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Harvard-MIT collaboration adds Lego-like genome analysis tool

Tools

The availability of open-source tools has broadened the reach of genome sequence analysis, but the need for programming skills has slowed uptake among biologists. GenePattern is aimed at these biologists, and a recent update has further tailored the tool to non-programmers.

Harvard and MIT collaboration the Broad Institute released GenePattern in 2004, and within two years it reported 30 biopharmas had registered to use the platform. Since then, users have created an estimated 10,000 genome analysis tools, and researchers have combined the programs to gain new insights. Analyzing genomics data using multiple tools required computer skills, though, and as such fell short of GenePattern's goal of making such capabilities available to all. A recent update aims to fix this weakness.

The new version better integrates GenePattern and its third-party software archive, GParc. Now, when users want to combine multiple genome analysis tools, they can add modules from GParc like Lego pieces, according to a Bio-IT World report. The output from each step is compatible with the next analysis module, allowing users to combine chain genomics tools. Previously some computer knowhow was needed to work around file format support issues and link multiple analysis programs.

Broad Institute's director for cancer informatics, Dr. Michael Reich, hopes the update will extend the reach of programs uploaded to GParc. "We want to let them release their own tools into the wild," Reich told Bio-IT World. Reich is part of a team that is working to make bioinformatics capabilities available to a wider audience. By pitching the tool at non-programmers--while still allowing advanced users to manipulate modules in MATLAB, R, or Java--GenePattern has grown to 50,000 users.

- read the Bio-IT World article

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