{bio,medical} informatics
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Genomeweb
Is Bioinformatics--and Open-Source Software--in ABI's
Future?
"Brenner, for example, stressed that while open sourcing "has potential in a generic sort of way," success depends on the operational and business models of specific companies.
Even considering a move to open sourcing can meet with resistance. "All of the instrument companies were brought up in closed-source shops, so they would have to change this fundamental attitude," explained Hood."
"THE OPEN SOURCE MOVEMENT has gained significant momentum of late, particularly within the bioinformatics field. While open source licenses vary widely, distribution of open source software typically requires delivery of both the object code and the source code. Most commercial software is delivered only in object code form, which is not easily read and modified by programmers.
The decision of whether to use open source software requires a careful analysis of various factors. In the right situations, open source software can be an excellent choice. In other cases, it can be disastrous."
redux [08.21.02]
"Want to make money from open-source bioinformatics? As long as it's not too much you might be OK.
This was the verdict of a panel of academics and business executives who had convened last week to talk broadly about open-source bioinformatics. But the discussion, which took place at the IEEE Computer Society bioinformatics conference at Stanford University, frequently veered to whether one could, or even should, make money from it.
The answer was a resounding maybe."
redux [01.16.02]
"A debate is heating up in the academic community over whether software that is generated by publicly funded research must be released with an open source license. The Internet is one example of how releasing research code benefited the public, but the trend seems to be changing now, and universities are more likely to consider the profit opportunity. The Bayh-Dole Act paved the way for the privatization of publicly funded resources, but not everyone is happy with the results.
Against the tide of privatization comes a group of bioinformatics researchers and programmers with an online petition to require that all software created by publicly funded research projects be licensed as open source. They have founded a group and a Web site, OpenInformatics.org, to further this cause.
Here we present two opposing viewpoints on this issue."
redux [01.07.01]
"The Open Source movement is infectious, it seems. It has bubbled up in the field of bioinformatics - gene research software. Gene research is already a burgeoning area of activity, which is predicted to deliver numerous benefits to the health industry. It is also an area where software counts and where universities have managed to prosper from their activities. US universities lodge about 2000 patents each year, many in bioinformatics, and these patents contribute a good deal of revenue - an amount estimated at about $5 billion per annum, or ten percent of their total budgets. Thus Open Source activities in this area are not universally welcomed."
"Over the past several years, open-source software development has won high-profile adherents in the business world -- including the likes of IBM and Sun Microsystems. But it has always had its strongest fans in the academic world, where open-source software is seen as a natural extension of the idea that the fruits of academic research should be shared with everyone.
But now some academic programmers on the cutting edge have found that the licensing office is proving a more formidable obstacle to progress than the limits of their imagination and skill."
redux [11.26.01]
"Before computer whiz Steven E. Brenner accepted his tenure-track research post at the University of California-Berkeley last year, he demanded that the school's intellectual property police leave him alone.
Brenner prevailed. He's now one of the few experts in the emerging field of bioinformatics with the freedom to distribute his work, software used in gene research.
``It's vital to what we do,'' says Brenner, who supports a movement to force universities to allow ``open source'' publishing of gene research software code."
redux [08.18.01]
"Steve Brenner, assistant professor and leader of a computational genomics research group at the University of California, Berkeley, said he fears that many academic bioinformaticists are unaware of a legal risk they face on a daily basis: contributing to open source software projects without explicit permission from their institutions.
While many employers have clauses in their employment contracts that restrict the creation and use of open source software, bioinformatics programmers at universities are often not as attuned to copyright issues as their industry counterparts. This fact, Brenner said, raises the possibility that a good portion of biological open source software is currently being produced illegally."
"The issue seems to be coming to a head in the academic world now, as more universities are exploiting the revenue stream made possible by their copyright and patent holdings. ?If you?re a software developer, the university holds rights to your software, but if you?re an English professor or Law professor and publish a book, they?re not the least bit interested in copyright,? said Thomas Field, an attorney at the Franklin Pierce Law Center affiliated with the Association of University Technology Managers."
redux [11.05.01]
"Computers are supposed to help biotechnology, right? Isn't bioinformatics all the rage right now? Well, it is, but with popularity comes legal questions that many companies don't address until it's too late."
