Process algebras in systems biology

  • Authors:

  • Federica Ciocchetta;Jane Hillston

  • Affiliations:

  • Laboratory for Foundations of Computer Science, The University of Edinburgh, Edinburgh, Scotland;Laboratory for Foundations of Computer Science, The University of Edinburgh, Edinburgh, Scotland

  • Venue:
  • SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
  • Year:
  • 2008

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Abstract

In this chapter we introduce process algebras, a class of formal modelling techniques developed in theoretical computer science, and discuss their use within systems biology. These formalisms have a number of attractive features which make them ideal candidates to be intermediate, formal, compositional representations of biological systems. As we will show, when modelling is carried out at a suitable level of abstraction, the constructed model can be amenable to analysis using a variety of different approaches, encompassing both individuals-based stochastic simulation and population-based ordinary differential equations. We focus particularly on Bio-PEPA, a recently defined extension of the PEPA stochastic process algebra, which has features to capture both stoichiometry and general kinetic laws. We present the definition of the language, some equivalence relations and the mappings to underlying mathematical models for analysis. We demonstrate the use of Bio-PEPA on two biological examples.