{bio,medical} informatics
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The Times of India
Indians discover three SARS virus genes
"Indian scientists missed the race to sequence the virus that causes SARS but they have scored a major victory by discovering three new genes of the virus - a step that should help speed up development of drugs or vaccine against the deadly disease that is feared to be reappearing."
"Indian scientists could not play a role in sequencing the SARS genome because they did not have access to the virus. However, availability of complete DNA sequence of SARS virus in the public domain provided them the opportunity for identification of protein coding genes using a novel gene prediction method called 'Gene Decipher' developed at IGIB."
redux [05.14.03]
"Researchers have made a three-dimensional image of a crucial part of the virus that causes severe acute respiratory syndrome (SARS). The model suggests that a drug being tested as a cold remedy is a good starting point in treating the killer disease."
""It's the Achilles' heel of the virus," says biochemist Rolf Hilgenfeld of the University of Luebeck in Germany, who led the team behind the model. "We're convinced that hitting this target will be enough to stop infection.""
redux [05.07.03]
"Scientists and commercial firms are scrambling to patent the genetic code of the virus thought to be responsible for Sars.
The group which produced the first entire genetic sequence of the coronavirus confirmed this week that it is seeking a patent to ensure that everyone has free access to the code.
It fears that a commercial patent could slow down research into vaccines and treatments."
redux [09.28.02]
"The Bay Area biotech firm that started the heretical campaign to ban gene patents hopes to stir more debate on the topic by sponsoring a scholarly smackdown in Washington, D.C., on Tuesday.
Santa Clara's Affymetrix broke ranks with the biotech industry in March by arguing that the United States should quit issuing gene patents because genes were invented by nature, not science."
redux [07.23.02]
"Patents on DNA sequences "inhibit innovation and development" and should be the exception rather than the norm, says a panel of leading UK bioethicists. In the past, biotech companies have said that without such patent protection they would not have the economic incentive to invest in expensive research towards new drugs.
A discussion paper, produced by the Nuffield Council on Bioethics (NCB), says that too many patents are of doubtful validity because they are being issued for genetic discoveries that are not adequately inventive. It recommends a number of significant changes to the way patents in the field are granted in the future and to limit possible adverse effects of those already issued."
redux [03.18.02]
"It's one of the toughest questions in biotechnology: Should businesses obtain patents on genetic information about plants, animals or humans? Michael Capellas, CEO of Compaq Computer Corp., surprised an audience of biotechnology specialists yesterday when he suggested that the answer should be "no.""
"In a comment that stunned the audience into several seconds of silence, Capellas responded to a question on the issue by flatly saying that companies shouldn't be able to patent genes. But he quickly backed away from the comment, pleading ignorance of all the ramifications of the issue. "If you're asking me what should be patentable," Capellas said, "I don't know.""
redux [02.07.02]
"Patents may make some genetic tests so expensive that ordinary labs cannot afford to offer them, says a team of researchers who interviewed staff at 119 US facilities.
Patents are meant to provide an incentive for companies to put their discoveries into the public domain. But some researchers wonder if prohibitive costs could in fact have the opposite effect, by keeping standard genetic tests out of the reach of all but a few laboratories. That would have far-reaching consequences not only for health care, but for clinical research and quality control, the researchers say."
redux [08.20.01]
""Like the Terrys, a rising number of patients, doctors and ethicists are questioning how the patent system handles genetic claims. Many say it awards too many patents, overly rewards their holders, and gives too little back to patients. Yet many industry voices complain the process is moving too slowly to keep up with galloping research and to yield medical care awaited by suffering patients."
"The gold rush days are about to begin,'' says Arthur Caplan, a bioethicist at the University of Pennsylvania. "There are so many targets that look so lucrative that they're falling all over one another to pursue opportunity after opportunity.""
redux [02.27.01]
"ONCE upon a time, pure and applied science were the same. Sir Humphry Davy discovered seven chemical elements, and invented the miner's safety lamp. Louis Pasteur investigated the properties of molecules, and worked out how to stop milk spoiling. Everybody thought that was admirable. Somehow, things have changed. Today the feeling is widespread that science and commerce should not - must not - mix. There is a queasy suspicion that the process of discovery is in some way corrupted if it is driven by profit."
