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June 15, 2003 | Mouse Brain Library may be a shortcut out of the maze of genomic database standards

The MBL started out in 1997 as a physical lending library for glass slides of mouse-brain cross-sections, which are a lot of work to prepare. "It seemed ridiculous to duplicate efforts between labs," says Glenn Rosen, associate professor of neurology at Beth Israel Deaconess Medical Center in Boston, and one of the MBL's founders. "But then we shipped slides to someone, and they arrived smashed."


Where's the cheese? MBL users can sort the database on two variables at a time, or can query for records matching specific criteria.
Meanwhile, Web technology improved enough to handle the resolution necessary to display a readable image of a mouse-brain slide, and the team won a five-year, $1-million grant from the Human Brain Project of the NIH. The MBL now resides on a server at the University of Tennessee Health Science Center, where principal investigator Robert Williams is co-director of the Center for Genomics and Bioinformatics.

Printed atlases of the mouse brain are available commercially for about $100, but, in addition to being unwieldy, they often don't do the job. "The problem with mouse brains is that there are huge differences among individual strains," Rosen says. The location of a particular brain region in one mouse strain might be several millimeters removed in another, creating problems if, for example, a researcher is trying to inject a substance into that region without the benefit of an atlas for that particular strain. The MBL provides the appropriate atlas to make sure he's aiming in the right place.

The site runs on a Linux cluster and is "a relatively conventional laboratory management information system," says Williams, whose son did a lot of design and programming for the project. It uses garden-variety HTML and some Java, and simple tools such as Filemaker Pro and MySQL.

"We're going for ease of use at this point," Rosen says. "The user interface is what we decided we would want if we didn't have physical access to the slides ourselves."

Despite, or perhaps because of, being narrowly focused in its research objectives, the MBL has its fans. The site gets about 1,500 hits a day. Desmond Smith from the University of California at Los Angeles is one appreciative user. "What you want is exactly there, and it's so transparent and simple to use," he says. "I wish they were all that easy!"

The MBL offers extensive crosslinks to other Web resources, and Rosen acknowledges the need to make Web databases compatible with one another — eventually. "You could spend years developing a methodology [for cross-referencing], or you could put it up not optimized and worry about it later," he says. "It might be difficult to put XML tags on now, but in five years it might not be."

The MBL is starting to work with other grantees in the Human Brain Project to synergize their data.

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For reprints and/or copyright permission, please contact  Terry Manning, 781.972.1349 , tmanning@healthtech.com.