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Transactions on Petri Nets and Other Models of Concurrency VI pp 123–145Cite as

A Domain Specific Language Approach for Genetic Regulatory Mechanisms Analysis

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Part of the Lecture Notes in Computer Science book series (TOPNOC,volume 7400)

Abstract

Systems biology and synthetic biology can be considered as model-driven methodologies. In this context, models are used to discover emergent properties arising from the complex interactions between components. Most available tools propose simulation frameworks to study models of biological systems. Simulation only explores a limited number of behaviors of these models. This may lead to a biased view of the system. On the contrary, model checking explores all the possible behaviors. The use of model checking in the domain of life sciences is limited. It suffers from the complexity of modeling languages designed by and for computer scientists. This article describes an approach based on Domain Specific Languages. It provides a comprehensible, yet formal, language called GReg to describe genetic regulatory mechanisms and their properties, and to apply powerful model checking techniques on them. GReg’s objective is to shelter the user from the complexity of those underlying techniques.

Keywords

  • Model Check
  • Synthetic Biology
  • System Biology Markup Language
  • Concrete Syntax
  • Genetic Regulatory Network

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Authors and Affiliations

  1. Université de Genève, 7 route de Drize, 1227, Carouge, Switzerland

    Nicolas Sedlmajer, Didier Buchs, Steve Hostettler, Alban Linard, Edmundo López Bóbeda & Alexis Marechal

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  1. Nicolas Sedlmajer
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  2. Didier Buchs
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  3. Steve Hostettler
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  4. Alban Linard
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  5. Edmundo López Bóbeda
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  6. Alexis Marechal
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Editor information

Editors and Affiliations

  1. Faculty of Science, Department of Computer Science, University of Aarhus, IT-parken, Aabogade 34, 8200, Aarhus N, Denmark

    Kurt Jensen

  2. Department of Mathematics and Computer Science, Eindhoven University of Technology, P.O. Box 513, NL-5600, Eindhoven, MB, The Netherland

    Wil M. van der Aalst

  3. Dipartimento di Elettronica e Telecomunicazioni, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Torino, Italy

    Marco Ajmone Marsan

  4. Dipartimento di Informatica, Università del Piemonte Orientale ”Amedeo Avogadro”, Viale T. Michel 11, 15121, Alessandria, Italy

    Giuliana Franceschinis

  5. Leiden Institute of Advanced Computer Science, LIACS, P.O. Box 9512, 2300, Leiden, RA, The Netherlands

    Jetty Kleijn

  6. Department of Computer Engineering, Faculty of Engineering, Bergen University College, Nygaardsgaten 112, Postbox 7030, 5020, Bergen, Norway

    Lars Michael Kristensen

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Sedlmajer, N., Buchs, D., Hostettler, S., Linard, A., López Bóbeda, E., Marechal, A. (2012). A Domain Specific Language Approach for Genetic Regulatory Mechanisms Analysis. In: Jensen, K., van der Aalst, W.M., Ajmone Marsan, M., Franceschinis, G., Kleijn, J., Kristensen, L.M. (eds) Transactions on Petri Nets and Other Models of Concurrency VI. Lecture Notes in Computer Science, vol 7400. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-35179-2_6

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  • DOI: https://doi.org/10.1007/978-3-642-35179-2_6

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