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Title:A Language for Biochemical Systems
Authors: Michael Pedersen ; Gordon Plotkin
Date:Oct 2008
Publication Title:Computational Methods in Systems Biology
Publication Type:Conference Paper Publication Status:Published
Volume No:5307/2008 Page Nos:63-82
DOI:10.1007/978-3-540-88562-7_9 ISBN/ISSN:978-3-540-88561-0
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; it 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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Bibtex format
author = { Michael Pedersen and Gordon Plotkin },
title = {A Language for Biochemical Systems},
book title = {Computational Methods in Systems Biology},
publisher = {Springer},
year = 2008,
month = {Oct},
volume = {5307/2008},
pages = {63-82},
doi = {10.1007/978-3-540-88562-7_9},
url = {},

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