Taming the complexity of biological pathways through parallel computing

Paolo Ballarini, Rosita Guido, Tommaso Mazza, Davide Prandi

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish
Pages (from-to)278-288
Number of pages11
JournalBriefings in Bioinformatics
Volume10
Issue number3
DOIs
Publication statusPublished - 2009

Keywords

  • Biological pathways
  • Model checking
  • ODE numerical solutions
  • Parallel computing
  • Stochastic simulation

ASJC Scopus subject areas

  • Molecular Biology
  • Information Systems

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