{bio,medical} informatics
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The Scientist
High-Performance Computing On-Demand
[requires 'free' registration]
"Various software packages are designed to build and manage internal grids using an enterprise's own computing resources, the market leader being Grid MP(TM) from United Devices of Austin, Texas.
Such solutions may be robust and help mop up otherwise wasted computing resources, but they still require considerable expertise to run efficiently and ensure that jobs are scheduled correctly and meet agreed priorities. The major cost of a grid lies in managing the resources rather than in the hardware itself, says Atkinson. Therefore, the cost saved by utilizing spare computing resources may be more than outweighed by the cost of additional IT staff. For this reason alone, Atkinson expects many laboratories will make use of external grids."
redux [10.01.03]
"Using the computing power of 2.5 million PCs donated by volunteers from around the world, researchers have narrowed the search for a new treatment for smallpox, now seen as a possible terrorist weapon, to 44 drug molecules that may render the smallpox protein inactive.
The volunteered computing power, set up in a grid through grid.org, contributed more than 250,000 years of computing time in the eight-month Smallpox Research Grid Project, project leaders said. "
""When this project was first explained to me, I thought it was rather Jules Verne-ish," said Army Brig. Gen. Patricia L. Nilo, acting deputy assistant for chemical and biological defense."
Collectively, the 2.5 million PCs running the grid screensaver constituted the world's largest supercomputer, said Todd S. Ramsey, IBM Corp.'s general manager for global government industry."
redux [07.17.03]
"The U.S. is falling behind Japan in the area of supercomputing, as federal research agencies have shifted their focus toward grid computing in the past decade, according to witnesses at a congressional hearing Wednesday.
The result is that U.S. companies have less access to supercomputing resources because demand from the U.S. government has traditionally driven the supercomputing industry in the U.S., critics of the government's efforts in high-performance computing told the U.S. House Science Committee."
redux [06.28.03]
""The language really matters, and confusion on language can be really damaging," Gage said. Citing Sun's experience with Java as an example, he warned developers about the dangers of hype and cautioned them that grid computing risks becoming a catch-all phrase that promises more than it ever can deliver."
"The term has been used to describe a myriad of computing scenarios, from harnessing the processing power in networked PCs build a vast, distributed "supercomputer," to an alternative architecture for the Internet that will provide the underpinnings for Web services and other distributed applications."
redux [05.21.03]
" The American Diabetes Association is using Gateway Inc.'s grid program to run a compute-intensive application designed to accelerate diabetes-related research.
The association, based in Alexandria, Va., is running the Archimedes software application, which Richard Kahn, chief scientific and medical officer for the ADA, called "the Sims City of health care." Using the program, the association can create an environment with any number of variables--such as doctors, hospitals, rooms, costs, patients and treatments--and run numerous what-if scenarios as a way of researching multiple aspects of diabetes care and running clinical studies."
redux [01.09.03]
"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]
"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."
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SciDev.Net
Latin America gets new bioinformatics network
"A second network has been launched in Latin America to boost regional collaboration in bioinformatics Ñ the use of information technology to store and analyse biological information, particularly in genomics.
"The Iberoamerican Network for Bioinformatics, launched last month, aims to improve training, increase research coordination and encourage student exchanges in the region. It links more than 20 research groups from Argentina, Bolivia, Brazil, Chile, Colombia, Cuba, Mexico, Paraguay, Uruguay and Venezuela, as well as Spain."
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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]
"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."
"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]
"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]
"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]
"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]
"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]
"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]
"Apple Computer has become the first member of a program launched by open-source advocacy-group Bioinformatics.org 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 Bioinformatics.org president and founder Jeff Bizarro."
redux [05.19.02]
"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."
" 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]
"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.""
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Biomedcentral
Homegrown scientists
"Saying that the "future strength of the US [science and engineering] workforce is imperiled," the National Science Board (NSB) is urging increased federal funds to support US science students and improved science teaching."
