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Bioinformatics Is Going Back to School


By John Otrompke

Sept. 18, 2006 | A spate of government-funded initiatives are helping to develop innovative bioinformatics curricula, providing more up-to-date and integrated training needed by industry, and preparing incumbent workers to meet the needs of the developing industry.

Ann Reed became director of the Bioinformatics training program (BITMAP) in 2004. “In two years, I’ve seen this dramatic shift,” she says. “Employers used to tell me bioinformaticians must have a Ph.D. in the life sciences... Now companies are starting to say, ‘We work in interdisciplinary teams. We want domain experts who can communicate with our Ph.D. scientists.’”

BITMAP is funded by a Department of Labor (DOL) grant and operated by the Chicago Technology Park, although student training occurs at the University of Illinois at Chicago (UIC). “Many programs teach informatics, and then biology,” says Hui Lu, academic director and associate professor in bioengineering. UIC received a $3 million grant for the BITMAP program, $500,000 of which funds tuition.

“Many of the 1,100 community colleges in the nation don’t have biotech programs,” says Patricia Dombrowski, director of the sciences informatics center at Bellevue Community College in Washington, which is under contract with the DOL to develop a new bioinformatics curriculum for community colleges nationwide.

Centers of Excellence
Bellevue is one of five community colleges designated as national community college life science centers of excellence by the DOL in 2004. The others, which shared a $5 million DOL grant to create a new curriculum, are Mira Costa College in San Diego (biomanufacturing); New Hampshire Community Technical College (bioprocessing); Indian Hills Community College in Iowa (bio-agriculture); and Forsyth Technical Community College in Winston-Salem, N.C. (research and development).

While most of the students in the UIC BITMAP program are either underemployed or unemployed, the program, which graduated its first 10 students in August 2005, has a 50 percent placement rate so far. Salaries are better too; a survey of IT workers from last year showed that earnings averaged around $54,000 per year, whereas the average salary upon graduation from BITMAP is about $75,000, Reed says.

Part of the reason for the program’s success has been the ability of schools to leverage the prestige of the DOL to work with biotechnology employers, who have provided curriculum guidance and offered internships.

“If you hire an IT person off the street, there’s a pretty steep learning curve in getting the employee to understand the complexities of the life sciences field,” says Rob Arnold, president of Geospiza, a software company that has helped develop the Bellevue curriculum. “It can take four to six months for them to get their head around the business, whereas if you brought in somebody who had already taken a course, my hope is that we could probably cut that time down to a month or less.”

Compounding the shortage of IT job opportunities, there is a shortage of bioinformaticians in some markets. Litholink, one of some 30 biotech companies in the Chicago Technology park, has an internship program that works with German students. “This is one of the reasons BITMAP was founded, because there was a shortage of trained workers,” says Reed.

Training in Emerging Technologies
Part of the challenge of retraining IT workers as bioinformaticians is exposing them to the most current technology and concepts in a rapidly evolving field. “IT programs that focus on bioinformatics tend to have more rapidly changing curricula,” explains Peter Tarczy-Hornoch, professor and division head for biomedical and health informatics at the University of Washington, which has graduated about 20 Ph.D. students since 2001.

Among concepts under development at the University of Washington is the Semantic Web. “In our knowledge and data research course, we’re teaching students to start extracting meaning from Web-based resources as opposed to extracting raw data,” says Tarczy-Hornoch. Students are assigned projects involving gathering information across disparate databases, with different underlying data models.

Another core subject is metabolomics — the study of metabolic activity. “[This] is going to generate a number of interesting informatics questions which are going to change the nature of what students need to know in this field,” says Tarczy-Hornoch.

Students are being trained not only in new concepts but also in new technologies. Stephanie Tatem Murphy, program manger in life sciences informatics at Bellevue, says, “There are some easily accessible free tools that are pretty easy to build into the classroom.” One example is the software program Ontology, produced by the National Center for Biotechnology Information. “Ontology relates to a function of genes and proteins, helping the scientist relate one piece of RNA to its function,” says Murphy.

Another area of potential interest at Bellevue is nanotechnology, although Dombrowski says, “In order to deliver the curriculum, we’ll need to find further funding.”

A New Model of Teaching Bioinformatics
In addition to new materials and new economics, the bioinformatics initiatives are using new models for teaching students. “For example, we would provide these students a clinical trials example, rather than a banking example, in which to manipulate the date in class,” says Murphy.

UIC’s Lu agrees that new approaches to teaching are important, including Hidden Markov Models for sequence analysis and phylogenetic tree analysis for studying gene relationships. Students receive integrated training in bioinformatics problems, as opposed to learning IT skills, then biology, under the old teaching model.

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