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.
Type de document :
Communication dans un congrès
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〉
Liste complète des métadonnées

Littérature citée [29 références]  Voir  Masquer  Télécharger
https://hal.inria.fr/hal-01613600
Contributeur : Jérôme Feret <>
Soumis le : mercredi 11 octobre 2017 - 07:45:57
Dernière modification le : lundi 15 janvier 2018 - 09:14:22
Document(s) archivé(s) le : vendredi 12 janvier 2018 - 12:44:50

Fichier

kade-tool-paper.pdf
Fichiers produits par l'(les) auteur(s)

Licence

Copyright (Tous droits réservés)

Identifiants

Collections

INRIA | PSL | INRIA2017

Citation

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〉

Exporter

BibTeX TEI DC DCterms EndNote

Partager

Métriques

Consultations de la notice

113

Téléchargements de fichiers

23

Contact


archive-ouverte@inria.fr