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Simulation of Kohn’s Molecular Interaction Maps through Translation into Stochastic CLS+

  • Roberto Barbuti
  • Daniela Lepri
  • Andrea Maggiolo-Schettini
  • Paolo Milazzo
  • Giovanni Pardini
  • Aureliano Rama
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5947)

Abstract

Kohn’s Molecular Interaction Maps (MIMs) are a graphical notation for describing bioregulatory networks at the molecular level. Even if the meaning of Kohn’s diagrams can be often easily understood, in many cases, due to the lack of a precise mathematical semantics, the notation can be ambiguous. By this paper we achieve two goals. Firstly, we give a precise meaning to MIMs by their translation into a formalism, the Stochastic Calculus of Looping Sequences (SCLS+), with a mathematical semantics. Further, by this translation we provide MIMs with all the tools developed for SCLS+, namely analysers and simulators. The ability of SCLS+ to specify compartments allows us to easily translate MIMs descriptions also when membranes are involved in the interactions.

Keywords

Parallel Composition Loop Sequence Continuous Time Markov Chain Biochemical Network Graphical Notation 
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 2010

Authors and Affiliations

  • Roberto Barbuti
    • 1
  • Daniela Lepri
    • 2
  • Andrea Maggiolo-Schettini
    • 1
  • Paolo Milazzo
    • 1
  • Giovanni Pardini
    • 1
  • Aureliano Rama
    • 1
  1. 1.Dipartimento di InformaticaUniversità di Pisa 
  2. 2.Institutt for InformatikkUniversitetet i Oslo 

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