StochKit2: Software for discrete stochastic simulation of biochemical systems with events

Kevin R. Sanft; Sheng Wu; Min Roh; Jin Fu; Rone Kwei Lim; Linda R. Petzold

doi:10.1093/bioinformatics/btr401

StochKit2: Software for discrete stochastic simulation of biochemical systems with events

Kevin R. Sanft, Sheng Wu, Min Roh, Jin Fu, Rone Kwei Lim, Linda R. Petzold

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113 Scopus citations

Abstract

StochKit2 is the rst major upgrade of the popular StochKit stochastic simulation software package. StochKit2 provides highly efcient implementations of several variants of Gillespie's stochastic simulation algorithm (SSA), and tau-leaping with automatic step size selection. StochKit2 features include automatic selection of the optimal SSA method based on model properties, event handling, and automatic parallelism on multicore architectures. The underlying structure of the code has been completely updated to provide a exible framework for extending its functionality.

Original language	English (US)
Article number	btr401
Pages (from-to)	2457-2458
Number of pages	2
Journal	Bioinformatics
Volume	27
Issue number	17
DOIs	https://doi.org/10.1093/bioinformatics/btr401
State	Published - Sep 2011
Externally published	Yes

Bibliographical note

Funding Information:
Funding: National Institute of Biomedical Imaging and Bioengineering (Grant No. R01EB007511); Institute for Collaborative Biotechnologies from the US Army Research Office (Grant No. DFR3A-8-447850-23002); DOE Contract No. DE-FG02-04ER25621; NSF Contract No. IGERT DG02-21715 and DMS-1001012; National Science Foundation Graduate Research Fellowships (to K.S. and R.K.L).

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title = "StochKit2: Software for discrete stochastic simulation of biochemical systems with events",

abstract = "StochKit2 is the rst major upgrade of the popular StochKit stochastic simulation software package. StochKit2 provides highly efcient implementations of several variants of Gillespie's stochastic simulation algorithm (SSA), and tau-leaping with automatic step size selection. StochKit2 features include automatic selection of the optimal SSA method based on model properties, event handling, and automatic parallelism on multicore architectures. The underlying structure of the code has been completely updated to provide a exible framework for extending its functionality.",

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note = "Funding Information: Funding: National Institute of Biomedical Imaging and Bioengineering (Grant No. R01EB007511); Institute for Collaborative Biotechnologies from the US Army Research Office (Grant No. DFR3A-8-447850-23002); DOE Contract No. DE-FG02-04ER25621; NSF Contract No. IGERT DG02-21715 and DMS-1001012; National Science Foundation Graduate Research Fellowships (to K.S. and R.K.L).",

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doi = "10.1093/bioinformatics/btr401",

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AU - Lim, Rone Kwei

AU - Petzold, Linda R.

N1 - Funding Information: Funding: National Institute of Biomedical Imaging and Bioengineering (Grant No. R01EB007511); Institute for Collaborative Biotechnologies from the US Army Research Office (Grant No. DFR3A-8-447850-23002); DOE Contract No. DE-FG02-04ER25621; NSF Contract No. IGERT DG02-21715 and DMS-1001012; National Science Foundation Graduate Research Fellowships (to K.S. and R.K.L).

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StochKit2: Software for discrete stochastic simulation of biochemical systems with events

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