Modeling and formal verification of biological regulatory networks: an integrative approach

The study of large models of biological networks by means of analysis and simulation tools leads to large amounts of predictions. This raises the question of how to identify interesting predictions of novel phenomena that can be confronted with experimental data. Formal verification techniques based on model-checking have recently been used to the analysis of these networks. The application of these techniques is hampered, however, by several key issues. First, properties of the network dynamics like multistability and oscillations, are not easily expressed using classical temporal logics. Second, the problem of posing relevant questions in temporal logic, is difficult for non-expert users. Finally, most of the existing modeling and simulation tools are not capable of applying model-checking techniques in a transparent way.