"It seems that many biotech companies don't realize that a computer vendor may have the rights to the software, and ultimately, the work that the biotech companies do.
For example, if a biotech company orders a computer network to help it sequence the genome of yeast, the company may ask the vendor to customize the software it will use to do the sequencing. However, the question is, who owns the right to that customized software--the biotech company or the software programmer?"
redux [08.23.01]
"This report outlines recent activity in open source software development within the discipline of bioinformatics. I present the relevant highlights of two bioinformatics meetings held in July 2001 in Copenhagen, Denmark: the Bioinformatics Open Source Conference and the Intelligent Systems for Molecular Biology Conference. The report also describes a large number of projects and groups important to bioinformatics open source software development. The appendices include meeting programs, the currently accepted definition of open source software, and descriptions of important online biological data sources."
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SFGate
Scholars to debate the wisdom of continuing to patent genes
"The Bay Area biotech firm that started the heretical campaign to ban gene patents hopes to stir more debate on the topic by sponsoring a scholarly smackdown in Washington, D.C., on Tuesday.
Santa Clara's Affymetrix broke ranks with the biotech industry in March by arguing that the United States should quit issuing gene patents because genes were invented by nature, not science."
redux [07.23.02]
"Patents on DNA sequences "inhibit innovation and development" and should be the exception rather than the norm, says a panel of leading UK bioethicists. In the past, biotech companies have said that without such patent protection they would not have the economic incentive to invest in expensive research towards new drugs.
A discussion paper, produced by the Nuffield Council on Bioethics (NCB), says that too many patents are of doubtful validity because they are being issued for genetic discoveries that are not adequately inventive. It recommends a number of significant changes to the way patents in the field are granted in the future and to limit possible adverse effects of those already issued."
redux [03.18.02]
"It's one of the toughest questions in biotechnology: Should businesses obtain patents on genetic information about plants, animals or humans? Michael Capellas, CEO of Compaq Computer Corp., surprised an audience of biotechnology specialists yesterday when he suggested that the answer should be "no.""
"In a comment that stunned the audience into several seconds of silence, Capellas responded to a question on the issue by flatly saying that companies shouldn't be able to patent genes. But he quickly backed away from the comment, pleading ignorance of all the ramifications of the issue. "If you're asking me what should be patentable," Capellas said, "I don't know.""
redux [02.07.02]
"Patents may make some genetic tests so expensive that ordinary labs cannot afford to offer them, says a team of researchers who interviewed staff at 119 US facilities.
Patents are meant to provide an incentive for companies to put their discoveries into the public domain. But some researchers wonder if prohibitive costs could in fact have the opposite effect, by keeping standard genetic tests out of the reach of all but a few laboratories. That would have far-reaching consequences not only for health care, but for clinical research and quality control, the researchers say."
redux [08.20.01]
""Like the Terrys, a rising number of patients, doctors and ethicists are questioning how the patent system handles genetic claims. Many say it awards too many patents, overly rewards their holders, and gives too little back to patients. Yet many industry voices complain the process is moving too slowly to keep up with galloping research and to yield medical care awaited by suffering patients."
"The gold rush days are about to begin,'' says Arthur Caplan, a bioethicist at the University of Pennsylvania. "There are so many targets that look so lucrative that they're falling all over one another to pursue opportunity after opportunity.""
redux [02.27.01]
"ONCE upon a time, pure and applied science were the same. Sir Humphry Davy discovered seven chemical elements, and invented the miner's safety lamp. Louis Pasteur investigated the properties of molecules, and worked out how to stop milk spoiling. Everybody thought that was admirable. Somehow, things have changed. Today the feeling is widespread that science and commerce should not - must not - mix. There is a queasy suspicion that the process of discovery is in some way corrupted if it is driven by profit."
