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Erschienen in:
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2015 | OriginalPaper | Buchkapitel

A Declarative View of Signaling Pathways

verfasst von : Davide Chiarugi, Moreno Falaschi, Carlos Olarte, Catuscia Palamidessi

Erschienen in: Programming Languages with Applications to Biology and Security

Verlag: Springer International Publishing

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Abstract

Due to the inherent limitations of wet-lab techniques, the experimental data regarding cellular signaling pathways often consider single pathways or a small subset of them. We propose a methodology for composing signaling pathways data in a coherent framework. Our method consists in specifying the signaling pathway as a computationally executable model. We rely on the timed concurrent constraint language ntcc to represent the system in hand as a set of stoichiometric-like equations resembling the essential features of molecular interactions. The main advantages of our approach stem from the use of constraints (formulas in logic) and from modeling of discrete time clocks in ntcc. We can deal with partial information, representing the fact that several features of the biological system may be undetermined. We can explicitly represent the time needed for a reaction to occur. We model and simulate some well known cross-talking networks, such as the TNF\(\alpha \), the EGF and the insulin signaling pathways as well as their interactions.

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Fußnoten
1
This is the more general case. It may happen that the consumption of a reactant does not lead to the production of other molecules or that, as in the case of enzymes, a molecule takes part to a reaction but is not consumed by it.
 
2
Proteins are composed by chains of aminoacyds. For biochemical reasons, aminoacyds are often called residues.
 
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Metadaten
Titel
A Declarative View of Signaling Pathways
verfasst von
Davide Chiarugi
Moreno Falaschi
Carlos Olarte
Catuscia Palamidessi
Copyright-Jahr
2015
Buch
Programming Languages with Applications to Biology and Security

Print ISBN: 978-3-319-25526-2

Electronic ISBN: 978-3-319-25527-9

Copyright-Jahr: 2015

DOI
https://doi.org/10.1007/978-3-319-25527-9_13