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{bio,medical} informatics

Wednesday, October 15, 2003

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find related articles. powered by google. Wired News Mac Supercomputer: Fast, Cheap

"Early benchmarks of Virginia Tech's brand new supercomputer -- which is strung together from 1,100 dual-processor Power Mac G5s -- may vault the machine into second place in the rankings of the worlds' fastest supercomputers, second only to Japan's monstrously big and expensive Earth Simulator."

""They're getting about 80 percent of the theoretical peak," Dongarra said. "If it holds, and it's unclear if it will, it has the potential to be the world's second most powerful machine.""

redux [09.12.03]
find related articles. powered by google. Businessweek A Mac-Style Supercomputer

" Here's a groundbreaker in computing, one that Apple can't take credit for: A group of scientists at Virginia Tech has figured out how to build the world's next supercomputer -- on the cheap no less -- using Macs. And they're in the process of doing it."

"And they would have it for chicken feed, relatively speaking. The Mac cluster will cost no more than $5.2 million, which is "quite modest," according to Tech officials. To save more money, the university is recruiting students to help set up 19.25 tons of computers, routers, and other equipment."

redux [09.03.03]
find related articles. powered by google. The Roanoke Times Va. Tech aims for computer ranking

"Apple Computer is shipping about 1,100 of the company's G5 Power Macs - a dual-processor computer being billed as the world's fastest personal computer - to Tech during the next month. Tech engineers and computer scientists then hope to connect, or "cluster," the G5s to create a supercomputer capable of handling massive calculations needed in such fields as nanoscale electronics and computational chemistry.

Tech is racing to complete the project by Oct. 1, the deadline for consideration in a popular ranking of the world's top supercomputers."

"The Virginia Bioinformatics Institute, a state institute run by Tech, has two supercomputers at its location in the Virginia Tech Corporate Research Center."

redux [03.30.03]
find related articles. powered by google. Bio-IT World Xserve and iPod simplify cluster setup

"iNquiry combines the technology The BioTeam developed for Texas A&M into a system that other bioscientists can use to create their own Xserve clusters in a matter of minutes instead of weeks, according to Van Etten. The secret is another Apple product -- the iPod.

Wholly self-contained in about 2GB of storage space on the iPod, iNquiry uses a Perl-based script that's controlled through a simple graphical configuration utility. The user tells the configuration utility how to configure the Xserve cluster, how many nodes it has, how the network is configured, and how to use the individual drive bays in each Xserve."

redux [11.06.02]
find related articles. powered by google. Wired News Beyond MP3s: iPod Holds Genome

"While it sounds neat to put the human genome on a hip-looking device people more commonly use to crank out Mos Def tunes, some researchers say using it to store the blueprint for humankind is not entirely practical."

""If you're walking back and forth (to transfer data) that's not good," said Richard Gibbs, director of the human genome sequencing center at Baylor College of Medicine. "It's often tempting to do that because of bandwidth, but the smart thing to do is make sure you have the proper infrastructure to (transfer data).""

redux [10.29.02]
find related articles. powered by google. Apple: Pro/Science Performing Feats of Bioinfomagic

"Dr. Will Gilbert likes to carry the human genome around on his iPod. It's the easiest way, he says, to transfer the genome -- 3 billion chemical "letters" that make up a person's genetic code, or DNA -- to the computers of other researchers at the Hubbard Center for Genome Studies at the University of New Hampshire.

Gilbert had set up a research project involving the human genome on his Power Mac, using the Apple/Genentech version of BLAST. A breakthrough implementation of the popular bioinformatics tool from the National Center for Biotechnology Information (NCBI), A/G BLAST conducts high-speed DNA searches in biomedical research and drug discovery. "But," says Gilbert, "I wanted to run the project down the hall on another Mac. Rather than copy it across the network, I'd pull out my iPod. Plug it in, drag, drop, zip, boom, bang and walk it down the hall.""

redux [08.20.02]
find related articles. powered by google. DigtalMass Apple's Mac muscles in

"High-powered computers are the "tech" in biotechnology. So it's no surprise that Cambridge-based biotech giant Genzyme Corp. uses lots of muscular workstation machines, most of them running the sophisticated Unix operating system.

But what is surprising is that some of these powerful Unix boxes bear the trademark of Apple Computer Inc. They're Macintoshes -- the same user-friendly computers that have earned Apple a loyal following among artists, publishers, and home computer users."

redux [07.01.02]
find related articles. powered by google. Genomeweb Apple Becomes First Corporate Member of's Co-Lab Program

"Apple Computer has become the first member of a program launched by open-source advocacy-group that aims at linking open-source developers with bioinformatics hardware and software vendors.

Apple's new Co-Lab program hopes to nurture industry involvement either by co-locating software projects at its SourceForge-based Open Lab project or by hosting and sharing those projects with developers at vendor sites via the web, according to president and founder Jeff Bizarro."

redux [05.19.02]
find related articles. powered by google. Grid Computing Planet Mac OS X Gets A Grid Solution

"Platform Computing plans to make its flagship Platform LSF software available for Apple's new Xserve, extending support for Mac OS X and Apple's new server, storage and systems management offerings.

"The combination of the Mac Xserve with Platform Computing's technology will enhance the quality and speed of work for Mac applications in life sciences, education and business," Ron Okamoto, Apple's vice president of Worldwide Developer Relations, said in a statement."

find related articles. powered by google. MacCentral Apple announces new rack-mount server

" Genentech -- Guy Kraines, vice president, Corporate IT. We got to use them, and we've got some observations. First, this is not a desktop box with rack-mount ears. From the physical design, the hot-swap capabilities, the remote monitoring -- this is a data center box. My guys in the data center are fully accepting of it. They did it right, right down to cable management. Second, performance. The G4 itself is a heck of a processor, especially with what we do. Velocity Engine doesn't just do Photoshop rendering well -- it does matching of genetic code really well too. The single most common application in bioinformatics is Blast. I'm not going to give you numbers today in terms of what we've done, but let's just say that this is not just a measurable improvement, but a meaningful improvement in helping us do what we need to do."

redux [12.16.01]
find related articles. powered by google. The O'Reilly Network Bioinformatics Meets Mac OS X

"Scientists are porting bioinformatics tools to the Macintosh platform because often they are already Macintosh users, and they want the convenience of being able to perform their research on their primary desktop computers. Traditionally scientific researchers have needed a desktop computer for all of their productivity applications, and a separate platform for the compute engine to support their research. "The tremendous benefit of Mac OS X is it gives you both," says Van Etten. "The only thing that comes close is Linux, but for most bioinformaticists, the Linux desktop user experience is a little sophisticated.""

[ rhetoric ]

Bioinformatics will be at the core of biology in the 21st century. In fields ranging from structural biology to genomics to biomedical imaging, ready access to data and analytical tools are fundamentally changing the way investigators in the life sciences conduct research and approach problems. Complex, computationally intensive biological problems are now being addressed and promise to significantly advance our understanding of biology and medicine. No biological discipline will be unaffected by these technological breakthroughs.


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