A Discrete Event Dynamic Systems Approach to Gene Regulatory Networks

S. Phoha and B.B. Madan (USA)


Gene regulatory networks, Bioinformatics, Gene expres sion, Discrete event systems, Supervisory control, Hypoth esis testing.


Representation of diverse data and biological processes in a single framework is a major challenge in bio-informatics for reasons of wide ranging varieties of available data and varying levels of fidelity at which biological processes can be considered. We propose an event based approach for representing both biological processes as well as data from different sources. Our aim is to integrate this approach with the discrete event framework to support qualitative reason ing for explaining gene expression in biological systems. We also identify some fundamental problems caused by state explosion that are dealt by introducing hierarchical layering in the proposed framework. Inherent differences between human engineered and biological systems lead us to believe that when dealing with biological systems, we need to use the forbiddance approach. Such an approach in turn requires us to model the controller part of biological systems as a multiple hypotheses testing problem.

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