"The situation in biology in general is not as dire as in the other natural sciences, George Langford, professor of biological sciences at Dartmouth and chair of the NSB Committee on Education and Human Resources, told The Scientist , but "it still is an area of concern, and that is particularly true in some of the fields of the life sciences." Langford said the problem is particularly acute in areas that require quantitative skills such as bioinformatics, protein structure, and crystallography."
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Eurekalert
International collaborators to form the Worldwide Protein Data
Bank
"Today the Research Collaboratory for Structural Bioinformatics (RCSB), the Macromolecular Structure Database at the EMBL-European Bioinformatics Institute (MSD-EBI), and Protein Data Bank Japan (PDBj) announced a collaboration to form the Worldwide Protein Data Bank (wwPDB; http://www.wwpdb.org/)."
""By providing a formal mechanism for standardizing the presentation of PDB data, software developers and users of the data will be assured of consistent data. At the same time, it is hoped that this wwPDB will allow for individual creativity in how the data are presented and made available to the community," said Helen Berman, director of the RCSB PDB and Board of Governors Professor of Chemistry at Rutgers, The State University of New Jersey"
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USA Today
Upstart science journals take on the powerhouses
"Science's Rocky-style publishing battle starts its second round Monday when a groundbreaking journal releases its latest issue.
The challenger, the upstart Public Library of Science: Biology, packed a strong punch last month with its first issue, which featured a headline-grabbing report of monkeys getting brain implants to control robot arms. The upcoming issue spotlights newly discovered genes for obesity and osteoporosis."
redux [10.14.03]
"There are lots of scientific journals, and the debut of another one normally would not raise many eyebrows.
But yesterday's online launch of Public Library of Science Biology drew so many curious browsers -- half-a-million Web hits in the first eight hours -- that the swamped site had to divert many to a backup site."
"Led by heavyweights such as Nobel laureate Harold Varmus, former director of the National Institutes of Health, the PLoS project aims to shake up the world of scholarly publishing by freely sharing its monthly contents."
redux [10.10.03]
"In the highly lucrative world of cutting-edge scientific research, it is nothing short of a revolution. A group of leading scientists are to mount an unprecedented challenge to the publishers that lock away the valuable findings of research in expensive, subscription-only electronic databases by launching their own journal to give away results for free.
The control of information on everything from new cancer treatments to space exploration is at stake, while caught in the crossfire are the world's publicly funded scientists, some of whom will soon face a choice between their career and their conscience."
redux [08.22.03]
[requires 'free' registration]
"Debate over open access to scientific articles is steadily moving into the mainstream, with the publication this month of an editorial in The New York Times, a recently introduced Congressional bill to promote open access publishing, and a television commercial sponsored by the Public Library of Science (PLoS), a California-based group that plans to launch an open-access journal in October.
As enthusiasm grows, however, some skeptics wonder whether open-access journals will succeed financially, since they charge relatively small "article processing fees," paid upfront by the researcher, instead of substantial fees for institutional library subscriptions."
redux [07.01.03]
""It's ridiculous," Eisen said in this voice during a recent phone interview from Washington. "All these things we're so used to doing with information on the Internet, we're preventing clever entrepreneurial people from doing with works of science. The idea that a narrow profit motive would prevent the dissemination of this information -- it's insane!"
Eisen was in Washington to lend his support to a congressional effort he believes will make scientific publishing less insane and less ridiculous. Most scientific journals -- such as Science, Nature or the New England Journal of Medicine -- require researchers to turn over all rights to the reports selected for publication; the publications then charge institutions and individuals subscription fees to view these reports, a model that Eisen believes inhibits scientific progress. The approach is especially galling, Eisen says, when you consider that a great deal of the money that funds the research published in these journals comes from the federal government. The public is paying for science that it never gets to see, he says."
redux [12.16.02]
[requires 'free' registration]
"A group of prominent scientists is mounting an electronic challenge to the leading scientific journals, accusing them of holding back the progress of science by restricting online access to their articles so they can reap higher profits.
