A process algebra framework for multi-scale modelling of biological systems

Degasperi, A. and Calder, M. (2013) A process algebra framework for multi-scale modelling of biological systems. Theoretical Computer Science, 488, pp. 15-45. (doi:10.1016/j.tcs.2013.03.018)

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Abstract

We introduce a novel process algebra for modelling biological systems at multiple scales, called process algebra with hooks (PAH). Processes represent biological entities, such as molecules, cells and tissues, while two algebraic operators, both symmetric, define composition of processes within and between scales. Composed actions allow for biological events to interact within and between scales at the same time. The algebra has a stochastic semantics based on functional rates of reactions. Two bisimulations are defined on PAH processes. The first bisimulation is used to aid model development by checking that two biological scales can interact correctly. The second bisimulation is a congruence that relates models, or part of models, that can perform the same timed events at a specified scale. Finally, we provide a PAH model of pattern formation in a tissue and illustrate reasoning about its behaviour using the PAH framework.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Calder, Professor Muffy
Authors: Degasperi, A., and Calder, M.
College/School:University Services > IT Services > Computing Service
Journal Name:Theoretical Computer Science
Publisher:Elsevier
ISSN:0304-3975
Copyright Holders:Copyright © 2013 Elsevier B.V.
First Published:First published in Theoretical Computer Science 488:15-45
Publisher Policy:Reproduced in accordance with the copyright policy of the publisher

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
441081SIGNAL - stochastic process algebra for biochemical signalling pathway analysisMuffy CalderEngineering & Physical Sciences Research Council (EPSRC)EP/E028519/1COM - COMPUTING SCIENCE