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Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments

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Transactions on Computational Systems Biology XI

Part of the book series: Lecture Notes in Computer Science ((TCSB,volume 5750))

Abstract

This paper introduces extended stochastic Petri nets to model wetlab experiments. The extentions include read and inhibitor arcs, stochastic transitions with freestyle rate functions as well as several deterministically timed transition types: immediate firing, deterministic firing delay, and scheduled firing. The extensions result into non-Markovian behaviour, which precludes analytical analysis approaches. But there are adapted stochastic simulation analysis (SSA) methods, ready to deal with the extended behaviour. Having the simulation traces, we apply simulative model checking of PLTL, a linear-time temporal logic (LTL) in a probabilistic setting.

We present some typical model components, demonstrating the suitability of the introduced Petri net class for the envisaged application scenario. We conclude by looking briefly at a classical example of prokaryotic gene regulation, the lac operon case.

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Author information

Authors and Affiliations

  1. Department of Computer Science, Brandenburg University of Technology, Postbox 10 13 44, 03013, Cottbus, Germany

    Monika Heiner & Sebastian Lehrack

  2. School of Information Systems, Computing and Mathematics, Brunel University, Uxbridge, Middlesex, UB8 3PH, UK

    David Gilbert

  3. Otto von Guericke University & Magdeburg Centre for Systems Biology c/o Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany

    Wolfgang Marwan

Authors
  1. Monika Heiner
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  2. Sebastian Lehrack
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  3. David Gilbert
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  4. Wolfgang Marwan
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Editor information

Editors and Affiliations

  1. Centre for Computational and Systems Biology, The Microsoft Research - University of Trento, Piazza Manci, 17, 38050, Povo, (TN), Italy

    Corrado Priami

  2. Department of Information Technologies, Ã…bo Akademi University, FI-20520, Turku, Finland

    Ralph-Johan Back

  3. Computational Biomodelling Laboratory, Turku Center for Computer Science, FIN-20520, Turku, Finland

    Ion Petre

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Heiner, M., Lehrack, S., Gilbert, D., Marwan, W. (2009). Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments. In: Priami, C., Back, RJ., Petre, I. (eds) Transactions on Computational Systems Biology XI. Lecture Notes in Computer Science(), vol 5750. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04186-0_7

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  • DOI: https://doi.org/10.1007/978-3-642-04186-0_7

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-04185-3

  • Online ISBN: 978-3-642-04186-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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