"Far from compromising science, profit in both these cases - the development of new medicines and the elucidation of the genome - has animated it, and directed it towards meeting pressing human needs. It is a happy marriage. Davy and Pasteur would surely have approved."
redux [08.26.00]
"Nowhere are patents more central to the creative process than in genetic drug development, where human genes and their expressed proteins themselves are developed as therapies. The biotechnology industry in the United States has brought a handful of these crucial new products (recombinant human insulin, to name one of the most familiar) to market and is on the threshold of a bonanza of genetic drugs and vastly greater relief for ill and aging populations around the world.
Patent protection is the sine qua non of that bonanza."
redux [04.26.00]
""The analogy that I would use is that of a minefield," said Bob Levy, senior VP of science and technology for American Home Products. "We are spending an incredible amount of time now, when we find exciting targets and begin to validate them, in trying to define who has rights to what. And we're finding, in almost every product that we look at, that someone has patented the protein, the gene, a fragment, a diagnostic test." Levy noted that untangling patent rights, and determining which patents are dominant, are increasingly time-consuming and expensive tasks. And patent-holders must be paid. "The royalties that will be involved soon in some of the products that we are bringing to market, they're already up into the ten, fourteen, fifteen percent [range]," said Levy. "And that may increase with time.""
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The New York Times
Here They Are, Science's 10 Most Beautiful Experiments
[requires 'free' registration]
"Whether they are blasting apart subatomic particles in accelerators, sequencing the genome or analyzing the wobble of a distant star, the experiments that grab the world's attention often cost millions of dollars to execute and produce torrents of data to be processed over months by supercomputers. Some research groups have grown to the size of small companies.
But ultimately science comes down to the individual mind grappling with something mysterious. When Robert P. Crease, a member of the philosophy department at the State University of New York at Stony Brook and the historian at Brookhaven National Laboratory, recently asked physicists to nominate the most beautiful experiment of all time, the 10 winners were largely solo performances, involving at most a few assistants. Most of the experiments -- which are listed in this month's Physics World -- took place on tabletops and none required more computational power than that of a slide rule or calculator."
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News.Com
Bioscience deal spurns HP for rival
"IBM and EMC have landed large contracts to install servers and storage systems at Applera, a major life-sciences company that once relied on Compaq Computer for its complex computing needs."
"HP's Alpha chip and the servers based around it are like the art film of the processor world. Academics, analysts and benchmark testers have consistently praised the chip, originally devised by Digital. The National Science Foundation, among others, has installed Alpha supercomputers.
But the broad market has largely ignored it."
redux [09.04.02]
"Billionaire Michael Dell is in the Buffalo area today to help the University at Buffalo unveil a powerful new computer cluster provided by the company that he founded and continues to run."
""We've installed hundreds of these clusters. (But UB's) would be one of the larger ones, not only for us but in the world," Dell said. "And the amazing thing is we got this up and running in 60 days.""
redux [12.05.01]
"The world's largest computer makers, faced with sagging consumer demand, are betting that the huge data crunching needs of nascent biotechnology firms will grow into a multi-billion dollar market for their equipment and consulting services over the next decade."
""The average individual can't comprehend what has happened in the last half dozen years, where the two greatest medical discoveries, the genome and the microchip, have converged," said Cal Stiller, chief executive of the $250 million Canadian Medical Discoveries Fund."
"We need companies that are on the informatics side that say 'holy cow', we have just stumbled onto the mother lode! We know nothing about mining that area, but we can build the best drilling equipment out there," added Stiller."
redux [06.26.01]
"In 1998, biotech upstart Celera Genomics needed a supercomputer to help it map the human genome. It didn't turn to IBM , which built 204 of the 500 fastest supercomputers. Both Celera and its academic competition, the Human Genome Project, used machines built by Compaq Computer. Two years later, Compaq is the leading seller of supercomputers to biological researchers.
