{bio,medical} informatics
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Wired News
DNA Could Speed Flu Vaccines
"The flu vaccine-making system that serves as the best available protection against a pandemic relies on millions of chicken eggs, takes nine months to produce each year's flu shots and has changed little since the 18th century. This creaky system poses a big problem if a new, deadly strain emerges once the annual and inflexible production process begins.
Several biotechnology companies are at work on a new and quicker way of making a flu vaccine they hope can replace one that requires people to be inoculated with the entire influenza virus. Their technique: extract just a few genes from the virus and inject it into people."
redux [10.17.05]
[requires 'free' registration]
"AFTER a decade of painstaking research, federal and university scientists have reconstructed the 1918 influenza virus that killed 50 million people worldwide. Like the flu viruses now raising alarm bells in Asia, the 1918 virus was a bird flu that jumped directly to humans, the scientists reported. To shed light on how the virus evolved, the United States Department of Health and Human Services published the full genome of the 1918 influenza virus on the Internet in the GenBank database.
This is extremely foolish. The genome is essentially the design of a weapon of mass destruction. No responsible scientist would advocate publishing precise designs for an atomic bomb, and in two ways revealing the sequence for the flu virus is even more dangerous."
redux [10.06.05]
""There most definitely is reason for concern," says Richard Ebright, a bacteriologist at Rutgers University in Piscataway, New Jersey, who serves on biosecurity panels. "Tumpey et al. have constructed, and provided procedures for others to construct, a virus that represents perhaps the most effective bioweapons agent now known."
"This would be extremely dangerous should it escape, and there is a long history of things escaping," says Barbara Hatch Rosenberg, a molecular biologist and member of the Federation of American Scientists' Working Group on Biological Weapons. "What advantage is so much greater than that risk?" "
"“This work will help us make vaccines and antivirals against pandemic strains,” says Tumpey. It is unclear how, as the next pandemic is likely to be a different kind of flu.
But, says Taubenberger, the 1918 sequences are already helping in another way: they prove that a bird flu can go pandemic without combining with a human flu, and suggest which mutations it needs. The most likely pandemic candidate, H5N1 bird flu, already has some of the mutations. We should watch out for more, he warns."
[requires 'free' registration]
"It was the culmination of work that began a decade ago and involved fishing tiny fragments of the 1918 virus from snippets of lung tissue from two soldiers and an Alaskan woman who died in the 1918 pandemic. The soldiers' tissue had been saved in an Army pathology warehouse, and the woman had been buried in permanently frozen ground.
"This is huge, huge, huge," said John Oxford, a professor of virology at St. Bartholomew's and the Royal London Hospital who was not part of the research team. "It's a huge breakthrough to be able to put a searchlight on a virus that killed 50 million people. I can't think of anything bigger that's happened in virology for many years.""
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Sys-Con
Applicability of the .NET Platform to Bioinformatics Research
"In all, bioinformatics is a field of research that has undergone a rapid explosion in terms of the numbers of tools and techniques that it has produced. While much of this progress can be attributed to the adaptability and flexibility of open source technologies such as Linux and Perl, it is important for bioinformatics professionals to consider that disseminating their bioinformatics tools to users can be as critical to scientific progress as developing new tools. A key way to facilitate the widespread dissemination of bioinformatics applications to biologists will likely be the development of an open sourced .NET class library to serve as framework for Windows-based bioinformatics applications."
redux [05.27.04]
"The Cornell Theory Center currently operates a cluster consisting of more than 900 processors based on Intel chips housed in Dell computers operating on Microsoft's Windows software. It represents the first steps in the development of Windows for a wide range of supercomputing applications.
Microsoft Research says its workshop brings together about 75 scientists to discuss data-intensive scientific computing as it pertains to Windows and .NET . The participants represent such fields as astronomy, material sciences, physics, archeology, oceanography, and bio-informatics and computational biology."
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News.Com
Blue Gene/L tops its own supercomputer record
"Lawrence Livermore National Laboratory and IBM unveiled the Blue Gene/L supercomputer Thursday and announced it's broken its own record again for the world's fastest supercomputer.
The 65,536-processor machine can sustain 280.6 trillion calculations per second, called 280.6 teraflops, IBM said Thursday. That's the top end of the range IBM forecast and more than twice the previous Blue Gene/L record of 136.8 teraflops, set when only half the machine was installed."
redux [09.07.05]
"Researchers at IBM’s Thomas J. Watson Research Center and Columbia University have used a small (single-rack) Blue Gene system from IBM to discover a new phenomenon having to do with the folding of a melittin protein in water.
