Article

A Language for Biochemical Systems

Authors:

Michael Pedersen,

Gordon PlotkinAuthors Info & Claims

CMSB '08: Proceedings of the 6th International Conference on Computational Methods in Systems Biology

Pages 63 - 82

https://doi.org/10.1007/978-3-540-88562-7_9

Published: 12 October 2008 Publication History

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.

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Cited By

Krivine J(2017)Systems biologyACM SIGLOG News10.1145/3129173.31291824:3(43-61)Online publication date: 28-Jul-2017
https://dl.acm.org/doi/10.1145/3129173.3129182
Pedersen MPlotkin G(2010)A language for biochemical systemsTransactions on Computational Systems Biology XII10.5555/2172311.2172314(77-145)Online publication date: 1-Jan-2010
https://dl.acm.org/doi/10.5555/2172311.2172314
Paulevé LYoussef SLakin MPhillips AQuaglia P(2010)A generic abstract machine for stochastic process calculiProceedings of the 8th International Conference on Computational Methods in Systems Biology10.1145/1839764.1839771(43-54)Online publication date: 29-Sep-2010
https://dl.acm.org/doi/10.1145/1839764.1839771

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Published In

cover image Guide Proceedings

CMSB '08: Proceedings of the 6th International Conference on Computational Methods in Systems Biology

October 2008

401 pages

ISBN:9783540885610

Editors:
Monika Heiner
Department of Computer Science, Brandenburg University of Technology, Cottbus, Germany 03013
,
Adelinde M. Uhrmacher
University of Rostock, Rostock, Germany D-18059

Publisher

Springer-Verlag

Berlin, Heidelberg

Publication History

Published: 12 October 2008

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Cited By

Krivine J(2017)Systems biologyACM SIGLOG News10.1145/3129173.31291824:3(43-61)Online publication date: 28-Jul-2017
https://dl.acm.org/doi/10.1145/3129173.3129182
Pedersen MPlotkin G(2010)A language for biochemical systemsTransactions on Computational Systems Biology XII10.5555/2172311.2172314(77-145)Online publication date: 1-Jan-2010
https://dl.acm.org/doi/10.5555/2172311.2172314
Paulevé LYoussef SLakin MPhillips AQuaglia P(2010)A generic abstract machine for stochastic process calculiProceedings of the 8th International Conference on Computational Methods in Systems Biology10.1145/1839764.1839771(43-54)Online publication date: 29-Sep-2010
https://dl.acm.org/doi/10.1145/1839764.1839771

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