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{bio,medical} informatics

Tuesday, February 19, 2002

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find related articles. powered by google. The New York Times Grid Project to Wed Web Services
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"A worldwide computing project known as grid, whose long-term vision is to bring the power of supercomputing to individuals, is taking a step out of the laboratory and into the commercial mainstream."

"The grid researchers in the labs have used their technology to enable far-flung groups of scientists to collaborate on complex projects that require lots of computing firepower including climate modeling, high-energy physics, genetic research and earthquake simulations."

redux [01.31.02]
find related articles. powered by google. The O'Reilly Network Lincoln Stein's Keynote: Building a Bioinformatics Nation

"Lincoln then summarized efforts to unify the bioinformatics data services. These efforts started 12 years ago with the Meetings of the Molecular Biology Databases (MMBD), which essentially ended in argument. Every member thought his or her way of doing things was the best way. Next came the federated models like Gaea and Kleisli , and then the data warehouses of Ensembl, UCSC, and others. This brings us to the ad hoc Web services that are currently in place. These allow programmatic access to data, as in the GenBank/EMBL example. To truly unify the services of bioinformatics data providers we need to move beyond this to a more formal Web services model.

In this Web services model, the data providers would register their services in a formalized service registry, and researchers' scripts would no longer need to be concerned with the interface details of the different databases. This model represents the unification that Lincoln, and judging by the response, apparently everyone in the audience, hopes to see in bioinformatics."

redux [02.06.01]
find related articles. powered by google. EyeForPharma GRID and distributed computing in pharmaceutical R&D

"Sixty-nine percent (69%) of respondents said they were addressing the lack of processing power by deploying GRID, clustered or distributed computing technologies. Of those, 100% are utilizing clusters. And according to the study, 69% of those are Linux clusters.

"In addition, 46% are deploying distributed computing technology and 23% are utilizing GRID computing somewhere in their organization."

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."

[ 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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