But IBM noticed that biologists now need microprocessors as much as microscopes. A year ago, it used $100 million to start a division that sells computers, software and services to biotechnology and drug companies. This life sciences division has had some success; pulling into second place behind Compaq, it must do better."
redux [08.14.01]
"For years, technologists have dreamed that information technology and biotechnology would someday converge into one seamless superscience that could crack the molecular code of disease and yield a gold mine of new treatments and cures. It always seemed so logical, even if it never quite seemed to happen. Some very big names in tech -- Bill Gates ( MSFT ), Paul Allen, and Jim Clark, among others -- for years have been placing bets on so-called convergence companies that promised to exploit the merging of computing and biotech. Allen alone has investments in more than 50 of them, mostly obscure companies that use words like "genomics," "bioinformatics," and "proteomics" to describe what they do. This industry is so new it hasn't settled on a single name yet."
"Now, like a middle-age actor who has just been discovered, convergence has hit the big time. Corporate giants such as IBM ( IBM ) and Compaq ( CPQ ) are pouring $100 million dollops of cash into "life science" projects that mesh computers and biotech."
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TechNews.Com
Make Room for Bioinformatics
"To many Washingtonians, the mention of Springfield conjures up nightmares of a highway free-for-all and an unfathomable tangle of half-finished concrete bridges.
But if Fairfax County economic development officials succeed, Springfield will one day be better known as a leading center of bioinformatics, the maturing field that applies information technology to speed up drug discovery and other biotech research."
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BioMedNet
Adam Smith
and science journals
[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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ABCNews.Com
Millionaires Lining Up to Buy Personal Gene Maps
"A service to map a person's entire genetic code is being offered by America's genome entrepreneur Craig Venter, according to the Sunday Times.
The newspaper said that for 400,000 (US$621,500), a person would get details of their entire genetic code within 1 week. "Armed with such information, the individual would be able to check for mutations linked with illnesses such as cancer and Alzheimer's," the Sunday Times reported."
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Genomeweb
Gathered at Gambling Mecca, Genomics Types Ask Why Pharmas Have
Quit Betting on Them
"In a so-called Masterminds Panel here this morning, four life sciences-industry execs pondered the question, "When and how will '-omic' technologies have a positive impact on pharma's output?" They were generally optimistic, and agreed that genomics and proteomics have had a significant effect on the drug-discovery trade--albeit a different one from what investors desired.
Genomic technologies have generated "lots of target ideas, but the bottleneck [exists] in understanding which target is for which disease," said Mark Crockett, executive director of functional genomics for Bristol Myers Squibb. The effect so far from genomic technologies has been to create more work for pharmas, Crockett said. "New targets have no literature associated with them. There are an average of seven publications on any given protein, which means that pharmas have to do a lot more basic biology.""
redux [12.14.01]
"And although the drug industry remains the most profitable worldwide--it generated profits as a percentage of revenues four times the median rate for all Fortune 500 firms during the end of the last decade, according to a Kaiser Family Foundation report released that day--an editorial in this month's Nature Biotechnology by David Horrobin, CEO of Laxdale Research, in Stirling, Scotland, had this to say: "With rare exceptions, most of the top 20 multinational pharmaceutical companies are not generating in-house the new products needed to sustain the rates of growth they have enjoyed in the past.
redux [05.26.00]
""The data suggest that the biotechnology industry used to be more productive than Big Pharma, but not any longer," said Rebecca Henderson, a professor at MIT's Sloan School of Management whose been studying the question for six years. "The public biotechs have declining productivity... and look as if they are running into the same problems as Big Pharma."
On every metric that Henderson has studied---number of scientific papers and patents per R&D dollar, cost per new drug--she found that biotech and Pharma productivity were quickly converging, and both were getting worse. After spending six years of studying the question, Henderson says she has found "no systematic evidence that small firms are more productive.""
redux [11.29.01]
[requires 'free' registration]
"Glenn Giovanetti at Ernst & Young Life Sciences Industry Services, comments "You could really compare [today's situation] to a large degree with the first biotech boom in the late eighties and early nineties where the thought was, 'Hey, this is going to lead to better drugs faster,' and clearly that hasn't been the case." Having the genome in hand has brought about more drug targets, but, explains Ma, "People are getting more concerned that novel targets are going to have a higher rate of failures because there is less information on them." And when working in 10-year drug-development cycles, failures are costly.
Ma points to a trend of growth in clinical informatics that would effectively garner more information from expensive clinical trials instead of simply treating them as regulatory hurdles. "People are beginning to think through to how ... to take greater advantage of that information," he adds. But increasingly, the suppliers of genomic information have been looking to do the same thing.
