{bio,medical} informatics
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The Straits Times: Singapore
Bioinformatics: finding a needle in a haystack
"One striking feature that is advancing the cause for open-source is Apple's decision to adopt it for its OS X, making the operating system the ideal choice for bioinformatics software, said the event's organiser, Mr Elia Stupka.
Mr Stupka is director of bioinformatics at Temasek Life Sciences Laboratory. In his view, sharing software on the open-source platform does not mean sharing database information, which means companies can still continue to have a firm hold over their proprietary data.
Open-source improves, and does not kill, business models, he said."
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The New York Times
For the History of Science, the First Draft Is Often Late
[requires 'free' registration]
"Just exactly when the readers of this newspaper first heard about the double helix is a mystery, and there is a lesson in that.
If journalism is the first draft of history, as the saying goes, then it's often a terrible draft."
"One might expect that such an accomplishment would be trumpeted in newspaper headlines around the world. But this was before the days when every advance in science, marginal or not, was preceded by a drumroll of missives from press agents. In fact, the double helix was a dog that did not bark, at least not at first, in this or any other newspaper."
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InfoWorld
Sun backs bio-IT research
"On Tuesday, Sun announced that it was forming the Sun North Carolina Research Triangle Center of Excellence (COE) in Bioinformatics and Computational Biology."
"The total value of the hardware, software and services from Sun will be approximately $6 million, according to Sun."
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News.Com
Intel gets inside life sciences
"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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The Boston Globe
Data glut
"To some extent, the life sciences market, which relies heavily on computational biology, has lived up to the promise. Research centers in both the private and public sectors placed orders last year for thousands of servers and storage systems capable of handling terabytes of the new genomic, proteomic, drug, and health care data generated hourly.
That's the good news. The bad news is that, during the past year, companies that develop software tools for managing and exploiting all of the new data struggled mightily. Red ink, consolidation, and layoffs were the norm. Welcome to the tumultuous world of ''bioinformatics,'' the underachieving wonder child of a genomics revolution-in-waiting."
redux [12.12.02]
"Bioinformatics: In life-sciences establishments around the world, the laboratory rat is giving way to the computer mouse—as computing joins forces with biology to create a bioinformatics market that is expected to be worth nearly $40 billion within three years."
"Welcome to the world of bioinformatics—a branch of computing concerned with the acquisition, storage and analysis of biological data. Once an obscure part of computer science, bioinformatics has become a linchpin of biotechnology's progress. In the struggle for speed and agility, bioinformatics offers unparalleled efficiency through mathematical modelling. In the quest for new drugs, it promises new ways to look at biology through data mining. And it is the only practical way of making sense of the ensuing deluge of data."
redux [11.30.02]
"Bioinformatics as a business, not to be confused with bioinformatics as a field of study, is at an interesting crossroads. As an academic branch of learning, bioinformatics remains mostly what it always was -- a cross-disciplinary endeavor between computer science and molecular biology. But bioinformatics as a money-making proposition has different criteria for success, and it has received a lot of bad press lately, some of it deserved."
"During this golden age, bioinformaticists developed software that computational biologists could use to make biological discoveries based on genomic data. But the industry swerved off course by selling expensive systems that focused on the individual pieces of a solution, without heeding downstream processes that were the actual bread-and-butter of our customers. Bioinformatics has always been about integrating data and converting it into information. When it loses that focus, it loses its value to the customer."
redux [11.05.02]
[requires 'free' registration]
"The biotechnology industry is facing one of its worst financial squeezes ever. The prices of many biotechnology stocks have plummeted, and Wall Street's vaults have snapped nearly shut, making it almost impossible for capital-hungry companies to finance themselves."
"Another sector that has suffered is bioinformatics, which uses computers to analyze masses of genetic data. Several young companies have gone out of business or been acquired for a pittance after sales did not meet expectations."
redux [07.09.02]
"Most agree that venture money is there for companies -- but the pressure must seem insurmountable for entrepreneurs, who probably feel like they have to give the perfect business pitch to venture capitalists just to get a foot in the door.
"If people aren't rethinking their models, they're nuts; if they were waiting for Viaken to be their wake-up call, they're nuts," Nelson says."
redux [04.18.02]
""Bioinformatics is heterogeneous, but many bioinformatics [tools] fulfill a narrow niche," said Williamson. "There is room for someone to consolidate, but I don't know if that is needed or necessary. Plus there's always an academic coming up with the next thing. So it's a hard business to sustain."
