Applications of a formal approach to decipher discrete genetic networks

Background: A growing demand for tools to assist the building and analysis of biological networks exists in systems biology. We argue that the use of a formal approach is relevant and applicable to address questions raised by biologists about such networks. The behaviour of these systems being complex, it is essential to exploit efficiently every bit of experimental information. In our approach, both the evolution rules and the partial knowledge about the structure and the behaviour of the network are formalized using a common constraint-based language. Results: In this article our formal and declarative approach is applied to three biological applications. The software environment that we developed allows to specifically address each application through a new class of biologically relevant queries. We show that we can describe easily and in a formal manner the partial knowledge about a genetic network. Moreover we show that this environment, based on a constraint algorithmic approach...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Fabien Corblin, Eric Fanchon, Laurent Trilling
• Keywords: BMCBI 2010, Formal Approach, Partial Knowledge, Systems Biology