Extending BioD to Describe Gene Regulation

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DESCRIPTION (provided by applicant): We have proposed that a computerized, internet-based graphical description language for systems biology will be essential for describing, archiving and analyzing complex problems of biological function in health and disease. Toward this we suggest a conceptual basis for designing such a language and describe BioD, a prototype language that we have used to explore the utility and feasibility of this approach to functional biology. Using example models, we demonstrate that a rather limited lexicon of icons and arrows suffices to describe complex cell biological systems as discrete models that can be posted and linked on the internet. Given available computer and internet technology, we also suggest that BioD may be implemented as an extensible, multidisciplinary language that can be used to archive functional systems knowledge and be extended to support both qualitative and quantitative functional analysis. In this application, we propose to test three critical assertions about the BioD language approach using the lambda phage lysis/lysogeny "genetic switch" as a classical, well characterized test case. First, we want to determine whether the BioD language can be extended to comprehensively describe gene regulation and expression mechanism found in the lambda phage genetic switch. Second, we aim to determine whether the BioD icon and arrow objects in the lambda phage system can be rigorously mapped to computational expressions for simulating model behavior. And third, we aim to establish the framework and basic patterns of a novel BioD Functional Pattern Language for defining, identifying and analyzing higher-order principles of organization of biological systems as an aid to understanding cell biological and genetic function.