"Far from compromising science, profit in both these cases - the development of new medicines and the elucidation of the genome - has animated it, and directed it towards meeting pressing human needs. It is a happy marriage. Davy and Pasteur would surely have approved."
redux [08.26.00]
"Nowhere are patents more central to the creative process than in genetic drug development, where human genes and their expressed proteins themselves are developed as therapies. The biotechnology industry in the United States has brought a handful of these crucial new products (recombinant human insulin, to name one of the most familiar) to market and is on the threshold of a bonanza of genetic drugs and vastly greater relief for ill and aging populations around the world.
Patent protection is the sine qua non of that bonanza."
redux [04.26.00]
""The analogy that I would use is that of a minefield," said Bob Levy, senior VP of science and technology for American Home Products. "We are spending an incredible amount of time now, when we find exciting targets and begin to validate them, in trying to define who has rights to what. And we're finding, in almost every product that we look at, that someone has patented the protein, the gene, a fragment, a diagnostic test." Levy noted that untangling patent rights, and determining which patents are dominant, are increasingly time-consuming and expensive tasks. And patent-holders must be paid. "The royalties that will be involved soon in some of the products that we are bringing to market, they're already up into the ten, fourteen, fifteen percent [range]," said Levy. "And that may increase with time.""
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BBC
Free software to aid poor doctors
"Free software developed to care for US Vietnam War vets could help provide better healthcare in poor countries.
A group of open source evangelists are looking to take the program called Vista beyond the borders of the US."
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Bio-IT World
The '04 Forecast for Bio-IT
"Earlier this year, Bio-IT World Senior Informatics Editor Malorye Branca interviewed 50 leaders in the bio-IT industry for their perspective on the completion of the human genome project, and their predictions/resolutions for the New Year and beyond.
As 2003 draws to a close, we present a three-part series of the highlights of that exclusive online report -- "50/50: Reflections on the Double Helix" -- with particular emphasis on the experts' predictions of the most important industry and technology trends for the year(s) ahead."
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Wired News
Mayo Amasses Mounds of Data
"The Mayo Clinic and IBM Life Sciences are close to activating an advanced database that doctors believe will help improve the accuracy and speed of diagnoses.
The database, called the Mayo Clinic Life Sciences System, will be used for research beginning in January by a limited number of doctors. It groups 4.4 million patients according to factors they have in common and includes both historical data and comprehensive information on Mayo Clinic patients dating back to 1997."
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News.Com
IBM thinks Fast for bioscience searches
"Oslo-based Fast Search & Transfer said on Monday that the two companies will look to integrate Fast's data search technology with Big Blue's products for bioscience customers in Europe and North America. The combined technology aims to help life sciences professionals track down information more quickly by providing a single point of access to massive amounts of data in internal systems and in external databases, in a disparate range of storage formats."
"We expect this partnership to help improve the discovery process for those in the life sciences sector who require real-time access to scientific information that is highly relevant to their research needs," Martin Stoddart, a senior marketing manager in IBM's Life Science Discovery Solutions unit, said in a statement."
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Mass High Tech
Biomed Rounds: Small companies step up to the plate in large
trials
"A half-dozen years ago it appeared that bioinformatics companies would take care of the data explosion. You know, big computers crunching large numbers in the hope that quick -- or quicker -- answers would be returned following an outsourcing of expensive software solutions.
But come to find out bioinformatics has not emerged as a dynamic space. The reason is that a fledging flock of geeks can never know enough about a client's science to make their software services worthwhile."
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BioMedNet
Scientists urged to take responsibility for bioterrorism
[requires 'free' registration]
"Although many scientific journals are now aware of their responsibility regarding publication of such research, what about when they receive manuscripts on work that is not intentionally related to dangerous pathogens, but which could nevertheless be misused?"
"Even though publishers are now becoming more aware of their responsibilities, the Internet presents a threat that has so far received little attention. An audience member noted, however, that in many cases, "the cat is out of the bag" with work that is posted onto the Internet which has not been submitted for peer review in a scientific journal."
redux [09.20.03]
[requires 'free' registration]
"As exemplified by the well-publicized cases of Thomas Butler, David Kelly, and Steven J. Hatfill, the fallout from the War on Terror has been particularly hazardous for scientists. Donald A. Henderson, who was inaugural director of the US Office of Public Health Preparedness, which coordinates the national response to public health emergencies, has accused the FBI of losing "all perspective" and of being "out of control" in the Butler and Hatfill investigations.