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The Straights Times
China opens way for 'super rice'
"Coming soon: a 'super rice' that is pest and disease resistant and which also tastes good.
And the credit will go to China, which yesterday created a public bank of thousands of genes it had discovered during a project to map out the basic genetic code of the indica rice."
"Scientists from the Beijing Genomics Institute at the Chinese Academy of Sciences pledged yesterday to share a set of 54,000 genes, or what is called a microarray, it had sequenced this year with the world's research community."
redux [09.06.02]
"Unravelling the blueprint of rice may be the most important breakthrough genetic science has achieved."
"Because rice is mankind's most important food crop - the staple diet for half of humanity - the researchers say reading its genome is of more importance than decoding mankind's own genetic code."
redux [04.06.02]
[requires 'free' registration]
"Rice is "the Rosetta stone of the cereals," Dr. Wing said. Once researchers have found an important gene in rice, they can look for its counterpart in other crop plants, or insert the rice gene itself since the genes of all these crops are thought to be largely interchangeable."
"Syngenta has already developed a microchip holding an array of DNA fragments that recognizes some 24,000 rice genes and can tell which genes are switched on at each stage of the plant's development. Because of corn's genetic similarity to rice, the rice gene chip can also recognize 90 percent of the genes in corn.""
redux [03.28.02]
"One of the world's largest agricultural companies is putting finishing touches on a plan to make public huge amounts of genetic information about the rice plant, an effort to accelerate research aimed at improving one of mankind's most important crops."
"The plan Syngenta is working on is, in part, an effort to stave off an incipient controversy."
"Syngenta's decision to share some data with the International Rice Genome Sequencing Project may help to quiet a growing controversy about public access to data gathered through privately funded sequence projects. But the decision by Science to allow Syngenta to publish without making its data available in Genbank will undoubtedly spur further debate."
redux [03.19.02]
"Prominent gene researchers fear that access to the complete DNA sequence of rice, the world's most important food crop, will be restricted when it is published in a scientific journal."
"Science says the issue is complex. "We have to weigh the benefit of publishing some data so that it is in the public domain or having it all deposited as privately held trade secrets," says Science spokesperson Ginger Pinholster. "In the case of the human genome it was felt that publishing was the best option - for rice, the case is even stronger.""
"Twenty leading geneticists are protesting against a deal that will allow a multinational company to control who has access to the complete DNA sequence of the rice genome - the most important food crop in the developing world.
The scientists, who include British Nobel laureates Sir Paul Nurse and Sir Aaron Klug, are up in arms against a plan to lock away the entire rice sequence on a company database rather than having it published in the open scientific literature."
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Bio-IT World
ABI's Smeltzer building Amazon.com of biology
"Breaking several months of silence, Applied Biosystems' Deborah Smeltzer is finally going public about her plans for the company's new Knowledge Business. Smeltzer has the unenviable task of leading an informatics initiative after a major reorganization and during the peak of the "bioinformatics backlash." In this, her first media interview since her appointment, she sounded clearly focused on the challenging task ahead of her.
"Our objective is to become the Amazon.com of biology," she says. "Think of how easy it is for customers on Amazon to get what they want. Our offerings are much more complex, but scientists deserve the same type of easy access to them.""
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Nature: Science Update
Cow
and dog genomes next up
"The cow genome could also help "make beef less fat but still tender and tasty - a worthy goal from an agricultural view", says Womack. Sequencing cattle bred for meat, dairy or plough-pulling might also reveal a genetic basis for differences among humans.
As for man's best friend: it shares some of man's worst maladies. Researchers hope the dog genome will shed light on heart disease, cancer, deafness and even narcolepsy and obsessive-compulsive disorder."
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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."
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BBC
Privacy fears over DNA database
"The inventor of DNA fingerprinting has launched an outspoken attack on the way the genetic profiles of suspects in the UK who have been cleared of any crime are still stored by the authorities."
"And he called for the creation of a national database, storing the profiles of the entire UK population, which would be managed by an independent body.
