StochKit-FF: Efficient Systems Biology on Multicore Architectures

Details StochKit-FF: Efficient Systems Biology on Multicore Architectures StochKit-FF: Efficient Systems Biology on Multicore Architectures

2010-07-11

arxiv.org/abs/1007.1768v1

Computer Science

Computational Engineering, Finance, and Science

14 pages + cover page

Scientific paper

The stochastic modelling of biological systems is an informative, and in some cases, very adequate technique, which may however result in being more expensive than other modelling approaches, such as differential equations. We present StochKit-FF, a parallel version of StochKit, a reference toolkit for stochastic simulations. StochKit-FF is based on the FastFlow programming toolkit for multicores and exploits the novel concept of selective memory. We experiment StochKit-FF on a model of HIV infection dynamics, with the aim of extracting information from efficiently run experiments, here in terms of average and variance and, on a longer term, of more structured data.

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