Book Chapter

StochKit-FF: Efficient systems biology on multicore architectures


Aldinucci M, Bracciali A, Lio P, Sorathiya A & Torquati M (2011) StochKit-FF: Efficient systems biology on multicore architectures. In: Guarracino M, Vivien F, Träff J, Cannatoro M, Danelutto M, Hast A, Perla F, Knüpfer A, Martino B & Alexander M (eds.) Euro-Par 2010 Parallel Processing Workshops. Lecture Notes in Computer Science, 6586. Berlin, Heidelberg: Springer, pp. 167-175.

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 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 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.

Stochastic biological models; simulation; multicore

Title of seriesLecture Notes in Computer Science
Number in series6586
Publication date31/12/2011
Publisher URL…103ad85e9652c57e
Place of publicationBerlin, Heidelberg
ISSN of series0302-9743