{bio,medical} informatics
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The New York Times
Three Universities Join Researcher to Develop Drugs
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"Saying that venture capitalists and drug companies are becoming reluctant to invest in academic medical discoveries, three leading California universities are planning to take on more of the task of developing drugs.
The universities -- Stanford and the University of California branches in San Francisco and San Diego -- are joining with SRI International, a nonprofit research institute, to form PharmaStart, a consortium aimed at moving discoveries made at the schools into clinical trials."
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ITWorld
IBM plans world's most powerful Linux supercomputer
"A Japanese national research laboratory has placed an order with IBM Corp. for a supercomputer cluster that, when completed, is expected to be the most powerful Linux-based computer in the world."
"IBM said it expects to deliver the cluster to AIST in March, 2004. AIST will link the machine with others as part of a supercomputer grid that will be used in research of grid technology, life sciences bioinformatics and nanotechnology, IBM said."
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EurekAlert
NYU scientists develop more accurate mathematical method to
analyze genetic data
""In spite of the fact that mathematics has been around for thousands of years, it is extremely new to biology, and our research in this area has focused on how best to leverage quantitative thinking in order to improve biological research," said Mishra. "This is not about data mining, or computation dealing with large amounts of data; it's about developing a better, more intelligent way of looking at things."
The current standard method used in the analysis of microarray data, pioneered by Eisen et al., is predicated on an arbitrary formulation. Mishra's team's algorithm replaces this method with a mathematically rigorous correlation coefficient of two gene expression vectors, based on James-Stein shrinkage estimators. Its research shows that the new algorithm corrects for many kinds of errors."
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WOAI.Com
Local Gene Detectives Open 'Computer Ranch'
"Once again San Antonio is a world champion. Not just in pro basketball, but also high-speed genetic research.
Doctor John Blangero showed us the new SBC Genomics Computing Center on the campus of the southwest foundation for biomedical research. It is the world's largest computer ranch devoted to DNA analysis."
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Bio-IT World
Congress Questions US Supercomputing Efforts
"The U.S. is falling behind Japan in the area of supercomputing, as federal research agencies have shifted their focus toward grid computing in the past decade, according to witnesses at a congressional hearing Wednesday.
The result is that U.S. companies have less access to supercomputing resources because demand from the U.S. government has traditionally driven the supercomputing industry in the U.S., critics of the government's efforts in high-performance computing told the U.S. House Science Committee."
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The New York Times
3 More Biotech Firms File Suit Against Columbia Over Patent
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"Columbia University is coming under increasing legal attack from biotechnology companies, which accuse it of illegally trying to extend the life of a patent that has brought the institution hundreds of millions in revenue."
"The suits say Columbia abused the patent system by obtaining a new patent covering the same invention that an expired patent had covered. The suits seek to invalidate the new patent and establish that the companies do not owe any more money to Columbia."
[requires 'free' registration]
"When universities license discoveries made by scientists to companies for commercialization, the whims of the marketplace determine the results. As with anything else in business, the odds of scoring a major financial hit are slight, but the payoff can be exceedingly large. This is especially true for the life sciences, where discoveries and patents in medicine and biology continue to produce the lion's share of revenues for universities and research institutions. Life science patents also contributed the most to overall research strength at US universities last year, outpacing discoveries in information technology and other fields."
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Wired Magazine
The End of Cancer (As we Know it)
"Even now, researchers are split over just how complicated cancer will turn out to be in the end - and some argue that our growing understanding of its molecular biology may also reveal intractable new levels of complexity. (One example: Researchers at UCLA's Jonsson Cancer Center recently investigated how overexpression by the Her2 gene affected the behavior of other genes - and found more than 500 changes.) But for now, optimism still holds sway. And if we succeed, at long last, in charting a tumor's mysterious mechanisms, getting diagnosed with cancer in 2015 could be a distinctly different experience than it is today. Much as AIDS evolved from being a mysterious disease that killed healthy young men in six months to a mostly survivable condition, so cancer might become a manageable illness. "More like an annoying mole in your garden than an alien taking over your body," as one researcher puts it. Either way, Golub believes, students of biology 10 years from now won't be able to imagine a time when cancer was treated without a molecular understanding of how it works."
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Financial Express
Indian Bioinformatics Market To Touch $20 M By '06: Report
"The report estimates that currently up to 10 per cent of investment in R&D is IT-related, and hence there is huge potential for Indian biotech and IT companies to enter into collaborative bioinformatics research with global pharma majors in the near term.
