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Modelling biological compartments in bio-PEPA. (English) Zbl 1348.92069
Ciobanu, Gabriel (ed.), Proceedings of the 2nd international meeting on membrane computing and biologically inspired process calculi (MeCBIC 2008), Iaşi, Romania, September 3–4, 2008. Amsterdam: Elsevier. Electronic Notes in Theoretical Computer Science 227, 77-95 (2009).
Summary: 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 \(\mathrm{Ca}^{2+}\) oscillations.
For the entire collection see [Zbl 1279.68011].

92C42 Systems biology, networks
68Q85 Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.)
Full Text: DOI
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