Supported by a $9 million grant from the Gordon and Betty Moore Foundation, the scientists say that this week they will announce the creation of two peer-reviewed online journals on biology and medicine, with the goal of cornering the best scientific papers and immediately depositing them in the public domain."
redux [11.15.02]
"Having persuaded the Energy Department to pull the plug on PubScience, a Web site that offered free access to scientific and technical articles, commercial publishers are taking aim at government-funded information services offering free legal and agricultural data.
"We're delighted with the decision [to shut down PubScience]," LeDuc said. "The administration has done a tremendous job of hearing our concerns and responding to what we've always considered to be our legitimate concern."
redux [09.24.02]
[requires 'free' registration]
"The UK's Office of Fair Trading says that the prices for scientific, technical, and medical (STM) journals are too high because normal competitive forces have been suspended. Libraries are paying too much. The prices of STMs are rising faster than inflation, and the disparity between for-profit and not-for-profit journals is obvious. Part of the problem is that the journals compete on quality, not price, so libraries are prone to skip the cheaper journals for the better, more expensive ones. Bundling journals also skews the market.
Goodman, S. 2002. "Unusual forces" are pushing journal market off course. Nature 419(6904):239.
redux [09.05.01]
[requires 'free' registration]
"Publishers of established scientific journals have thus far resisted demands for freer access. In its campaign to make biomedical research literature available free online, Public Library of Science is now taking a new tack: It hopes to publish peer-reviewed, electronic journals.
"If we really want to change the publication of scientific research, we must do the publishing ourselves," says an announcement posted Sept. 1 on the group's Web site. "It is time for us to work together to create the journals we have called for."
redux [04.24.01]
"When a molecular biologist or a biochemist has made a discovery - often after many months or even years of tedious experiments - they tell the rest of the world by publishing their results in a scientific journal. So far, these journals have controlled who can read them and who cannot - but maybe not for much longer.
E-mail, Internet discussion groups, electronic databases and pre- or e-print servers have already transformed the way scientists openly exchange their results. And in the life sciences, researchers are now demanding that their work be included in at least one free central electronic archive of published literature, challenging the traditional ownership of publishers. The demand has sparked widespread discussions among scientists, publishers, scientific societies and librarians about the future of scientific publishing. The outcome may be nothing short of a revolution in the scientific publishing world."
redux [09.20.00]
"How should biomedical research be communicated? How should research be assessed and validated?"
"Below are abstracts, transcripts, and biographies from the conference. Some presentations did not lend themselves to transcription. Where possible we have supplemented them with editorials from the speakers.
We have also commissioned editorial articles from several speakers and delagates at the meeting."
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The New York Times
Smaller Computer Chips Built Using DNA as Template
[requires 'free' registration]
"The recipe for a computer chip of the future may read something like this: Take some wires. Add DNA. Stir.
In an advance that might provide a practical method for making molecular-size circuits, the smallest possible, scientists in Israel used strands of DNA, the computer code of life, to create tiny transistors that can literally build themselves."
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Bio-IT World
New Life Science Systems Make 'Top500' Supercomputers List
"The list of the world's top 500 supercomputers, presented at this week's SC2003 Igniting Innovation conference in Phoenix, contains several notable new life science entries."
"A trend that was evident last year and continues this year is the increased adoption of clusters in high-performance computing environments."
redux [07.17.03]
"The U.S. is falling behind Japan in the area of supercomputing, as federal research agencies have shifted their focus toward grid computing in the past decade, according to witnesses at a congressional hearing Wednesday.
The result is that U.S. companies have less access to supercomputing resources because demand from the U.S. government has traditionally driven the supercomputing industry in the U.S., critics of the government's efforts in high-performance computing told the U.S. House Science Committee."
