{bio,medical} informatics
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Nature: Science Update
250
years of Linnaeus' plant names celebrated
"Although most botanists remain diehard fans of Linnaean nomenclature, the system does throw up a problem. When new research shifts a species from one group into another, it has to swap names to reflect its new position. Tomato, for example, can go under both Solanum lycopersicum and Lycopersicon esculentum.
Because of such problems, a renegade band of scientists wants to ditch Linnaeus' names for a system called the PhyloCode, which names organisms according to their evolutionary relationships. Linnaeus' scheme places organisms in groups based on shared characteristics that do not necessarily reflect their position on the evolutionary tree."
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The Scientist
Chip Critics Countered
[requires 'free' registration]
"Since their rise to fame in the mid 1990s, microarrays have been both lauded and criticized. Enthusiasm about this technology, which many researchers say has forever fundamentally changed biology, is tempered by the recognition that the microarray, like any tool or technology, has its limits. Results are often hard to reproduce and interpret, and the data-driven approach encouraged by the technology can make microarray studies little more than what critics call "fishing expeditions.""
"Microarrays also have been criticized for being, at best, "semi-quantitative," meaning specific gene expression measures may not consistently be confirmed on separate occasions or by other methods. Some debate the issue's significance. "Your ability to look at so many pathways at one time really points to the virtue," says Sistare. "I may not get the exact same numbers, but I'm seeing the same pathways activated. The biology, the interpretation I'm getting is the same.""
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China Post
ITRI, HP team up to boost bioinformatics
"Taiwan's Industrial Technology Research Institute (ITRI) and Hewlett-Packard (HP) Taiwan Ltd. signed a memorandum of understanding yesterday to spearhead research into system biology bioinformatics, setting the stage for Taiwan's future developments in biotechnology.
"It's a milestone for Taiwan's biotechnology development," stated Rosemary Ho, HP Taiwan country manager. "The project stands for a vital step for ITRI to integrate its past achievements into research on genes, proteins and diseases, by taking the system biology approach," said Johnsee Lee, executive vice president of ITRI and general director of the Biomedical Engineering Center (BMEC), a research laboratory under ITRI."
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Seattle Post-Intelligencer
11.8-teraflop computer powers up
"The nation's fastest "unclassified" supercomputer will power up to full strength today in Richland to tackle some of the toughest problems in biology and the environment.
"There's that stuff in the ground at the Hanford site, to begin with," said Scott Studham, manager of computing at the computer's home at the U.S. Department of Energy's Pacific Northwest National Laboratory."
""It's also tailored for bioinformatics and computational biology," he said. With the recently completed sequencing of the entire human genetic code, or genome, biologists need powerful computers to work with all of the 3 billion bits of DNA."
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The New York Times
I.B.M. Looks to Genetics to Map a New Business
[requires 'free' registration]
""We're talking to scientists at the bench, the head of informatics, the head of R & D. Linking into that community can only be done by people who truly understand it."
At a time when information technology sales are sluggish in areas like financial services and retail, the life-sciences segment will grow at close to a 20 percent clip over the next three years, according to analysts. Along with its competitors, I.B.M. is investing in it heavily."
redux [06.03.03]
""There's been an explosion of data," says Roehr, who nowadays sits in his New Jersey branch office behind an advanced computer system that automatically pulls together all relevant project data onto a single screen. "We're looking to the information technology industry to play catch-up.""
"Biosciences organizations will spend an estimated $30 billion on technology-related purchases in 2006, up from $12 billion in 2001, according to research firm International Data Corp."
redux [11.15.02]
"The Santa Clara, Calif.-based chipmaker said this week that it is working with universities, software developers and server manufacturers to come up with supercomputer-class systems, built around Intel technology, for pharmaceutical engineering, genetic research and other biotech projects, said Rick Herrmann, Intel's manager for worldwide high-performance computing.
"There seems to be a rush toward building out the infrastructure around life sciences," Hermann said. "Every country in the world is looking for bioinformatics to be the next technology pillar: Singapore...Taiwan...the U.S. Even Ireland is looking at 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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Wired News
Genetic Tests in Your Bedroom
""This technology could really empower people," said Dr. Michael Burkart, an assistant professor of biochemistry at the university and a co-author of the paper. "The existing technologies that laboratories use to identify molecules cost hundreds of thousands of dollars. Our method uses equipment that is almost ubiquitous."
