Process Algebra Modelling Styles for Biomolecular Processes

Authors:
Muffy Calder;Jane Hillston
Affiliations:
Department of Computing Science, University of Glasgow, Glasgow, Scotland G12 8QQ;Laboratory for Foundations of Computer Science and Centre for Systems Biology, Edinburgh, The University of Edinburgh, Edinburgh, Scotland EHA 9AB
Venue:
Transactions on Computational Systems Biology XI
Year:
2009

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Abstract

We investigate how biomolecular processes are modelled in process algebras, focussing on chemical reactions. We consider various modelling styles and how design decisions made in the definition of the process algebra have an impact on how a modelling style can be applied. Our goal is to highlight the often implicit choices that modellers make in choosing a formalism, and illustrate, through the use of examples, how this can affect expressability as well as the type and complexity of the analysis that can be performed.