CellMC--a multiplatform model compiler for the Cell Broadband Engine and x86.
BACKGROUND
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 x86 PCs.


BACKGROUND
The code is freely available from http://www.cellmc.org. It will run on a wide variety of x86 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.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Caulfield
Emmet
E
Department of Information Technology, Uppsala University, Box 337, SE-751 05, Uppsala, Sweden.
Hellander
Andreas
A
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D012984:Software; D049490:Systems Biology