Computational Proxies for Genomic Databases

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9224726 Cushing SDB/RUI: Computational Proxies for Genomic Databases This is the first year funding of a three-year continuing award. In a perfect world output from one program could easily be used as input to another. The world of scientific computing is far from perfect, however, and scientists are plagued with the task of writing special purpose data conversion programs. Business data processing are solving interoperability problems by using shared databases. Unfortunately, current database systems do not serve scientific applications well. This research addresses the problems of interoperability in the scientific realm by interfacing databases to computational biology programs. It builds on previous research in object-oriented databases for computational chemistry conducted jointly by the Oregon Graduate Institute in Portland, Oregon; Battelle Pacific Northwest Laboratories in Richland, Washington; Cold Spring Harbor Laboratories, New York. Results of previous research are being extended to cover genomic databases by using T4 bacteriophage data (perhaps the most nearly complete representation of genetic information for any individual organism). The genomic database is extended to include a "computational proxy mechanism", which allows for parameterized interface of the T4 data to existing computation-intensive distributed applications. The research has three objectives: (1) to demonstrate that previous database work is generalizable to scientific domains other than computational chemistry, and serviceable as a model for database interface with so-called "legacy" applications; (2) to make computational operations as well as genomic data available to the T4 researchers; and (3) to demonstrate that previous genomic database work in yeasts is transferable to other sites and organisms. The long term impact of this research is to transfer the current computing environment that the computational scientists find too complex to a data-centered approach that improves the interoperability of scientific data and programs. ***