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Allen Brain Atlas Updated with Powerful New Tools

Sept. 13, 2007 | Less than a year after its launch, the Allen Brain Atlas has been updated with powerful new search tools and options that make it easier for researchers to use.

A project of the Seattle-based Allen Institute for Brain Science, the atlas is an open access, Web-based, 3D database of the mouse brain that shows the location of expression sites of more than 21,000 genes at the cellular level. Because of the similarity between mouse and human brains, the database has implications for research into disorders that affect humans.

“This update offers neuroscientists more and better ways to tap into the Allen Brain Atlas data and extract the information most relevant to their research,” said Allan Jones, chief scientific officer of the Allen Institute for Brain Science, in a press release.

Updates to the atlas include:
•            NeuroBlast, a data mining tool that helps extract relevant data quickly. It helps users easily find genes similar to the one they are searching for by retrieving a list of genes with similar expression patterns.

•           Easy browsing and quick view options let users quickly access and scan images, data summaries, and anatomic reference plates from the integrated Allen Reference Atlas.

•            Improved navigation lets users zoom and pan through data while tracking where in the brain they are looking. 

•            Programmatic access allows third-party search programs to see and retrieve Allen Brain Atlas metadata programmatically for research, Semantic Web, or other applications. 

Additional fine structure annotation options direct researchers to the 50 genes most specific to defined fine brain structures of interest.

In addition, the Allen Institute for Brain Science has released Version 1.4 of its downloadable viewing application, Brain Explorer — an interactive 3D version of the Allen Reference Atlas, the anatomic map integrated with the Allen Brain Atlas.

Related story: Completion of Allen Brain Atlas Hailed as "Epoch-Making," Bio-IT World, Sept. 2006.

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