StochKit-FF: Efficient Systems Biology on Multicore Architectures

  • Marco Aldinucci
  • Andrea Bracciali
  • Pietro Liò
  • Anil Sorathiya
  • Massimo Torquati
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6586)

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 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Marco Aldinucci
    • 1
  • Andrea Bracciali
    • 2
  • Pietro Liò
    • 3
  • Anil Sorathiya
    • 3
  • Massimo Torquati
    • 4
  1. 1.Computer Science DepartmentUniversity of TorinoItaly
  2. 2.ISTI - CNRItaly
  3. 3.Computer LaboratoryCambridge UniversityUK
  4. 4.Computer Science DepartmentUniversity of PisaItaly

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