Bioinformatics "is great for smaller companies," he went on. And there are "people who can tie the islands of analysis together, and who have the resources to pull it off, but is that a business? That's the million dollar question. And will anyone buy it if you can pull it together? Everybody wants to be the Microsoft Office of bioinformatics, but I'm not sure that's going to happen.""
redux [03.11.02]
"The emerging field of bioinformatics, the use of computers to analyze the inner workings of biology, is transforming an industry that just a decade ago relied on the manual labor of chemists and biologists. But even as it does so, bioinformatics is floundering as a business.
Shares of public companies that sell biological data or software are trading at a fraction of what they did two years ago. Dozens of companies have crowded into the field. Some have folded; others have survived only by morphing into drug-discovery companies.
''It's a hard market to build a business around,'' said Oliver Fetzer, a vice president at Boston Consulting Group."
redux [02.11.02]
"LIKE EVERY BUBBLE, this one had to burst. Stock prices of many bioinformatics firms have fallen sharply in recent years. LION Biosciences of Germany went public at $40 a share and now trades at about $13. Iceland's DeCode is worth a fourth of its former high. Even Celera, the U.S. firm that helped decode the human genome, is off its peak.
Falling stock prices are a symptom of a greater disappointment in bioinformatics. A few years ago the laborious and quirky process of drug discovery seemed on the verge of giving way to new streamlined, data-driven methods. Some firms organized the blizzard of genetic data into databases that researchers could mine with search engines from still other firms. Software companies built computer programs that modeled what goes on in human cells and even whole organs. Many investors came to believe that bioinformatics would open a new avenue to the discovery of drugs. But this avenue simply hasn't materialized. Says biotech analyst Earling Refsum at Nomura Bank in London: "Bioinformatics has not helped Big Pharma get more drugs into the pipeline.""
redux [01.03.02]
"Inside the laboratories of the world's major pharmaceutical companies and biotechnology start-ups, an emerging science is quietly transforming the drug industry. Bioinformatics -- the use of computers to analyze the inner workings of biology -- is helping researchers pinpoint the roots of diseases and design sophisticated medicines to treat them.
But even as it becomes a vital part of drug research, bioinformatics as a business is losing favor with investors. Shares of publicly traded firms that sell biological data and software tools are slumping, and venture capitalists are increasingly wary of investing in such companies.
redux [12.18.01]
"There comes a point in the life cycle of every organism when it must change or perish. For bioinformatics, the time for metamorphosis is now. Though computational biology is already an intrinsic part of the drug discovery process, the business models adopted by most bioinformatics firms have failed to produce profits. Competition -- from the IT industry and big pharma itself -- is growing and investors, both public and private, are unimpressed. While some companies are hoping persistence pays off, many are pursuing new business models that should allow them to retain a bigger share of the profits they are helping to create."
redux [03.14.01]
"The story proclaimed in its lead, "Move over Information Age. Make room for the age of bioinformation." You could picture bleary eyes opening all over the Bay Area. The story went on to note that a San Jose consulting firm was predicting a 10 percent annual growth in the bioinformatics market for years to come; and that the National Science Foundation estimated that 20,000 new jobs in the field would be created in the field in just the next four years.
If that wasn't enough, the rest of the section was filled with page after page of biotech firms listing job openings - in powerful juxtaposition to the endless lists of dot-com layoffs just a few pages earlier. Picture Starbucks spit-takes from Marin to Santa Cruz.
Wow! Rewrite that resume to emphasize that biology course you took in college. Roll your Aeron chair down to the nearest lab. Trade that black turtleneck for a white lab coat..."
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The Scientist
Systems Biology: A Pale Beacon For Biotechs
[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 [01.10.03]
"At last count, 103 of the 341 faculty in MIT's engineering school-and we're talking aeronautic, astronautic, chemical, civil, electrical, environmental, materials science, mechanical, and nuclear engineering--were using the term "bio" to describe the nature of their research.
At a luncheon for 175 invited guests in the MIT faculty club here today, Vest gave a plug for the institute's nascent Computational and Systems Biology Initiative, an interdisciplinary program that will facilitate cross-fertilization among all of MIT's bio-interested faculty and students, whether they be engineers or in the departments of biology, chemistry, computer science, or physics."
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 [02.05.02]
"The project has been a pet of Gov. Gray Davis, who helped seed QB3 with $75 million in state funding. Intel co-founder Gordon Moore has quietly pledged an additional $10 million to launch this novel high-tech/biotech collaboration."
