StochKit2: software for discrete stochastic simulation of biochemical systems with events | Zendy

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

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

Author(s) -

Kevin R. Sanft,

Sheng Wu,

Min K. Roh,

Jin Fu,

Rone Kwei Lim,

Linda Petzold

Publication year - 2011

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btr401

Subject(s) - computer science , unix , software , upgrade , multi core processor , implementation , selection (genetic algorithm) , programming language , stochastic simulation , code (set theory) , parallel computing , discrete event simulation , event (particle physics) , operating system , theoretical computer science , artificial intelligence , simulation , mathematics , statistics , physics , set (abstract data type) , quantum mechanics

StochKit2 is the first major upgrade of the popular StochKit stochastic simulation software package. StochKit2 provides highly efficient 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 flexible framework for extending its functionality.

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