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Bioinformatics Advance Access originally published online on July 3, 2009
Bioinformatics 2009 25(17):2289-2291; doi:10.1093/bioinformatics/btp387
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Efficient stochastic simulation of reaction–diffusion processes via direct compilation

Mieszko Lis 1,*, Maxim N. Artyomov 2, Srinivas Devadas 1 and Arup K. Chakraborty 2,3,4

1 Computer Science and Artificial Intelligence Laboratory and the Departments of2 Chemistry, 3 Chemical Engineering and 4 Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

* To whom correspondence should be addressed.


  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.

Availability: SSC currently runs on Linux and Mac OS X, and is freely available at http://web.mit.edu/irc/ssc/.

Contact: mieszko{at}csail.mit.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Olga Troyanskaya

Received on February 2, 2009; revised on June 13, 2009; accepted on June 19, 2009

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