Compositional modelling of signalling pathways in timed concurrent constraint programming

Davide Chiarugi (1) , Moreno Falaschi (1) , Carlos Olarte (2) , Catuscia Palamidessi (3)

1 DSMI - Department of Mathematics and Computer Science / Dipartimento di Scienze Matematiche e Informatiche "Roberto Magari"
2 AVISPA Resarch Group - Ambientes VISuales de Progamación Aplicativa
3 COMETE - Concurrency, Mobility and Transactions

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.

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]

Davide Chiarugi, Moreno Falaschi, Carlos Olarte, Catuscia Palamidessi. Compositional modelling of signalling pathways in timed concurrent constraint programming. First ACM International Conference on Bioinformatics and Computational Biology (BCB '10)., Aug 2010, Niagara Falls, New York, United States. pp.414-417, ⟨10.1145/1854776.1854843⟩. ⟨hal-00548213⟩