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eWeek
IBM Takes Wraps Off PowerPC-Based Blade System
"The two-way BladeCenter JS20, featuring the 1.6GHz PowerPC 970 chip, will run both SuSE AG Linux Enterprise Service 8 and Turbolinux Inc.'s Enterprise Service 8, according to Karl Freund, vice president of pSeries products and strategy for the Armonk, N.Y., company."
"In a related move, IBM also is announcing the BladeCenter for Bioinformatics. The offering includes such applications as BLAST, FASTA and HMMER, which have been pretested and ported onto the servers to ensure they run well on the system."
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The Age
Biotech wins battle for junk justice
"Investors piled into Genetic Technologies yesterday after the biotech company announced that two US groups it was suing for patent infringement had settled out of court."
"The Melbourne-based Genetic Technologies has consistently warned it would sue any company, research institution or university that infringed its patent over the so-called junk DNA."
redux [08.18.03]
"An Australian biotech company, Genetic Technologies Ltd. (GTG), is stirring up controversy over its decision to enforce a series of patents, granted in the 1990s by the US Patent and Trademark Office, over the genetic diagnostic and mapping applications of non-coding, or junk, DNA."
"Scientists, including NHGRI chief Francis Collins and Sir John Sulston, are also upset over GTG's recent decision to ask academic institutions to sign research licenses."
redux [05.19.03]
[requires 'free' registration]
The dark side of the moon is a misnomer. Light reaches la luna's entire surface, but one half is unviewable from Earth. The human genome, the now essentially decoded map of life, likewise has a light side--the genes encoding mRNA and protein--and a dark side, which is coming into view for the first time. The dark side encompasses more than its opposite: The majority of the genome comprises intronic regions, stretches of repeat sequence, and other assorted gibberish that has attained the ignoble dubbing, "junk."
The first exploratory missions to the human genome's faceted surface are turning up traces regarding the extent of the junk."
redux [11.21.02]
"In a provisional patent application filed July 31, Pellionisz claims to have unlocked a key to the hidden role junk DNA plays in growth -- and in life itself.
Rather than being useless evolutionary debris, he says, the mysteriously repetitive but not identical strands of genetic material are in reality building instructions organized in a special type of pattern known as a fractal. It's this pattern of fractal instructions, he says, that tells genes what they must do in order to form living tissue, everything from the wings of a fly to the entire body of a full-grown human."
redux [08.28.02]
"In a new study in the August 29 issue of Nature, researchers at The Wistar Institute identify a cohesin-containing protein complex that reshapes chromatin to allow cohesins to bind to DNA. In doing so, they also identified the locations on the human genome where the cohesins bind. Somewhat to their surprise, the binding sites were found to be a repetitive DNA sequence found throughout the human genome for which no previous role had ever been identified. These bits of DNA, known as Alu sequences, are liberally represented along those vast stretches of the human genome not known to directly control genetic activity, sometimes referred to as junk DNA."
redux [08.09.02]
"Results of a new University of Michigan study suggest that junk DNA - dismissed by many scientists as mere strings of meaningless genetic code - could have a darker side.
In a paper published in the Aug. 9 issue of Cell, scientists from the U-M Medical School report that, in cultured human cancer cells, segments of junk DNA called LINE-1 elements can delete DNA when they jump to a new location - possibly knocking out genes or creating devastating mutations in the process."
"Scientists in the past decade have discovered that remnants of ancient germ line infections called human endogenous retroviruses make up a substantial part of the human genome. Once thought to be merely "junk" DNA and inactive, many of these elements, in fact, perform functions in human cells.
Now, a new study by John McDonald of the University of Georgia and King Jordan at the National Center for Biotechnology Information at the National Institutes of Health, suggests for the first time that a burst of transpositional activity occurred at the same time humans and chimps are believed to have diverged from a common ancestor - 6 million years ago."
redux [01.20.01]
[requires 'free' registration]
"Speaking at a National Institutes of Health conference on ethical and social issues in genetics, Dr. Francis Collins said that a "spate of papers in public journals'' due out within a month will signify the incredibly rapid pace of scientific discovery seen since the announcement of the nearly complete sequencing of the human genome last summer.
