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Petri Nets for Systems and Synthetic Biology

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Formal Methods for Computational Systems Biology (SFM 2008)

Part of the book series: Lecture Notes in Computer Science ((LNPSE,volume 5016))

Abstract

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which unifies the qualitative, stochastic and continuous paradigms. Each perspective adds its contribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how qualitative descriptions are abstractions over stochastic or continuous descriptions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks.

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Authors and Affiliations

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

    Monika Heiner

  2. Bioinformatics Research Centre, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK

    David Gilbert & Robin Donaldson

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  1. Monika Heiner
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  2. David Gilbert
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  3. Robin Donaldson
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Marco Bernardo Pierpaolo Degano Gianluigi Zavattaro

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Heiner, M., Gilbert, D., Donaldson, R. (2008). Petri Nets for Systems and Synthetic Biology. In: Bernardo, M., Degano, P., Zavattaro, G. (eds) Formal Methods for Computational Systems Biology. SFM 2008. Lecture Notes in Computer Science, vol 5016. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-68894-5_7

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  • DOI: https://doi.org/10.1007/978-3-540-68894-5_7

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