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A Domain Specific Language Approach for Genetic Regulatory Mechanisms Analysis

  • Nicolas Sedlmajer
  • Didier Buchs
  • Steve Hostettler
  • Alban Linard
  • Edmundo López Bóbeda
  • Alexis Marechal
Chapter
Part of the Lecture Notes in Computer Science book series (LNCS, 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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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Nicolas Sedlmajer
    • 1
  • Didier Buchs
    • 1
  • Steve Hostettler
    • 1
  • Alban Linard
    • 1
  • Edmundo López Bóbeda
    • 1
  • Alexis Marechal
    • 1
  1. 1.Université de GenèveCarougeSwitzerland

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