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Bioinformatics Advance Access published online on July 3, 2009
Bioinformatics, 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 2–4

1Computer Science and Artificial Intelligence Laboratory and the Departments of 2Chemistry, 3Chemical Engineering, and 4Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

To whom correspondence should be addressed. Mieszko Lis, E-mail: mieszko{at}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. SSC currently runs on Linux and Mac OS X, and is freely available at http://web.mit.edu/irc/ssc/.

Associate Editor: Dr. Olga Troyanskaya

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

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