StochKit-FF: efficient systems biology on multicore architectures

Authors:
Marco Aldinucci;Andrea Bracciali;Pietro Lio;Anil Sorathiya;Massimo Torquati
Affiliations:
Computer Science Department, University of Torino, Italy;ISTI - CNR, Italy;Computer Laboratory, Cambridge University, UK;Computer Laboratory, Cambridge University, UK;Computer Science Department, University of Pisa, Italy
Venue:
Euro-Par 2010 Proceedings of the 2010 conference on Parallel processing
Year:
2010

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Abstract

The stochastic modelling of biological systems is informative and often very adequate, but it may easily be more expensive than other modelling approaches, such as differential equations. We present Stoch-Kit-FF, a parallel version of StochKit, a reference toolkit for stochastic simulations. StochKit-FF is based on the FastFlow programming toolkit for multicores and on 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.