Brain Institute's Clever Move

One of the more unexpected interests of Microsoft co-founder Paul Allen is the Allen Human Brain Atlas:

Using an innovative approach to human brain mapping, the Allen Institute is developing a one-of-a-kind resource for understanding genes at work in the human brain. Launched in May 2010, the ALLEN Human Brain Atlas is expected to provide insights that propel researchers to understand and discover new treatments for a variety of brain diseases and disorders, including Alzheimer’s disease, autism, schizophrenia and drug addiction.

To its credit, it has adopted a reasonably liberal licence:

You may use, copy, distribute, publicly perform, publicly display or create derivative works of the Materials for research or noncommercial educational purposes or for your own personal noncommercial purposes.

Interestingly, it has this rider:

Freedom to Innovate and Rights to Improvements

You may, and are encouraged to, develop new methods, applications, interfaces or other inventions or works that improve the use of, and build upon, the Materials (collectively, “Improvements”). In order to make the Materials available to you and others in the research community, however, the Allen Institute must preserve its freedom to innovate. If you develop an Improvement based on or utilizing the Materials, and you obtain any proprietary rights in or to that Improvement, you and your successors or assigns agree not to assert such proprietary rights against the Allen Institute or its successors or assigns for its or their use of any Improvement independently developed by or on behalf of the Allen Institute that might otherwise infringe such proprietary rights. Additionally, the Allen Institute retains its rights, title and interest in any Materials that are part of or are used by you to create an Improvement.

That's a clear recognition of the fact that "proprietary rights" like patents cut across the "freedom to innovate". It's a pity that the Allen Institute didn't go further, and insist that all improvements be made freely available to everyone, but it's a start.

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The Open Source Brain

At first sight, there's something appropriate about Paul Allen paying for the Allen Brain Atlas:

an interactive, genome-wide image database of gene expression in the mouse brain. A combination of RNA in situ hybridization data, detailed Reference Atlases and informatics analysis tools are integrated to provide a searchable digital atlas of gene expression. Together, these resources present a comprehensive online platform for exploration of the brain at the cellular and molecular level.

After all, he did work on an "electronic brain" as they were mockingly called back in those dim, dark days of early computing. And it comes as no surprise that the freely-available and rather impressive 3D Brain Explorer - think Google Earth for the mouse brain - is only available for Windows XP and the Macintosh.

But dig a little deeper, and you find something rather telling about the real "brain" behind this brain:

Processing the amount of data produced during the Atlas project (approximately 1 terabyte/day) requires a fully automated data processing and analysis pipeline. A goal of informatics is to provide the infrastructure that will allow scaling of an increase in image data and complexity of image processing. The IDP was designed to be modularized and scalable to support a library of informatics algorithms and to function so that additional incorporation of informatics modules does not interrupt production systems. The system must also have the flexibility to accommodate defining multiple workflows using some or all algorithms and is iterative in its processing of gene image series. Parts of the process are computationally intensive, such as image quality assurance/quality control (QA/QC) and preprocessing, registration, and signal quantification. These tasks are scheduled and run in parallel on the server cluster.

Right. And just as a matter of interest, what might that cluster be running?

The cluster consists of a total of 148 CPUs, 32 HP BL35p blades with dual AMD 2.4Ghz, 4GB RAM and 21 IBM HS20 blades with dual Intel 2.8Ghz Hyperthreaded, 4GB RAM, all running Fedora Linux.

Obviously someone used their brain.