Allen Institute for Brain Science launches its Brain Atlas on December 13, 2004.

  • By Patrick Marshall
  • Posted 2/24/2013
  • Essay 10336

On December 13, 2004, the Allen Institute for Brain Science launches its Allen Brain Atlas, an online resource available to the public. The first batch of released data maps the location of nearly 2,000 genes actively operating in the mouse brain.  (Genes express amino acids, which fold together to make proteins, which do most of the work of the body.) That’s only one-tenth of the final goal of mapping all 20,000 genes in the mouse brain, a goal that will be reached in 2006. The data is displayed in a Web interface, and researchers can search the database for specific genes.

The Allen Institute for Brain Science was launched in 2003, with a $100 million donation from Paul Allen (1953-2018). It is an independent, nonprofit medical research organization located in the Fremont neighborhood of Seattle and dedicated to accelerating the understanding of how the human brain works.

The institute chose to focus first on analyzing the mouse brain because it is similar -- both structurally and genetically -- to the human brain. Indeed, the human and mouse genome share 99 percent of genes. Researchers hope that mapping genes expressing proteins in the mouse brain will not only enhance our understanding of the brain, but  may explain the cause of such diseases as Alzheimer’s and Parkinson’s. 

(Allen’s mother, Faye, was diagnosed with Alzheimer’s disease in 2003 and died of complications from the disease in 2012.) 

By 2006, the Mouse Brain Atlas was receiving 250 hits a day from researchers. "I really can't live without it," Ben Barres, professor of neurobiology and developmental biology at Stanford University, told a reporter in 2006 (Doughton). 

According to Dr. Thomas Insel, director of the National Institute of Mental Health, the federal government would have been reluctant to fund a project like this one. "For a private donor to build this kind of a spectacular electronic atlas and just say to the world: 'Have at it' -- I can't think of a precedent for that," he told The Seattle Times (Doughton).

The Mouse Brain Atlas had cost approximately $40 million as of 2006. 

In May 2010, the institute launched the Allen Human Brain Atlas, a publicly available online atlas charting genes at work throughout the human brain. The atlas offers a 3D framework that includes over 700 distinct anatomic locations throughout the brain and containing information for over 62,000 gene probes with 93 percent of known genes.  The first release provides nearly 50 million gene expression measurements from a single brain. Future releases will include data from additional brains and from brainstems.

In November 2011, the institute launched a new resource, the Allen Mouse Brian Connectivity Atlas. The Mouse Brain Connectivity Atlas is a 3D high-resolution map of neural connections throughout the mouse brain. Major enhancements were also delivered to the Mouse Brain Atlas, the Human Brain Atlas, the NIH Blueprint Non-Human Primate Atlas, and the BrainSpan Atlas of the Developing Human Brian.

The institute released another round of updates to its atlases in 2012. At the same time, Allen announced his commitment of an additional $300 million to cover the first four years of a new 10-year plan.

In addition to its original research and its creation of online resources for researchers, the institute in 2013 announced a series of free workshops around the world for those wanting to learn to use the provided tools.


The Allen Institute for Brain Science website accessed February 23, 2013 (; Sandi Doughton, “Paul Allen's 'Brain Atlas' Unlocking Mysteries of the Ultimate Computer,” The Seattle Times, September 26, 2006 (; Sandi Doughton, “Paul Allen Gives $300 Million to Fund Brain Research,” The Seattle Times, March 21, 2012 (

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