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Quantitative Pathway Logic for Computational Biology

  • Michele Baggi
  • Demis Ballis
  • Moreno Falaschi
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5688)

Abstract

This paper presents an extension of Pathway Logic, called Quantitative Pathway Logic (QPL), which allows one to reason about quantitative aspects of biological processes, such as element concentrations and reactions kinetics. Besides, it supports the modeling of inhibitors, that is, chemicals which may block a given reaction whenever their concentration exceeds a certain threshold. QPL models can be specified and directly simulated using rewriting logic or can be translated into Discrete Functional Petri Nets (DFPN) which are a subclass of Hybrid Functional Petri Nets in which only discrete transitions are allowed. Under some constraints over the anonymous variables appearing in the QPL models, the transformation between the two computational models is shown to preserve computations. By using the DFPN representation our models can be graphically visualized and simulated by means of well known tools (e.g. Cell Illustrator); moreover standard Petri net analyses (e.g. topological analysis, forward/backward reachability, etc.) may be performed on the net model. An executable framework for QPL and for the translation of QPL models into DFPNs has been implemented using the rewriting-based language Maude. We have tested this system on several examples.

Keywords

Cell State Linear Temporal Logic Discrete Transition Forward Simulation Input Connector 
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 2009

Authors and Affiliations

  • Michele Baggi
    • 1
  • Demis Ballis
    • 2
  • Moreno Falaschi
    • 1
  1. 1.Dip. di Scienze Matematiche e InformaticheSienaItaly
  2. 2.Dip. Matematica e InformaticaUdineItaly

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