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Bio-PEPA with Events

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Transactions on Computational Systems Biology XI

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

Abstract

In this work we present an extension of Bio-PEPA, a language recently defined for the modelling and analysis of biochemical systems, to handle events. Events are constructs that represent changes in the system due to some trigger conditions. The events considered here are simple, but nevertheless able to describe most of the discontinuous changes in models and experiments.

Events are added to our language without any modification to the rest of the syntax in order to keep the specification of the model as straightforward as possible. Some maps are defined from Bio-PEPA with events to analysis tools. Specifically, we map our language to Hybrid Automata (HA) and we consider a modification of Gillespie’s algorithm for stochastic simulation. In order to test our approach, we present the translation in Bio-PEPA of a biochemical network describing the functional properties of the Acetylcholine receptor with the addition of an event that causes the inactivation of some reactions at a given time.

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Author information

Authors and Affiliations

  1. Laboratory for Foundations of Computer Science, The University of Edinburgh, Edinburgh, EH8 9AB, Scotland

    Federica Ciocchetta

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  1. Federica Ciocchetta
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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, Åbo 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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Ciocchetta, F. (2009). Bio-PEPA with Events. 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_3

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  • DOI: https://doi.org/10.1007/978-3-642-04186-0_3

  • 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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