Specifically, the Blue Gene system’s processing power allowed the researchers to perform simulations that were impractical to run on previously available high-performance computing systems."
""It's a big game changer," says Ajay Royyuru, a computational biologist in charge of IBM's life science research. "We now have the ability to think about the whole system, not just parts. We can start to build a robust model of how a system is behaving or misbehaving and ask, 'How can I correct it?' If I knock a gene out, how will the whole system behave?"
The ability to simulate how an entire system behaves is the modus operandi of Blue Gene, which ties the brute strength of tens of thousands of processors with a sophisticated architecture that lets processors share information on the fly. The record-breaking versions are running in elite institutions such as the Lawrence Livermore Lab--its behemoth consists of 32 e-Servers lashed together--and Japan's Advanced Institute of Science and Technology, but the basic 5.7-teraflop "e-Server" system is available for roughly $2 million. IBM is also renting space on Blue Gene systems for about $10,000 a week."
redux [08.19.05]
"IBM and Argonne have agreed to augment Argonne's Innovative and Novel Computational Impact on Theory and Experiment (INCITE) computer capacity with compute cycles on IBM's Blue Gene "BGW" supercomputer system at IBM T.J. Watson Research Center in Yorktown Heights, N.Y."
""What we're really talking about about is over 1 million CPU hours over the course of a year, running 24 x 7, minus maintenance and upgrades," Herb Schultz, a Blue Gene manager at IBM, told internetnews.com. "Depending on the project, the workload could take 10 racks at a time. We're trying to learn what these kinds of applications are all about, so it's a good exercise for us." Each of the twenty racks at the IBM facility has 2,048 CPUs."
redux [06.21.04]
"The latest list of the top 500 performing supercomputers in the world was released today and it shows IBM has placed two Blue Gene/L prototype systems in the top 10. Additionally, clusters are now the most common supercomputer architecture."
"Coming in at number four and eight were the Blue Gene/L DD1 and DD2 Prototype systems. The systems’ performance benchmarks were 11.68 teraFLOPS sustained speed and 16 teraFLOPS peak performance for the DD1 and 8.66 teraFLOPS sustained, 11.47 tearFLOPS peak for the DD2."
redux [02.20.04]
"IBM will install a second Blue Gene/L supercomputer as part of a radio telescope project in the Netherlands, the company plans to announce Monday.
The supercomputer will be used for a new radio telescope project called Lofar, short for low frequency array, run by a Dutch organization called Astron. The system, which is expected to be complete in 2005, will run the Linux operating system, use about 12,000 processors and perform more than 30 trillion calculations per second, sources familiar with the plan said."
redux [11.15.03]
"IBM on Friday talked up its Blue Gene/L supercomputer, the first module of which is a relatively small, dishwasher-size machine that can perform 1.4 trillion calculations per second.
The performance is enough to make the machine the world's 73rd fastest supercomputer, according to a ranking of the top 500 to be released Sunday. By the time IBM has upgraded the box's 512 chips, each with two processors, and linked it with another 127 identical systems in 2005, Big Blue hopes to take the top spot."
redux [09.19.03]
"WHATEVER happened to Blue Gene, IBM's ambitious attempt to build the world's fastest computer? The project, launched in 1999, called for the construction of a "massively parallel" computer with over 36,000 processing chips, each containing 32 processing cores roughly equivalent in power to a desktop PC. Harnessing all that computing horsepower--more than one petaflop, or 1,000 trillion floating-point calculations per second--would, it was hoped, allow scientists to simulate the folding of a protein, an extraordinarily demanding task which might help to streamline the discovery of new drugs. The idea was to achieve all of this within five years--something that even enthusiasts thought ambitious.
Four years on, the chips that will power the first Blue Gene computer are now being manufactured and tested. But the plans have changed somewhat."
redux [05.08.03]
""Blue Gene is a completely oddball, you've-never-seen-anything-like-this-before design," said Illuminata analyst Jonathan Eunice. "It is not custom everything, (but) it is still very exotic compared to anything you can buy.""
"IBM already has spent more than the original $100 million budgeted for the project and won't meet its 2004 goal for the ultimate machine, but the company has made progress bringing its ideas to fruition."
redux [02.11.03]
"THE first version of IBM's revolutionary Blue Gene chip will roll off the production line this quarter, Ajay Royyuru, head of IBM's Computational Biology Centre, has revealed."
""We plan to build a 512-node prototype Blue Gene machine in our Watson Research Centre, in New York, where I am located, hopefully before the end of the year.