The dangers are summed up by the case of Butler, chief of the division of infectious diseases at Texas Tech University."
redux [09.13.03]
"In one telling situation, 32 scientists and editors connected to some of the most respected scientific journals have agreed to self-censor any advances they think might compromise national security.
"That's a chilling example of knowing whatever you do might not get published because an editor might decide that it will look bad for John Ashcroft," said Barry Bloom, dean of Harvard's School of Public Health."
redux [05.09.03]
"THE rapid progress of genomics means that the publication of yet another gene sequence for one of the Earth's many millions of species is not guaranteed to raise much interest. But this is no ordinary species. Bacillus anthracis is the bug that causes anthrax. The publication, in Nature, comes two months after a group of editors of the world's leading scientific journals announced they were worried about publishing information that could be used by terrorists to evil ends. New procedures had therefore been put into place to tackle this threat. The question is, do they work?"
redux [02.15.03]
"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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Bio-IT World
3rd Millennium Goes 'Open Source'
"3rd Millennium wants to cash in on the software it spent seven years developing for various government and commercial clients - by giving it away free.
The Waltham, Mass.-based informatics consultancy and services firm has released its Data Centric Knowledge Management System for biotech and drug R&D under a GNU general public license (GPL)."
"The company is betting that, of those life science organizations deploying the software, some will want to buy support and maintenance contracts."
redux [11.20.02]
"Until recently, open source has often appeared to bioscientists as some sort of novelty, or, worse, a threat to IP protection. In the last few years, though, solid achievements in clustering, genomic data management, Web publication, and scores of specific "vertical" applications have established open source as a serious technical alternative.
Big Pharma and other biosciences are just starting to realize how open source can systematically cut costs, improve security, allow their own workers to shift attention back to their "core competences" from proprietary IT expertise, and even promote better science. We're in the midst of a dramatic evangelical movement that teaches better ways for open source IT to support bioscientific goals. Perhaps the most consequential shift is that participants have begun to understand that standards-based open source can enhance biosciences' fundamental values. These are exciting times for open source bioinformatics."
redux [09.30.02]
"Brenner, for example, stressed that while open sourcing "has potential in a generic sort of way," success depends on the operational and business models of specific companies.
Even considering a move to open sourcing can meet with resistance. "All of the instrument companies were brought up in closed-source shops, so they would have to change this fundamental attitude," explained Hood."
"THE OPEN SOURCE MOVEMENT has gained significant momentum of late, particularly within the bioinformatics field. While open source licenses vary widely, distribution of open source software typically requires delivery of both the object code and the source code. Most commercial software is delivered only in object code form, which is not easily read and modified by programmers.
The decision of whether to use open source software requires a careful analysis of various factors. In the right situations, open source software can be an excellent choice. In other cases, it can be disastrous."
redux [08.21.02]
"Want to make money from open-source bioinformatics? As long as it's not too much you might be OK.
This was the verdict of a panel of academics and business executives who had convened last week to talk broadly about open-source bioinformatics. But the discussion, which took place at the IEEE Computer Society bioinformatics conference at Stanford University, frequently veered to whether one could, or even should, make money from it.
The answer was a resounding maybe."
redux [01.16.02]
"A debate is heating up in the academic community over whether software that is generated by publicly funded research must be released with an open source license. The Internet is one example of how releasing research code benefited the public, but the trend seems to be changing now, and universities are more likely to consider the profit opportunity. The Bayh-Dole Act paved the way for the privatization of publicly funded resources, but not everyone is happy with the results.
Against the tide of privatization comes a group of bioinformatics researchers and programmers with an online petition to require that all software created by publicly funded research projects be licensed as open source. They have founded a group and a Web site, OpenInformatics.org, to further this cause.
Here we present two opposing viewpoints on this issue."
redux [01.07.01]
"The Open Source movement is infectious, it seems. It has bubbled up in the field of bioinformatics - gene research software. Gene research is already a burgeoning area of activity, which is predicted to deliver numerous benefits to the health industry. It is also an area where software counts and where universities have managed to prosper from their activities. US universities lodge about 2000 patents each year, many in bioinformatics, and these patents contribute a good deal of revenue - an amount estimated at about $5 billion per annum, or ten percent of their total budgets. Thus Open Source activities in this area are not universally welcomed."
