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Bio-PEPA with Events

  • Federica Ciocchetta
Part of the Lecture Notes in Computer Science book series (LNCS, 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.

Keywords

Hybrid System Stochastic Simulation Functional Rate Jump Condition Simultaneous Event 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Federica Ciocchetta
    • 1
  1. 1.Laboratory for Foundations of Computer ScienceThe University of EdinburghEdinburghScotland

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