Temporal constraints in the logical analysis of regulatory networks

Starting from the logical description of gene regulatory networks developed by R. Thomas, we introduce an enhanced modeling approach based on timed automata. We obtain a refined qualitative description of the dynamical behavior by exploiting not only information on ratios of kinetic parameters related to synthesis and decay, but also constraints on the time delays associated with the operations of the system. We develop a formal framework for handling such temporal constraints using timed automata, discuss the relationship with the original Thomas formalism, and demonstrate the potential of our approach by analyzing an illustrative gene regulatory network of bacteriophage λ.