{bio,medical} informatics
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The New England Journal Of Medicine
The Triple Helix: Gene, Organism, and Environment""Like any large construction project in the public domain, sequencing the human genome has been a subject of discussion and controversy. Major issues have been the cost of the project, its scientific merit, and the effects of the knowledge gained on human affairs. The concern about cost subsided as the project proved viable and attracted private funding. That leaves the other two questions: What will we learn from this sequence, and how will it affect our lives? With fame and fortune to be made in the genome business, one can only be skeptical of the wondrous claims made by the project's protagonists. The Triple Helix examines these questions from a critical and biologically informed angle."
"In Lewontin's triple helix, the genes are placed in their natural context, where history and geography shape the nature of organisms and the genes they contain. His differences with the most modern of molecular and cellular biologists are irreconcilable and reflect the ever-widening gulf between biologists who have an affinity for what goes on outside the laboratory and those for whom the differences between individuals and between species represent "an annoyance [to be] ignored whenever possible." In many laboratories, organisms are now studied under conditions in which genetic variation is eliminated and the environment held constant. It is only under these special conditions, where neither variation nor natural selection is tolerated, that the triple helix collapses into the double helix and genes appear to be paramount.""
"The 'implication' that seems to worry people most of all is so-called 'genetic determinism'. It's the notion that, if human nature was shaped by evolution, then it's fixed and so we're simply stuck with it — there's nothing we can do about it. We can never change the world to be the way we want, we can never institute fairer societies; policy-making and politics are pointless.
Now, that's a complete misunderstanding. It doesn't distinguish between human nature — our evolved psychology — and the behavior that results from it. Certainly, human nature is fixed. It's universal and unchanging — common to every baby that's born, down through the history of our species. But human behavior — which is generated by that nature — is endlessly variable and diverse. After all, fixed rules can give rise to an inexhaustible range of outcomes. Natural selection equipped us with the fixed rules — the rules that constitute our human nature. And it designed those rules to generate behavior that's sensitive to the environment. So, the answer to 'genetic determinism' is simple. If you want to change behavior, just change the environment. And, of course, to know which changes would be appropriate and effective, you have to know those Darwinian rules. You need only to understand human nature, not to change it."
"In the late 1970s I attended meetings at which sociobiologists E. O. Wilson and David Barash, critic Stephen J. Gould, and others were on a panel. Standing blocked by the crowd in the hall outside the doorway to the packed hall I was unable hear the speakers. I spied a little door near the stage, and figured that if I could get to that door, I could get next to the stage and the front row. I sneaked through the hotel kitchen and found the door. Just as I opened it I was passed by a number of African American students who ran up on stage and poured water on Wilson's head. Wilson responded by saying to the audience that he felt like he had been speared by an aborigine. The crowd applauded the martyred Wilson (on crutches at the time--from a skiing accident) and some in the front row muttered epithets at the disrupters and at me, who appeared to have held the door for the demonstrators. The water pitcher story has been repeated scores of times in journalistic accounts, but none of these mention Wilson's racially tinged response. Two decades later the debate concerning the genetic determination of human behavior has been reanimated in the general intellectual and middle-brow media with a somewhat more restrained tone. The study of evolutionary accounts of human behavior is now called "evolutionary psychology" to avoid some of the justifiably bad connotations that were associated with sociobiology. During the last few years the linguist Steve Pinker, (1997) philosopher Daniel Dennett, (1995) New Republic editor and science popularizer Robert Wright,(1994) and science writer Matt Ridley (1994, 1997) have produced feisty, polemical expositions of evolutionary psychology for a broad audience. Stephen J. Gould has returned to the breach to criticize evolutionary psychology, but several writers considered to be on the left have defended sociobiological approaches and criticized postmodern rejection of biologism.
The core theories of evolutionary psychology are the same as those of sociobiology. Several of the commonly made distinctions between evolutionary psychology and sociobiology turn out not to distinguish the two. So what has changed and what is new?"
redux [08.10.00]
"US researchers believe they have identified the parts of the human genome involved in developing a person's intelligence.