"If we're all on the database, we're all in exactly the same boat - the issue of discrimination disappears," he said."
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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]
"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]
"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]
"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]
"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."
"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]
"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."
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Bio-IT World
The New, New Pharmacogenomics
"Collins is unimpressed by the hubbub that has shaken the industry lately. "In some quarters there was a misunderstanding, or naivete, about how having the sequence was going to solve everything. And there were some business models built solely upon the notion of quick profits, particularly selling subscription databases."
He dismisses talk about a foundering industry. "I think that every pharmaceutical company is still expecting that genomics will be the platform upon which they will build the next generation of drugs," says Collins. Others echo Collins' perspective. "We will change the treatment of cancer," says Variagenics' Adams. And there is no hint of doubt in his voice."
redux [08.08.01]
"Pharmacogenomics requires the integration and analysis of genomic, molecular, cellular, and clinical data, and thus offers a remarkable set of challenges to biomedical informatics. These include infrastructural challenges such as the creation of data models and data bases for storing this data, the integration of these data with external databases, the extraction of information from natural language text, and the protection of databases with sensitive information. There are also scientific challenge in creating tools to support gene expression analysis, three-dimensional structural analysis, and comparative genomic analysis. In this review, we summarize the current uses of informatics within pharmacogenomics, and show how the technical challenges that remain for biomedical informatics are typical of those that will be confronted in the post-genomic era."
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Genomeweb
Urging Researchers to 'Forget the Genome,' Sydney Brenner Sells
a Cell Map
"Consistent with his lifelong reputation as a visionary and provocateur, Brenner challenged a crowd of over 250 bioinformaticists gathered at the Wellcome Trust Genome Campus in Hinxton, UK, to "forget the genome."
"The more you annotate the genome, the more you make it opaque," he warned in a keynote speech delivered at the joint Cold Spring Harbor Laboratory/Wellcome Trust Genome Informatics conference on Saturday. "We need to focus on our cells."
Brenner questioned the ability of computational approaches to derive functional knowledge from genomic sequence alone--a "hideously difficult task," he said--because some problems are simply "not soluble or computable." The future, according to Brenner, requires going back to the bench. Old-fashioned data on the biochemistry of the cell would then be used to flesh out the cell map, which would serve as "a framework to think of genomes and their products.""
redux [07.29.02]
"Colin Hill, president and CEO of GNS, said the adoption of modeling will be slow, but even the largest and most stubborn pharmas will soon realize they have to adopt it if they want to compete.
He has seen more success selling pharmas the baby steps toward modeling: tools, such as its Diagrammatic Cell Language, software and database information, rather than actual models."
redux [11.27.00]
"What do a Boeing 777 and the human body have in common? Both are complex systems, dependent on millions of complex parts, whether they be a jet-propelled engine or a pumping organ such as the heart. The big difference: Engineers can design and build highly accurate computer models of the way a Boeing 777 will behave in flight. The human heart? Its complexity has long stymied efforts by researchers intent on turning drug development into a predictive science, much like building airplanes.
But that's changing. A handful of companies are developing software that can model single cells, whole organs, cellular metabolism and toxicology, diseases throughout a patient's body, and even an entire clinical trial."
redux [02.16.01]
"Computers capable of mimicking life have long been the stuff of sci-fi nightmares - think The Terminator or 2001's HAL 9000. But for researchers struggling to make sense of vast amounts of new biological data, and for drug companies anxious to cut costs and speed development, having accurate computer simulations of living systems is still a dream. To make that dream come true, they are turning to "in silico biology," building computer models of the intricate processes that take place inside cells, organs, and even people. The ultimate goal: an entire organism modeled in silicon, allowing researchers to test new therapies much as engineers "fly" new airplane designs on supercomputers."
redux [05.15.01]
[requires 'free' registration]
""We in physics are used to studying complex systems, but the level of complexity inherent in biological systems ... is way beyond what we have experience dealing with," said Rajagopal, assistant director of research at the Cavendish Laboratory in the University of Cambridge. "Biological systems are much harder to model as they are in highly non-equilibrium states and you not only have to take into account the flow of matter and energy, but also the flow of information!"
