2015
DOI: 10.1371/journal.pone.0114296
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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 sign… Show more

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Cited by 10 publications
(4 citation statements)
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“…196 In collaborative model development, approaches used in computer programming are likely to prove useful because teams of programmers routinely write, maintain, and extend complex codes. Two products of recent efforts to bring software engineering concepts to modeling in systems biology are PySB 152 and LBSκ, 197 which are tools designed to ease the specification of models. A model specified using PySB takes the form of a Python-language program, which can be executed to obtain models in other formats and to direct simulations and analyses.…”
Section: High-level Modeling Languagesmentioning
confidence: 99%
“…196 In collaborative model development, approaches used in computer programming are likely to prove useful because teams of programmers routinely write, maintain, and extend complex codes. Two products of recent efforts to bring software engineering concepts to modeling in systems biology are PySB 152 and LBSκ, 197 which are tools designed to ease the specification of models. A model specified using PySB takes the form of a Python-language program, which can be executed to obtain models in other formats and to direct simulations and analyses.…”
Section: High-level Modeling Languagesmentioning
confidence: 99%
“…PySB transforms the Python code into either BioNetGen or Kappa rules, and provides methods that make it easier to create macros that encode recurrent biochemical patterns and to define complex networks as reusable modules. Pedersen et al [53] also introduce a modular extension to Kappa that provides a means for writing modular rule-based models.…”
Section: Biological Modelingmentioning
confidence: 99%
“…The main examples of rule-based languages are: BNGL [10] and Kappa [9] supporting the detailed expression of molecule binding; Chromar [18] associating objects with physical attributes allowing to describe observed system quantities; rxncon [6,19] focusing on regulatory interactions and allowing construction of rules from experimental evidence; LBS [20] and LBS-κ [21] enriching rule-based framework with modularity; PySB [22] embedding BNGL into Python; BioCHAM [23] explicitly separating rules from their mathematical semantics. An important work is ML-rules [24], which allows linkage of species with unique values in a highly flexible manner (e.g.…”
Section: Introductionmentioning
confidence: 99%