The method was conceived in 1999 when chemist and co-author James La Clair accidentally spilled laboratory chemicals on a compact disc. The new technology relies on counting the errors detected by the laser in a CD player whenever particles in a solution cross its path."
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MIT Technology Review
An Emphasis on Compassion
"To help the New York City medical examiner identify the remains of the thousands of victims of 9/11, tiny bioinformatics company Gene Codes created M-FISys--the first software capable of managing such massive amounts of genetic evidence."
"M-FISys brings together three types of DNA analysis--some standard, some not generally used for identification purposes--for repeated "all-against-all" comparisons among victim and kinship samples. The program constructs "virtual" DNA profiles where actual ones have literally gone up in smoke and permits users to add or subtract sample analyses from the composites as the evidence changes. It can link to other databases, such as those containing descriptions of, say, family relationships or what the victim wore to work the day of the disaster, or the medical examiner's postmortem findings. It can present a snapshot of not just every test done on a sample but of the progression of those tests, as well as the forensic scientists' comments. "M-FISys allows us to do quality checks on the software, on the samples, on the analysis," says Robert C. Shaler, director of the Department of Forensic Biology for New York City. "We can, at a glance, get an idea of what samples we have and what results we have on them so that we can quickly go through and ascertain what else we need to do.""
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The Scientist
Economics of open access
[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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Computerworld Singapore
Beyond bioinformatics
"Some time last year, the "gene bubble" burst when the investment community became disenchanted with the deliverables of genomics, which were not quite as spectacular as promised. Now, a local researcher has predicted that the current hot topic of bioinformatics will not exist within the next ten years. Instead, its position will eventually be usurped by disciplines such as system biology and transcriptome research, which will be the focus for pharmaceutical research in the near future."
"System biology is an emergent field that aims at system-level understanding of biological systems. While system-level understanding has been a long-standing goal of biological sciences, it was only recently that system-level analysis, grounded on discoveries at molecular-level, could be made."
redux [06.24.03]
"The study of systems biology, the field of research that creates predictive models of complex biological processes, will lead to advances in pharmaceuticals and medical treatment, but also to advances in computer science, a leading systems biologist predicted Monday.
""I think biology is going to give fundamental new insights to IT," Hood said. "Really understanding the evolution of gene regulatory networks is going to provide completely new strategies for how one deals with this horrendous computational problem of taking big programs ... and restructuring them really efficiently so that you don't restructure them simply by adding more onto them.""
redux [04.21.03]
"One of the critical priorities now is to take all the components we can detect, and reconstruct the interaction networks inside cells that underlie biological processes. This type of reconstruction is very tricky: People call it 'integration of heterogeneous databases.' Collating these data files is like stacking playing cards -- each piece of data stands upon, and influences, the reliability of other pieces.
The next priority is then to generate computer models that can be used for simulations -- in silico biology. There are three categories of models we need to build: models for metabolism, DNA regulation, and cell signaling."
redux [02.2.03]
[requires 'free' registration]
"Systems biology, a siren in a sea of dark prospects, has lured investors frustrated with low returns in biotechnology and anxious to set a new course of drug discovery. Institutions have also geared up training programs, but the excitement in the new field has failed to arrest downsizing in the biotech industry."
"Despite the interest of the pharmaceutical industry, prospective systems biologists should think carefully before investing in training in hopes of landing a job in the new field."
redux [03.08.02]
[ summary can be viewed for free once registered ]
"To understand biology at the system level, we must examine the structure and dynamics of cellular and organismal function, rather than the characteristics of isolated parts of a cell or organism. Properties of systems, such as robustness, emerge as central issues, and understanding these properties may have an impact on the future of medicine. However, many breakthroughs in experimental devices, advanced software, and analytical methods are required before the achievements of systems biology can live up to their much-touted potential."
redux [02.26.02]
"Over the last few years, there's been an explosion of information in biology. The mapping of the human genome gave biologists unprecedented detail about some 30,000 to 40,000 genes. Efforts are also under way to identify the thousands--and potentially millions--of proteins encoded by those genes. Researchers are now pursuing the next logical step in integrating all this data: systems biology.
