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Erschienen in:
2018 | OriginalPaper | Buchkapitel
KaSa: A Static Analyzer for Kappa
verfasst von : Pierre Boutillier, Ferdinanda Camporesi, Jean Coquet, Jérôme Feret, Kim Quyên Lý, Nathalie Theret, Pierre Vignet
Erschienen in: Computational Methods in Systems Biology
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Abstract
KaSa is a static analyzer for Kappa models. Its goal is two-fold. Firstly, KaSa assists the modeler by warning about potential issues in the model. Secondly, KaSa may provide useful properties to check that what is implemented is what the modeler has in mind and to provide a quick overview of the model for the people who have not written it.
The cornerstone of KaSa is a fix-point engine which detects some patterns that may never occur whatever the evolution of the system may be. From this, many useful information may be collected: KaSa warns about rules that may never be applied, about potential irreversible transformations of proteins (that may not be reverted even thanks to an arbitrary number of computation steps) and about the potential formation of unbounded molecular compounds. Lastly, KaSa detects potential influences (activation/inhibition relation) between rules.
In this paper, we illustrate the main features of KaSa on a model of the extracellular activation of the transforming growth factor, TGF-b.