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.
|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 Berlin Heidelberg|
|Number of pages||20|
|Publication status||Published - 2008|