This means scientists could soon test the potential intelligence of new-born babies."
"The researchers, working for the US National Institutes of Health, analysed the DNA of 200 of the brightest kids in America and compared them with the genetic material from ordinary children.
The results are due out next year, but the BBC Newsnight programme has learned that key differences have been found. In other words, the scientists are homing in on the genes for genius."
redux [07.07.00]
"Kaplan examines the roles genetic explanations for these types of differences play in our culture -- and how science has been used inappropriately to "medicalize" problems that should be more properly addressed as complex social issues.
Kaplan explores six specific areas -- intelligence (IQ), criminality and violence, homosexuality, depression, obesity, and the centrality of genetics in defining parenthood."
"He also explains the problems involved in "finding genes" for complex human behaviors by comparing the genomes of people who have a particular trait with the genomes of those who do not. The resulting medicalization centers the problem on the individual."
"... an emphasis on the biochemical and the genetic share the property that they make the condition out to be internal to the patient. Once a genetic explanation is offered, and any plausible sounding pathway proposed, the opportunities for claiming that there are other ways of approaching the problem are radically curtailed."
The problem becomes entirely that of personal biochemistry: the danger is in adopting easy solutions without looking at other reasons for the problem -- and without questioning the framework in which certain temperaments or sexual orientations become defined as problems."
redux [05.28.00]
"Suddenly, I'm picturing a new conclusion to "Casablanca," in which Rick walks up to the teary-faced Ilsa as she's about to board the plane with her husband and says: "I was gonna tell you that the problems of three little people don't amount to a hill of beans in this crazy world. But then I saw your BRCA-1 code. Baby, you're staring at the c-stuff. Let's just stay here and party to the bitter end."
"In the Brave New World ahead, are we (and the characters who reflect us) going to run dry of choice? Are we doomed to a movie-viewing future of genetically savvy detectives who catch their man armed with a genetoscope? I mean, what if Jack Nicholson were to turn his back on Faye Dunaway in "Chinatown" because, well, he'd already checked out that family incest history at the GenBank file at the National Institutes of Health."
redux [04.25.00]
"In the current issue of Advances in Complex Systems (February-April), Dr. Yaneer Bar-Yam, president of the New England Complex Systems Institute and an expert on the application of mathematical analysis to complex systems, contends that the selfish-gene theory of evolution is fatally flawed.
If his mathematical proof gains general acceptance, it will shut the door on controversial "gene-centered" views of evolution.
Bar-Yam, in the upcoming article, proves that the "selfish gene" approach is not valid in the general case. He demonstrates that the gene-centered view, expressed in mathematical form, is only an approximation of the dynamics actually at work."
"The key to Bar-Yam's analysis lies in recognizing three levels of structure in nature: the gene, the organism and the group (or network) of organisms."
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BioMedNet News
Iceland cold-shoulders genetics company[requires 'free' registration]
"The Icelandic Medical Association and deCODE, the company set to run a national database of health information in Iceland, are unable to reach a compromise over whether the "anonymized" data should automatically include all patients' health records without consent. The company is playing down the problem, but most Icelandic doctors are opposed to "presumed consent." The CEO of deCODE says that the database still will be useful without needing to represent 100% of the population.
Reference: Abbott, A. 2000. Iceland's doctors rebuffed in health data row. Nature 406(6798):819."
[requires 'free' registration]
"Should genetic material be collected from individuals for the purpose of studying human disease in specific populations? The native genome of Iceland offers a powerful and rare resource in genomic research -- a relatively homogeneous population. In this setting, the proposed Icelandic Healthcare Database, which would integrate medical information with genealogy and molecular genetic data, has driven a number of issues -- both ethical and scientific -- to the fore."
redux [03.20.00]
"The Icelandic public is accusing its government of taking huge payments from the company licensed to create a nationwide genetic database of the country's entire population.
