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DOE Seeks to Share its Computational Experience with the Genomics Community


The US Department of Energy recently announced a proposed program called Genomes to Life that is intended to complement the work of DOE genomics efforts under the Joint Genome Institute and the DOE Microbial Cell Project. The new program has set forth specific goals centered around the identification and characterization of microbial cellular functions.

The first step in this ambitious undertaking will be the development of new bioinformatics tools that will build upon the success of the international genome sequencing effort, according to Walt Polansky, who heads the math, computing, and information sciences directorate at the DOE.

Polansky sees the DOE’s long history of high-performance computing in the fields of weapons research and high-energy physics as ideal precursors to its intended role as a bioinformatics developer.

“Some of the strengths of the DOE are the ability to bring teams of people from several different scientific disciplines together to work on a common problem, we have a history of using high-performance computing to help solve these problems, and we also have a history of dealing with some very large databases,” said Polansky. “Bioinformatics is the area of opportunity that we see for the department and it’s also an area to which I think we bring a lot of strength and unique capabilities.”

The department will sponsor a series of workshops in the fall for researchers in academia, industry, and federal labs in order to hash out the unique challenges the department will face as it moves its focus from the physical sciences to the life sciences.

Polansky anticipates that a principal challenge will be the dimensionality of biological data, which is much higher than physics data, making data querying and extraction more difficult. He foresees another hurdle in determining the best way to link biological databases together that contain information on sequencing as well as structural and functional annotation, protein interactions, and other data.

Genomes to Life will essentially pick up where the JGI leaves off — at the sequencing level. The program will first aim to identify and characterize the molecular machines that make up microbial cells. Additional goals include characterizing cellular regulatory networks, characterizing individual microbes and microbial communities, and ultimately developing computational capabilities to understand complex biological systems and predict their behavior.

Polansky pointed to the DOE’s record of successful collaboratory efforts in the fields of high-energy physics and global climate modeling as evidence that the agency is a fit partner to support genomics research. “In my view if we can successfully meld experimental results and data to high-performance computing and data querying, we can offer tremendous insights into biological systems,” he said.

Since Genomes to Life is still in the planning stages, and its funding level will not be finalized until the end of the year, Polansky was unable to speculate on specific bioinformatics initiatives the DOE would undertake under the program.

The math, computing, and information sciences directorate has allocated $3 million of its fiscal 2002 budget request to the program.

— BT

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