"Over the past several years, open-source software development has won high-profile adherents in the business world -- including the likes of IBM and Sun Microsystems. But it has always had its strongest fans in the academic world, where open-source software is seen as a natural extension of the idea that the fruits of academic research should be shared with everyone.
But now some academic programmers on the cutting edge have found that the licensing office is proving a more formidable obstacle to progress than the limits of their imagination and skill."
redux [11.26.01]
"Before computer whiz Steven E. Brenner accepted his tenure-track research post at the University of California-Berkeley last year, he demanded that the school's intellectual property police leave him alone.
Brenner prevailed. He's now one of the few experts in the emerging field of bioinformatics with the freedom to distribute his work, software used in gene research.
``It's vital to what we do,'' says Brenner, who supports a movement to force universities to allow ``open source'' publishing of gene research software code."
redux [08.18.01]
"Steve Brenner, assistant professor and leader of a computational genomics research group at the University of California, Berkeley, said he fears that many academic bioinformaticists are unaware of a legal risk they face on a daily basis: contributing to open source software projects without explicit permission from their institutions.
While many employers have clauses in their employment contracts that restrict the creation and use of open source software, bioinformatics programmers at universities are often not as attuned to copyright issues as their industry counterparts. This fact, Brenner said, raises the possibility that a good portion of biological open source software is currently being produced illegally."
"The issue seems to be coming to a head in the academic world now, as more universities are exploiting the revenue stream made possible by their copyright and patent holdings. ?If you?re a software developer, the university holds rights to your software, but if you?re an English professor or Law professor and publish a book, they?re not the least bit interested in copyright,? said Thomas Field, an attorney at the Franklin Pierce Law Center affiliated with the Association of University Technology Managers."
redux [11.05.01]
"Computers are supposed to help biotechnology, right? Isn't bioinformatics all the rage right now? Well, it is, but with popularity comes legal questions that many companies don't address until it's too late."
"It seems that many biotech companies don't realize that a computer vendor may have the rights to the software, and ultimately, the work that the biotech companies do.
For example, if a biotech company orders a computer network to help it sequence the genome of yeast, the company may ask the vendor to customize the software it will use to do the sequencing. However, the question is, who owns the right to that customized software--the biotech company or the software programmer?"
redux [08.23.01]
"This report outlines recent activity in open source software development within the discipline of bioinformatics. I present the relevant highlights of two bioinformatics meetings held in July 2001 in Copenhagen, Denmark: the Bioinformatics Open Source Conference and the Intelligent Systems for Molecular Biology Conference. The report also describes a large number of projects and groups important to bioinformatics open source software development. The appendices include meeting programs, the currently accepted definition of open source software, and descriptions of important online biological data sources."
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Bio-IT World
IBM, Harvard Team to Develop 'Crimson Grid'
"Harvard University and IBM Corp. are developing a university-wide computing grid for student and faculty research, data sharing, and collaboration in life sciences, engineering, and applied sciences, they announced Wednesday.
The "Crimson Grid" will be based on OGSA (Open Grid Services Architecture) and is expected to eventually be available to other universities in the region, said Robert Eades, IBM's worldwide executive for academic, government and health in the company's life sciences division."
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The Scientist
Thinking Beyond Tomorrow
[requires 'free' registration]
"That discovery is fraught with unpredictability poses an enormous problem when evaluating research priorities and allocating funding. It also sends many scientists scrambling for cover when they are asked to prognosticate the future. The Scientist asked anyway.
Research scientists, venture capitalists, patent attorneys, even a biomedical professor-turned-mystery author offered their opinions on what will be the hottest new technologies five years hence."
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The New York Times
Comparing Genomes Shows Split Between Chimps and People
[requires 'free' registration]
"In a preliminary screen, Dr. Clark and his colleagues have found that a large number of genes shows signs of accelerated evolution in the human lineage. Those are genes that, by a statistical test applied to changes in their DNA, appear to be under strong recent pressure of natural selection and so are likely to be those that make humans differ from chimpanzees.
