Journal Article

CellMC—a multiplatform model compiler for the Cell Broadband Engine and ×86

Emmet Caulfield and Andreas Hellander

in Bioinformatics

Volume 26, issue 3, pages 426-428
Published in print February 2010 | ISSN: 1367-4803
Published online December 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp662
CellMC—a multiplatform model compiler for the Cell Broadband Engine and ×86

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Motivation: Gillespie's stochastic simulation algorithm (SSA) is often the most tractable method to study stochastic models of biochemical systems. The algorithm itself is very simple and a natural target for implementation on specialized architectures such as the Cell Broadband Engine (Cell/BE). We have developed CellMC, a multiplatform SBML model compiler implementing a vectorized version of SSA for use on Cell/BE or ×86 PCs.

Availability: The code is freely available from http://www.cellmc.org. It will run on a wide variety of ×86 computers running Linux/MacOSX (Darwin) and on Cell/BE computers such as the Sony PlayStation3 (PS3) and the IBM BladeCenter QS22. CellMC requires gcc, libxml2 and libxslt, all of which are installed by default on most of the supported platforms.

Contact: info@www.cellmc.org; andreas.hellander@it.uu.se

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1878 words. 

Subjects: Bioinformatics and Computational Biology

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