Français Anglais
Accueil Annuaire Plan du site
Accueil > Evenements > Séminaires
Séminaire d'équipe(s)
A Rule-based driven knowledge representation model for signalling networks
Adrien Basso-Blandin

17 December 2015, 14h30
Salle/Bat : 465/PCRI-N
Contact :

Activités de recherche : Biologie des systèmes

Résumé :
The study of cellular signalling pathways and their deregulation in disease states, such as cancer, is a large and extremely complex task. Indeed, these systems involve many parts and processes but are studied piecewise and their literatures and data are consequently fragmented, distributed and sometimes—at least apparently—inconsistent. This makes it extremely difficult to build significant explanatory models with the result that effects in these systems that are brought about by many interacting factors are poorly understood. The rule-based approach to modelling has shown some promise for the representation of the highly combinatorial systems typically found in signalling where many of the proteins are composed of multiple binding domains, capable of simultaneous interactions, and/or peptide motifs controlled by post-translational modifications. However, the rule-based approach requires highly detailed information about the precise conditions for each and every interaction which is rarely available from any one single source. Rather, these conditions must be painstakingly inferred and curated, by hand, from information contained in many papers—each of which contains only part of the story. We introduce a graph-based meta-model, attuned to the representation of cellular signalling networks, which aims to ease this massive cognitive burden on the rule-based curation process. This meta-model is a generalization of that used by Kappa and BNGL which allows for the flexible representation of knowledge at various levels of granularity. In particular, it allows us to deal with information which has either too little, or too much, detail with respect to the strict rule-based meta-model. Our approach provides a basis for the gradual aggregation of fragmented biological knowledge extracted from the literature into an instance of the meta-model from which we can define an automated translation into executable Kappa programs.

Pour en savoir plus : https://bioinfo.lri.fr/seminars/2015-12-17-basso-blandin.html
Séminaires
Some recent results on the integer linear programm
Théorie des graphes
Friday 30 November 2018 - 00h00
Salle : 445 - PCRI-N
Hung Nguyen .............................................

Maximum Independent Set in H-free graphs
Théorie des graphes
Friday 05 October 2018 - 14h30
Salle : 445 - PCRI-N
Edouard BONNET .............................................

A Family of Tractable Graph Distances
Gestion de données du Web
Wednesday 04 July 2018 - 10h30
Salle : 465 - PCRI-N
Stratis Ioannidis .............................................

Binary pattern of length greater than 14 are abeli
Combinatoire
Friday 29 June 2018 - 14h30
Salle : 445 - PCRI-N
Matthieu Rosenfeld .............................................

Distributionally Robust Optimization with Principa
Optimisation combinatoire et stochastique
Friday 29 June 2018 - 11h00
Salle : 455 - PCRI-N
Dr. Jianqiang Cheng .............................................