"Kelly said the future will involve figuring out how millions upon millions of interactions between inanimate genes and proteins somehow give rise to life at the cellular level -- a field called systems biology."
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 [03.17.01]
"When Lee Hood started the Institute for Systems Biology, a project to build an integrated research supercenter for the biological sciences, few doubted the validity of the concept, but many wondered whether the technology existed to make it work.
Now, in a sign that others are also willing to gamble on the idea, systems biology is attracting commercial attention. Beyond Genomics (BG), a startup based in Cambridge, Mass., is attempting to glean medically-relevant information from multiple systems simultaneously, from genes to metabolites, by using software that identifies patterns in these systems caused by disease."
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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IBM Alphaworks
Web Services for Life Sciences
"Web Services for the Life Sciences are illustrated in this application targeted for Bio-informatics researchers using the National Center for Biotechnology Information (NCBI) databases, PubMed, GenBank, and BLAST. The Rochester Life Sciences Framework team developed Web Services wrappers around each of the applications and provides example programs that use each of the three Web services as well as an example program that combines all three as sequential searches. Each of these programs are downloadable and include both the Java sources and compiled codes to show developers how these Web services can be constructed."
[ via bioinformatics.org ]
redux [01.31.02]
"Lincoln then summarized efforts to unify the bioinformatics data services. These efforts started 12 years ago with the Meetings of the Molecular Biology Databases (MMBD), which essentially ended in argument. Every member thought his or her way of doing things was the best way. Next came the federated models like Gaea and Kleisli , and then the data warehouses of Ensembl, UCSC, and others. This brings us to the ad hoc Web services that are currently in place. These allow programmatic access to data, as in the GenBank/EMBL example. To truly unify the services of bioinformatics data providers we need to move beyond this to a more formal Web services model.
In this Web services model, the data providers would register their services in a formalized service registry, and researchers' scripts would no longer need to be concerned with the interface details of the different databases. This model represents the unification that Lincoln, and judging by the response, apparently everyone in the audience, hopes to see in bioinformatics."
"Web Services can't create a framework in which any two arbitrary applications can interact because XML doesn't provide shared languages, merely shared alphabets. The Web Services stack pushes this shared semantics problem into higher and higher layers without solving it. Humans often cannot create perfectly transparent descriptions even when they are trying to, and they simply won't try when there's an economic incentive to stretch the truth."
redux [09.27.01]
"As you might be aware of, flat-files have severe limitations, and we have been asked various times if we are going to distribute the EMBL data in different formats as well, XML being the one most prominently mentioned. In short, the XEMBL project will bring to the user several alternative formats of EMBL data."
"We have XEMBL running as a web service using SOAP (Simple Object Access Protocol) and WSDL (Web Service Definition Language)."
redux [11.06.00]
"The semantics of services -- what they do and what data elements they manipulate mean -- is the key issue. Business value results from B2B collaborations that do the right thing. If they do something else, the damage may be dramatic. How, then, do we trust that a service does the right thing before it is used? And how do we make that determination at Internet speeds?
In small-scale OO systems, interface compatibility usually implies semantic compatibility. That is, an object that implements the right set of messages with the right types of arguments probably does "the right thing." This is true, in part, because small-scale systems tend to be built by a small team of programmers with shared understanding of how the system operates and, in part, because small systems offer little opportunity for ambiguity. However, in large-scale OO systems, the semantics provided by a given class cannot be reliably deduced from the message interface alone. Clearly, in an Internet populated with many thousands of services offered by thousands of different companies with very different agendas, compliance with some specified message set will not be sufficient to deduce the semantics of the service."
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The Financial Express
Forget Bioinformatics, It’s ‘In Silico’ Now
"Bioinformatics is a bad word in the US, according to Strand Genomics CEO Srinivasan Seshadri. Speaking at a recent conference in the capital, Dr Seshadri said it is fashionable to use the term ‘‘in silico’’, instead of Bioinformatics. Thereby, he indicated that there’s a lot in a name, after all.
Agreeing with that view, Ocimum Biosolutions CEO Anuradha Acharya told eFE that ‘in silico’ is ‘‘unfortunately’’ being used as an alternative for bioinformatics. It is at once fashionable and trendy. But why? ‘‘Ever since bioinformatics companies have been doing badly in the US, people like to use in silico biology as the new buzzword,’’ Ms Acharya reasoned."
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Wired News
Complete DNA Map: All Your Genes
"A sweepstakes winner will be declared at the May meeting for guessing the number of genes in the human genome. A lively debate spawned the GeneSweep contest. The number had been so disputed that Ewan Birney of the European Bioinformatics Institute created an official betting pool in 2000 during CSHL's annual genome conference.