Then we will build a 64,000- node Blue Gene machine and deliver it to the Lawrence Livermore laboratory by late 2004, or early 2005."
redux [10.24.02]
"Linux will be the main operating system for IBM's upcoming family of "Blue Gene" supercomputers--a major endorsement for the OS and the open-source computing model it represents."
""We had two choices of operating systems for the Blue Gene family, either use a special purpose system or Linux," Bill Pulleyblank, director of Exploratory Server Systems at IBM Research, said in a statement. "We chose Linux because it's open and because we believed it could be extended to run a computer the size of Blue Gene. We saw considerable advantage in using an operating system supported by the open-source community so that we can get their input and feedback.""
redux [07.13.01]
""Ambuj Goyal, IBM Research's general manager for software, solutions, and strategy, was more ambitious than that. Why not build a machine to model molecular dynamics using general-purpose chips rather than specialized ones? That way you'd produce a prototype for a whole new family of supercomputers. Not only would it be great technology development, it would be great marketing, too. Whereas the Department of Energy has the greatest interest in top-end supercomputing - with its need to understand how nuclear weapons work - focusing on the life sciences rather than the death sciences could make supercomputing more widely appealing. What's more, a biology program would be a way of telling one of the newest markets for big iron - the post-genome biotech world - that IBM took its interests seriously. "We believe that the life sciences are going to be a rapidly growing area," says Blue Gene project manager Bill Pulleyblank, "a huge growth area for IBM.""
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Bio-IT World
I3C: Missing in Action
Sometime within the last year, the Interoperable Informatics Infrastructure Consortium (I3C) quietly disappeared. Sadly, perhaps, almost nobody noticed.
Researchers and vendors launched the I3C with the noble goal of developing interoperability standards for the life sciences that would make it easier to access, exchange, and share data."
"So why did the I3C just vanish with so little fanfare? Opinions among some of the I3C founding members vary, but the consensus is that the work of the I3C is being carried out today in other standards bodies."
redux [11.08.03]
"Loralyn Mears, Sun's market development group manager, life sciences, said, "Looking back the vision was grand: 'Let's create the solutions where everybody can plug everything in.' Well, you know it's hard to define what that everything is, especially when every couple of months there's a new everything to add."
"Over time, especially the last year, it became apparent that the I3C wanted to pursue a direction of formal specifications and standards, which was never really the original intent," said Mears."
redux [08.13.02]
"For researchers it's really about using the absolute best applications. Our universities are turning out a tremendous number of the most important applications that people are using -- there's huge innovation that happens in government and university labs. We need to be able to integrate the applications that come from both public and private sectors.
So the idea of I3C is to make this layer open, and agree on a set of standards. There will have to be a lot of domain specifics to this middleware architecture, probably done as XML vocabulary around particular areas of chemistry and biology and expression data analysis. And the applications will have to become compliant, so it is a little bit of work for the [informatics suppliers], but ultimately there's a value proposition for everybody."
redux [06.27.01]
"The Interoperable Informatics Infrastructure Consortium (I3C) unveiled its first demonstration of a working protocol Tuesday at the BIO 2001 Conference."
The XML-driven format allowed the exchange and analysis of sequence data across 10 different organizations? products. I3C views the demonstration as a bridge to the next step to defining components needed for a more general open architecture."
redux [05.23.01]
"The new coalition, led by the Biotechnology Industry Organization (BIO), a Washington trade group, plans to spend the next year or so creating a detailed specification for biological data. This specification would be available without fee to any company or scientist that wanted to use it to help organize and mine information."
The project has been dubbed the Interoperable Informatics Infrastructure Consortium, or I3C."
redux [02.21.01]
"Sun Microsystems said Wednesday it would partner with the Biotechnology Industry Organization, the National Cancer Institute, and several commercial bioinformatics vendors to support a collaborative effort to develop an open platform for the life sciences based on Java and XML.
The proposed initiative, temporarily referred to as Life Force or LI4 (Lifescience Informatics Interoperability Infrastructure Initiative) aims to develop an open platform to support data integration and interoperability and to focus the growing number of standards efforts."
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BusinessWeek
A New Roadmap for Genetics
"Gattaca, a science-fiction movie released in 1997, portrays a dystopian future in which a person's place in society is determined by an analysis of his or her DNA, and the likelihood of disease is ascertained at birth. The movie would seem to have little connection with reality -- except that an international consortium has just completed the groundwork for a version of this future. Ultimately, an individual's DNA could be decoded at an early age to spot a predisposition to illness. And here's where life improves on art: The goal will be to counter the risk of disease, not pigeonhole the person."
"And HapMap shows how differences between ethnic groups can be very subtle."