The report, however, indicated that despite India's IT capabilities, it may be difficuly to replicate this success in biotechnology as biotechnology differs from IT in many ways. Avendus suggests that Indian players will have to leverage upon the lower costs of infrastructure and human resources. The cost of setting up and running a bioinformatics company in India is a fraction of the cost in the US."
redux [03.18.03]
"Despite several strengths inherent, India's biotechnology industry is not able to take a quantum jump mainly due to lack of capital and low R&D spending, absence of industry-academic partnership and the mismatch between strategic research, product planning and effective collaboration.
The Associated Chambers of Commerce and Industry of India (Assocham) paper on Business of Biotechnology has pointed out that India has several options with the main focus on informatics. Bioinformatics is crucial for the advancement of the biotech industry by cutting the timeframe and costs in developing a product tremendously."
"Everyone in the room, from Sen. Hillary Rodham Clinton to Buffalo Mayor Anthony Masiello, was beaming at last week's announcement.
The news was that Asia's largest computer consultant has become a deep-pocket partner of the University at Buffalo. Under an agreement signed Monday, Tata Consultancy Services of India will partner with local researchers and help transform their discoveries into money-making products."
"But some in the tech community voiced concern that the state's $100 million-plus bioinformatics investment will wind up boosting the economy in Bombay instead of Buffalo."
redux [12.13.02]
[requires 'free' registration]
"India is set to reap substantial rewards in the field of functional genomics, thanks to an invaluable genetic resource and highly advanced IT expertise, predicts Samir Brahmachari, director of the country's Institute of Genomics and Integrative Biology in Delhi."
"Brahmachari sees India's genetic resource - not the biological samples themselves, but the associated information - as a tradable commodity. Data can be processed using India's unparalleled IT expertise, he says: The country's IT industry generated about $10 billion in revenues this year, and has continued to grow by 50% each year over the past decade. The information, once processed, represents an "intellectual-property protectable" commodity, he says."
redux [06.23.02]
"Also, India's success in information technology provides excellent opportunities in the field of bioinformatics.
"Traditional IT companies are translating their strong capabilities in data mining and warehousing to business models based on biological data," says the report, citing examples of IBM's India Research Lab and Satyam's five-year agreement with the Center for Cellular and Molecular Biology, Hyderabad."
redux [02.13.02]
"India's biotech boom could even dwarf software in coming years if you trust the most optimistic projections. Much of our $2.5-billion biotech market relies on low-end products like vaccines, but experts predict that as more start-ups come up, that could change dramatically."
"The need to dive into this ocean of genetic data for hidden treasures has created a whole new discipline--bio-informatics, the science of using information technology (IT) to decipher the genomic jumble. Thanks to a flourishing IT industry, bioinformatics is today the darling of venture capitalists, drug firms, and, of course, IT majors. So, Satyam Computers has signed a five-year alliance with CCMB to create, store, and annotate genetic databases, and it is angling for contracts from global bigpharma to sequence genes and build protein catalogs. Strand Genomics, a Bangalore-based bio-informatics start-up, is designing tools to accelerate drug discovery."
redux [09.17.01]
"India has the potential to garner 8-10 per cent of the global software market in the next few years from the current levels of just 1.5 per cent, but the country?s planners need to focus on improving computer penetration and use of Indian made software in the industry.
This was the view of FC Kohli, chairman, Tata Consultancy Services, while speaking at Connect 2001, an international conference and exhibition on information technology, communication technologies and bioinformatics, which opened on Thursday. Currently, India's IT exports are about $8.7 billion."
redux [08.27.01]
"THE mood is one of caution as far as bioinformatics is concerned. The beginning of the year saw hype building up around the fledgling industry as the next big gold rush for India.
But six months after the first bioinformatics seminar in the country, with the IT industry's lesson on hype fresh in mind, things are moving at a more sedate pace."
"In India, bioinformatics training institutes have already begun to mushroom. Bangalore and Hyderabad have around five private training institutes between them. However, the industry is sceptical about the quality of manpower these centres can supply because most of them have short-term courses offering basic skills, says Dr. Sabharwal. In all fairness to them she adds, "We need to wait for a few months to see the outcome of it all.""
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The New York Times: Editorials/Op-Ed
Is
Race Real?
[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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Wired News
Linux Reconstructing Tree of Life
"Demeter, Mother Earth to ancient Greeks, is now helping scientists unlock the mysteries of life.
Demeter is the name of the American Museum of Natural History's supercomputer. Built by biologist Ward Wheeler from off-the-shelf parts, the Linux cluster is now ranked the 107th-fastest computer in the world on the Top 500 supercomputers list.
Scientists are now using Demeter to create "The Tree of Life," a collaborative project involving biologists from around the world."