A prominent set of accelerated human genes are those involved in hearing, particularly the gene that makes a protein called alpha-tectorin, a component of the tectorial membrane of the inner ear."
"Another group of selected genes is involved in brain development."
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BioMedNet
Comparing genomes
[requires 'free' registration]
"About three billion As, Ts, Gs, and Cs make up the human genome sequence, but other organisms that are only slightly simpler can have up to 1000 times less DNA - implying that some human DNA is redundant, says Ewan Birney of the European Bioinformatics Institute (EBI) in Cambridge, UK. So which sections of DNA are redundant, he asks, and which sections correspond to specific genetic traits?
The most challenging aspect of this question, says Birney who heads Ensembl, an EBI project set up to develop software to facilitate annotation of the growing volume of data on eukaryotic genomes, is how to search for genes in the human genome when it is not clear what those genes look like."
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Nature: Science Update
Chimp
genome draft completed
"Researchers today released a draft version of the genetic sequence of our closest relative, the chimpanzee Pan troglodytes.
The differences between the chimp's genetic code and ours should reveal what makes us human, scientists hope. The disparities might, for example, lie in genes that control the development of the brain and language, or of human-specific diseases such as Alzheimer's, AIDS and malaria."
redux [05.20.03]
"Scientists from the Wayne State University, School of Medicine, Detroit, US, examined key genes in humans and several ape species and found our "life code" to be 99.4% the same as chimps.
They propose moving common chimps and another very closely related ape, bonobos, into the genus, Homo, the taxonomic grouping researchers use to classify people in the animal kingdom."
redux [04.29.03]
"By studying chimpanzees, scientists are honing their genetic view of humanity, researchers told this week's meeting of the Human Genome Organisation in Cancun, Mexico."
"The data call for some revision of the estimated genetic similarity between us and our closest relatives. Previously, human and chimp genetic sequences were quoted as being nearly 99% identical, with a difference of only a few DNA's letters. In fact, the similarity may be as low as 94-95%, says Todd Taylor of the RIKEN Genomic Sciences Center in Yokohama, Japan.
redux [03.04.03]
"Chimpanzees seem almost human, and scientists have maintained for decades that chimps are, in fact, 98.5 percent genetically identical to humans.
But the results of a new study call that figure into question, with a finding that there are actually large chunks of the human and chimp genomes that are vastly different."
"It involves sampling data from select regions of many different related species, and then comparing them within the context of their phylogenetic relationships. In the research described in the Science paper, Rubin and colleagues sampled 17 primate species closely related to human and spanning 40 million years of evolution -- insufficient time for significant genetic divergence to have taken place.
According to Rubin, phylogenetic shadowing compensates for the failure of traditional comparative genomics techniques, which "invariably miss recent changes in DNA sequence that account for primate-specific biological traits." The approach overcomes the primary challenge of comparing genomes of closely related species: the difficulty in distinguishing functional from nonfunctional sequences."
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Times Union
A vision has yet to spark rebirth
""Unfortunately, I think there's unreal expectations," said Skolnick, the Buffalo center director. Still, he said, the center "can play a role, and perhaps a significant role" in an economic turnaround.
Even so, not everybody is on board. At Ulrich's Tavern, which calls itself Buffalo's oldest and is sandwiched between the center and an old windshield-wiper factory, an elderly man nursed a midafternoon beer and said he'd never even heard of bioinformatics.
The bar's proprietor, Jim Daley Jr., was plenty aware of it.
"I think it's the most underrated thing in Buffalo," he said. "Most people talk about the casino.""
redux [07.14.03]
"If any doubts lingered among scientists, politicians or business executives about the future prospects for the University at Buffalo Center of Excellence in Bioinformatics, they were erased last Friday as nearly 200 scientists representing the U.S., Canada, India, the Netherlands, the United Kingdom, Italy and Japan gathered in the Adams Mark Hotel in Buffalo for the first annual "Frontiers in Bioinformatics" symposium."
"The day's events amounted to a grand show of support for the center of excellence, which was founded in 2001 by Gov. George E. Pataki"
redux [06.06.03]
"Despite the media barrage surrounding her new book, Senator Hillary Rodham Clinton made a brief appearance in Buffalo on Friday, June 6, to praise the University of Buffalo (UB)'s ambitious Bioinformatics Center of Excellence initiative."