The goal is to understand not just the functions of individual genes, proteins and smaller molecules like hormones, but to learn how all of these molecules interact within, say, a cell. Biologists hope to then use this information to generate more accurate computer models that will help unravel the complexities of human physiology and the underlying mechanisms of disease. The biggest payoff: faster development of more-effective drugs."
redux [04.05.00]
[requires 'free' registration]
"I suspect that although the new enthusiasm for computers in biology is genuine, it overlooks some basic problems in implementation. The basic difficulty, as I see it, is that although biologists use computers, they do not trust everything that comes out of them. It is one thing to use them to print up nice-looking graphs, but it is an entirely different matter to use them to think better."
"Francis Crick was once quoted as saying that no biologist had ever made a discovery using a mathematical model. I would reply that no biologist has ever made a discovery by running an electrophoretic gel. They make discoveries by using their brains. Computers, like all scientific tools, are only as good as the person who uses them. If biologists don't understand how computer models are constructed, they won't know their strengths and limitations. Without some foundation of trust, biologists will be unlikely to utilize or accept this powerful method of data analysis."
redux [01.19.02]
"The integration of bioinformatics with these systems approaches is an integral, essential feature. One of the things that we stress is that in the future it's going to be increasingly important for people in bioinformatics to be intimately associated with data producers, because no matter how smart you are you can't model biological complexity--it's just too complex. The only way we're going to understand it is through the integration of these global experimental observations, together with powerful computational tools for analysis, and ultimately, for modeling.
A mistake that a lot of people in bioinformatics have tended to make is thinking that you can set up a bioinformatics center and it can work in isolation from the biology, and it can study all these great databases and learn lots and lots about biology. In vitro biology and in silico biology are all popular terms, but it isn't true, and it isn't going to be true in the future."
redux [04.18.01]
[requires 'free' registration]
"Systems biology is a loosely defined term, but the main idea is that biology is an information science, with genes a sort of digital code. Moreover, while much of molecular biology has involved studying a single gene or protein in depth, systems biology looks at the bigger picture, how all the genes and proteins interact. Ultimately the goal is to develop computer models that can predict the behavior of cells or organisms, much as Boeing can simulate how a plane will fly before it is built.
But such a task requires biologists to team up with computer scientists, engineers, physicists and mathematicians. The structure of universities makes that difficult, Dr. Hood said."
redux [07.13.00]
"A new mathematical biology is emerging. Building on experimental data from developing organisms, it uses the power of computational methods to explore the properties of real gene networks."
"Our understanding of gene networks is at an early stage. We perceive their complexity only after it has been filtered by the limitations of the techniques used to study them. Genome databases and DNA-chip technology, which enables huge numbers of genes to be screened for activity, will undoubtedly provide more, and much more complicated, data than anything produced by Drosophila genetics. If a relatively simple gene network such as the segment-polarity system is hard to understand intuitively, we can be certain that modelling will be essential to make sense of the flood of new data.
But this will not be elegant theoretical modelling: rather, it will be rooted in the arbitrary complexity of evolved organisms. The task will require a breed of biologist-mathematician as familiar with handling differential equations as with the limitations of messy experimental data. There will be plenty of vacancies, and, on present showing, not many qualified applicants."
redux [05.15.01]
"Our Mission is to develop an integrated, easy-to-use environment, the workbench , which will enable biologists to create, manipulate, display and analyze biological models at molecular, cellular and multicellular levels. We are focusing on biochemical networks including mass action kinetics, metabolic pathways, stochastic simulation, gene expression and regulation."
"One of the key aspects of out project is to facilitate collaboration among existing developers and users of system biology software. We aim to do this by providing an open-source software infrastructure which will enable collaborators to freely use and share each other's computational resources."
redux [07.11.00]
"For most of us, formal biology education begins with complex systems--the traditional dissection of a frog in high school biology class is virtually a rite of passage in the U.S.
But the way many people learn about and invest in biotechnology is at the smallest end of the spectrum--the genome, now often described as the "periodic table" of biology. Genomics and all its related buzzwords have been responsible for much of the media attention, government grants, and investment capital heaped on the biotech industry over the past decade.