Birney leaned over the bar at the campus pub and took official bets in a lab notebook while scientists threw dollars over his shoulder. In 2000, it cost $1 to make a bet. By 2001, it had risen to $5 and in 2002 it was up to $20. Now, 165 bettors are waiting to find out who's won the pot."
redux [10.31.01]
[requires 'free' registration]
"Counting human genes ought to be straightforward. Tracking telltale signs--motifs for promoters, translation start sites, splice sites, CpG islands--gene counters must by now be mopping up, finalizing chromosomal locations of every human gene already known, and predicting whereabouts of all the rest. Insert one human genome sequence, turn the bioinformatics crank, and genes gush out like a slot machine jackpot, right?
"No, no, no," says Bo Yuan, of Ohio State University, having a laugh over the idea that computation is all you need to tally genes. To the contrary, states the director of the bioinformatics group in the division of Human Cancer Genetics at Ohio State, trawling for genes is so labor-intensive that several years may pass before researchers possess a highly accurate count."
redux [08.24.01]
[requires 'free' registration]
"After a humiliating deflation this February, human dignity is on the recovery path, at least as measured by the number of genes in the human genome.
Two new estimates put the likely number of human genes at around 40,000, up by a third from the estimate of about 30,000 in February by the two teams of scientists who decoded the human genome. The low estimate still has its defenders."
redux [01.18.01]
"Two rival teams that cracked the human genome may have underestimated the number of human genes, according to a new computer analysis."
Scientists in the United States claim humans are built from 66,000 genes, nearly twice as many as the current consensus."
"But the new analysis, published on the website of the journal Genome Biology, has been dismissed by the Sanger Centre, in Cambridgeshire, UK, which was responsible for about a third of the human genome sequencing effort."
""The experimental evidence actually points to 30-40,000 genes," Dr Hubbard told BBC News Online. "I don't believe the argument in this paper that there are a lot more genes. This is an entirely computational paper and I don't think it's very credible.""
redux [11.13.00]
[requires 'free' registration]
"If James Watson, co-discoverer of DNA's structure, says we don't know how many genes there are, you're inclined to believe him. So it was a great surprise to hear the legend denounced, albeit with due deference. At the last count, insisted Kay Davies, professor of anatomy at the University of Oxford, humans are reckoned to have 40,944 tiny protein factories.
She was drawing on statistics that define the proteome, the protein equivalent of the genome, as the set of all expressed proteins in humans, for which 40,944 genes are individually responsible. Not a huge figure, she noted, barely the equivalent of three flies or a couple of worms. "Apologies Jim, let's talk over tea," she added."
redux [05.13.00]
"Well, they weren't all men, but mostly. The betting in the pub continued, the lowest bet being 29,800 genes placed by Pat Tome and the highest number coming from John Quackenbush at 118,259.
The pool was organized by Erwin Birney, a team leader at the European Bioinformatics Institute. He tried to convince the bartender to oversee the betting, but was told in no uncertain terms that no gambling was allowed in the Cold Spring bar.
Guesses on the number of genes in the human genome have lowered considerably since the mapping of chromosome 21, which researchers found to contain only 225 genes, far fewer than previously predicted. The researchers on the chromosome 21 study predicted their results could mean that there are as few as 40,000 genes in the entire human genome.
"Someone from Incyte will probably show up and bet 150,000," one gambler said."
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Genomeweb
NAS Committee Says Published Researchers Should Share Data, No Exceptions
"An upcoming report from the National Academy of Sciences' Board on Life Sciences recommends that authors of scientific papers -- whether working in academia, government, or the commercial sector -- should allow unrestricted access to data and materials that support their published findings.
The report, "Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences," is the product of an initiative that the NAS launched in November 2001 to address growing uncertainty within the life science community regarding issues of data release and access in the post-genomic era."
"Prepublication Version Available for Online Reading; Final Version is Forthcoming"
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BBC
Bioterror fears impact free science
"A group of leading scientific journals has announced measures aimed at restricting the publication of research which could be used by bioterrorists.
In a joint statement, the journals' editors say it is crucial that concerns over terrorism do not affect the release of valuable medical research.
But they say they recognise there may be occasions when new research data should be withheld from publication because it could be abused.
redux [01.14.03]
"Despite fears that bioterrorists will use DNA sequence data to create 21st century superpathogens, genomic science should remain public, The Institute for Genomic Research head Claire Fraser said at a special National Academies meeting on national security and the life sciences last week.
