Design Issues for Qualitative Modelling of Biological Cells with Petri Nets

  • Elzbieta Krepska
  • Nicola Bonzanni
  • Anton Feenstra
  • Wan Fokkink
  • Thilo Kielmann
  • Henri Bal
  • Jaap Heringa
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5054)


Petri nets are a widely used formalism to qualitatively model concurrent systems such as a biological cell. We present techniques for modelling biological processes as Petri nets for further analyses and in-silico experiments. Instead of extending the formalism with ,,colours” or rates, as is most often done, we focus on preserving the simplicity of the formalism and developing an execution semantics which resembles biology – we apply a principle of maximal parallelism and introduce the novel concept of bounded execution with overshooting. A number of modelling solutions are demonstrated using the example of the well-studied C. elegans vulval development process. To date our model is still under development, but first results, based on Monte Carlo simulations, are promising.


Biological Cell Boolean Network Lateral Signal Qualitative Modelling Anchor Cell 
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 2008

Authors and Affiliations

  • Elzbieta Krepska
    • 1
  • Nicola Bonzanni
    • 1
  • Anton Feenstra
    • 1
  • Wan Fokkink
    • 1
  • Thilo Kielmann
    • 1
  • Henri Bal
    • 1
  • Jaap Heringa
    • 1
  1. 1.Department of Computer ScienceVrije UniversiteitAmsterdamThe Netherlands

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