A Language for Biochemical Systems

Michael Pedersen, Gordon D. Plotkin

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

Abstract

CBS is a Calculus of Biochemical Systems intended to allow the modelling of metabolic, signalling and regulatory networks in a natural and modular manner. In this paper we extend CBS with features directed towards practical, large-scale applications, thus yielding LBS: a Language for Biochemical Systems. The two main extensions are expressions for modifying large complexes in a step-wise manner and parameterised modules with a notion of subtyping; LBS also has nested declarations of species and compartments. The extensions are demonstrated with examples from the yeast pheromone pathway. A formal specification of LBS is then given through an abstract syntax, static semantics and a translation to a variant of coloured Petri nets. Translation to other formalisms such as ordinary differential equations and continuous time Markov chains is also possible.
Original languageEnglish
Title of host publicationComputational Methods in Systems Biology
Subtitle of host publication 6th International Conference, CMSB 2008, Rostock, Germany, October 12-15, 2008. Proceedings
PublisherSpringer Berlin Heidelberg
Pages63-82
Number of pages20
Volume5307
ISBN (Electronic)978-3-540-88562-7
ISBN (Print)978-3-540-88561-0
DOIs
Publication statusPublished - 2008

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