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

  • Authors:

  • Monika Heiner;Sebastian Lehrack;David Gilbert;Wolfgang Marwan

  • Affiliations:

  • Department of Computer Science, Brandenburg University of Technology, Cottbus, Germany 03013;Department of Computer Science, Brandenburg University of Technology, Cottbus, Germany 03013;School of Information Systems, Computing and Mathematics, Brunel University, Uxbridge, Middlesex, UK UB8 3PH;Otto von Guericke University & Magdeburg Centre for Systems Biology c/o Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany 39106

  • Venue:
  • Transactions on Computational Systems Biology XI
  • Year:
  • 2009

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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.