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news:summary [06/10/2015 23:22]
aspicher [Application de certains outils d’aide à la conception de la microélectronique à la biologie de synthèse (10/07/2014)]
news:summary [07/10/2015 17:41] (Version actuelle)
aspicher [Simplicité en biologie : le cas du cycle cellulaire (14/10/2015)]
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 +===== A knowledge representation meta-model for rule-based modeling of signalling networks (14/10/2015) ====
 +// Adrien Basso-Blandin - Post-doctorant Lip - ENS Lyon / Fontana Lab - Harvard medical school //
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 +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.
 +In this context, 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.