A public outcry escalated last week following newspaper editorials and a forum sponsored by Mannvernd, an organization strongly opposed to deCODE Genetic's plans to create the Icelandic Health Sector Database."
redux [02.06.00]
"It has never been done before and no-one really knows how successful it will be, but it has already divided the country and now the whole world is watching and waiting."
"The Icelandic Government has given a licence to a US-funded corporation to study the medical records, family trees and genetic information of each and everyone of the country's 270,000 citizens."
redux [06.15.00]
"A centralised database is an idea that requires this form of temporary protection in order to flourish, just as the author of a book requires copyright and, for a fixed period, exclusive right to sell the work. Without a special or exclusive licence of some form, it is impossible to establish a privately-run database."
"DNA molecules are entirely separate from medical records. In the future, however, the DNA molecule and the medical record are likely to merge into one when it becomes possible to sequence a person's entire genome and put that information on a computer chip or disk. This is not deCODE's current project, but we should not wait until this step is taken to explore its implications. The most important questions would then be who has the authority to make such a disk in the first place; who owns the disk; who controls the use of the disk; and whether the disk containing the genome should be treated as specially protected medical information, as is the case for psychiatric and drug-dependency records? In clinical settings, it seems reasonable to treat such a disk as containing particularly private and sensitive medical information. It also seems reasonable to permit patients to agree to have their entire genome scanned without detailing the tens of thousands of tests that would be run. This is akin to consent to a battery of tests during an annual physical examination.
On the other hand, in a research setting, or when a specific genetic disorder is suspected, the creation and use of an individual patient's genome disk should be subject to the informed consent of the patient. And since they can be both separated from the medical record and readily recreated, research subjects should retain the right to have the files containing their genetic information destroyed at any time.
Iceland's experience with deCODE provides a useful catalyst for formulating fair and ethical rules for research on genetic variation. The Icelandic experience demonstrates that people are concerned about how genetic research is done, that medical-records research and DNA-based research are not the same, that community consultation is necessary but not sufficient to justify DNA-based research ethically, that the probable benefits of such research should be spelled out as clearly as possible, and that international standards for consent to and withdrawal from research should apply directly to research on human genetic variation. Rules for such research will retain their relevance even after it becomes possible to transfer all the genetic-sequence information in a DNA molecule to a computer disk."
redux [02.13.00]
"By the spring of this year, the first draft of the human genome -- the sequence of all the genetic instructions needed to make up a human being -- will be published on the Web. But that is only the end of the beginning. Scientists still have very little idea of what most of the 100,000 or so human genes actually do, and finding out will take them into a very different area of research.
The raw material of the genome program has been anonymous samples of DNA, manipulated by complex laboratory machines that turn out information like a production line turns out widgets. But the new era of post-genome research involves analysing real people and their confidential medical records. The records are needed to match the genes that people carry with the diseases they may develop. Only then will gigabytes of genetic data into new treatments for cancer or heart disease. And that is why socialised healthcare is a vital part of post-genome research.
Countries such as the U.S., which provide healthcare through private enterprise, are useless for this sort of genetic inquiry. Only those countries which have organized the delivery of healthcare to their population in a way that is independent of the marketplace have built up the universal medical records necessary to make sense of the patterns of disease."
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Genome Biology
Genomics: what is realistically achievable?"Since I am a computer scientist by training, I tend to think of the current situation in which the field of genomics is being driven forward by rapid technological advances as quite analogous to the sequence of events in computing that were triggered by advances in microcomputer and network technologies. I distinctly remember the early period in which it seemed clear to most computer scientists (including myself) that technical advances were very desirable and interesting, but could have little impact on either the fundamental research issues or the overall advance of the field. Most of us completely underestimated the impact of exponential price improvements in key-enabling technologies. Certainly no one that I know of foresaw in any detail the current world of computing (although a few had rare insights into the potential). As we face the world generated by the web, we should remember that as late as the early 1990s common wisdom indicated that 'movies on demand' would be the application that drove increased network bandwidth."
