Incorporating time delays into the logical analysis of gene regulatory networks
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
Petri net representation of multi-valued logical regulatory graphs
Natural Computing: an international journal
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For modeling and analyzing regulatory networks based on qualitative information and possibly additional temporal constraints, approaches using hybrid automata can be very helpful. The formalism focussed on in this paper starts from the logical description developed by R. Thomas to capture network structure and qualitative behavior of a system. Using the framework of timed automata, the analysis of the dynamics can be refined by adding a continuous time evolution. This allows for the incorporation of data on time delays associated with specific processes. In general, structural aspects such as character and strength of interactions as well as time delays are context sensitive in the sense that they depend on the current state of the system. We propose an enhancement of the approach described above, integrating both structural and temporal context sensitivity.