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{bio,medical} informatics

Monday, October 03, 2005

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find related articles. powered by google. Bio-IT World Apple Adds Analysis Apps to Workgroup Cluster

"Adding to its support of The BioTeam’s iNquiry informatics software, Apple announced this week that it will now offer pre-configured Workgroup Clusters with two popular numerical analysis programs: Wolfram’s gridMathematica and MathWorks’ MATLAB.

With the bioinformatics cluster [the Workgroup Cluster with iNquiry pre-installed], we found a broader base of scientists wanted to use the combination of pre-configured Xserve hardware with Mac OS X and other [system] software,” says Liz Kerr, Apple’s director, science and technology markets."

redux [05.11.04]
find related articles. powered by google. Macworld Apple's $200,000 research-donation

"Apple will donate a Workgroup Cluster for Bioinformatics to five of "America's most important, innovative and visionary scientific research projects."

"The purpose of program is to provide innovative scientists with computer hardware that will enhance their ability to conduct their research in unique ways," according to Apple."

redux [03.23.04]
find related articles. powered by google. The Mac Observer Xserve G5 Shipping, Apple Introduces Bio Sciences Cluster

"The Xserve G5 uses a new version of the G5 processor from IBM that uses less power and generates less heat than the version used in Apple's current Power Mac G5 models. The Xserve line itself is a major component of Apple's push into the new server-oriented markets such as rendering farms, IT server rooms, and even scientific uses, which brings us to Apple's other announcement today, a new bio sciences cluster.

The company has announced the Apple Workgroup Cluster for Bioinformatics. The Cluster is based on the Xserve G5, and, as the name implies, is configured specifically for bio sciences. The solution comes with a software package from The Bio Team."

redux [02.12.04]
find related articles. powered by google. Macworld Scientists: The Latest Mac Converts

""For our [Mars] landing site work, we always get the highest-end desktop Mac we can find, so we just got one of the G5s with dual 2-GB processors and 8 GB of RAM," Matt Golombek, a planetary geologist at NASA's Jet Propulsion Laboratory, told the E-Commerce Times."

""If you pull up a shot of NASA after the [first] Mars landing and look at the desktops, you'll see a couple of PC laptops there, but you'll see more PowerBooks," Jon Rubinstein, senior vice president for hardware engineering at Apple, told the E-Commerce Times."

redux [01.22.04]
find related articles. powered by google. Macworld Xserve G5 cluster unveiled

"Apple's focus on creating products that should be of use to the high-performance computing markets has spawned a new, little-known product combo - the Apple Workgroup Cluster for Bioinformatics.

This is a pre-configured bioinformatics cluster built around the new Xserve G5. The cluster includes between four and 16 servers, a rack to hold the them, cabling, and systems and application software. The bundled system includes The BioTeam's iNquiry software with 200 informatics applications including BLAST and HMMER. It costs from $27,999."

redux [01.06.04]
find related articles. powered by google. MacDailyNews Apple previews Xgrid technology; uses Rendezvous to make cluster computing easy

"Apple today previewed Xgrid, a computational clustering technology from Apple's Advanced Computation Group (ACG). Xgrid helps scientists and others working in compute intensive environments to fully utilize all IT resources, including desktops and servers, by creating a grid enabled "virtual" IT environment that takes advantage of unused computing capacity to run batch and workload processing."

""The Xgrid BLAST application enables bioinformatics researchers to perform distributed BLAST searches on a cluster running the Xgrid software," said Richard H. Scheller, Ph.D., senior vice president of Research, Genentech in the press release. "We tested Xgrid BLAST by querying DNA sequence files for matches against multi- gigabyte genomic databases on a cluster of four dual-processor Xserves.""

redux [11.26.03]
find related articles. powered by google. Computerworld Singapore Muscling up apple power

"Dr Elia Stupka (left), Bioinformatics Programme manager, Laboratory of Computational Biology said, "The Xserve is suitable to TTL because the operating system (OS) X Unix-based open source application can be ported and run easily. And integration with specific software tools is seamless.""

"In addition, he could use the same OS on his desktops, portable computers and network cluster. Stupka sought to tap on the unused computing power of all the devices in the cluster."

redux [10.31.03]
find related articles. powered by google. Wired News Mac Supercomputer Just Got Faster

"The latest semi-official numbers concerning the speed of Virginia Tech's "Big Mac" supercomputer rank it as the third-fastest machine on the planet.

The system's architect, Srinidhi Varadarajan, said Tuesday evening that the newly completed supercomputer operates at 9.55 trillion operations a second, or 9.55 teraflops."

find related articles. powered by google. O'Reilly Network: MacDevCenter Confessions of the World's Largest Switcher

"It's a shame that Apple no longer runs the "Switch" campaign on television. Dr. Srinidhi Varadarajan would make an excellent spokesperson for moving to the Mac."

" His ad might go something like this. "I was in the market for a new machine. I was hoping to get ten teraflops by the end of the year. I'd never used a Mac and had been looking at Dells and IBMs. Then Apple released the G5 on June 23. A week later I bought 1,100 duals online at the Apple Store. I'm Srinidhi Varadarajan and I build Supercomputers at Virginia Tech.""

redux [10.25.03]
find related articles. powered by google. Bio-IT World Scientific Computing: Apple's Next Big Leap?

"Tribble, one of the designers of the original Macintosh user interface, said that with the advent of the Power Mac G5 and the OS X operating system, the Macintosh now has the Unix backbone, 64-bit processing power, Windows interoperability, and open source credibility to be a viable computing platform in the life sciences space.

"Really, for the first time in this industry, you have a computer that can do all the scientific applications, and you can run Microsoft Office," he said. "It's been kind of a Holy Grail that started with Mac OS X.""

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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