"But although the absolute differences between the various ethnic backgrounds are tiny, there are genetic trends that differ between ethnic groups. A given set of SNPs may be linked in one way in Asian populations for example, but in a different way in Europeans. Over the whole genome there are more differences between individuals than there are between ethnic groups, but such trends are still thought to be useful for targeting drugs.
Hudson stresses that not all people within an ethnic group share the same SNP pattern, so pharmaceutical companies should bear this in mind. "We would want to give a drug not based on the colour of someone's skin but based on the presence or absence of the genetic markers," he says."
redux [07.27.05]
"So, what's in it for me? That question probably crossed many minds five years ago following the news that scientists had successfully assembled the first draft of the human genome -- the genetic blueprint of a human being. The answer for most of us was ''not much."
What a difference five years can make. Today, we are witnessing a revolution in the understanding of health and disease, spurred on by the sequencing of the human genome and the subsequent creation of a map of human genetic variation. And, like most historic movements, this revolution has been given a name: personalized medicine."
"Will access to genomic technologies be equitable? Will knowledge of human genetic variation reduce prejudice or increase it? What boundaries will need to be placed on this technology, particularly when applied to enhancement of traits rather than prevention or treatment of disease? Will we succumb to genetic determinism, neglecting the role of the environment and undervaluing the power of the human spirit?"
redux [07.12.03]
[requires 'free' registration]
"Genetics increasingly shows that racial and ethnic distinctions are real -- but often fuzzy and greatly exaggerated. Genetics will increasingly show that most humans are mongrels, and it will make a mockery of racism.
"There are meaningful distinctions among groups that may have implications for disease susceptibility," said Harry Ostrer, a genetics expert at the New York University School of Medicine. "The right-wing version of this is `The Bell Curve,' and that's pseudoscience -- that's not real. But there can be a middle ground between left-wing political correctness and right-wing meanness.""
redux [05.28.03]
"Howard University officials yesterday announced plans to create the first large-scale collection of genetic profiles of African Americans, an endeavor they described as a bid for a "place at the table in genetic research" and a pathway to improved medical care for blacks."
"However, other genetics experts question the premise that the program can help as much as Howard officials say."
redux [05.13.03]
"The use--and often misuse--of genetics to explain racial and ethnic differences is, of course, nothing new. But the HapMap, together with a series of powerful genomic tools developed over the last several years, will make it possible to spell out in great detail the genetic differences between peoples from different parts of the world. Sociologists, bioethicists, and anthropologists worry that the genetic data could be manipulated to give an air of biological credence to ethnic stereotypes, to revive discredited racial classifications, and even to fuel bogus claims of fundamental genetic differences between groups."
redux [01.25.03]
"Race doesn't exist, the mantra went. The DNA inside people with different complexions and hair textures is 99.9 percent alike, so the notion of race had no meaning in science. At a National Human Genome Research Institute (NHGRI) meeting five years ago, geneticists were all nodding in agreement. Then sociologist Troy Duster pulled a forensics paper out of his briefcase. It claimed that criminologists could find out whether a suspect was Caucasian, Afro-Caribbean or Asian Indian merely by analyzing three sections of DNA.
"It was chilling," recalls Francis S. Collins, director of the institute. He had not been aware of DNA sequences that could identify race, and it shocked him that the information can be used to investigate crimes. "It stopped the conversation in its tracks.""
redux [12.20.02]
"Inuit or Basque, Laotian or Pashtun: we're much more similar than we are different, says the most detailed analysis of human genetic variation to date.
When it comes to sensitivity to drugs or diseases, the analysis also suggests that a person's account of their ethnic origin is almost as reliable an indicator as intrusive genetic tests.""
redux [11.01.02]
"In response to early concerns about racial profiling, scientists at the Human Genome Project went out of their way to downplay ethnic variations. Humans are 99.9 per cent alike, the sequencing showed, a figure that was leveraged into a call for global harmony. "The concept of race has no genetic or scientific basis," said Francis Collins, head of the Human Genome Project, at the White House ceremony to celebrate the genome completion.
Yet a great deal of controversy is now brewing over that 0.1 per cent. A growing number of scientists want to use such information as a way to find cures for devastating diseases. If we know more about the genes that cause susceptibility to cystic fibrosis in whites, or sickle cell anaemia in blacks, they argue, we will move closer to a solution for these illnesses. "Ancestry is imperative to biomedical research," says Mark Shriver, an anthropologist at Pennsylvania State University."
redux [10.30.01]
"Race should not influence drug prescriptions, warn geneticists. Genetic differences between individuals give a better indication of who will respond well to a medicine, a new study shows."
