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College Briefs

We Are the Champions of Computational Genomics


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It pays to stand up for something you believe in. Plant and microbial biology professors Brian Staskawicz and John Taylor saw a need to bring the tools of genomics to the campus's multifarious biology researchers, who had questions ready-made for genomics but lacked the computational expertise to make use of the new, inexpensive data.

"It's a special kind of data—researchers need to understand where it came from and how it was created," said Donna Hendrix, chief administrator for the Department of Plant and Microbial Biology (PMB).

"Berkeley was in a very strange position," said Taylor. "Many of the world's top developers of computational methods for next-generation genomic sequence data were in the statistics, mathematics, and bioengineering departments, but there were very few faculty in biology departments—among them PMB; Environmental Science, Policy, and Management; and Integrative Biology—with the computational expertise to use the methods."

Staskawicz and Taylor wrote grants and garnered support from campus upper management, offered PMB space for a center, and coordinated with Susan Marqusee, Berkeley director of the California Institute for Quantitative Biosciences, or QB3, who shared their vision. Hendrix worked the balance-sheet magic. The result is the new QB3 Computational Genomics Resource Lab, launched in June 2011 and housed in Koshland Hall.

"There was a lot of synergy with QB3, since they already had two genomics labs," said Staskawicz. "They wanted it to be compatible with their existing labs, and they provided the funds to allow that to happen." The result is a resource for the entire campus—equipment, classes and workshops, and support for researchers.

"The new lab will allow scientists to spend more time focusing on extracting meaning from genomics data, and less time struggling with the complex logistics of building computer systems and installing software to analyze the data," said Staskawicz, who is co-director with Taylor.

"Our aim is to put the infrastructure in place that allows knowledgeable users to teach novices, creating a self-sustaining and self-perpetuating exchange of expertise," said Taylor.

-Ann Brody Guy

SOCIETY NEWS: Cooperative Extension specialist Peggy Lemaux has been elected president of the 5,000-member American Society of Plant Biologists.