Design of a support system for modelling gene regulatory networks

Mémoire de WATTIEZ Morgan

The understanding of gene regulatory networks depends upon the solving of questions related to the interactions in those networks. This study shows how a promising programming paradigm, constraint logic programming, can be used to design a support tool for modelling biological networks, with the emphasis on gene regulatory networks. We describe the most important elements of those complex regulatory networks, as well as popular formal methods and tools designed for their modelling. Then we introduce to the constraint logic programming paradigm and its advantages for solving real world as biological problems. Our approach is to use this paradigm to design a simple support tool with the aiming to help in modelling gene regulatory networks. For instance we set the emphasis on the understanding of the nature of interactions in those networks. To illustrate our approach, we designed BioNet, and present its interesting capabilities. Finally, we illustrate some of its features with the modelling of the regulation in the lac operon.

 

Keywords: Gene regulatory networks, biological networks, network inference, Prolog, constraint logic programming.

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