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Erschienen in:
2008 | OriginalPaper | Buchkapitel
Cells in Silico: A Holistic Approach
verfasst von : Davide Chiarugi, Pierpaolo Degano, Jan Bert Van Klinken, Roberto Marangoni
Erschienen in: Formal Methods for Computational Systems Biology
Verlag: Springer Berlin Heidelberg
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This paper reports on our experience in modelling whole cells with process calculi. We followed a holistic approach, aiming at investigating the behaviour of biological objects at the system level, in particular of a hypothetical and a of real prokaryote. These cells, namely VICE and
Escherichia coli
, have been specified through the
π
-calculus, endowed with a stochastic semantics. We describe a couple of variants of the
π
-calculus and briefly survey three interpreters of it, with increasing efficiency. We show how the usage of tools based on process calculi greatly helped us in designing the virtual cell VICE, and in comparing it with other prposals. The main properties of the
in silico
experiments on VICE and on
Escherichia coli
are then discussed and shown in agreement with those of real prokaryoptes acting
in vivo/vitro
.