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Design Issues for Qualitative Modelling of Biological Cells with Petri Nets

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Formal Methods in Systems Biology (FMSB 2008)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5054))

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Abstract

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.

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Authors and Affiliations

  1. Department of Computer Science, Vrije Universiteit, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands

    Elzbieta Krepska, Nicola Bonzanni, Anton Feenstra, Wan Fokkink, Thilo Kielmann, Henri Bal & Jaap Heringa

Authors
  1. Elzbieta Krepska
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  2. Nicola Bonzanni
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  3. Anton Feenstra
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  4. Wan Fokkink
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  5. Thilo Kielmann
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  6. Henri Bal
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  7. Jaap Heringa
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Editor information

Jasmin Fisher

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© 2008 Springer-Verlag Berlin Heidelberg

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Krepska, E. et al. (2008). Design Issues for Qualitative Modelling of Biological Cells with Petri Nets. In: Fisher, J. (eds) Formal Methods in Systems Biology. FMSB 2008. Lecture Notes in Computer Science(), vol 5054. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-68413-8_4

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  • DOI: https://doi.org/10.1007/978-3-540-68413-8_4

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-68410-7

  • Online ISBN: 978-3-540-68413-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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