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Using Bioinformatics in the Undergraduate Classroom

AIBS Eye on Education

Susan Musante

During a BioQUEST workshop five years ago, Garry Duncan discovered the potential of bioinformatics. Using innovative software to manipulate biological data and solve problems, he realized, held enormous promise for him not just as a researcher but also as an educator. Duncan returned to his university a changed man. His cell biology and molecular biology students at Nebraska Wesleyan University began using bioinformatics tools to investigate DNA sequence homology and protein structure. Next, he challenged them to ask questions for which he had no answer--for example, do the evolutionarily conserved and variable regions of certain proteins make functional sense? (That is, do the conserved regions correspond to important functions of the molecule?) And this became the most exciting aspect of using bioinformatics: He, a PhD biologist trained in molecular biology, genetics, and evolution, was learning alongside his students.

The BioQUEST Curriculum Consortium, founded in 1986 by John R. Jungck and 17 other developers, collaboratively develops innovative student-centered curriculum materials for teaching undergraduate biology. These materials reflect BioQUEST's pedagogical philosophy: to engage faculty and students as colearners in the science process through problem posing, problem solving, and peer persuasion. Jungck, BioQUEST principal investigator and biology faculty member at Beloit College in Wisconsin, has dedicated his career to improving undergraduate education both in the United States and abroad, and his efforts have not gone unrecognized. In March 2004, the American Institute of Biological Sciences presented Jungck with its Education Award for his significant contributions to biological sciences education.

When Duncan attended the workshop in 1999, BioQUEST had long been investigating the role of computers and technology in education, strategies to engage students in real science, and ways to use evolution as a basis for understanding biological systems. In 2002, BioQUEST received funding from the National Science Foundation for a new program called BEDROCK, Bioinformatics Education Dissemination: Reaching Out, Connecting, and Knitting-together (http://bioquest.org/bedrock/). The three-year grant supports the development of innovative curricular tools that use molecular data in the classroom to explore biological questions.

"We have a new and unprecedented opportunity to engage students in doing science," says Sam Donovan, BEDROCK program director and assistant professor in the Department of Instruction and Learning at the University of Pittsburgh. Bioinformatics "grew up" in a networked computer environment, meaning that both data resources and analytic tools are available in the public domain. Instead of limiting students' science learning to memorizing facts or studying outcomes, Donovan says, "we have the opportunity to include a much broader set of science experiences...[such as] developing and testing hypotheses using the existing computer equipment available in most undergraduate teaching labs."

Rebecca Roberts, biology faculty member at Ursinus College in Collegeville, Pennsylvania, enjoys the rewards of exploring data with her students. Roberts used bioinformatics tools in graduate school, so transitioning to their use in the classroom was a natural progression for her. "Science is like telling a story," Roberts tells her students. "You explore the data, either primary or your own, and find a story that fits." Roberts was introduced to BEDROCK during a faculty development workshop and returned home full of ideas. "It takes a lot of time to prepare bioinformatics teaching materials for your students," she says, but "the BEDROCK community has collectively done a lot of the prep work by posting data, resources, and tools for faculty to use."

Indeed, BEDROCK provides a venue for faculty to develop and share ideas not only during workshops (see http://bioquest.org/bedrock/events.php) but also through an online community. Faculty materials are posted in the "problem spaces" section of the BEDROCK Web site, defined as "a way to organize diverse kinds of resources to support student inquiry." According to Donovan, "The goal is to support innovative bioinformatics education by having faculty share teaching ideas through the problem spaces, thus creating a rich set of resources for others to use and/or modify. It's an open curriculum model...[that] fits well with the general BioQUEST philosophy."

There are currently six problem spaces: chimpanzee conservation, HIV, prion, TRP cage, West Nile Virus, and Whippo (see http://bioquest.org/bedrock/problem_spaces/). Each offers questions to investigate with students and includes introductory materials, background, sequence data, curricular resources, and links to tools such as the Biology Workbench and NCBI (National Center for Biotechnology Information). "Each presents a set of ideas and resources, then you can take this core and do what you want with it," Roberts noted.

Both Rebecca Roberts and Garry Duncan encourage faculty members to give the inquiry-based, open-ended approach a try, though students may initially resist. "Engaging students in biology courses is challenging," acknowledges Duncan, "but using BioQUEST's approach to teaching bioinformatics provides opportunities for students to create their own knowledge, and there's no doubt that they have a more positive, inquisitive attitude."

Susan Musante (e-mail: ) is AIBS education and outreach program manager.

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