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How Might Petri Nets Enhance Your Systems Biology Toolkit

  • Monika Heiner
  • David Gilbert
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6709)

Abstract

“How might Petri nets enhance my Systems Biology toolkit?” – this is one of the questions that we get on a regular basis, which motivated us to write an answer in the form of this paper.

We discuss the extent to which the Petri net approach can be used as an umbrella formalism to support the process of BioModel Engineering. This includes the facilitation of an active and productive interaction between biomodellers and bioscientists during the construction and analysis of dynamic models of biological systems. These models play a crucial role in both Systems Biology, where they can be explanatory and predictive, and synthetic biology, where they are effectively design templates. In this paper we give an overview of the tools and techniques which have been shown to be useful so far, and describe some of the current open challenges.

Keywords

BioModel Engineering Systems Biology synthetic biology biomolecular networks qualitative stochastic and continuous Petri nets model checking 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Monika Heiner
    • 1
  • David Gilbert
    • 1
  1. 1.School of Information Systems, Computing and MathematicsBrunel UniversityUxbridgeUK

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