He added: "In biology, the whole is greater than the sum of its parts. We have to move on from the "reductionist" towards an "integrationist" approach."
redux [05.15.01]
[requires 'free' registration]
"For a brief period, supplying the data was enough. More genes meant more potential drug targets. But now the victims of the data flood are crying for help. Companies like Entelos, Inc. (Menlo Park, California) are coming to the rescue by building models that integrate all those data into a single, homeostatic, interconnected whole. The models allow researchers to run virtual drug trials to determine the best drug targets, treatment regimens, and patient populations."
Modelers feel that their time has come. "Leaders in the genomics field are all coming to this realization that model building is becoming the rate-limiting step," says Palsson. "There's a major shift taking place in the biological sciences." Math is back, he says, and "biology is going to become quantitative."
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BBC News
Rice code is 'greatest achievement'
"Unravelling the blueprint of rice may be the most important breakthrough genetic science has achieved."
"Because rice is mankind's most important food crop - the staple diet for half of humanity - the researchers say reading its genome is of more importance than decoding mankind's own genetic code."
redux [04.06.02]
[requires 'free' registration]
"Rice is "the Rosetta stone of the cereals," Dr. Wing said. Once researchers have found an important gene in rice, they can look for its counterpart in other crop plants, or insert the rice gene itself since the genes of all these crops are thought to be largely interchangeable."
"Syngenta has already developed a microchip holding an array of DNA fragments that recognizes some 24,000 rice genes and can tell which genes are switched on at each stage of the plant's development. Because of corn's genetic similarity to rice, the rice gene chip can also recognize 90 percent of the genes in corn.""
redux [03.28.02]
"One of the world's largest agricultural companies is putting finishing touches on a plan to make public huge amounts of genetic information about the rice plant, an effort to accelerate research aimed at improving one of mankind's most important crops."
"The plan Syngenta is working on is, in part, an effort to stave off an incipient controversy."
"Syngenta's decision to share some data with the International Rice Genome Sequencing Project may help to quiet a growing controversy about public access to data gathered through privately funded sequence projects. But the decision by Science to allow Syngenta to publish without making its data available in Genbank will undoubtedly spur further debate."
redux [03.19.02]
"Prominent gene researchers fear that access to the complete DNA sequence of rice, the world's most important food crop, will be restricted when it is published in a scientific journal."
"Science says the issue is complex. "We have to weigh the benefit of publishing some data so that it is in the public domain or having it all deposited as privately held trade secrets," says Science spokesperson Ginger Pinholster. "In the case of the human genome it was felt that publishing was the best option - for rice, the case is even stronger.""
"Twenty leading geneticists are protesting against a deal that will allow a multinational company to control who has access to the complete DNA sequence of the rice genome - the most important food crop in the developing world.
The scientists, who include British Nobel laureates Sir Paul Nurse and Sir Aaron Klug, are up in arms against a plan to lock away the entire rice sequence on a company database rather than having it published in the open scientific literature."
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GenomeBiology
Design and implementation of microarray gene expression markup
language (MAGE-ML)
"Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one publication to another. Only when data can be easily exchanged will the entire biological community be able to derive the full benefit from such microarray studies.
To this end we have developed three key ingredients towards standardizing the storage and exchange of microarray data. First, we have created a minimal information for the annotation of a microarray experiment (MIAME)-compliant conceptualization of microarray experiments modeled using the unified modeling language (UML) named MAGE-OM (microarray gene expression object model). Second, we have translated MAGE-OM into an XML-based data format, MAGE-ML, to facilitate the exchange of data. Third, some of us are now using MAGE (or its progenitors) in data production settings. Finally, we have developed a freely available software tool kit (MAGE-STK) that eases the integration of MAGE-ML into end users' systems."
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Buffalo News
New UB computer hikes capacity tenfold
"Billionaire Michael Dell is in the Buffalo area today to help the University at Buffalo unveil a powerful new computer cluster provided by the company that he founded and continues to run."
""We've installed hundreds of these clusters. (But UB's) would be one of the larger ones