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Extended stochastic Petri nets for model-based design of wetlab experiments. (English) Zbl 1260.68268

Priami, Corrado (ed.) et al., Transactions on Computational Systems Biology XI. Berlin: Springer (ISBN 978-3-642-04185-3/pbk). Lecture Notes in Computer Science 5750. Lecture Notes in Bioinformatics. Journal Subline, 138-163 (2009).
Summary: 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.
For the entire collection see [Zbl 1175.92022].

MSC:

68Q85 Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.)
68Q87 Probability in computer science (algorithm analysis, random structures, phase transitions, etc.)
92-08 Computational methods for problems pertaining to biology
92C40 Biochemistry, molecular biology

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APMC; SNOOPY; INA
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References:

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