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DOD Uses HPC Modernization Funds to Launch Cross-Service Biomedical Informatics Resource


The US Department of Defense has launched the first institute dedicated to providing biomedical informatics support for researchers engaged in Army, Navy, and Air Force R&D projects.

The Biotechnology High Performance Computing Software Applications Institute, or BHSAI, kicked off at the beginning of the year. The institute is one of four software institutes that the DOD created in late 2004 under its High Performance Computing Modernization Program, an initiative launched in 1992 to improve the armed forces' computational resources.

The BHSAI was awarded around $11 million over six years. Eight staffers have been hired so far, and the center is still seeking a deputy director, according to Jaques Reifman, institute lead for the BHSAI.

Reifman told BioInform that the BHSAI marks the first cross-service commitment by the DOD in the area of biomedical informatics, which "is truly a new area of investment" for the department.

The DOD currently categorizes its high-performance computing activities under 10 computational technology areas, which all focus on the physical sciences — structural mechanics, fluid dynamics, image processing, and the like — a focus that has left bioinformatics without an obvious home, Reifman said. BHSAI's fellow software institutes — the Institute for Maneuverability and Terrain Physics Simulation, the Battlespace Environments Institute, and the HPC Software Applications Institute for Space Situation Awareness — only serve to highlight the unique role of the center under the DOD's HPC umbrella.

DOD has "bent over backwards to say, 'We see that this is a growth area, it's an important area, and we want to make an investment in this area, where there's no history of the community using high-performance computing.'"

DOD has "bent over backwards to say, 'We see that this is a growth area, it's an important area, and we want to make an investment in this area, where there's no history of the community using high-performance computing,'" Reifman said.

Reifman said that many DOD projects "will require that we harvest information from the genomics and proteomics data that's being generated." While the department has "a vast investment in the experimental side" of life science research, Reifman said that the center will enable for the first time "synergies between experimentation and simulation" and that it will allow DOD biologists and chemists "to do things that [they] couldn't do without high-performance computation."

The BHSAI's primary task is to develop software, and it doesn't have any hardware of its own, Reifman said. Instead, it relies on the computational assets of the DOD's four major shared resource centers at the US Army Research Laboratory, Aeronautical Systems Center, US Army Engineer Research and Development Center, and Naval Oceanographic Office. So far, Reifman said, these resources have proved sufficient, and there are no plans to acquire dedicated hardware at this time.

BHSAI has already embarked upon a number of projects. In a collaboration with the US Army Medical Research Institute of Infectious Diseases, the center is developing software to identify genomic and proteomic "fingerprints" for pathogens of military interest that can be detected with microarrays. This project is the most advanced of the BHSAI's current activities, according to Reifman. "We might have a pipeline with a graphical user interface that a biologist could use between now and the end of the fiscal year," he said.

In another project, the center is integrating several open source virtual screening software packages, such as Dock and AutoDock, into a single, user-friendly package for DOD researchers developing drugs and vaccines. In a related project, the team is integrating several computational methods for protein structure prediction.

One of the center's longer-term projects is in the area of biosimulation. In a collaboration with the Air Force, the BHSAI team is using discrete stochastic modeling to simulate subcellular interactions with the goal of one day developing "cell-like devices that one would be able to control," Reifman said.

The BHSAI is only one example of the DOD's push to create bioinformatics resources that span the R&D activities of all the armed services. Reifman said that under a more recent initiative, he is chairing a joint technology coordinating group on biomedical informatics under the DOD's Armed Services Biomedical Research Evaluation and Management (ASBREM) committee.

"The objective is to coordinate activities in bioinformatics across the services," he said. One of the first objectives for this effort will be coordinating the department's Small Business Innovation Research and Small Business Technology Transfer grant activities, in order to better share the fruits of funded projects across the services and eliminate duplication in funding. "We want to make sure we are a smart buyer," Reifman said.

Reifman also wears a third hat as director of the Bioinformatics Cell at the US Army Medical Research and Materiel Command — the Army's primary medical R&D resource. The MRMC launched its bioinformatics program around four years ago in a bid to keep up with the onslaught of genomics and proteomics data that was being generated in its research labs [BioInform 07-14-03].

While Reifman was unable to pin a number on how many biologists currently work under the auspices of the DOD, he said that around "half a dozen different laboratories" across the armed services are engaged in biomedical research that would require access to bioinformatics resources.

— Bernadette Toner ([email protected] )

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