A high-level language for rule-based modelling.
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ABSTRACT:
SUBMITTER: Pedersen M
PROVIDER: S-EPMC4456403 | biostudies-literature | 2015
REPOSITORIES: biostudies-literature
Publications
A high-level language for rule-based modelling.
Pedersen Michael M Phillips Andrew A Plotkin Gordon D GD
PloS one 20150604 6
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 ...[more]
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