Geneticists have known this for a while. "It's no surprise that skin pigment is a lousy predictor of physiology," says Howard McLeod of Washington University School of Medicine in St Louis, Missouri. This study is the first to prove it."
redux [07.20.01]
[requires 'free' registration]
"Scientists planning the next phase of the human genome project are being forced to confront a treacherous issue: the genetic differences between human races."
"With the decoding of the human genome largely complete, government scientists are beginning to construct a special kind of genetic map that would provide a shortcut to locating the variant human genes that predispose people to common diseases."
"The question the scientists face is whether that map should chart possible differences that may emerge among the principal population groups, those of Africans, Asians and Europeans."
redux [03.18.01]
"Genetics research is demonstrating that the differences in appearance among groups are profoundly incidental, but these differences do have a genetic basis. And although it's true that all people have inherited the same genetic legacy, the genetic differences among groups have important implications for our understanding of history and for biomedical research. These complications in an otherwise reassuring story have thoroughly spooked the leaders of the public and private genome efforts. The NIH has been collecting information about genetic variants from different ethnic groups in the United States, but it has refused to link specific variants with ethnicity. Celera has been sequencing DNA from an Asian, a Hispanic, a Caucasian, and an African-American, but it, too, declines to say which DNA is which.
This strategy of avoiding the issue is almost sure to backfire. It seems to imply that geneticists have something to hide. But the message emerging from laboratories around the world should be hailed, not muzzled. It is one of great hope and promise for our species."
redux [06.11.01]
[requires 'free' registration]
"Scientists have long suspected that the racial categories recognized by society are not reflected on the genetic level.
But the more closely that researchers examine the human genome -- the complement of genetic material encased in the heart of almost every cell of the body -- the more most of them are convinced that the standard labels used to distinguish people by "race" have little or no biological meaning.""
""Ethnicity is a broad concept that encompasses both genetics and culture," Dr. Anand said. "Thinking about ethnicity is a way to bring together questions of a person's biology, lifestyle, diet, rather than just focusing on race. Ethnicity is about phenotype and genotype, and, if you define the terms of your study, it allows you to look at differences between groups in a valid way."
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Nature
Y chromosomes reveal founding father
"About 1.5 million men in northern China and Mongolia may be descended from a single man, according to a study based on Y chromosome genetics."
Historical records suggest that this man may be Giocangga, who lived in the mid-1500s and whose grandson founded the Qing dynasty, which ruled China from 1644 to 1912.
The analysis is similar to a controversial study in 2003, which suggested that approximately 16 million men alive today are descended from the Mongolian conqueror Genghis Khan."
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The Wall Street Journal
A Better Idea
"Gene sequencing -- the process of unlocking an individual's DNA -- could one day revolutionize medicine, allowing doctors to quickly identify someone's genetic makeup and craft individual treatments for such diseases as cancer and tuberculosis. But first, there has to be a way to speed the cumbersome, slow and expensive sequencing process."
"The genome-sequencing technique from 454 Life Sciences was selected as the Gold winner in The Wall Street Journal's 2005 Technology Innovation Awards competition. Innovative technologies from around the world were eligible for awards in categories including biotechnology, software, security, energy and the environment, among others."
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Bio-IT World
Venter Raises Stakes for “$1,000 Genome”
"Adding even greater incentive to scientists striving to realize the era of the $1,000 genome sequence, J. Craig Venter announced today that he is seeking to increase the size of his foundation’s prize from $500,000 to as much as $10 million."
"“We’re thinking of a timeline that this has to be done sometime between 2008 and 2010. We’re trying to raise the prize value to reward the scientists that actually come up with these breakthroughs, not by calculation but by actual demonstration.”"
redux [08.05.05]
"A thousand dollars can buy a lot of things. Scientists hope to soon add an individual's genetic sequence to that list. Full-genome DNA decoding, estimated to now cost $20 million, could soon be done for about $2.2 million, experts say, and will continue to drop in price as researchers develop new ways to conquer the task. A report published online yesterday by the journal Science suggests one such method: a technique that used off-the-shelf instruments and reagents to successfully sequence the E. coli genome."
"Unlike the 454 approach, the method developed by Church and colleagues is a form of DNA resequencing – that is, it requires a reference sequence with which to compare the new sequence, because each fragment of DNA sequenced is so short. Nevertheless, many likely lab applications – from genotyping haplotypes in a disease study, searching for mutations in cancer resistance, or as in the Science paper, identifying microbial strain variants – would fall into this category."
redux [08.01.05]
"When Jonathan Rothberg's son was born six years ago, the baby was sent to the infant intensive care unit. Rothberg worried all night that something might be wrong with his child, and he found himself wishing he could just read the boy's genome to find out.