"As microarray data from genomic sequences become increasingly available, the expression data that will be produced will obviously be directly relevant. There will probably be other forms of data, as well, but these adequately illustrate the point: the generation of hypotheses will flow from integrating a number of such sources of data. The existence of a growing number of hypotheses will guide the rate-limiting 'wet' lab efforts."
redux [08.12.00]
"The flood of data from genome-wide analysis is transforming biology. We need to develop new, interdisciplinary approaches to convert these data into information about the components and structures of individual biological pathways and to use the resulting information to yield knowledge about general principles that explain the functions and evolution of life."
"Genomics increases the chance that biology will experience a split like the one in physics, between those who collect and those who analyze data. This will challenge the majority of biologists who believe that modeling, simulation, and theory have little to contribute to biology. This prejudice rests on insecurity engendered by most biologists' weakness in mathematics (including my own) and previous efforts to model systems using more variables than there were data points. If we keep clinging to this prejudice, we will drown in a sea of data."
redux [07.13.00]
"A new mathematical biology is emerging. Building on experimental data from developing organisms, it uses the power of computational methods to explore the properties of real gene networks."
"Our understanding of gene networks is at an early stage. We perceive their complexity only after it has been filtered by the limitations of the techniques used to study them. Genome databases and DNA-chip technology, which enables huge numbers of genes to be screened for activity, will undoubtedly provide more, and much more complicated, data than anything produced by Drosophila genetics. If a relatively simple gene network such as the segment-polarity system is hard to understand intuitively, we can be certain that modelling will be essential to make sense of the flood of new data.
But this will not be elegant theoretical modelling: rather, it will be rooted in the arbitrary complexity of evolved organisms. The task will require a breed of biologist–mathematician as familiar with handling differential equations as with the limitations of messy experimental data. There will be plenty of vacancies, and, on present showing, not many qualified applicants."
redux [04.05.00]
[requires 'free' registration]
"I suspect that although the new enthusiasm for computers in biology is genuine, it overlooks some basic problems in implementation. The basic difficulty, as I see it, is that although biologists use computers, they do not trust everything that comes out of them. It is one thing to use them to print up nice-looking graphs, but it is an entirely different matter to use them to think better."
"Francis Crick was once quoted as saying that no biologist had ever made a discovery using a mathematical model. I would reply that no biologist has ever made a discovery by running an electrophoretic gel. They make discoveries by using their brains. Computers, like all scientific tools, are only as good as the person who uses them. If biologists don't understand how computer models are constructed, they won't know their strengths and limitations. Without some foundation of trust, biologists will be unlikely to utilize or accept this powerful method of data analysis."
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Scientific American
Beyond the First Draft"Unprecedented fanfare greeted the June 26 announcement that scientists had completed a draft of the human genome sequence. The truth is, however, that figuring out the order of the letters in our genetic alphabet was the easy part. Now comes the hard part: deciphering the meaning of the genetic instruction book.
The next stage goes by a deceptively prosaic name: annotation. Strictly speaking, "annotation" comprises everything that can be known about a gene: where it works, what it does and how it interacts with fellow genes. Right now, scientists often use the term simply to signify the first step: gene finding. That means discovering which parts of a stretch of DNA belong to a gene and distinguishing them from the other 96 percent or so that have no known function, often called junk DNA.