""It has taken a lot of work to make the case to fund bioinformatics," Clinton said. "When we started, the response was, 'What's that?' " Despite this, Clinton and Reynolds have helped to earmark more than $9 million in federal funding for the project."
"Scientists on the cutting edge of drug development were comparing notes in Buffalo Friday during a symposium aimed at introducing the city's developing bioinformatics center to the scientific world."
"In Buffalo, bioinformatics is viewed as perhaps the best hope to generate jobs lost with the demise of its steel and grain-milling industries. But with several other cities around the country also investing heavily in life sciences, the center's directors are well aware of the competition for staff and resources."
redux [03.02.03]
"Jeff Skolnick didn't sign up for all this hype.
He did not apply to the following posting:
Savior wanted: A wunderkind in cutting-edge technology who can help build a new economy and carry the hopes of a Rust Belt region of 1.2 million people.
He just took a job heading a new academic program, the University at Buffalo's Center of Excellence in Bioinformatics."
redux [07.26.02]
"New York's U.S. Senators Charles Schumer and Hillary Rodham Clinton jointly announced that the Senate Appropriations Committee has approved $1 million in funding for Buffalo's planned Center of Excellence in Bioinformatics.
The $1 million was included as part of a an appropriations measure for the Departments of Veterans Affairs and Housing and Urban Development."
redux [05.01.02]
"An optimistic Pataki declared the center "will transform western New York into a 21st Century economy."
The lofty predictions come as upstate's largest city struggles to reinvent itself from a past-its-peak industrial center losing not only jobs but people: U.S. Census figures show the population has dropped to under 300,000, down from a 1950s peak of 580,000."
redux [12.07.01]
"Buffalo will be the site of a Center of Excellence for Bioinformatics thanks to a $200 million collaboration between the public and private sectors.
Gov. George Pataki announced during a swing through Buffalo on Dec. 6 that the state will contribute $50 million to help establish the 150,000 square-foot facility to be located adjacent to the emerging Buffalo Niagara Medical Campus. It is part of Pataki's $1 billion high-tech and biotech Centers of Excellence planned for across the state."
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eWeek
Analytics Tools Mine Text
"With predictive analytics at the core of many marketing initiatives, software developers are adding predictive capabilities to text mining so that enterprises can act on information in unstructured as well as structured data."
"The University of Pennsylvania's Abramson Cancer Center is using Clementine and LexiQuest in combination to better analyze years' worth of textual data to gain new insights into cancer diagnosis and treatment. "We took 10 years of [medical] journal articles and mined them for terms and syntax," said Michael Liebman, the center's director of computational biology and biomedical informatics, in Philadelphia. That analysis helps the center find patterns in the data showing relationships among diseases, symptoms, treatment and other factors, Liebman said, patterns that would otherwise have to be subjectively discerned by researchers poring over the data."
redux [10.27.03]
"SO YOU THINK you've found a cure for psoriasis. But first you need to check 12 million journal article abstracts on the National Library of Medicine's PubMed database, piling up at the rate of 40,000 new citations a month from 4,600 journals. You missed the latest issue of the Journal of Investigative Dermatology? PubMed's Medical Subject Headings (MeSH) vocabulary might help -- a little. It has 300,000 synonyms for 19,000 basic medical terms. But if you type in "epidermopoiesis," a key concept in the MeSH entry for psoriasis, you will find ... nothing.
Can software put an end to tortured searching? Researchers and vendors say text mining in the life sciences is on the verge of a long-sought dream: distilling oceans of inchoate data into insights and hypotheses."
redux [10.17.03]
[requires 'free' registration]
"MICHAEL N. LIEBMAN knows his limitations. Even with a Ph.D. and a long career in medical research, he cannot keep up with all the developments in his area of interest, breast cancer. Medline, the database that already houses more than 10 million abstracts for journal articles, is adding 7,000 to 8,000 abstracts per week. Only a fraction of these are about cancer, but the volume of information is daunting nonetheless."