At the time that was impossible: it cost tens of millions of dollars and took more than a decade to decipher the first complete human genome, published in 2001 in Nature. But Rothberg's parental panic and frustration inspired him to design a faster, cheaper sequencing technique. Now Rothberg and his co-workers at the 454 Life Sciences Corporation, which he founded, report their success. "
[requires 'free' registration]
""What they have done here is very significant," Dr. Ronaghi said, noting that the company had already sequenced 50 microbial genomes. "This is the first step toward $1,000 human genome sequencing," he said."
"Jonathan Rothberg, board chairman of 454 Life Sciences, said the company was already able to decode DNA 400 units at a time in test machines. It was working toward sequencing a human genome for $100,000, and if costs could be further reduced to $20,000 the sequencing of individual genomes would be medically worthwhile, Dr. Rothberg said."
redux [10.03.02]
"Mapping and reading J. Craig Venter's genome took 15 years, $5 billion and some of the world's most sophisticated computers.
Wouldn't you, too, like your genome decoded?
Venter says he plans to offer the service, with the goal of burning individual human's entire DNA sequences onto shiny compact discs."
"Tonight's plenary panel discussion at GSAC, "The Future of DNA Sequencing: Advancing Toward the $1,000 Genome," hosted by Craig Venter and Gerald Rubin, quickly turned into a genomics version of the game show "The Price is Right."
"I had to do a little better than the thousand-dollar genome," said VisiGen Biotechnologies CEO Susan Hardin, one of the panelists, about her company's efforts to develop a single-molecule sequencing method using both a modified polymerase and nucleotides. "So we're going for the $995 genome.""
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Nature
You say genomics, I say genetics...
"Training as a geneticist or genomicist today involves mastering a lot more than the mendelian ratios, central dogma and population equations of times past. Not only has the conceptual focus shifted from genes to genomes, but that change has added the new realm of bioinformatics. As a result, today's genetic scientists have skill sets that dwarf those of their mentors."
"Over the past few years, familiarity with, if not expertise in, bioinformatics has become not just desirable, but expected. "Classical and molecular genetics are still part of the training, but it is hard to believe that anyone with a PhD in genetics nowadays would not also have a background in bioinformatics," says Richard Gregory, director of research at Genzyme in Cambridge, Massachusetts."
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Science Daily
Online journal to cover clinical trials
"PLoS Clinical Trials, a new online journal, will be launched next spring to report results of all randomized controlled clinical trials on humans in all medical and public-health disciplines, its sponsor said Monday."
"PLoS will charge a publication fee to authors to offset the journal's costs, but the fee will be waived for authors with insufficient funds, the library said in a statement."
"Dr. Catherine DeAngelis, editor-in-chief of the Journal of the American Medical Association, said the entire scientific community is concerned about getting research information into the public domain.
"I think the idea of getting things out there is fine," DeAngelis told UPI, "but I'd like to see the (journal's) business plan. I think they will find this is a more expensive proposition than they thought.""
redux [09.28.05]
"IT USED to be so straightforward. A team of researchers working together in the laboratory would submit the results of their research to a journal. A journal editor would then remove the authors' names and affiliations from the paper and send it to their peers for review. Depending on the comments received, the editor would accept the paper for publication or decline it. Copyright rested with the journal publisher, and researchers seeking knowledge of the results would have to subscribe to the journal.
No longer. The internet—and pressure from funding agencies, who are questioning why commercial publishers are making money from government-funded research by restricting access to it—is making free access to scientific results a reality. This week, the Organisation for Economic Co-operation and Development (OECD) issued a report describing the far-reaching consequences of this. The report, by John Houghton of Victoria University in Australia and Graham Vickery of the OECD, makes heavy reading for publishers who have, so far, made handsome profits. But it goes further than that. It signals a change in what has, until now, been a key element of scientific endeavour."
redux [08.15.05]
"Now, after a study that sent reverberations through the medical profession by finding that almost one-third of top research articles have been either contradicted or seriously questioned, some specialists are calling for radical changes in the system."
In advance of a world congress on peer review next month in Chicago, these specialists are suggesting that reviewers drop their anonymity and allow comments to be published."
""It would be lovely to start anew and to set up a trial of peer review against no peer review," Rennie said. "But no journal is willing to risk it.""
redux [06.25.04]
[requires 'free' registration]
"More than money and success is at stake. Free and widespread distribution of new research has the potential to redefine the way scientific and intellectual developments are recorded, circulated and preserved for years to come.