Several companies have sprouted up to provide bioinformatics tools, software and services [see "The Business of the Human Genome," Scientific American, July]. Their success, though, may hinge on a peaceful spot south of England's University of Cambridge. It is home to the Sanger Center, the U.K. partner in the publicly funded Human Genome Project (HGP) consortium, and the European Bioinformatics Institute (EBI), Europe's equivalent of the National Center for Biotechnology Information (NCBI) at the National Institutes of Health. Sanger and EBI are collaborating on the Ensembl project, which consists of computer programs for genome analysis and the public database of human DNA sequences. New DNA sequences arrive in bits and pieces; automated routines scan the sequences, looking for patterns typically found in genes. "One of the important things about Ensembl is that we're completely open, so you can see all our data, absolutely everything," says EBI's Ewan Birney." [via bioinformatics.org]
redux [07.25.00]
The Scientist Automatic annotations of the human genome will produce different interpretations
[requires 'free' registration]
"To translate the billions of sequenced bases of the human genome into meaningful information, investigators in the private and public sectors continue to use computer prediction to automatically annotate the human genome--to attach biological footnotes about genes, the proteins they encode, and the ailments to which they may be linked. But as with any translation, there's potential for multiple interpretations. Annotation projects could present geneticists with significantly different genome schematics.
"I think that for the moment scientists are going to have to revel in the variety," maintains Robert Waterston, director of the genome sequencing center at Washington University in St. Louis. A joint effort in the United Kingdom from the European Bioinformatics Institute (EBI) and the Sanger Centre, U.S. efforts at the National Center for Biotechnology Information (NCBI) and Oak Ridge National Laboratory (ORNL), and commercial efforts will present different annotations based on the data available, algorithms employed, and weight given to different data points. "
redux [06.23.00]
"Bioinformatics is the science of life as a software problem. An international co-operation called the Human Genome Project is about to finish putting the human DNA blueprint on the internet.
And a team working closely with them is about to distribute a software package that will turn the world of biology into a co-operative research laboratory. The exploration of the human software will become a kind of global interactive game, with a new tool called Ensembl."redux [04.24.00]
"Ensembl provides complete and consistent annotation across the human genome. It will soon also process mouse, (in conjunction with other projects, hopefully people like the Jackson Lab). To understand how Ensembl fits into the human genome project, please read EnsemblHGP"
"A central element of the Ensembl project is openness: all data is freely available; all code is freely available. You can read about the EnsemblSoftwareDesign and about how to DownloadEnsembl software and data and how to go about InstallingEnsembl on your own site in our developers area. You can follow Ensembl announcements, user discussion or development issues via a number of mailing lists as well as view previous emails here."
"Now that the age of the genome is upon us, scientists must find a way to spin mountains of DNA code into biological gold. To do it, they are building their own Rumpelstiltskins: powerful computer programs that automatically scrutinize the code and decipher its genetic elements. The April issue of Genome Research reports a new enterprise to test the state of the art in computer "genome annotation." Organized by a team from University of California, Berkeley, 12 international groups compared the power of their computer programs to predict gene elements within a 3 million base pair stretch of Drosophila DNA.The groups compared the results of their programs against each other and against the results of an exhaustive experimental and computational effort to locate all the genes in this region (not available to the participants during the test).
When the results were in, many programs had detected the genes in the region with 95% accuracy compared to the experimental effort. Furthermore, the programs made predictions of genes that had not been found in that effort, which researchers are now investigating. However, the programs were less accurate in defining the exact boundaries of the genes within the code, and groups that attempted to find elements controlling gene activity (e.g., promoters) made a large number of false predictions."
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[requires 'free' registration]
"Kwang-I Yu, president of Paracel Inc., will not say which secretive government agency buys his company's specialized supercomputers. "We sell to the federal government," he demurs.
But J. Craig Venter, the president of Celera Genomics, is less circumspect. Paracel's machines, he said, are used by the National Security Agency, the code-breaking unit that eavesdrops on other nations. And Dr. Venter should know. Celera Genomics, the company that mapped the human genome, acquired Paracel for nearly $250 million in stock in June." The machines are being snapped up to sift the blizzard of data being generated by the Human Genome Project and various private genomics efforts. "They're all character strings," said Dr. Yu, comparing the gene sequence to a text message."
