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.

The Mega-Important MicroRNAs

Yesterday, when I was writing about the structures found in DNA, I said

Between the genes lie stretches of the main program that calls the subroutines

This is, of course, a gross over-simplification. One of the most interesting discoveries of recent years is that between your common or garden genes there are other structures that do not code for proteins, but for strings of RNA. It turns out that the latter play crucial roles in many biological processes, for example development. Indeed, they are fast emerging as one of genomics' superstars.

So it is only right that Nature Genetics should devote an entire issue to the subject; even better, it's freely available until August 2006. So get downloading now. Admittedly, microRNAs aren't the lightest of subject-matters, but they're mega-important.