But just as there is a whole lot of chemistry that happens in between the periodic table and a birthday cake, there is a lot of biology in between the genome and a living organism. With the completion of biology's periodic table within sight, academics and industry players alike are pondering the best way to apply our hard won knowledge.
The only problem is, the path from genome to system seems to get harder the more we learn."
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EyeForPharma
Knowledge management in an unordered world
"David Snowden, Director of the Cynefin Center for Organizational Complexity, told attendees at the recent eyeforpharma Knowledge Sharing Strategies for the Pharma Lifecycle conference that their knowledge management initiatives will only be successful when those initiatives include a new set of tools and techniques for unordered domains. "If you carry on using ordered techniques for unordered systems, you are doomed to repeat the knowledge management failures everybody's been going through for the past eight years or so," Snowden warned."
redux [11.07.02]
"Large companies relying on in-house knowledge to maintain market dominance have highly evolved IT systems for capturing, storing and analyzing that knowledge."
"Just take GlaxoSmithKline PLC (GSK). The $27.5 billion, London-based pharmaceutical firm is a Lotus Notes shop. It uses an array of customized Notes templates and databases to track just about everything it does."
"The problem: Capturing external knowledge, and discretely sharing internal knowledge, weren't possible."
redux [02.21.02]
"However, according to Victor Newman, Chief Learning Officer at Pfizer, knowledge management can only be capitalized on by pharma when we recognize that it's not the knowledge itself that gives us power, but the way we use it."
""Unless you involve people in your vision of what you want the technology to achieve, then they don't actually start to change their psychology in preparation of how they are going to change the way they perform in order to make it happen. We have realized that KM is a more personal activity than it was. It's now more about how we design conversations so people know who to talk to when they need specific knowledge. I believe knowledge management is about managing dialogue.""
redux [11.05.01]
"One of the major problems with expert communities, according to Snowden, is that they train behaviour and prevent innovation. Encouraging multiple informal communities throughout the company is a critical step toward innovation, he said.
"Identify people with like interests and pull them together. Allow people to cluster and form communities, then reinforce the ones you want." Snowden said. "Informal communities keep organisations together and make things work.""
redux [06.12.01]
"Within IBM, there's an interesting disconnect between Cooper's team and Larry Prusak's IBM Institute for Knowledge Management, a research group located just across the street from Cooper in Cambridge. While Cooper is trying to sell a sophisticated piece of software that uses automated spiders, linguistic analysis, and Bayesian arithmetic to create topical clusters of documents and identify in-house gurus, Prusak is publishing books and articles that say that the key to developing the kind of strong relationships that make companies more effective -- what he calls social capital -- has nothing to do with software.
In an article in the June issue of the Harvard Business Review, Prusak argues that virtuality -- collaborating with colleagues in an online chat-room, for example -- can eat away at the social fabric of an organization."
redux [08.04.00]
"The Web was invented so that scientists could use computer networks to collaborate -- that is, exchange documents, discuss them, coordinate work, create and publish collective knowledge. It was, in other words, supposed to be a groupware application.
Despite the popularity of the Web -- or, perhaps, because of that popularity -- it has yet to fulfill that original mission. Today's Web is more like a shotgun marriage of electronic publishing and broadcast television than it is like an engineered solution for group collaboration. True, the Internet empowers today's working scientist in ways only dreamed of even a decade ago. Yet our use of it often remains rooted in pre-Web idioms and habits -- partly because we don't fully exploit today's Internet communication tools, but mainly because we're still missing key tools and infrastructure."
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New Scientist
First game-playing DNA computer revealed
"The first game-playing DNA computer has been revealed - an enzyme-powered tic-tac-toe machine that cannot be beaten.
The human player makes his or her moves by dropping DNA into 3 by 3 square of wells that make up the board. The device then uses a complex mixture of DNA enzymes to determine where it should place its nought or cross, and signals its move with a green glow."
"It almost sounds too fantastic to be true, but a growing amount of research supports the idea that DNA, the basic building block of life, could also be the basis of a staggeringly powerful new generation of computers.
