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.

• Type: Conference
• Year: 2008
• Where: CMSB
• Authors: Michael Pedersen, Gordon D. Plotkin
• Keywords: Applied Computing, Biochemical Systems, CMSB 2008, Coloured Petri Nets, Yeast Pheromone Pathway