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Briefings in Bioinformatics Advance Access originally published online on April 1, 2009
Briefings in Bioinformatics 2009 10(3):278-288; doi:10.1093/bib/bbp020
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© The Author 2009. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Taming the complexity of biological pathways through parallel computing

Paolo Ballarini, Rosita Guido, Tommaso Mazza and Davide Prandi

Corresponding author. Paolo Ballarini, The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manci 17 38100 Povo, Trento, Italy. Tel: +39-0461-882841; Fax: +39-0461-882814; E-mail: ballarini{at}cosbi.eu

Biological systems are characterised by a large number of interacting entities whose dynamics is described by a number of reaction equations. Mathematical methods for modelling biological systems are mostly based on a centralised solution approach: the modelled system is described as a whole and the solution technique, normally the integration of a system of ordinary differential equations (ODEs) or the simulation of a stochastic model, is commonly computed in a centralised fashion. In recent times, research efforts moved towards the definition of parallel/distributed algorithms as a means to tackle the complexity of biological models analysis. In this article, we present a survey on the progresses of such parallelisation efforts describing the most promising results so far obtained.

Keywords: ODE numerical solutions, stochastic simulation, model checking, parallel computing, biological pathways

Submitted: November 8, 2008. Received (in revised form): March 2, 2009.


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