Compositional modelling of signalling pathways in timed concurrent constraint programming

Authors:
Davide Chiarugi;Moreno Falaschi;Carlos Olarte;Catuscia Palamidessi
Affiliations:
Università di Siena, Italy;Università di Siena, Italy;Universidad Javeriana, Cali, Colombia;INRIA and LIX, Ecole, Polytechnique, France
Venue:
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Year:
2010

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Abstract

The biological data regarding the signalling pathways often consider single pathways or a small number of them. We propose a methodology for composing this kind of data in a coherent framework, in order to be able to investigate a bigger number of signalling pathways. We specify a biological system by means of a set of stoichiometric-like equations resembling the essential features of molecular interactions. We represent these equations by a timed concurrent constraint (ntcc) language, which can deal with partial information and the time for a reaction to occur. We describe a freely available prototypical implementation of our framework.