a flexible and generic stochastic simulator for polymerization processes

Abstract Detailed whole-cell modeling requires an integration of heterogeneous cell processes having different modeling formalisms, for which whole-cell simulation could remain tractable. Here, we introduce BiPSim, an open-source stochastic simulator of template-based polymerization processes, such...

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Autores principales:	Stephan Fischer, Marc Dinh, Vincent Henry, Philippe Robert, Anne Goelzer, Vincent Fromion
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ac317034f0994e66bdcdba31c8db31dd
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spelling	oai:doaj.org-article:ac317034f0994e66bdcdba31c8db31dd2021-12-02T16:14:46ZBiPSim: a flexible and generic stochastic simulator for polymerization processes10.1038/s41598-021-92833-52045-2322https://doaj.org/article/ac317034f0994e66bdcdba31c8db31dd2021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-92833-5https://doaj.org/toc/2045-2322Abstract Detailed whole-cell modeling requires an integration of heterogeneous cell processes having different modeling formalisms, for which whole-cell simulation could remain tractable. Here, we introduce BiPSim, an open-source stochastic simulator of template-based polymerization processes, such as replication, transcription and translation. BiPSim combines an efficient abstract representation of reactions and a constant-time implementation of the Gillespie’s Stochastic Simulation Algorithm (SSA) with respect to reactions, which makes it highly efficient to simulate large-scale polymerization processes stochastically. Moreover, multi-level descriptions of polymerization processes can be handled simultaneously, allowing the user to tune a trade-off between simulation speed and model granularity. We evaluated the performance of BiPSim by simulating genome-wide gene expression in bacteria for multiple levels of granularity. Finally, since no cell-type specific information is hard-coded in the simulator, models can easily be adapted to other organismal species. We expect that BiPSim should open new perspectives for the genome-wide simulation of stochastic phenomena in biology.Stephan FischerMarc DinhVincent HenryPhilippe RobertAnne GoelzerVincent FromionNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-16 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Stephan Fischer Marc Dinh Vincent Henry Philippe Robert Anne Goelzer Vincent Fromion BiPSim: a flexible and generic stochastic simulator for polymerization processes
description	Abstract Detailed whole-cell modeling requires an integration of heterogeneous cell processes having different modeling formalisms, for which whole-cell simulation could remain tractable. Here, we introduce BiPSim, an open-source stochastic simulator of template-based polymerization processes, such as replication, transcription and translation. BiPSim combines an efficient abstract representation of reactions and a constant-time implementation of the Gillespie’s Stochastic Simulation Algorithm (SSA) with respect to reactions, which makes it highly efficient to simulate large-scale polymerization processes stochastically. Moreover, multi-level descriptions of polymerization processes can be handled simultaneously, allowing the user to tune a trade-off between simulation speed and model granularity. We evaluated the performance of BiPSim by simulating genome-wide gene expression in bacteria for multiple levels of granularity. Finally, since no cell-type specific information is hard-coded in the simulator, models can easily be adapted to other organismal species. We expect that BiPSim should open new perspectives for the genome-wide simulation of stochastic phenomena in biology.
format	article
author	Stephan Fischer Marc Dinh Vincent Henry Philippe Robert Anne Goelzer Vincent Fromion
author_facet	Stephan Fischer Marc Dinh Vincent Henry Philippe Robert Anne Goelzer Vincent Fromion
author_sort	Stephan Fischer
title	BiPSim: a flexible and generic stochastic simulator for polymerization processes
title_short	BiPSim: a flexible and generic stochastic simulator for polymerization processes
title_full	BiPSim: a flexible and generic stochastic simulator for polymerization processes
title_fullStr	BiPSim: a flexible and generic stochastic simulator for polymerization processes
title_full_unstemmed	BiPSim: a flexible and generic stochastic simulator for polymerization processes
title_sort	bipsim: a flexible and generic stochastic simulator for polymerization processes
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/ac317034f0994e66bdcdba31c8db31dd
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BiPSim: a flexible and generic stochastic simulator for polymerization processes

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