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Bio-PEPA with events. (English) Zbl 1260.92021
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, 45-68 (2009).
Summary: 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 simulations. 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.
For the entire collection see [Zbl 1175.92022].

MSC:
92C40 Biochemistry, molecular biology
92-04 Software, source code, etc. for problems pertaining to biology
92C45 Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.)
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