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Natural Computing

, 8:865 | Cite as

Rule-based programming for integrative biological modeling

Application to the modeling of the λ phage genetic switch
  • Olivier Michel
  • Antoine Spicher
  • Jean-Louis Giavitto
Article

Abstract

Systems biology aims at integrating processes at various time and spatial scales into a single and coherent formal description to allow computer modeling. In this context, we focus on rule-based modeling and its integration in the domain-specific language MGS . Through the notions of topological collections and transformations, MGS allows the modeling of biological processes at various levels of description. We validate our approach through the description of various models of the genetic switch of the λ phage, from a very simple biochemical description of the process to an individual-based model on a Delaunay graph topology. This approach is a first step into providing the requirements for the emerging field of spatial systems biology which integrates spatial properties into systems biology.

Keywords

Domain-specific languages Rule-based modeling Spatial systems biology 

Notes

Acknowledgments

The authors gratefully acknowledge the reviewers for their valuable comments on a first version of this article.

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Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Olivier Michel
    • 1
  • Antoine Spicher
    • 1
  • Jean-Louis Giavitto
    • 2
  1. 1.LACL – EA 4213, Faculté des Sciences et TechnologieUniversité de Paris 12Creteil CedexFrance
  2. 2.IBISC Lab. - FRE 3190 CNRSUniversité d’Évry & GenopoleEvryFrance

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