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Wired News
Mapping an 'Unlucky' Chromosome
"The number seven is not so lucky when it comes to chromosomes. Chromosome seven is the home of genes associated with cystic fibrosis, deafness, several cancers and a protein that resists cancer drugs.
The good news is, researchers now know more about chromosome seven than ever. Research at five centers around the world has culminated in the publication of the complete DNA sequence of chromosome seven in the July 10 issue of Nature."
"The most challenging region of the chromosome to sequence was that containing genes for Williams-Beuren syndrome (WBS), a rare genetic disorder characterized by mild mental retardation, unusual facial appearance and a narrowing of the aorta, the major artery leaving the heart. The WBS region was difficult to decipher because it contains large segments DNA with many duplicated genes, and the number of duplicated genes differs among individuals. Children with WBS are missing long stretches of these duplicated genes.
"It seems that multiple copies of these genes are necessary for normal development, and if any are lost, developmental abnormalities occur," Wilson says. "People who study this disease may find the chromosome 7 sequence data very helpful.""
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Herald Sun
Roos' genes in spotlight
"KANGAROOS will be next to join the select club of animals whose full genomes have been mapped."
" Professor Jenny Graves, who will today announce the creation of the Centre for Kangaroo Genomics, said it was important to map a marsupial genome to compare with humans.
"Kangaroos are very distantly related to humans," Professor Graves said yesterday. "Mice are too close to humans, so it's really useful to go a step away and compare genomes."
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BioMed Central
Using BioMed Central's open access full text corpus for data
mining research
"BioMed Central has so far published 2489 articles of peer-reviewed biomedical research, all of which are covered by our open access license agreement which allows free distribution and re-use of the full text article, including the highly structured XML version.
As a result, BioMed Central's research article corpus is ideally suited for use by data mining researchers."
"For more information on using BioMed Central's articles for data mining research, please contact Matthew Cockerill, Technical Director, BioMed Central (matt@biomedcentral.com)." [ via bioinformatics.org ]
[requires 'free' registration]
"Open-access publishing received official support this month when UK funding bodies agreed on a deal with BioMed Central (a partner of The Scientist)."
Under the terms of the deal with BioMed Central, the Joint Information Systems Committee (JISC), a committee of the UK's further and higher education funding bodies, is making a blanket payment covering university membership of BioMed Central. As a result, from July 1 university researchers in the United Kingdom whose work is accepted for publication in one of the company's peer-reviewed, online journals will not have to pay an author fee. In these journals, all research articles can, of course, be accessed free of charge by anyone with an Internet connection, and copyright is retained by the author."
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Computerworld Malaysia
Aiming for a suite spot
"SYNAMATIX. This is the name that is likely going to be on everyone's lips come the next year 2004. This local company, which is currently developing a special database for use in the life sciences industry, may not be an easily recognised entity among the many IT-related companies in the country. But what it plans to do in the bioinformatics field--should it prove successful--will surely make many sit up and take notice. The name that will hog column spaces in every technology and business newsprint in Malaysia. The name that will actually put Malaysia on the world map. All these might just be hypothetical statements and wishful thinking. But like many who came and fail before them, when an ambitious bioinformatics company like Synamatix is trying something so different, it makes you sit up and take notice."
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Genomeweb
PLoS Gets Lift With Introduction of Sabo Bill
"In a new TV spot, a man walks out his front door with his briefcase, and stops at the sidewalk to tie his shoe, as a voiceover says "in the year 2003, the Public Library of Science made it possible for people all over the world to have access to the latest scientific discoveries. Shortly thereafter, things began to change." The man stands up. And flies away.
The Public Library of Science, or Plos, is airing this 30-second spot as part of an awareness campaign,this coming fall, in hopes that its own initiative to make all scientific research publicly available online will take off as well."
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The Register
Los Alamos lends open source hand to life sciences
"Researchers at Los Alamos National Labs have struck computing gold once again with an open source project that could benefit genetic research."
"The group decided to chop up a BLAST database and spread it across a number of servers instead of throwing lots of horsepower at a single data set. In so doing, the need to run I/O requests to disk was eliminated and the researchers saw huge, super-linear performance gains.
The experiment to put little bits of a database in memory instead of on disk proved a success and has since drawn considerable attention to mpiBLAST from pharmaceutical companies, researchers and even Microsoft."
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Salon
The free research movement
""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."
[ rhetoric ]
“Bioinformatics will be at the core of biology in the 21st century. In fields ranging from structural biology to genomics to biomedical imaging, ready access to data and analytical tools are fundamentally changing the way investigators in the life sciences conduct research and approach problems. Complex, computationally intensive biological problems are now being addressed and promise to significantly advance our understanding of biology and medicine. No biological discipline will be unaffected by these technological breakthroughs.”
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