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

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Computational Methods in Systems Biology (CMSB 2017)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 10545))

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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.

This material is based upon works partially sponsored by the Defense Advanced Research Projects Agency (DARPA) and the U. S. Army Research Office under grant number W911NF-14-1-0367, and by the ITMO Plan Cancer 2014. The views, opinions, and/or findings contained in this article are those of the authors and should not be interpreted as representing the official views or policies, either expressed or implied, of DARPA, the U.S. Department of Defense, or ITMO.

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Authors and Affiliations

  1. INRIA, École normale supérieure, CNRS, PSL Research University, 75005, Paris, France

    Ferdinanda Camporesi, Jérôme Feret & Kim Quyên Lý

  2. Département d’informatique de l’ÉNS, École normale supérieure, CNRS, PSL Research University, 75005, Paris, France

    Ferdinanda Camporesi, Jérôme Feret & Kim Quyên Lý

Authors
  1. Ferdinanda Camporesi
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  2. Jérôme Feret
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  3. Kim Quyên Lý
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Correspondence to Jérôme Feret .

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Editors and Affiliations

  1. Inria & École normale supérieure, Paris, France

    Jérôme Feret

  2. Technische Universität Darmstadt, Darmstadt, Germany

    Heinz Koeppl

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Camporesi, F., Feret, J., Lý, K.Q. (2017). KaDE: A Tool to Compile Kappa Rules into (Reduced) ODE Models. In: Feret, J., Koeppl, H. (eds) Computational Methods in Systems Biology. CMSB 2017. Lecture Notes in Computer Science(), vol 10545. Springer, Cham. https://doi.org/10.1007/978-3-319-67471-1_18

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  • DOI: https://doi.org/10.1007/978-3-319-67471-1_18

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