Her explanation: genomics just isn't good enough yet to provide the kind of tools terrorists need."
redux [12.01.02]
[requires 'free' registration]
"Scientific information that the US government wants to keep mum, but which can't officially be labeled "classified," has been designated "sensitive but unclassified." One example is the National Academy of Science's recent report on agricultural bioterrorism. Its chapter on bioterror case studies is available only on a need-to-know basis. Other professional groups may find themselves in the same boat, but the rules governing the category are anything but clear.
Reference: Enserink, M. 2002. Entering the twilight zone of what material to censor. Science 298(5598):1548."
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Wired News
Happy Birthday, Dear Double Helix
"Fifty years after Watson's groundbreaking discovery, his fellow geneticists are keen to honor him and his ongoing contributions to science.
"Jim Watson is one of the great figures of the century, and one of the great humans of all time," said Richard Gibbs, director of the Human Genome Sequencing Center at Baylor College of Medicine in Houston. "Not just for this kind of pivotal contribution, but the long-term leadership role that he's played. He's really iconic, and there just really aren't many icons.""
"I have never seen Francis Crick in a modest mood." James Watson's mischievous opening line of The Double Helix raised many eyebrows at the time, but even Crick wouldn't quarrel with it now. Still brash and outspoken at 86, even without the booming laugh that once echoed through Cambridge's Cavendish lab, Crick has no reason for modesty. In the years since their discovery of the double helix, Crick, unlike Watson, has continued to do significant research, mostly by pondering big—and often controversial—theoretical questions rather than by toiling in the lab. Says his longtime colleague and fellow Nobel laureate Sydney Brenner: "He's the only molecular biologist I know who has managed to make a living as a theoretician.""
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Nature: Science Update
Strands of life are like a sticky zip
"DNA is like a sticky zip. So say researchers who have been pulling apart the two strands of the famous double helix by hand.
"The strands unzipped in jumps, repeatedly getting stuck for up to half an hour. The harder the researchers pulled, the bigger the jumps, until the process became almost an all-or-nothing affair: recalcitrant sticking or sudden unzipping of nearly the whole chain."
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BioMedNet
Improving drug response with pharmacogenomics
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""The need to incorporate the teaching of pharmacogenomics into the medical curriculum is quite urgent," said Gurwitz, who this academic year has launched such a course at Tel-Aviv University, which he hopes will stimulate other medical schools to follow. "Pharmacogenomics must be incorporated within a few years ... into the general MD curriculum," he said.
The consequence of not doing so, he says, could be that any therapeutic benefits of the Human Genome Project will be severely delayed. The next generation of doctors will not have an adequate understanding of the interplay between genetics and drug metabolism, he warns."
redux [01.07.03]
"Much like the giant Homer Simpson Pez dispenser in his office, John Quackenbush, PhD, dispenses tasty tidbits when he opens his mouth."
" I think if you review the microarray literature, everybody in the early days was saying, oh, we're going to find out what all the pathways are. And now I think everyone is realizing that what comes out of the arrays are associations. It's the whole link, the disjunction between correlation and causality. I may discover that mass murderers drink more milk than anybody else but that doesn't mean drinking milk makes you a mass murderer."
redux [12.17.02]
"Investors may have stopped watching, but drug companies are finally beginning to wrench tangible benefits from the human genome. Two years after a boom fed by hype, a revolution finally is starting to take hold not in how drugs are invented, but in how they are tested.
Merck (nyse: MRK - news - people ), the world's third-largest drug company, is using gene expression arrays, also known as DNA chips, to keep clinical duds from reaching expensive animal or human trials. Separately, Millennium Pharmaceuticals (nasdaq: MLNM - news - people ) used similar chips in its late-stage clinical studies of its cancer drug, Velcade. Millennium's work is a big step toward so-called personalized medicine, in which treatment would be tailored toward individual patients based on genetic makeup."
redux [10.07.02]
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"Pharmacogenomics holds the promise of delivering safer, better designer drugs--and profits--to pharmaceutical manufacturers. But the technology also poses a challenge to the industry's current, highly successful business model that relies on one-size-fits-all blockbuster drugs.
