KaDE: A Tool to Compile Kappa Rules into (Reduced) ODE Models

Ferdinanda Camporesi 1 Jérôme Feret 1 Kim Quyen Ly 1
1 ANTIQUE - Analyse Statique par Interprétation Abstraite
DI-ENS - Département d'informatique de l'École normale supérieure, Inria de Paris
Abstract : Kappa is a formal language that can be used to model sys- tems of biochemical interactions among proteins. It offers several se- mantics to describe the behaviour of Kappa models at different levels of abstraction. Each Kappa model is a set of context-free rewrite rules. One way to understand the semantics of a Kappa model is to read its rules as an implicit description of a (potentially infinite) reaction net- work. KaDE is interpreting this definition to compile Kappa models into reaction networks (or equivalently into sets of ordinary differential equations). KaDE uses a static analysis that identifies pairs of sites that are indistinguishable from the rules point of view, to infer backward and forward bisimulations, hence reducing the size of the underlying reaction networks without having to generate them explicitly. In this paper, we describe the main current functionalities of KaDE and we give some benchmarks on case studies.
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Jérôme Feret; Heinz Koeppl. CMSB 2017 - 15th Conference on Computational Methods in Systems Biology, Sep 2017, Darmstadt, Germany. Springer, LNCS/LNBI, 10545, pp.291-299, 2017, Computational Methods in Systems Biology. 〈http://www.etit.tu-darmstadt.de/cmsb2017/cmsb_2/home/index.en.jsp〉. 〈10.1007/978-3-319-67471-1_18〉
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Ferdinanda Camporesi, Jérôme Feret, Kim Quyen Ly. KaDE: A Tool to Compile Kappa Rules into (Reduced) ODE Models. Jérôme Feret; Heinz Koeppl. CMSB 2017 - 15th Conference on Computational Methods in Systems Biology, Sep 2017, Darmstadt, Germany. Springer, LNCS/LNBI, 10545, pp.291-299, 2017, Computational Methods in Systems Biology. 〈http://www.etit.tu-darmstadt.de/cmsb2017/cmsb_2/home/index.en.jsp〉. 〈10.1007/978-3-319-67471-1_18〉. 〈hal-01613600〉

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