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GSEA (Gene Set Enrichment Analysis), IQbase 2.0,dbSNP, GenomeBrowser 1.1.1, Joo Setubal, Bruno Sobral, Ewan Birney, Lincoln Stein, James Kent, Michael Eisen


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The Broad Institute has released GSEA (Gene Set Enrichment Analysis), an analytical tool that "moves microarray analysis from the level of individual genes to whole networks of genetic interactions," according to a statement from the institute. GSEA relies on a curated database of gene sets, such as genes that are known to interact in biochemical pathways. So far, the Broad researchers have gathered around 1,500 gene sets, and made them publicly available with the GSEA software package at The researcher also published a paper on the method in the Proceedings of the National Academy of Sciences (see In Print, this issue).

Media Cybernetics has released IQbase 2.0, enterprise image asset management software. Features include new display, measurement, and collaboration tools that enable organizations to store, query, and share scientific or industrial images and data, the company said. The upgrade also includes new functionality that enables IQbase users to export archived images to Microsoft PowerPoint presentations.

Concurrent with the completion of the first phase of the International HapMap project last week, the National Center for Biotechnology Information released accessioned haplotype content at Users can also download the data from the dbSNP FTP site by organism at

UniPro has released UniPro GenomeBrowser 1.1.1, a sequence analysis, annotation, and visualization tool. New features include a dialog to configure features, a new "Density of Features" chart, and interface improvements. The software is available at


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The Virginia Bioinformatics Institute at Virginia Tech has appointed João Setubal as deputy director. Setubal will act on behalf of Bruno Sobral, VBI's executive and scientific director, "handling internal administrative functions, as well as scientific decision-making," VBI said. Before coming to VBI, Setubal was an associate professor at the Institute of Computing at the University of Campinas in Brazil from 1992 to 2004. He has a PhD in computer science from the University of Washington and served in the Department of Genome Sciences at the University of Washington from 2000 to 2001.

The Bioinformatics Organization is seeking nominees for the 2006 Benjamin Franklin Award in Bioinformatics, which is presented annually by the members of the non-profit open source bioinformatics advocacy group "to an individual who has worked to promote open access to the materials and methods used in the field." Past awardees include Ewan Birney, Lincoln Stein, James Kent, and Michael Eisen. Information on the award and the nomination process is available at

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