title: A high-level language for rule-based modelling.
abstract: Rule-based languages such as Kappa excel in their support for handling the combinatorial complexities prevalent in many biological systems, including signalling pathways. But Kappa provides little structure for organising rules, and large models can therefore be hard to read and maintain. This paper introduces a high-level, modular extension of Kappa called LBS-κ. We demonstrate the constructs of the language through examples and three case studies: a chemotaxis switch ring, a MAPK cascade, and an insulin signalling pathway. We then provide a formal definition of LBS-κ through an abstract syntax and a translation to plain Kappa. The translation is implemented in a compiler tool which is available as a web application. We finally demonstrate how to increase the expressivity of LBS-κ through embedded scripts in a general-purpose programming language, a technique which we view as generally applicable to other domain specific languages.
authors.affiliation: Department of Plant Sciences, Cambridge University, Cambridge, England; Biological Computation Group, Microsoft Research, Cambridge, England.
authors.forename: Michael
authors.initials: M
authors.lastname: Pedersen
authors.affiliation: Biological Computation Group, Microsoft Research, Cambridge, England.
authors.forename: Andrew
authors.initials: A
authors.lastname: Phillips
authors.affiliation: Laboratory for Foundations of Computer Science, School of Informatics, Edinburgh University, Edinburgh, Scotland.
authors.forename: Gordon D
authors.initials: GD
authors.lastname: Plotkin
mesh_terms: D000818:Animals; D003198:Computer Simulation; D006801:Humans; D020935:MAP Kinase Signaling System; D008954:Models, Biological; D011381:Programming Languages