The first, Collins said, will be a paper that puts the total count of human genes at between 30,000 and 35,000. "That's less than half the number most people have been predicting.'' The second is a study ascribing previously unknown biological missions to genes scientists thought were inactive, or so-called "junk genes."
"There is now clear evidence that (the junk genes) have been performing a number of functions for tens or hundreds of thousands of years,'' he said."
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News.Com
IBM gives glimpse of Blue Gene performance
"IBM on Friday talked up its Blue Gene/L supercomputer, the first module of which is a relatively small, dishwasher-size machine that can perform 1.4 trillion calculations per second.
The performance is enough to make the machine the world's 73rd fastest supercomputer, according to a ranking of the top 500 to be released Sunday. By the time IBM has upgraded the box's 512 chips, each with two processors, and linked it with another 127 identical systems in 2005, Big Blue hopes to take the top spot."
redux [09.19.03]
"WHATEVER happened to Blue Gene, IBM's ambitious attempt to build the world's fastest computer? The project, launched in 1999, called for the construction of a "massively parallel" computer with over 36,000 processing chips, each containing 32 processing cores roughly equivalent in power to a desktop PC. Harnessing all that computing horsepower--more than one petaflop, or 1,000 trillion floating-point calculations per second--would, it was hoped, allow scientists to simulate the folding of a protein, an extraordinarily demanding task which might help to streamline the discovery of new drugs. The idea was to achieve all of this within five years--something that even enthusiasts thought ambitious.
Four years on, the chips that will power the first Blue Gene computer are now being manufactured and tested. But the plans have changed somewhat."
redux [05.08.03]
""Blue Gene is a completely oddball, you've-never-seen-anything-like-this-before design," said Illuminata analyst Jonathan Eunice. "It is not custom everything, (but) it is still very exotic compared to anything you can buy.""
"IBM already has spent more than the original $100 million budgeted for the project and won't meet its 2004 goal for the ultimate machine, but the company has made progress bringing its ideas to fruition."
redux [02.11.03]
"THE first version of IBM's revolutionary Blue Gene chip will roll off the production line this quarter, Ajay Royyuru, head of IBM's Computational Biology Centre, has revealed."
""We plan to build a 512-node prototype Blue Gene machine in our Watson Research Centre, in New York, where I am located, hopefully before the end of the year.
Then we will build a 64,000- node Blue Gene machine and deliver it to the Lawrence Livermore laboratory by late 2004, or early 2005."
redux [10.24.02]
"Linux will be the main operating system for IBM's upcoming family of "Blue Gene" supercomputers--a major endorsement for the OS and the open-source computing model it represents."
""We had two choices of operating systems for the Blue Gene family, either use a special purpose system or Linux," Bill Pulleyblank, director of Exploratory Server Systems at IBM Research, said in a statement. "We chose Linux because it's open and because we believed it could be extended to run a computer the size of Blue Gene. We saw considerable advantage in using an operating system supported by the open-source community so that we can get their input and feedback.""
redux [07.13.01]
""Ambuj Goyal, IBM Research's general manager for software, solutions, and strategy, was more ambitious than that. Why not build a machine to model molecular dynamics using general-purpose chips rather than specialized ones? That way you'd produce a prototype for a whole new family of supercomputers. Not only would it be great technology development, it would be great marketing, too. Whereas the Department of Energy has the greatest interest in top-end supercomputing - with its need to understand how nuclear weapons work - focusing on the life sciences rather than the death sciences could make supercomputing more widely appealing. What's more, a biology program would be a way of telling one of the newest markets for big iron - the post-genome biotech world - that IBM took its interests seriously. "We believe that the life sciences are going to be a rapidly growing area," says Blue Gene project manager Bill Pulleyblank, "a huge growth area for IBM.""
[ 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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