Virtual Mouse Brain is Penguin-Powered

One of GNU/Linux's unique properties is its ability to run on dozens of platforms (whereas Windows runs on precisely one, that of Intel's processors). GNU/Linux can power anything from an embedded processor in a tiny industrial device, through mobile phones, PCs, minicomputers, mainframes right up to massively-parallel supercomputers.

One of these, IBM's Blue Gene/L, has recently been used to model part of a mouse brain in near-real-time. Which means that GNU/Linux has just added a platform, albeit as an emulation. (Via Jamais Cascio.)

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.

I'll Have What Doug's Having

Doug Engelbart is The Man: he invented practically everything clever in recent computing, from the mouse through to hypertext. One of his lesser-known but more ambitious projects was the Open Hyperdocument System. Or rather is, since it's back as HyperScope 1.0:

The HyperScope is a high-performance thought processor that enables you to navigate, view, and link to documents in sophisticated ways. It's the brainchild of Doug Engelbart, the inventor of hypertext and the mouse, and is the first step towards his larger vision for an Open Hyperdocument System.

The HyperScope is written in JavaScript using the Dojo toolkit and works in Firefox (recommended) and Internet Explorer. It uses OPML as its base file format. It is open source and available under the GPL.

In practice, this sounds like fine-grained navigation and presentation of documents (although it seems to be much more). There's even a demo you can try out.

After just a brief perusal of this stuff, I can confidently say I don't really know what's going on. But if it's good enough for Doug, it's good enough for me. (Via Techmeme.)