If it happens, the revolution someday might be traced to the night a decade ago when University of Southern California computer scientist Leonard Adleman lay in bed reading James Watson's textbook "Molecular Biology of the Gene.""
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Bio-IT World
Guardians of the Genome
"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 [05.07.03]
"Scientists and commercial firms are scrambling to patent the genetic code of the virus thought to be responsible for Sars.
The group which produced the first entire genetic sequence of the coronavirus confirmed this week that it is seeking a patent to ensure that everyone has free access to the code.
It fears that a commercial patent could slow down research into vaccines and treatments."
redux [09.28.02]
"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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Computerworld
Biotech a healthy market for chips
""Couple that with a personalised detection mechanism that shows the heart is suffering failure by monitoring blood flow and pressure in the aorta, and it's possible for your phone to ring and say 'your heart is about to stop - get to hospital quick; you have 20 minutes' thanks to the extra oxygen in your blood keeping you alive," he said.
Blatt was expanding on Intel's new push into the BioInformatics arena, which is to concentrate on both the improvement of existing IT services throughout the healthcare industry, and the development of new technologies within the device market."
redux [02.25.03]
"The Santa Clara, Calif., chipmaker, which began an effort to boost its presence in life sciences in November, said on Tuesday that 15 universities and other research institutes in Australia, India, China and Singapore--all focused on areas such as medicine and genetics--are using or will soon put into place new computers based on Intel chips."
"The chipmaker isn't alone among tech companies angling for a stake in the life sciences."
redux [01.23.03]
"IBM and Icelandic company Decode Genetics will announce on Thursday a partnership to offer technology and services for applying genetic information to the hunt for new drugs."
"IDC ranks IBM near the top of the heap when it comes to outfitting life sciences organizations with information technology. IBM pulled in $1.36 billion in life sciences sales in 2001, according to IDC, while Hewlett-Packard and Compaq Computer--now merged--combined for $1.77 billion. Dell Computer ranked third with $821 million."
redux [12.10.02]
"Gateway Inc., the PC maker best known for its consumer systems and talking cow, is linking thousands of display PCs in its nationwide chain of stores to create a grid computing environment capable of scaling to 14 teraflops of performance."
In a pilot test, Inpharmatica Ltd. reproduced the results of a bioinformatics job run on the Processing on Demand system and its own computer farm, said CIO Pat Leach. The London-based company turned to Gateway because it wants to cut the amount of time it spends managing its 2,300-processor computer farm. "We are a drug discovery company, not an IT shop," Leach said. "We would much rather employ people to do innovative analysis of the data than spend time building computers.""
redux [11.15.02]
"The Santa Clara, Calif.-based chipmaker said this week that it is working with universities, software developers and server manufacturers to come up with supercomputer-class systems, built around Intel technology, for pharmaceutical engineering, genetic research and other biotech projects, said Rick Herrmann, Intel's manager for worldwide high-performance computing.
"There seems to be a rush toward building out the infrastructure around life sciences," Hermann said. "Every country in the world is looking for bioinformatics to be the next technology pillar: Singapore...Taiwan...the U.S. Even Ireland is looking at 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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Genomeweb
New Breed of Genomics Centers Works Disease-Down, Not
Genes-Up
""The concept can work if it's a really integrated center," says Michael Liebman, director of computational biology at the Abramson Family Cancer Research Institute at the University of Pennsylvania. He likes the disease focus because it makes more sense from a clinical standpoint - starting from the disease and its effect in patients and stripping that down, layer by layer, to understanding "how genomics and proteomics can help differentiate between subtypes of disease" - than starting with genomics and working up from genes."
redux [05.17.02]
"An unprecedented wealth of biological data has been generated by the human genome project and sequencing projects in other organisms. The huge demand for analysis and interpretation of these data is being managed by the evolving science of bioinformatics. Bioinformatics is defined as the application of tools of computation and analysis to the capture and interpretation of biological data. It is an interdisciplinary field, which harnesses computer science, mathematics, physics, and biology. Bioinformatics is essential for management of data in modern biology and medicine. This paper describes the main tools of the bioinformatician and discusses how they are being used to interpret biological data and to further understanding of disease. The potential clinical applications of these data in drug discovery and development are also discussed."
