Phd student at I3S (SPARKS team)
Phd student in Computer Science
at Université Côte d'Azur.
My research interests are in the area of modelisation, Bioinformatics. I'm doing my PhD under the supervision of Pr. Jean-Paul Comet, Pr. Gilles Bernot and Dr. Hélène Collavizza. The title of my thesis is Discrete model life cycle and application to the regulation of pancreatic cancer cells.
The modelling of complex biological systems does not benefit from the methods and tools that exist for the development of technological products in software engineering. The main reason for this is the impossibility of implementing a modular design: in biology, the introduction of a new element in a previously validated model can drastically change its behaviour. Nevertheless, this thesis provides an incremental methodology, in order to design discrete models for biology, which has some similarities to software spiral development model. The principal goal is to preserve the feasibility of proofs allowing to verify the non-regression at each enrichment. Although the proposed method was developed within the framework of René Thomas’ formalism, it can be adapted to any other discrete modelling framework. It includes three distinct phases: requirements analysis, model enrichment combined with validation by formal methods and finally a prediction phase. The substantial case study that anchors this work is a model of metabolic regulation at different stages of progression in pancreatic ductal adenocarcinoma (PDAC). In this work, we adopt an abstract modelling incremental approach, whose starting point is an already consequent general model of eukaryotic metabolic regulation. Our method allows us to enrich this initial model step by step to reach our aim, that is, a model covering the evolution from the healthy cell to the aggressive cell through the non-aggressive cancer cell. One has only little molecular a priori knowledge on the metabolic deregulation involved, and the level of abstraction of this model is chosen to best guide biologists in their research and in the choice of their working hypotheses.
