The Allen Institute for Brain Science is making its first batch of scientific results available to the public today, through a map that shows where nearly 2,000 genes are actively...

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The Allen Institute for Brain Science is making its first batch of scientific results available to the public today, through a map that shows where nearly 2,000 genes are actively operating in the mouse brain.

The data release puts the nonprofit research center about one-tenth of the way toward its goal of mapping out where 20,000 genes are active in the mouse brain. The results will be displayed online to scientists through a Web browser, where they can run database searches for a particular gene they study. The massive digital image files of brain tissue that show where genes are active will be stored on servers at the institute’s headquarters in Seattle’s Fremont neighborhood.

Allan Jones, senior director of operations, said the institute remains on track to finish the map by mid-2006, its goal. During the first 15 months, he said, much of the time was spent setting up automated processes and working on the computational challenge of displaying a 3-D organ through a 2-D format on the Internet.

Because the mouse brain is similar to the human brain, the institute’s founders hope mapping it will lead to better understanding of how the brain works, as well as the causes of diseases such as Alzheimer’s and Parkinson’s.

The precise methods of the project and findings are not yet being published in a peer-reviewed scientific journal, but they may be at some point. The institute is continually seeking funding and validation from credible sources such as the National Institutes of Health, Jones said.

“Early on, I had doubts as to what kind of resource this could be, but this will be an incredible resource for scientists,” he said.

Allen Institute for Brain Science

Founded: 2003

Status: Nonprofit

Located: Seattle, in Fremont

Employees: 53

Investor: Microsoft co-founder Paul Allen has committed $100 million to its first project, the Allen Brain Atlas

Senior director of operations: Allan Jones

What it does:
Developing a cellular map of the mouse brain to put on display for scientists through a Web browser

Web sites:,

The nonprofit research center was launched in September 2003 with a $100 million commitment from Microsoft co-founder Paul Allen.

The institute still has some leadership matters to clear up. It lost its founding director, Mark Boguski, in its first year. It is looking to hire a chief operating officer, who will spearhead the institute’s development, fund raising and relationships with academic and industrial collaborators. When asked about the institute’s long-term future beyond the three-year mouse-brain mapping project, Jones said that will be up to the new leaders.

If the data prove to be high quality and reproducible, that could go a long way toward establishing the institute, scientists say.

Denis Baskin, a professor of medicine at the University of Washington who uses brain-mapping techniques to study obesity, said a map could be especially useful if it went into high-resolution detail. For example, he knows the gene he’s looking for, and the region of the brain where it operates, but he wants to pin down the precise sorts of nerve cells where it is active.

He said he’d be curious to see what he can learn from the atlas. “As a reference volume, I’m sure it will be useful. I’m excited to see it,” he said.

Luke Timmerman: 206-515-5644 or