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Coloured stochastic multilevel multiset rewriting

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

Original languageEnglish
Title of host publicationProceedings of the 9th International Conference on Computational Methods in Systems Biology
PublisherACM
Pages171-181
Number of pages11
ISBN (Print)978-1-4503-0817-5
DOIs
Publication statusPublished - 2011

Abstract

From the phosphorylation state of a molecule to the volume of a cell, parameters are ubiquitous in systems biology. At the same time, most models involve static or dynamic compartments, for example to separate cells from their environment. We introduce coloured stochastic multilevel multiset rewriting, an expressive formalism for modelling systems with parameters and complex dynamic, multilevel compartment structures, and an extension of both multilevel multiset rewriting and coloured Petri nets. While being very expressive, it allows the direct and natural expression of biological ideas. We give some illustrative examples, demonstrating the use of parameters to handle cell states, position and volume, and variable rates. We further demonstrate the use of rules with complex right-hand sides for reproduction. We regard these examples as paving the way for more biologically relevant models.

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