"Society pays for science," said Dr. Nicolelis, whose article in the October issue of PLoS got worldwide attention. "We have the technology, we have the expertise. Why is it that the only thing that has remained the same for 50 years is the way we publish our results? The whole system needs overhaul.""
redux [11.22.03]
"Science's Rocky-style publishing battle starts its second round Monday when a groundbreaking journal releases its latest issue.
The challenger, the upstart Public Library of Science: Biology, packed a strong punch last month with its first issue, which featured a headline-grabbing report of monkeys getting brain implants to control robot arms. The upcoming issue spotlights newly discovered genes for obesity and osteoporosis."
redux [10.14.03]
"There are lots of scientific journals, and the debut of another one normally would not raise many eyebrows.
But yesterday's online launch of Public Library of Science Biology drew so many curious browsers -- half-a-million Web hits in the first eight hours -- that the swamped site had to divert many to a backup site."
"Led by heavyweights such as Nobel laureate Harold Varmus, former director of the National Institutes of Health, the PLoS project aims to shake up the world of scholarly publishing by freely sharing its monthly contents."
redux [10.10.03]
"In the highly lucrative world of cutting-edge scientific research, it is nothing short of a revolution. A group of leading scientists are to mount an unprecedented challenge to the publishers that lock away the valuable findings of research in expensive, subscription-only electronic databases by launching their own journal to give away results for free.
The control of information on everything from new cancer treatments to space exploration is at stake, while caught in the crossfire are the world's publicly funded scientists, some of whom will soon face a choice between their career and their conscience."
redux [08.22.03]
[requires 'free' registration]
"Debate over open access to scientific articles is steadily moving into the mainstream, with the publication this month of an editorial in The New York Times, a recently introduced Congressional bill to promote open access publishing, and a television commercial sponsored by the Public Library of Science (PLoS), a California-based group that plans to launch an open-access journal in October.
As enthusiasm grows, however, some skeptics wonder whether open-access journals will succeed financially, since they charge relatively small "article processing fees," paid upfront by the researcher, instead of substantial fees for institutional library subscriptions."
redux [07.01.03]
""It's ridiculous," Eisen said in this voice during a recent phone interview from Washington. "All these things we're so used to doing with information on the Internet, we're preventing clever entrepreneurial people from doing with works of science. The idea that a narrow profit motive would prevent the dissemination of this information -- it's insane!"
Eisen was in Washington to lend his support to a congressional effort he believes will make scientific publishing less insane and less ridiculous. Most scientific journals -- such as Science, Nature or the New England Journal of Medicine -- require researchers to turn over all rights to the reports selected for publication; the publications then charge institutions and individuals subscription fees to view these reports, a model that Eisen believes inhibits scientific progress. The approach is especially galling, Eisen says, when you consider that a great deal of the money that funds the research published in these journals comes from the federal government. The public is paying for science that it never gets to see, he says."
redux [12.16.02]
[requires 'free' registration]
"A group of prominent scientists is mounting an electronic challenge to the leading scientific journals, accusing them of holding back the progress of science by restricting online access to their articles so they can reap higher profits.
Supported by a $9 million grant from the Gordon and Betty Moore Foundation, the scientists say that this week they will announce the creation of two peer-reviewed online journals on biology and medicine, with the goal of cornering the best scientific papers and immediately depositing them in the public domain."
redux [11.15.02]
"Having persuaded the Energy Department to pull the plug on PubScience, a Web site that offered free access to scientific and technical articles, commercial publishers are taking aim at government-funded information services offering free legal and agricultural data.
"We're delighted with the decision [to shut down PubScience]," LeDuc said. "The administration has done a tremendous job of hearing our concerns and responding to what we've always considered to be our legitimate concern."
redux [09.24.02]
[requires 'free' registration]
"The UK's Office of Fair Trading says that the prices for scientific, technical, and medical (STM) journals are too high because normal competitive forces have been suspended. Libraries are paying too much. The prices of STMs are rising faster than inflation, and the disparity between for-profit and not-for-profit journals is obvious. Part of the problem is that the journals compete on quality, not price, so libraries are prone to skip the cheaper journals for the better, more expensive ones. Bundling journals also skews the market.
Goodman, S. 2002. "Unusual forces" are pushing journal market off course. Nature 419(6904):239.
redux [09.05.01]
[requires 'free' registration]
"Publishers of established scientific journals have thus far resisted demands for freer access. In its campaign to make biomedical research literature available free online, Public Library of Science is now taking a new tack: It hopes to publish peer-reviewed, electronic journals.
