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Jason Moore directs the Bioinformatics Core of the Program in Human Genetics. The core’s 11 computer programmers provide database design services and support, Web interfacing, and software design in various programming languages.

Genetics group tackles range of computing needs

by Mary Beth Gardiner

With its 11 computer programmers, the Bioinformatics Core is one of the largest bioinformatics groups on the Medical Center campus. The operation spans from the core’s home base on the fifth floor of Light Hall to the Information Technology Services networking center on Peabody campus, where the VAMPIRE supercomputer is housed.

The Bioinformatics Core was organized by Jonathan Haines as part of the Program in Human Genetics, and is under the scientific direction of Jason Moore. The efforts of the facility are focused primarily on genetics-related projects, though not exclusively.

“We’ve taken on a range of projects, from molecular genetics to population genetics to genomics to microarray work,” Moore says. “And we’re getting into proteomics now, too.”

As part of the services offered, the staff programmers provide database design services and support, Web page design and support services, Web interface to the database, and software design in various programming languages. Scheduling of programming and design services can be arranged with Janey Wang, the core’s manager.

In addition, the core manages Vanderbilt’s subscription to the Celera database, and supports a wide variety of bioinformatics software packages, such as the Wisconsin GCG Package for nucleic acid and protein sequencing analysis. Charles Alexander, who is responsible for this area of the core’s services, conducts training workshops and is available for one-on-one training in the use of Celera and the various software products.

According to Moore, it’s a simple matter for the bioinformatics core to coordinate services with other core facilities, such as the Microarray Shared Resource. While the microarray core is responsible for processing the raw data generated there and formatting it for the researcher, the bioinformatics core is able to generate the databases that facilitate analysis of the data.

For example, Moore and Shawn Levy, director of the Microarray Shared Resource, are both principal investigators on a Program Project Grant that Jacek Hawiger directs, which has as its goal to identify markers of inflammation in the blood.

“The group is trying to identify genes that are turned on and off during the inflammatory process,” Moore says. “We’re working together to create a seamless database and analysis system for that project, which will require a lot of microarray work.”

Moore and his programmers have devised a number of computational methods for analyzing microarray data and genetic epidemiological data that wouldn’t be possible, he says, without the use of a supercomputer, such as VAMPIRE. With its 110 linked CPUs, VAMPIRE, which stands for Vanderbilt Multiple Processor Integrated Research Engine, provides the boosted speed and power needed to perform sophisticated computations in a reasonable time frame.

One example of VAMPIRE’s power can be seen in its application to the proteomics work of Richard Caprioli, whose lab is investigating whether mass spectrometry can be used to correlate tumor proteins with tumor grade. Comparing mass spectra of different tissue samples to identify common proteins can be problematic, however, since the protein peaks sometimes shift in a non-linear fashion. Moore devised an algorithm that corrects for such shifts.

In the graphic depiction of results from this algorithm, identical proteins appear as dots within vertical bins, the color of each dot reflecting the relative abundance of that protein. Variation in mass among the proteins is evident in the “wobble” seen in the stacked tower of dots.

The algorithm must simultaneously figure out the optimal size of the bins and what proteins belong in each. Analyzing 500 tissue samples using this algorithm, as in one of Caprioli’s brain tumor studies, can be computationally intensive, to say the least. Even with VAMPIRE, it takes a couple of days to run the program; without VAMPIRE, Moore says, it would be impossible.

Those responsible for VAMPIRE, including Alan Tackett, who has direct oversight of the system, are anxious to give it more teeth. Moore envisions a resource large enough to service the entire University. Moore, along with Tackett and Paul Sheldon, a professor in the department of Physics, have been marinating the idea of creating a scientific computing center. Attempts to find the funding needed for this leap include an application to the NIH’s High End Instrumentation Program, an NSF proposal, and a proposal to the University’s Academic Venture Capital Fund.

“I think VAMPIRE will be a tremendous asset for anybody doing computational studies,” Moore says, “not just in bioinformatics, but across the university. The system will open doors for a lot of people to do things they never dreamed they could do.”