Electronic Proceedings in Theoretical Computer Science (Oct 2009)

BioDiVinE: A Framework for Parallel Analysis of Biological Models

  • David Šafránek,
  • Jan Láník,
  • Jana Fabriková,
  • Sven Dražan,
  • Ivana Černá,
  • Luboš Brim,
  • Jiří Barnat,
  • Hongwu Ma

DOI
https://doi.org/10.4204/EPTCS.6.3
Journal volume & issue
Vol. 6, no. Proc. COMPMOD 2009
pp. 31 – 45

Abstract

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In this paper a novel tool BioDiVinEfor parallel analysis of biological models is presented. The tool allows analysis of biological models specified in terms of a set of chemical reactions. Chemical reactions are transformed into a system of multi-affine differential equations. BioDiVinE employs techniques for finite discrete abstraction of the continuous state space. At that level, parallel analysis algorithms based on model checking are provided. In the paper, the key tool features are described and their application is demonstrated by means of a case study.