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

  • Ferdinanda Camporesi
  • Jérôme FeretEmail author
  • Kim Quyên Lý
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10545)

Abstract

Kappa is a formal language that can be used to model systems of biochemical interactions among proteins. It offers several semantics 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 network. 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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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Ferdinanda Camporesi
    • 1
    • 2
  • Jérôme Feret
    • 1
    • 2
    Email author
  • Kim Quyên Lý
    • 1
    • 2
  1. 1.INRIAÉcole normale supérieure, CNRS, PSL Research UniversityParisFrance
  2. 2.Département d’informatique de l’ÉNSÉcole normale supérieure, CNRS, PSL Research UniversityParisFrance

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