"If we really want to change the publication of scientific research, we must do the publishing ourselves," says an announcement posted Sept. 1 on the group's Web site. "It is time for us to work together to create the journals we have called for."
redux [04.24.01]
"When a molecular biologist or a biochemist has made a discovery - often after many months or even years of tedious experiments - they tell the rest of the world by publishing their results in a scientific journal. So far, these journals have controlled who can read them and who cannot - but maybe not for much longer.
E-mail, Internet discussion groups, electronic databases and pre- or e-print servers have already transformed the way scientists openly exchange their results. And in the life sciences, researchers are now demanding that their work be included in at least one free central electronic archive of published literature, challenging the traditional ownership of publishers. The demand has sparked widespread discussions among scientists, publishers, scientific societies and librarians about the future of scientific publishing. The outcome may be nothing short of a revolution in the scientific publishing world."
redux [09.20.00]
"How should biomedical research be communicated? How should research be assessed and validated?"
"Below are abstracts, transcripts, and biographies from the conference. Some presentations did not lend themselves to transcription. Where possible we have supplemented them with editorials from the speakers.
We have also commissioned editorial articles from several speakers and delagates at the meeting."
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The New York Times
Recipe for Destruction
[requires 'free' registration]
"AFTER a decade of painstaking research, federal and university scientists have reconstructed the 1918 influenza virus that killed 50 million people worldwide. Like the flu viruses now raising alarm bells in Asia, the 1918 virus was a bird flu that jumped directly to humans, the scientists reported. To shed light on how the virus evolved, the United States Department of Health and Human Services published the full genome of the 1918 influenza virus on the Internet in the GenBank database.
This is extremely foolish. The genome is essentially the design of a weapon of mass destruction. No responsible scientist would advocate publishing precise designs for an atomic bomb, and in two ways revealing the sequence for the flu virus is even more dangerous."
redux [10.06.05]
""There most definitely is reason for concern," says Richard Ebright, a bacteriologist at Rutgers University in Piscataway, New Jersey, who serves on biosecurity panels. "Tumpey et al. have constructed, and provided procedures for others to construct, a virus that represents perhaps the most effective bioweapons agent now known."
"This would be extremely dangerous should it escape, and there is a long history of things escaping," says Barbara Hatch Rosenberg, a molecular biologist and member of the Federation of American Scientists' Working Group on Biological Weapons. "What advantage is so much greater than that risk?" "
"“This work will help us make vaccines and antivirals against pandemic strains,” says Tumpey. It is unclear how, as the next pandemic is likely to be a different kind of flu.
But, says Taubenberger, the 1918 sequences are already helping in another way: they prove that a bird flu can go pandemic without combining with a human flu, and suggest which mutations it needs. The most likely pandemic candidate, H5N1 bird flu, already has some of the mutations. We should watch out for more, he warns."
[requires 'free' registration]
"It was the culmination of work that began a decade ago and involved fishing tiny fragments of the 1918 virus from snippets of lung tissue from two soldiers and an Alaskan woman who died in the 1918 pandemic. The soldiers' tissue had been saved in an Army pathology warehouse, and the woman had been buried in permanently frozen ground.
"This is huge, huge, huge," said John Oxford, a professor of virology at St. Bartholomew's and the Royal London Hospital who was not part of the research team. "It's a huge breakthrough to be able to put a searchlight on a virus that killed 50 million people. I can't think of anything bigger that's happened in virology for many years.""
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National Geographic News
One-Fifth of Human Genes Have Been Patented, Study Reveals
"A new study shows that 20 percent of human genes have been patented in the United States, primarily by private firms and universities."
"The top patent assignee is Incyte, a Palo Alto, California-based drug company whose patents cover 2,000 human genes."
"[Critics] caution that patents that are very broad can obstruct future innovations by preventing researchers from looking for alternative uses for a patented gene."
[via the personal genome ]
redux [05.19.04]
"A controversial patent on a breast cancer gene has been revoked by the European Patent Office, paving the way for cheaper screening across the continent. The verdict reflects the transatlantic disparities that make gene patents much tougher to uphold in Europe than in the US."
"The EPO has yet to spell out its precise reasons for revoking the BRCA1 patent, but New Scientist understands that the primary justification was that the application was not deemed "inventive"."
redux [08.18.03]
"An Australian biotech company, Genetic Technologies Ltd. (GTG), is stirring up controversy over its decision to enforce a series of patents, granted in the 1990s by the US Patent and Trademark Office, over the genetic diagnostic and mapping applications of non-coding, or junk, DNA."
"Scientists, including NHGRI chief Francis Collins and Sir John Sulston, are also upset over GTG's recent decision to ask academic institutions to sign research licenses."
redux [05.07.03]
"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.""