A Language for Biochemical Systems

  • Authors:

  • Michael Pedersen;Gordon Plotkin

  • Affiliations:

  • LFCS, School of Informatics, University of Edinburgh,;LFCS, School of Informatics, University of Edinburgh,

  • Venue:
  • CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
  • Year:
  • 2008

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Abstract

CBS is a Calculus of Biochemical Systemsintended 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.