"Complex diseases have complex phenotypes, and proper diagnosis requires that the analysis take into account the patient's history and exposure to environmental factors, as well as genetic information. Signaling information is one aspect of a grander "biomedical informatics" approach advocated for a better understanding of a patient's medically relevant disease phenotype."
redux [04.17.02]
"Research into human genetics is being limited by a lack of knowledge in other areas of science, say delegates at the Seventh International Human Genome Meeting (HUGO) in China.
Professor Lap-Chee Tsui, HUGO's outgoing president, says that our poor understanding of even basic human anatomy means that the human genome project is not delivering cures for genetic diseases as was hoped."
redux [12.08.01]
"The goal now is to redefine disease based on the underlying biological mechanisms, Lander said. By that token, diseases are going to surprise us. Reclassifying them means that some diseases will get split in half and other diseases will get lumped together because they have the same mechanism, although they may look different to us, he said.
What this portends commercially is up to smart companies to figure out, he said. Companies will need the ability to integrate scale and informatics; they'll need what he called a "fleetness" with technologies—not just one favored technology, but many kinds. They shouldn't worry too much about hoarding intellectual property rights nor depend on one technology platform. It is more important to understand the big picture in the first place in order to choose the right target, Lander said."
redux [08.01.01]
"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."
redux [11.16.00]
"Neither we nor our critics defined a revolution in medicine. We mean a paradigm shift in theory or practice. Sotos and Rienhoff's plea for "precise diagnosis" epitomizes the current paradigm. In most of those who will have common disorders, the interaction of genetic, environmental, and behavioral factors makes the quest for precise diagnosis illusive."
"The revolution in medicine will come with the recognition, based in part on genetic research, that the quest for single causes for common diseases will seldom be fruitful and that a new paradigm of a causal web must be adopted. Interventions must be directed at the most vulnerable points in the web. Sometimes this will involve biomedical interventions. At other times, it will involve modifying aspects of our social structure, lifestyle, or environment that increase the risk of disease."
redux [08.06.01]
[ summary can be viewed for free once registered ]
"The human genome sequence will dramatically alter how we define, prevent, and treat disease. As more and more genetic variations among individuals are discovered, there will be a rush to label many of these variations as disease-associated. We need to define the term disease so that it incorporates our expanding genetic knowledge, taking into account the possible risks and adverse consequences associated with certain genetic variations, while acknowledging that a definition of disease cannot be based solely on one genetic abnormality."
"In thinking about how clinicians use the term disease, we think that three elements should be considered: disease is a state that places individuals at increased risk of adverse consequences . Treatment is given to those with a disease to prevent or ameliorate adverse consequences. The key element in this definition is risk: deviations from normal that are not associated with risk should not be considered synonymous with disease. Our definition has three definable elements and should serve clinicians well. Of course, its success will depend on whether it becomes clinically useful."
redux [07.11.00]
"For most of us, formal biology education begins with complex systems--the traditional dissection of a frog in high school biology class is virtually a rite of passage in the U.S.
But the way many people learn about and invest in biotechnology is at the smallest end of the spectrum--the genome, now often described as the "periodic table" of biology. Genomics and all its related buzzwords have been responsible for much of the media attention, government grants, and investment capital heaped on the biotech industry over the past decade.
But just as there is a whole lot of chemistry that happens in between the periodic table and a birthday cake, there is a lot of biology in between the genome and a living organism. With the completion of biology's periodic table within sight, academics and industry players alike are pondering the best way to apply our hard won knowledge.
The only problem is, the path from genome to system seems to get harder the more we learn."
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Infoworld
Memo to software vendors: Biotech wants smart pitches
"Those charged with hearing pitches from software vendors who want to sell wares to biotechnology companies don't like these words: "enterprise-wide solution." They don't want to hear the generic wonders of the "solution" being pitched, they don't want to hear marketing buzzwords or that the software will revolutionize the pharmaceutical business. They won't believe that kind of approach and they will show the software vendor the door, perhaps within minutes, without an invitation back."
"But perhaps the largest issue has little to do with technology, but with getting recalcitrant scientists excited about tools available to them."
redux [04.28.03]
"Leading executi