While the pioneering work of Adam Arkin's team at the University of California, Berkeley, relies on a remarkably broad range of tools and techniques, such versatility may soon become standard operating procedure in biology labs.

Consider the University of Pittsburgh's undergraduate course on computational biology, which apparently has no trouble luring biology students. They're already computer-savvy, so what might have seemed overly technical, complex or irrelevant to their predecessors is challenging and downright exciting to this next generation of researchers.

"The idea that they can apply their interest in computers to biology is very appealing to them," says Lewis Jacobson, associate professor of biological sciences and project director for the grant from HHMI that supports the course. The goal, he says, is to enhance the undergraduates' research skills through the use of sophisticated programs and Web sites.

A prime attraction is access to the Pittsburgh Supercomputing Center—a joint effort of the University of Pittsburgh and Carnegie Mellon University—that enables the students to work on some of the world's fastest machines. "Their sheer power is enormous," Jacobson says. "The kind of stuff that would take your desktop [computer] hundreds of years to do, these computers can do in a second."

The supercomputing center also has a large selection of software and databases, says Hugh B. Nicholas, Jr., one of its senior scientific specialists. "In the neurosciences, we have programs that simulate neurotransmitters going back and forth between nerve cells and muscle cells," he says. "That is invaluable if you're trying to study how the brain functions." Throughout the course, students hear guest lecturers—from at least a dozen biological disciplines—who discuss the creative ways they've been integrating computers and biology. The undergrads take a shot at it themselves; at the beginning of the course, each student chooses a specific gene or protein and uses computers to learn more about it, explains course coordinator Eric Polinko.

One student studied a protein kinase that is associated with Alzheimer's disease. He compared versions of the protein in everything from cows to fruit flies, finding that only portions of the protein remained identical in them all. These portions should represent the most important parts of the protein, and thus, the most interesting to study, Polinko says. "The computational tools will never replace experimental research, but they can point you in the right experimental directions."

"These students get hands-on experience and come out with computer skills that will make them highly employable," Nicholas adds.

—Marlene Cimons

Photo: Scott Goldsmith

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Reprinted from the HHMI Bulletin,
September 2002, pages 20-23.
©2002 Howard Hughes Medical Institute