Logical Modeling and Analysis of Regulatory Genetic Networks in a Non Monotonic Framework

  • Nicolas Mobilia
  • Alexandre Rocca
  • Samuel Chorlton
  • Eric Fanchon
  • Laurent Trilling
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9043)

Abstract

We present a constraint based declarative approach for analyzing qualitatively genetic regulatory networks (GRNs) with the discrete formalism of R. Thomas. For this purpose, we use the logic programming technology ASP (Answer Set Programming) whose related logic is non monotonic. Our aim is twofold. First, we give a formal modeling of both Thomas’ GRNs and biological data like experimental behaviors and gene interactions and we evaluate the declarative approach on three real biological applications. Secondly, for taking into account both gene interaction properties which are only generally true and automatic inconsistency repairing, we introduce an optimized modeling which leads us to exhibit new logical expressions for the conjunction of defaults and to show that they can be applied safely to Thomas’ GRNs.

Keywords

computational systems biology gene networks discrete modeling AI-oriented declarative approach non monotonic logic Answer Set Programming 

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Nicolas Mobilia
    • 1
  • Alexandre Rocca
    • 1
  • Samuel Chorlton
    • 2
  • Eric Fanchon
    • 1
  • Laurent Trilling
    • 1
  1. 1.Laboratoire TIMC-IMAGUniversité de GrenobleFrance
  2. 2.Department of MedicineMcMaster UniversityHamiltonCanada

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