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{bio,medical} informatics

Friday, April 04, 2003

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find related articles. powered by google. Genomeweb "Grid Nirvana" Beckons Genomics Researchers

"What if you could call off your hunt for all the data you need? Forget about trying to run analyses of your favorite gene from your desktop, or whether you'll have to book time on a supercomputer or ship out to a Linux cluster.

Imagine, instead, simply punching in your query and something called "the grid" would just do it all for you. It would pull together all the bioinformatics applications, shuffle the data from the appropriate databases, and crunch various components of your analyses on just the right arrangement of computer processors.

Grid nirvana," as Abbas Farazdel calls this fantasy, is the future for basic biological research, drug discovery and development, and even diagnostics research. Or at least that's what some academics and industry players such as IBM, Sun Microsystems, HP, SGI, Dell, Platform Computing - to name a few - would like you to believe."

redux [01.09.03]
find related articles. powered by google. Bio-IT World Grids: When Concepts Collide

"Clearly, grid computing means different things to different people, often at different times. To its most visionary pundits, grids symbolize the penultimate step in the evolution of computing architecture into a universal source of pervasive, utility-like computing power that companies can purchase as needed, much as they purchase electricity today. Most stalwart advocates believe that grids not only represent the IT environment of the future but also will ultimately eclipse in significance what the Internet is today."

"All hype aside, it is unlikely that grids will fundamentally change the way that scientific and technical computing is done in the near term, particularly in the private sector."

redux [09.13.02]
find related articles. powered by google. Genomeweb Pharma Eases onto the Grid, but Desktop Deals Highlight Remaining Obstacles

"A final obstacle that Stuart pointed out is of the self-inflicted variety: Grid, distributed, peer-to-peer, and other similar incarnations have become victims of their own hype. Increasing media coverage of these technologies has led to confusion in the marketplace, Stuart posited, "and when a prospect becomes confused, the easiest thing is not to do anything.""

"However, he added, there is a bright side to the publicity deluge. Citing the Gartner Group's annual "Hype Cycle of Emerging Technologies" report, which tracks new methods from the initial "tech trigger" period through the "peak of inflated expectations," the "trough of disillusionment," the "slope of enlightenment," and onto the final "plateau of productivity," Stuart noted that desktop grid computing might be working its way from the trough to the slope phase right now, largely because users are discovering which applications work best with the architecture."

redux [09.11.02]
find related articles. powered by google. Eyeforpharma Platform Computing builds enterprise grid for Bristol-Myers Squibb

"Platform Computing recently announced Bristol-Myers Squibb (BMS) has selected Platform ActiveCluster to build one of the largest enterprise desktop grids in production for pharmaceutical research to date. BMS, after an extensive competitive evaluation and pilot stage, is currently deploying Platform ActiveCluster to several thousand desktop computers housed in its research sites across the northeast United States."

"BMS will use the Platform technology, Rozenman said, to link a large number of desktop PCs and existing dedicated computer clusters. The resulting grid initially will be utilized to run both cheminformatic applications, such as Dock, Autodock, Think and GOLD. Ultimately, the grid also will be used to run a variety of bioinformatics applications. "

redux [08.30.02]
find related articles. powered by google. Genomeweb San Diego Supercomputer Center Using Entropia Grid to Build Protein-Structure Databases

"A research team at the San Diego Supercomputer Center is using a grid-based computer system from Entropia to build a set of protein structure databases."

"With the help of 250 desktop computers with processing power ranging from 180 MHz to 2.2 GHz, the platform has so far completed calculations on almost 1,000 proteins, said Elbert."

""What they've done in principle they could have done on one of their supercomputers, but those machines are heavily used for other projects," he said. "This is a way of expanding capacity. And it's a whole lot cheaper.""

redux [11.28.01]
find related articles. powered by google. News.Com IBM computers picked for cancer research

"IBM will supply the University of Pennsylvania and four hospitals with computers that will link into a computing "grid" to check for breast cancer, the company will announce Wednesday.

The grid will be used to detect breast cancer in patients, store mammograms in digital form and identify populations that are particularly susceptible, the company said in a statement. The system can be used, for example, to compare a new mammogram to a previous year's image to detect changes.

IBM, along with rivals such as Sun Microsystems and Compaq Computer, have been backing grid computing, which joins computers and storage systems into a large pool of computing power.

redux [11.21.01]
find related articles. powered by google. Scientific Computing World Scientific sharing across computer networks in USA

"The US National Science Foundation has announced a $12 million programme - called the NSF Middleware Initiative (NMI) - to develop middleware: software that allows scientists to share applications, scientific instruments and data, and collaborate with their colleagues across high-performance networks.

The effort will build on the success of the Globus project in developing middleware tools for grid computing, and will integrate Globus and other emerging middleware components into a well-tested, comprehensive, commercial-quality, middleware distribution package that runs on multiple platforms. These middleware distributions will be disseminated to research labs and universities worldwide."

redux [11.12.01]
find related articles. powered by google. ZDNet News New boost for open-source supercomputing

"Platform Computing, a company that tries to harness the collective computing power on computer networks, has signed a deal to commercialize an open-source supercomputing project.

Platform is working with the Globus Project to commercialize the Globus Toolkit for governing the use of computers and storage systems joined into a large computing "grid," Platform said Wednesday."

"Grid computing, though, often uses higher-powered computers than mere desktop PCs, and has attracted the interest of IBM, which thinks corporate customers as well as academics will use grid methods. IBM is working with Globus to boost this expansion.

Grid computing has long held potential for some types of computing tasks--typically those that don't require as much communication between one computing task and another. For this reason, they don't replace single mammoth supercomputers such as those from Cray. However, grid computing is popular among pharmaceutical companies and others."

find related articles. powered by google. Technical Report, Monash University The Virtual Laboratory: Enabling On-Demand Drug Design with the World Wide Grid

"Computational Grids are emerging as a popular paradigm for solving large-scale compute and data intensive problems in science, engineering, and commerce. However, application composition, resource management and scheduling in these environments is a complex undertaking. In this paper, we illustrate the creation of a virtual laboratory environment by leveraging existing Grid technologies to enable molecular modeling for drug design on distributed resources. It involves screening millions of molecules of chemical compounds against a protein target, chemical database (CDB) to identify those with potential use for drug design. We have grid-enabled the molecular docking process by composing it as a parameter sweep application using the Nimrod-G tools. We then developed new tools for remote access to molecules in CDB small molecule database. The Nimrod-G resource broker along with molecule CDB data broker is used for scheduling and on-demand processing of jobs on distributed grid resources. The results demonstrate the ease of use and suitability of the Nimrod-G and virtual laboratory tools."

redux [10.09.00]
find related articles. powered by google. ACM CrossRoads The SETI@Home Problem

"The SETI@Home problem can be thought of as a special case of the distributed computation verification problem: "given a large amount of computation divided among many computers, how can malicious participating computers be prevented from doing damage?" This is not a new problem. Distributed computation is a venerable research topic, and the idea of "selling spare CPU cycles" has been a science fiction fixture for years."

"The Internet makes it possible for computation to be distributed to many more machines. However, distributing computing around the internet requires developers to consider the possibility of malicious clients."

"The general study of secure multiparty computation has produced much interesting work over the last two decades. Less well studied, unfortunately, are the tools and techniques required to move the theoretical results to the real world. The old dream of massively distributed computations is finally coming true, and yet our tools for building and analysing real systems still seem primitive. The challenge of the next few years will be to bridge this gap."

[ 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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