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Book Chapter

StochKit-FF: Efficient systems biology on multicore architectures

Citation
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. http://www.scopus.com/inward/record.url?partnerID=yv4JPVwI&eid=2-s2.0-80051706079&md5=286ea3e23e0a0be6103ad85e9652c57e

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 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.

Keywords
Stochastic biological models; simulation; multicore

StatusPublished
Author(s)Aldinucci, Marco; Bracciali, Andrea; Lio, Pietro; Sorathiya, Anil; Torquati, Massimo
Title of seriesLecture Notes in Computer Science
Number in series6586
Publication date31/12/2011
PublisherSpringer
Publisher URLhttp://www.scopus.com/…103ad85e9652c57e
Place of publicationBerlin, Heidelberg
ISSN of series0302-9743
ISBN978-3-642-21877-4
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