Temporal Logic Modeling of Biological Systems

  • Jean-Marc Alliot
  • Robert Demolombe
  • Martín Diéguez
  • Luis Fariñas del CerroEmail author
  • Gilles Favre
  • Jean-Charles Faye
  • Naji Obeid
  • Olivier Sordet
Part of the Intelligent Systems Reference Library book series (ISRL, volume 110)


Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of these reactions. Cancer, for example, can sometimes appear in a cell as a result of some pathology in a metabolic pathway. Most of these pathways are formed by an intricate and complex network of chain reactions, and can be represented in a human readable form using graphs which describe the cell signaling pathways. In this paper, we define a logic, called Molecular Interaction Logic (MIL), able to represent these graphs and we present a method to automatically translate graphs into MIL formulas. Then we show how MIL formulas can be translated into linear time temporal logic, and then grounded into propositional classical logic. This enables us to solve complex queries on graphs using only propositional classical reasoning tools such as SAT solvers.


Metabolic networks Molecular interaction logic (MIL) Temporal reasoning 



This work is partially supported by ANR-11-LABX-0040-CIMI within the program ANR-11-IDEX-0002-02, by IREP Associated European Laboratory and by project CLE from Région Midi-Pyrénées.


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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Jean-Marc Alliot
    • 1
  • Robert Demolombe
    • 1
  • Martín Diéguez
    • 1
  • Luis Fariñas del Cerro
    • 1
    Email author
  • Gilles Favre
    • 1
  • Jean-Charles Faye
    • 1
  • Naji Obeid
    • 1
  • Olivier Sordet
    • 1
  1. 1.INSERM/IRITUniversity of ToulouseToulouseFrance

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