"Yet Dr. Liebman is convinced that new cures could someday emerge for breast cancer if only someone could read all the literature and synthesize it. So he has found a solution: enlisting a computer program to read the articles for him."
redux [11.09.02]
"The analysis of large-scale genomic information (such as sequence data or expression patterns) frequently involves grouping genes on the basis of common experimental features. Often, as with gene expression clustering, there are too many groups to easily identify the functionally relevant ones. One valuable source of information about gene function is the published literature. We present a method, neighbor divergence, for assessing whether the genes within a group share a common biological function based on their associated scientific literature. The method uses statistical natural language processing techniques to interpret biological text. It requires only a corpus of documents relevant to the genes being studied (e.g., all genes in an organism) and an index connecting the documents to appropriate genes. Given a group of genes, neighbor divergence assigns a numerical score indicating how "functionally coherent" the gene group is from the perspective of the published literature. We evaluate our method by testing its ability to distinguish 19 known functional gene groups from 1900 randomly assembled groups. Neighbor divergence achieves 79% sensitivity at 100% specificity, comparing favorably to other tested methods. We also apply neighbor divergence to previously published gene expression clusters to assess its ability to recognize gene groups that had been manually identified as representative of a common function."
redux [10.08.01]
"The literature of the field of biology is the largest of all the sciences. The volume of biology literature each year, measured in bytes, is about fifty times the size of the entire human genome, junk and all. But locked in this literature is an enormous amount of information that can tell us much about the structure and function of genes, proteins, cells and organisms -- how they work as well as how they can fail.
The newly emergent interest in natural language processing for biology has been christened "Information Extraction". But work in this area has been going on for many decades under different names and this site includes a good deal of information about past and current work in NLP and in information extraction for biology in particular."
redux [04.30.01]
"Biologists in Norway have used a computer program to "read" the scientific literature and successfully predict gene interactions.
This data-mining of the "biobibliome" provides a way of dealing with the ever-increasing torrent of biological data - millions of papers a year. But even more impressively, the completely automated process can make new genetic discoveries - essentially free research."
"Annotating the tremendous amount of sequence information being generated requires accurate automated methods for recognizing homology. Although sequence similarity is only one of many indicators of evolutionary homology, it is often the only one used. Here we find that supplementing sequence similarity with information from biomedical literature is successful in increasing the accuracy of homology search results. We modified the PSI-BLAST algorithm to use literature similarity in each iteration of its database search. The modified algorithm is evaluated and compared to standard PSI-BLAST in searching for homologous proteins. The performance of the modified algorithm achieved 32% recall with 95% precision, while the original one achieved 33% recall with 84% precision; the literature similarity requirement preserved the sensitive characteristic of the PSI-BLAST algorithm while improving the precision."
"And the future of data-mining technology? Wide open, says Fayyad - especially as researchers begin to move beyond the field's original focus on highly structured, relational databases. One very hot area is "text data mining": extracting unexpected relationships from huge collections of free-form text documents. The results are still preliminary, as various labs experiment with natural-language processing, statistical word counts and other techniques. But the University of California at Berkeley's LINDI system, to take one example, has already been used to help geneticists search the biomedical literature and produce plausible hypotheses for the function of newly discovered genes."
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Triangle Tech Journal
Duke Researchers will reap benefits from cluster farm
"Tom Kepler, a professor of biostatistics and bioinformatics, cited another problem. "To hire good faculty," he said, "we have to show we're really serious about computation. Attractive candidates are going to be expecting significant resources.""
"Duke's cluster farm takes the concept to the next step by allowing researchers to buy as many clusters as they need. They literally own the processors and determine their use, he said. "In no way are we trying to take control away from anybody," he emphasized. Researchers can buy different-sized "plots" of computer clusters for different-sized "crops" of research problems. The farm currently has 200 nodes, each with two processors, including a core cluster of 64 nodes. It's a work in progress, said Harer. CSEM will add capacity as it learns from the process both technical and administratively."
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Australian IT
Forum to address sluggish bio-IT
"THE possibility of creating a "big science" project to boost Australia's profile in bio-IT and health informatics is to be discussed at a high-level meeting in Melbourne this week."
""Australia's growth in bioinformatics is currently slower than in other countries, especially in Asia," a GAP spokesman said."
""Informatics in biology and medicine requires the input of feeder industries, government and investors. It's agreed the industry here is fragmented and there is a need for centralisation.""
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ABC Science Online
Push to free up biotech tools for all
"Jefferson called for a "democratisation of innovation" based on "open source genetics". Central to this concept was a distinction between the tools of innovation and the products of innovation."
