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The Computational Biology Resource of the Center for Structural Biology boasts a 64-processor Silicon Graphics Origin supercomputer. The system is key to determining, analyzing, and modeling biomolecular structure, says Jarrod Smith, the resource’s director.

Resource aids structure analysis, modeling

by Mary Beth Gardiner

Providing support for the specialized needs of the growing population of structural biologists on campus, the Computational Biology Resource is one of four core technological facets of Vanderbilt’s Center for Structural Biology. The resource provides outreach to scientists in other disciplines, as well, on projects that cross over into the structural biology field. In fact, you could say that the mission of the resource, in general, is to promote thinking on a molecular level, says director Jarrod Smith.

Smith and Walter Chazin, director of the Center, have spent the past two years building the Computational Biology Resource. Though the resource resembles a traditional core facility, it differs in a fundamental way. The facility provides the resources – the hardware, software, and expertise to use them – but the investigator needing the services provides the manpower to come and actually do the work.

The resource assists with traditional bioinformatics needs, such as deciding how to use information once it is collected. But the bulk of what they do, according to Smith, falls more into one of the “fringe-definitions” of bioinformatics.

“Our piece of bioinformatics in structural biology would be determining, analyzing, and modeling biomolecular structure,” he says.

To that end, the resource boasts an impressive collection of high-end equipment.

“Currently, we’ve got a 64-processor Silicon Graphics Origin supercomputer, as well as a 32-processor Linux cluster, for a total of 96 CPUs dedicated to running biomolecular simulations, biomolecular analysis tools, and ab-initio calculations for small molecules,” Smith says.

Even though the VAMPIRE computer cluster has more CPUs, the bandwidth on this parallel system is greater, and the latency – the amount of time it takes for a packet of information to travel between two processors – is very low. These qualities are critical to many algorithms used in computational biology.

“That’s what makes a supercomputer to us,” Smith says. “It’s not only how fast the processors are, it’s how tightly coupled they are and how you can use the thing as a whole. The Origin has 32 gigabytes of shared memory; all the processors see that memory and they all see it with the same bandwidth.”

The facility also offers what Smith calls a “visualization lab.” At this time, there are four high-end Silicon Graphics Octane workstations, specifically designed for real-time, 3-D graphics rendering.

“This is where people go to bring their molecules up into the computer, rotate them around, and interact with them,” he says. “We also have the capability to use stereoscopic glasses, so you can actually see the object in three dimensions. That’s an important tool for researchers doing modeling and drug design, or for X-ray crystallographers needing to put atoms into electron density clouds.”

The software packages available through the resource are listed on their Web page (http://structbio.vanderbilt.edu/ comp/), though the list grows faster than they are able to update the site. It’s a good idea to ask if you don’t see the one you’re interested in, Smith says. Each package comes with instructions on how to install and begin, plus links to manuals and customized user hints. For some of the packages, Smith has written tutorials for more advanced interactions with the software.

As far as infrastructure goes, the resource has several servers that handle Web, database, software, and file serving tasks, and they have just installed a two terabyte RAID (redundant array of inexpensive disks) array that dramatically increases storage capacity.

“The RAID device does its work in the background,” says Smith. “The advantage of that is you can get massive amounts of storage in one, easy to maintain system. And there is a redundancy built in, so you could lose a disk and nobody would know except us.”

The two terabytes of space – that’s 2000 gigabytes – are necessary to handle the data collected at the NMR Center, the simulations that are run on the supercomputers, and the data brought back by the X-ray crystallographers from the synchrotron.

Smith and his staff, which currently consists of two system administrators, are available as consultants to share their expertise in how to get started and how to solve particular problems. Ultimately, they plan to offer workshops in addition to one-on-one interactions.

“The goal is that over time the required knowledge and skills to take advantage of these technologies will start to percolate through the community,” Smith says.

Smith got his Ph.D. at the Scripps Research Institute, jointly advised by Chazin, an NMR spectroscopist, and David Case, a computational biologist.

“My background is in NMR structure determination, but most of the work I did was in the computational methods for resolving the structures,” he says. “This job really takes advantage of my skills. Plus, I enjoy helping people solve problems, and that’s perhaps the most important aspect of the job.”

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