Researchers from the Broad Institute of MIT and Harvard have announced that GenomeSpace, a software environment that seamlessly connects genomic analysis tools, is now available to the scientific community. During her keynote address at Bio-IT World Conference and Expo on Tuesday, Jill Mesirov, director of computational biology and bioinformatics at the Broad Institute, invited biomedical researchers and tool developers to explore this beta release of the new resource and to use it in their work.
Currently, in order to make use of multiple analysis tools and data sources, biologists need to convert between the different data formats they use. This often involves error-prone spreadsheet manipulations or requires programming skills to write scripts. Mesirov's team and her collaborators set out to change that.
"Our goal is to bring the ever-changing wealth of genomic analysis methods and whatever data are required to the fingertips of any biologist," said Mesirov.
The GenomeSpace environment currently connects six tools: GenePattern, Galaxy, Integrative Genomics Viewer (IGV), Cytoscape, Genomica, and the UCSC Genome Browser. Many projects in genomic research rely on one or more of these tools. For instance, if researchers want to test a hypothesis about genetic differences between two stages of breast cancer, they might first use an analytical tool such as GenePattern to detect genes of interest; then IGV to view their genetic sequence; and then Cytoscape to see protein-protein interactions. GenomeSpace allows them to seamlessly transition between all of these tools to carry a project through to completion.
But GenomeSpace can also be used for smaller inquiries or simple conversions from one tool to another. GenomeSpace's designers worked closely with scientists from the Broad Institute and beyond to determine many kinds of scientific problems for which GenomeSpace could be used. "We strove to identify a range of critical biol
|Contact: Haley Bridger|
Broad Institute of MIT and Harvard