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A process algebra framework for multi-scale modelling of biological systems
Author(s)
Date Issued
2013-06
Date Available
2013-11-29T13:14:35Z
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.
Other Sponsorship
Lord Kelvin/Adam Smith Scholarship of the University of Glasgow and by the EPSRC & SIGNAL project
Type of Material
Journal Article
Publisher
Elsevier
Journal
Theoretical Computer Science
Volume
488
Start Page
15
End Page
45
Copyright (Published Version)
2013 Elsevier
Language
English
Status of Item
Peer reviewed
This item is made available under a Creative Commons License
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