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A Declarative View of Signaling Pathways

  • Davide Chiarugi
  • Moreno Falaschi
  • Carlos Olarte
  • Catuscia Palamidessi
Chapter
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9465)

Abstract

Due to the inherent limitations of wet-lab techniques, the experimental data regarding cellular signaling pathways often consider single pathways or a small subset of them. We propose a methodology for composing signaling pathways data in a coherent framework. Our method consists in specifying the signaling pathway as a computationally executable model. We rely on the timed concurrent constraint language ntcc to represent the system in hand as a set of stoichiometric-like equations resembling the essential features of molecular interactions. The main advantages of our approach stem from the use of constraints (formulas in logic) and from modeling of discrete time clocks in ntcc. We can deal with partial information, representing the fact that several features of the biological system may be undetermined. We can explicitly represent the time needed for a reaction to occur. We model and simulate some well known cross-talking networks, such as the TNF\(\alpha \), the EGF and the insulin signaling pathways as well as their interactions.

Keywords

Partial Information Insulin Signaling Pathway Concurrent System Cellular Signaling Pathway Stochastic Simulation Algorithm 
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.

Notes

Acknowledgements

We thank the anonymous referees for their helpful comments.

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Davide Chiarugi
    • 1
  • Moreno Falaschi
    • 2
  • Carlos Olarte
    • 3
  • Catuscia Palamidessi
    • 4
  1. 1.Department of Theory and Bio-SystemsMax Planck Institute for Colloids and InterfacesPotsdamGermany
  2. 2.Dipartimento di Ingegneria dell’Informazione e Scienze MatematicheUniversità di SienaSienaItaly
  3. 3.ECT, Universidade do Rio Grande do NorteNatalBrazil
  4. 4.INRIA and LIX, École PolytechniqueParisFrance

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