Neurome goes with `big iron' from Big Blue

The crew at Neurome Inc., a gene expression database concern, is going seriously mainframe with IBM Corp.'s Regatta p690 eServers.

Neurome Chief Technology Officer Warren Young says the p690 servers and IBM's FAStStorage system will be used to process 2-D and 3-D models of "mouse brain structures, circuits and cells to pinpoint gene expression patterns."

Neurome, he says, conducted it own benchmark tests, and IBM won out over Compaq Alphaservers and Sun Microsystems Inc. UltraSPARC servers. However Neurome uses Compaq Proliant and Sun servers for other tasks, such as firewall management, Young adds.

Just as important as benchmarks was buying the complete system from a single vendor. The system will run 64-bit Java technology, custom applications software, and IBM's flavor of Unix known as AIX. The year-and-a-half old company is also in the middle of a two-month evaluation of IBM's DB2 database. Currently, it's an Oracle Corp. shop.

"[One-stop shopping] was important because too often vendors won't accept blame and accountability [if something goes wrong]. I really don't want to deal with that. IBM will have no one to blame but itself [when something goes wrong]," Young says. In exchange for testimonials about the system, IBM gave Neurome discounts on the hardware, Young says, adding the company spent well over US$1 million on the system.

The hardware was set up in one day on June 24. However, it will take several weeks to install and fine-tune the software, he adds.

Neurome's new system will be used in preparing 3-D atlas databases for mapping out "gene and protein data of mice brains to determine how genes are expressed -- turned on or off -- in diseased or healthy states." The company hopes the work will "shed light" on human neurological disorders such as epilepsy, Parkinson's disease, and schizophrenia.

The databases stores 2-D images of mice brain cells and structures that can range in size from 150 MB to 20 GB, Young says. A 3-D image of an entire mouse brain, divided up into hundreds of thousands of images known as "tiles," can be up to a terabyte.

"We are trying to set up an encyclopedic knowledge base of circuitry, structural, and genetic information about mice brains," he says.

IBM's p690 was first shipped Dec. 14 and is based on the company's POWER4 silicon architecture, incorporating I/O, a large cache, and two 1-GHz microprocessors on a single chip, making it a "system on a chip," according to IBM.

Five years in development, the p690, nicknamed "Regatta," is a product of IBM's Project eLiza initiative, offering self-healing technologies designed to keep the system running through component failures and system errors. That's reassuring to Young.

"We are very computation intensive and run [tasks] overnight for hours and hours," he says, adding images from microscopes are digitized and fed directly into the database. Next up for Neurome's datacenter and laboratories - robotics, Young says.

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