Journal Article

Efficient stochastic simulation of reaction–diffusion processes via direct compilation

Mieszko Lis, Maxim N. Artyomov, Srinivas Devadas and Arup K. Chakraborty

in Bioinformatics

Volume 25, issue 17, pages 2289-2291
Published in print September 2009 | ISSN: 1367-4803
Published online July 2009 | e-ISSN: 1460-2059 | DOI:

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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.

Availability: SSC currently runs on Linux and Mac OS X, and is freely available at


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  2217 words. 

Subjects: Bioinformatics and Computational Biology

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