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Bioinformatics gains momentum
New planning grant, shared efforts move research forward

by Leigh MacMillan

If you ask ten different scientists, “what is bioinformatics?,” you will likely hear ten different responses. There will be common elements – computers and databases top the list – but the definition will depend on who’s doing the defining. Nancy Lorenzi, assistant vice chancellor for Health Affairs, sums it up nicely. “Bioinformatics is like an amoeba,” she says. “It comes in various shapes and sizes.”

At Vanderbilt Medical Center, advancing bioinformatics is “a very distributed effort,” says Mark Magnuson, assistant vice chancellor for Research. “Bioinformatics is probably involved in one way or another in seven or more of our shared resources, and individual laboratories are making use of these tools as well.” Magnuson has spearheaded an effort to bring different investigators together over lunch, to stimulate discussion and development of new bioinformatics resources. Although the definition of bioinformatics may be vague, he says, there is momentum at Vanderbilt for improving and expanding efforts in the bioinformatics arena.

So what is bioinformatics?

According to the National Institutes of Health, bioinformatics is “research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data.”

“The term bioinformatics is not very specific to any one effort,” says Al George, director of Genetic Medicine. “Bioinformatics is a toolbox that can be configured to perform a wide variety of research needs; it is not one flavor.”

Mary Edgerton, director of the Molecular Profiling and Data Mining Shared Resource, sees bioinformatics as a spectrum “that goes from storage and retrieval of massive amounts of information to techniques used to interpret that information.” In her view, bioinformatics is a large field with many subspecialties, including biomedical informatics and computational biology.

Others, including the NIH, define these disciplines as distinct entities, recognizing that there is significant overlap and activity at their interfaces.

Lorenzi explains that biomedical informatics usually refers to clinical or medical informatics – the application of computing to patient-related data, while the term bioinformatics more often implies the computing tools that handle the research information of the genomic era.

Vanderbilt is particularly strong in the realm of biomedical informatics. The department of Biomedical Informatics and its faculty members, including chair Randy Miller and Bill Stead, are internationally recognized for initiatives like StarChart and WizOrder. Bioinformatics for basic science areas of research has been slower to develop at Vanderbilt, but thanks to the efforts of many investigators, it is gaining ground.

A newly awarded pre-Center grant to develop a National Program of Excellence in Biomedical Computing will allow Vanderbilt to build on existing efforts to establish the organizational and infrastructure components needed for a full-fledged Center.

This issue of Peer Review takes a look at some of the areas at VUMC where bioinformatics plays a key role. Shared resources like the microarray, proteomics, structural biology, and imaging resources rely heavily on bioinformatics tools and are developing some of their own. The bioinformatics cores of the Program in Human Genetics and VICC are writing code and developing databases to store, retrieve and analyze information. Investigators in the department of Biomedical Informatics are writing new algorithms to find relationships among the elements of huge genomic datasets. And ongoing efforts seek to recruit new faculty members with bioinformatics expertise and to expand and improve computing resources such as the VAMPIRE system.

The stories in this issue do not present an exhaustive review of bioinformatics at the Medical Center. They are intended to highlight some of the advances, to provide a glimpse into the changing shape and movement of the amoeba that is bioinformatics.