For small biotech companies and large drug manufacturers alike, pharmacogenomics remains only one component of genome-based research and consumes only a small part of the $30 billion (US) in annual pharmaceutical research and development funding, according to the Pharmaceutical Research and Manufacturers of America (PhRMA). "It's an area where we are seeing movement, but it's not there yet," says Gillian Woollett, associate vice president for biologics and biotechnology at PhRMA."
redux [09.10.02]
"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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AustraianIT
Blue Gene to crunch biotech's biggest numbers
"THE first version of IBM's revolutionary Blue Gene chip will roll off the production line this quarter, Ajay Royyuru, head of IBM's Computational Biology Centre, has revealed."
""We plan to build a 512-node prototype Blue Gene machine in our Watson Research Centre, in New York, where I am located, hopefully before the end of the year.
Then we will build a 64,000- node Blue Gene machine and deliver it to the Lawrence Livermore laboratory by late 2004, or early 2005."
redux [10.24.02]
"Linux will be the main operating system for IBM's upcoming family of "Blue Gene" supercomputers--a major endorsement for the OS and the open-source computing model it represents."
""We had two choices of operating systems for the Blue Gene family, either use a special purpose system or Linux," Bill Pulleyblank, director of Exploratory Server Systems at IBM Research, said in a statement. "We chose Linux because it's open and because we believed it could be extended to run a computer the size of Blue Gene. We saw considerable advantage in using an operating system supported by the open-source community so that we can get their input and feedback.""
redux [07.13.01]
""Ambuj Goyal, IBM Research's general manager for software, solutions, and strategy, was more ambitious than that. Why not build a machine to model molecular dynamics using general-purpose chips rather than specialized ones? That way you'd produce a prototype for a whole new family of supercomputers. Not only would it be great technology development, it would be great marketing, too. Whereas the Department of Energy has the greatest interest in top-end supercomputing - with its need to understand how nuclear weapons work - focusing on the life sciences rather than the death sciences could make supercomputing more widely appealing. What's more, a biology program would be a way of telling one of the newest markets for big iron - the post-genome biotech world - that IBM took its interests seriously. "We believe that the life sciences are going to be a rapidly growing area," says Blue Gene project manager Bill Pulleyblank, "a huge growth area for IBM.""
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Complexity Digest Virtual Conference Network
INSC 2003, International Nonlinear Sciences Conference Research and Applications in the Life Sciences
"Note: Audio files are in downloadable mp3 format for portable mp3 players or any mp3 software players. Video files are in asf format and can be played e.g. with windows media player. For the sound codec a (free) plugin might be required, but the download should be automatic.)"
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Nature: Science Update
DNA: Beyond the double helix
""The way I think about DNA is different," says Gasser, who is not alone. Watson and Crick transformed biology by revealing the three-dimensional structure of DNA - and in so doing, set the stage for a lasting obsession with its sequence of chemical letters. But 50 years on, researchers are realizing that DNA has a fascinating life in three dimensions - and the fourth dimension of time - that makes it far more than a simple string of code.
Today's studies paint a more complete picture of DNA by examining the molecule as it coils in the cell's nucleus. In this context, structural biologists now believe that DNA is frequently unfaithful to its famous structure. The double helix, it has emerged, regularly morphs into alternative shapes and weaves itself into knots."
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O'Reilly Network
Bioinformatics Technology Conference Coverage Page
"rather than link to any one article, i'd suggest just going over to the coverage page to browse at your leisure. there really is too much goodness to link to any one article, including lincoln stein's prognostication that bioinformatics will be extinct by 2012. as usual, oreilly does a good job of integrating weblog coverage with the conference.
sigh. maybe one of these year's i'll get a break and get to attend the conference."
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O'Reilly Network
Jim Kent Keynotes O'Reilly's Bioinformatics Conference
"Ben Franklin is remembered for his many great ideas, inventions, and accomplishments. In presenting this year's Ben Franklin Award on behalf of Bioinformatics.Org, J.W. Bizarro reminded us that Franklin also refused to profit from many of his ideas and instead made them freely available. Bizarro pointed out that Jim Kent, this year's recipient of the award, embodies those characteristics in his work, which includes creating a browser for the human genome that is used by many thousands of biomedical researchers every day.
"You've got to admire a man who will flirt with lightning," Kent begins."
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The New York Times
Smallpox Researchers Seek Help From Millions of Computer
Users
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"Responding to worries that smallpox could become a weapon of bioterrorism, a group of research universities and corporations and the Defense Department are announcing today a networked computer project intended to accelerate the search for a cure for smallpox.
The project is to use computing power contributed by a few million personal computer owners linked to the Internet worldwide to try to winnow the number of chemical compounds that might show promise in combating smallpox."
redux [01.09.03]