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Bioinformatics. 2009 Sep 1;25(17):2289-91. doi: 10.1093/bioinformatics/btp387. Epub 2009 Jul 3.

Efficient stochastic simulation of reaction-diffusion processes via direct compilation.

Author information

1
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. mieszko@csail.mit.edu

Abstract

We present the Stochastic Simulator Compiler (SSC), a tool for exact stochastic simulations of well-mixed and spatially heterogeneous systems. SSC is the first tool to allow a readable high-level description with spatially heterogeneous simulation algorithms and complex geometries; this permits large systems to be expressed concisely. Meanwhile, direct native-code compilation allows SSC to generate very fast simulations.

PMID:
19578038
PMCID:
PMC2734316
DOI:
10.1093/bioinformatics/btp387
[Indexed for MEDLINE]
Free PMC Article

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