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Programming for the curious biologist

To advise biologists navigating the unfamiliar terrain of computer programming, Wheaton professors Betsey Dyer (biology) and Mark LeBlanc (computer science) have written a guidebook, Perl for Exploring DNA, that serves as an introduction to computer-aided searching of biological sequences.

The emerging field of bioinformatics has opened up exciting new research opportunities for biologists, but it also has presented them with a problem: learning how to harness the computational power of computers.

To advise travelers navigating the unfamiliar terrain of computer programming, Wheaton professors Betsey Dyer (biology) and Mark LeBlanc (computer science) have written a guidebook, Perl for Exploring DNA, that serves as an introduction to computer-aided searching of biological sequences.PerlCover

The book, which was published by Oxford University Press, represents an accessible approach to the use of Perl for genomic research, a subject that Dyer and LeBlanc have been exploring with students in laboratory research and through "connected" courses in biology and computer science that they began teaching in 1998. The text for the book began in 2003 with a series of primers written for students in the pair's team-taught class, DNA, and grew from there.

"Mark and I realized that we ourselves needed this book and so did colleagues that we were meeting at various workshops and conferences," says Professor Dyer. Professor LeBlanc adds that "our Wheaton students were our first readers" for the second complete draft of the book, which was used as a text for one of the pair's courses. Programs written by students working with the professors are included in the book, and its companion Web site, as examples from which readers can build their own customized program.

"The book is for students of all ages (including professors) who are moving in an interdisciplinary direction," says Dyer. "This is such a new field that everyone is a student."

Indeed, professors at other institutions are finding the book as they try to learn the field themselves. "Having been assigned the task of starting a three-class bioinformatics programming intensive..., I researched every available resource and had chosen a combination of texts with which I was not completely satisfied," one college professor wrote in an Amazon.com review of the book. "Then I got a copy of this text and had the bookstore send the others back."

LeBlanc confirms that he and Dyer have heard from a number of colleagues who are adopting their text. "We are receiving good feedback from professors who were looking for a new book to help programmers enter the field of bioinformatics," he says. "Colleagues at UNH, WIT, Vassar, Hiram and more have either used it or are about to this coming spring semester."

The swift response reflects the intense interest in the use of computers to map and translate genes and proteins. Large-scale genome-mapping projects, such as the human genome effort, have developed enormous amounts of DNA sequence data that is, for the most part, not yet understood. In their collaborative research with students, Dyer and LeBlanc have put computers' power and their students' curiosity and energy to work in exploring this massive new field.

"Biology has returned to an age of discovery, perhaps not seen since the days of nineteenth century scientific expeditions," Dyer and LeBlanc write in the book's introduction. "If Charles Darwin had taken a couple of undergraduate interns with him on the Beagle, those students would have discovered, described and cataloged their share of new species. It would have been almost unavoidable, because so few neotropical flora and fauna had been examined and characterized at the time of that voyage.

"Likewise undergraduates today, exploring the vast, mostly unknown terrains of genomes can make discoveries and be among the first to describe a new genetic sequence."

LeBlanc and Dyer's research have yielded a number of journal articles in this field, many of which boast students as contributing authors. And their work has been funded by several grants, including awards from the National Science Foundation, the college's Mars Student-Faculty Research Collaborative Fellowships, Davis Educational Grants, Wheaton Research Partners and Wheaton Foundation Grants.

If you would like to learn more, the professors' Web site offers a more in-depth look at the history of their project as well as at their current findings and software tools.