Tools of genetics and modern biology should be made freely available just as computer programming tools were shared in the open source software movement, he said."
redux [05.09.01]
"The toolbox of biochemistry, the parts list--"the kernel," to stretch the software analogy--is shared by all organisms on the planet. In general, organisms differ from one another because of their order of gene expression or because of relatively subtle perturbations to protein structures common to all forms of terrestrial life. That is, innovation in the natural world in some sense has always followed the idea of a service and flow economy. If the environment is static, only when an organism figures out how to use the old toolbox to provide itself, or another organism, with a new service is advantage conferred.
The analogy to future industrial applications of biology is clear: When molecular biologists figure out the kernel of biology, innovation by humans will consist of tweaking the parts to provide new services. Because of the sheer amount of information, it is unlikely that a single corporate entity could maintain a monopoly on the kernel. Eventually, as design tasks increase in number and sophistication, corporations will have to share techniques and this information will inevitably spread widely, reaching all levels of technical ability--the currency of the day will be innovation and design. As with every other technology developed by humans, biological technology will be broadly disseminated."
Technology based on intentional, open-source biology is on its way, whether we like it or not, and the opportunity it represents will just begin to emerge in the next 50 years."
redux [11.20.02]
"Until recently, open source has often appeared to bioscientists as some sort of novelty, or, worse, a threat to IP protection. In the last few years, though, solid achievements in clustering, genomic data management, Web publication, and scores of specific "vertical" applications have established open source as a serious technical alternative.
Big Pharma and other biosciences are just starting to realize how open source can systematically cut costs, improve security, allow their own workers to shift attention back to their "core competences" from proprietary IT expertise, and even promote better science. We're in the midst of a dramatic evangelical movement that teaches better ways for open source IT to support bioscientific goals. Perhaps the most consequential shift is that participants have begun to understand that standards-based open source can enhance biosciences' fundamental values. These are exciting times for open source bioinformatics."
redux [09.30.02]
"Brenner, for example, stressed that while open sourcing "has potential in a generic sort of way," success depends on the operational and business models of specific companies.
Even considering a move to open sourcing can meet with resistance. "All of the instrument companies were brought up in closed-source shops, so they would have to change this fundamental attitude," explained Hood."
"THE OPEN SOURCE MOVEMENT has gained significant momentum of late, particularly within the bioinformatics field. While open source licenses vary widely, distribution of open source software typically requires delivery of both the object code and the source code. Most commercial software is delivered only in object code form, which is not easily read and modified by programmers.
The decision of whether to use open source software requires a careful analysis of various factors. In the right situations, open source software can be an excellent choice. In other cases, it can be disastrous."
redux [08.21.02]
"Want to make money from open-source bioinformatics? As long as it's not too much you might be OK.
This was the verdict of a panel of academics and business executives who had convened last week to talk broadly about open-source bioinformatics. But the discussion, which took place at the IEEE Computer Society bioinformatics conference at Stanford University, frequently veered to whether one could, or even should, make money from it.
The answer was a resounding maybe."
redux [01.16.02]
"A debate is heating up in the academic community over whether software that is generated by publicly funded research must be released with an open source license. The Internet is one example of how releasing research code benefited the public, but the trend seems to be changing now, and universities are more likely to consider the profit opportunity. The Bayh-Dole Act paved the way for the privatization of publicly funded resources, but not everyone is happy with the results.
Against the tide of privatization comes a group of bioinformatics researchers and programmers with an online petition to require that all software created by publicly funded research projects be licensed as open source. They have founded a group and a Web site, OpenInformatics.org, to further this cause.
Here we present two opposing viewpoints on this issue."
redux [01.07.01]
"The Open Source movement is infectious, it seems. It has bubbled up in the field of bioinformatics - gene research software. Gene research is already a burgeoning area of activity, which is predicted to deliver numerous benefits to the health industry. It is also an area where software counts and where universities have managed to prosper from their activities. US universities lodge about 2000 patents each year, many in bioinformatics, and these patents contribute a good deal of revenue - an amount estimated at about $5 billion per annum, or ten percent of their total budgets. Thus Open Source activities in this area are not universally welcomed."
"Over the past several years, open-source software development has won high-profile adherents in the business world -- including the likes of IBM