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Formal methods for biochemical signalling pathways

Calder, Muffy and Gilmore, S. and Hillston, Jane and Vyshemirsky, Vladislav (2010) Formal methods for biochemical signalling pathways. In: Formal Methods: State of the Art and New Directions. Springer, London, pp. 185-215. ISBN 9781848827363

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We apply quantitative formal methods to a domain from the life sciences: biochemical signalling pathways. The key idea is to model pathways as stochastic continuous time distributed systems. Components of the system are molecular species (rather than individual molecules) and are modelled by concurrent processes that interact with each other via biochemical reactions. Through an application, we show how high level languages and analysis techniques rooted in computer science theory add significantly to the analysis presently available to computational biologists.