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Researchers announce GenomeSpace environment to connect genomic tools
Date:4/25/2012

ogical problems from 'microproblems' involving a couple of steps in two tools, to complex scenarios on the scale of an extensive research paper," said Aviv Regev, a core faculty member of the Broad Institute. Regev, who is also an associate professor at MIT and an Early Career Scientist of the Howard Hughes Medical Institute, and members of her lab have made examples of ways to solve these kinds of problems available on GenomeSpace as tutorials for others.

Michael Reich, director of informatics development for the Broad Institute's Cancer Program, is one of the architects of GenomeSpace. He describes GenomeSpace as a connection layer that allows different tools to communicate it can detect the different data formats each tool requires and make the necessary conversions. "GenomeSpace acts as a broker, automatically detecting and converting files from one format to another for the user," said Reich.

Anton Nekrutenko, an associate professor at Pennsylvania State University and one of the developers of the aggregation tool Galaxy, notes that tools like Galaxy and GenePattern already integrate hundreds of tools. GenomeSpace pulls these aggregation tools together.

"GenomeSpace is an integration of integrators," Nekrutenko said. "The benefit to the user is that this brings together distinctive collections of functionalities offered by individual tools."

"We couldn't be more pleased that Cytoscape is plugged into GenomeSpace," said Trey Ideker, Division Chief of Medical Genetics at University of California, San Diego School of Medicine. "GenomeSpace will connect our network analysis tools with hundreds of other state-of-the-art programs and enable our users quick access to expression clustering and classification and browsing, access to the genome sequence, and so on."

Mesirov, Reich, and their colleagues are eager for other biologists to test drive GenomeSpace and offer feedback on its utility. "We're committed to rapidly resp
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Contact: Haley Bridger
hbridger@broadinstitute.org
617-714-7968
Broad Institute of MIT and Harvard
Source:Eurekalert

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