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 language | English |
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Title of host publication | Computational Methods in Systems Biology |
Subtitle of host publication | 6th International Conference, CMSB 2008, Rostock, Germany, October 12-15, 2008. Proceedings |
Publisher | Springer |
Pages | 63-82 |
Number of pages | 20 |
Volume | 5307 |
ISBN (Electronic) | 978-3-540-88562-7 |
ISBN (Print) | 978-3-540-88561-0 |
DOIs | |
Publication status | Published - 2008 |