Process Algebras in Systems Biology

Federica Ciocchetta, Jane Hillston

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract / Description of output

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.
Original languageEnglish
Title of host publicationFormal Methods for Computational Systems Biology
Subtitle of host publication8th International School on Formal Methods for the Design of Computer, Communication, and Software Systems, SFM 2008 Bertinoro, Italy, June 2-7, 2008 Advanced Lectures
EditorsMarco Bernardo, Pierpaolo Degano, Gianluigi Zavattaro
PublisherSpringer Berlin Heidelberg
Pages265-312
Number of pages48
Volume5016
ISBN (Electronic)978-3-540-68894-5
ISBN (Print)978-3-540-68892-1
DOIs
Publication statusPublished - 2008

Publication series

NameLecture Notes in Computer Science
PublisherSpringer Berlin Heidelberg
Volume5016

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