A Language for Biochemical Systems

10 years 3 months ago
A Language for Biochemical Systems
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 specificaLBS 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.
Michael Pedersen, Gordon D. Plotkin
Added 18 Oct 2010
Updated 18 Oct 2010
Type Conference
Year 2008
Where CMSB
Authors Michael Pedersen, Gordon D. Plotkin
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