Modelling Biological Compartments in Bio-PEPA

  • Authors:

  • Federica Ciocchetta;Maria Luisa Guerriero

  • Affiliations:

  • Laboratory for Foundations of Computer Science, The University of Edinburgh, Edinburgh EH8 9AB, Scotland;Laboratory for Foundations of Computer Science, The University of Edinburgh, Edinburgh EH8 9AB, Scotland

  • Venue:
  • Electronic Notes in Theoretical Computer Science (ENTCS)
  • Year:
  • 2009

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Abstract

Compartments and membranes play an important role in cell biology. Therefore it is highly desirable to be able to represent them in modelling languages for biology. Bio-PEPA is a language for the modelling and analysis of biochemical networks; in its present version compartments can be defined but they are only used as labels to express the location of molecular species. In this work we present an extension of Bio-PEPA with some features in order to represent more details about locations of species and reactions. With the term location we mean either a membrane or a compartment. We describe how models involving compartments and membranes can be expressed in the language and, consequently, analysed. We limit our attention to static locations (i.e. with a fixed structure) whose size can depend on time. We illustrate our approach via a classical model used to represent intracellular Ca^2^+ oscillations.