"I.B.M. estimates that the market for hardware and software for life sciences will grow from $3.5 billion now to more than $9 billion by 2002. Carolyn Kovac, who heads a newly formed life sciences division at I.B.M., said biologists had replaced physicists as the main scientific users of supercomputers."
redux [06.14.00]
Scientific Computing World Biotech and clusters dominate Mannheim Supercomputing Conference
"Biotechnology and cluster computing were the main focus of attention in the corridors and private conversations at the recent Mannheim Supercomputing Conference, even though US Defense Department machines again dominated the upper ranks of the most recent Top500 listing of the world's fastest supercomputers, published at the meeting. "
"...in the breaks between the formal sessions at the conference, many of the delegates appeared to be focusing more on the prospective growth in bioinformatics and the demands that this is creating for high performance computing. In an interview, Dr Martin Walker from Compaq reviewed the figures for the growth of the supercomputing market. At present, according to the International Data Corporation figures, the high performance computing market was worth about $5.6 billion in 1999 and is expected to grow by about 9 per cent annually through to 2003. However, bioinformatics may change all that, he noted. The total R&D budget of the pharmaceutical industry is about $40 billion annually and so if some 10 per cent of it were to go on IT, this would provide $4bn for computing, especially high performance computing applications. Thus bioinformatics could grow, relatively quickly, from a minor component of the market to a 40 per cent share. 'This is a phase transition,' he commented. "redux [06.03.00]
"Here is the plan: IBM scientists intend to spend five years building the fastest computer in the world, 500 times faster than anything in existence today. It will suck down every spare watt of electricity and throw off so much heat that engineers have bought a gas turbine the size of a jet engine to cool it.
The machine, dubbed Blue Gene, will be turned loose on a single problem. The computer will try to model the way a human protein folds into a particular shape that gives it unique biological properties. Obscure as it may sound, that kind of puzzle is at the heart of mankind's efforts to understand the nature of consciousness, the origins of sex, the causes of disease and many other mysteries."
redux [03.29.00]
"Gone are the days when any pioneer with a bit of hardware, hard code, and hard work could run a small Linux farm and compete with the best plantations. The smart folks at biotech firm Incyte Genomics of Palo Alto, Calif., have just invented agribusiness. You remember everything you ever tried to tell your boss or colleagues about Linux's stability, price performance, and reliability? Well, Incyte has put those ideas to the test and come up grinning like a bandit.
To map the human genome, Incyte runs the world's largest commercial Linux farm, with more than 2,000 Linux processors chomping away on tens of millions of jobs per day. In its datacenter, laid out like a temple in the middle of Incyte's corporate headquarters, space costs a king's ransom -- but the company has come up with clever ways to address that problem..."
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"Biotech companies are snapping up patents on human genes. Will the trend mean powerful new medicines, or will it quash biomedical innovation?"
MIT Technology Review The Case for Gene Patents
"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."
MIT Technology Review Toward Sharing the Genome
"The raw data of the human genome should be an “IP-free zone,” opines author Seth Shulman, to preserve our precious shared genetic heritage and update outmoded notions of intellectual property."
redux [07.17.00]
GeneLetter Committee examines gene patents
"Scientists and biotechnology experts on Thursday sharply disagreed before a House subcommittee over whether it should be easier or harder to patent human genes and genomic inventions.
Dr. Harold Varmus, former head of the National Institutes of Health and current president of the Memorial Sloan-Kettering Cancer Center, said that it is currently too easy to patent genetic discoveries."
"But other witnesses said that patents should be even more available to encourage the development of critically needed medical advances. "The development of cures for uncured diseases, such as kidney cancer, will come out of the Human Genome Project only if commercial development can take place," testified Carl Dixon, President and Chief Executive Officer of the Kidney Cancer Association."redux [04.26.00]redux [03.18.00]
Signals Homestead 2000: The Genome
""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.""
White House Judiciary Archive OVERSIGHT HEARING ON "GENE PATENTS AND OTHER GENOMIC INVENTIONS"
HMS Beagle Patenting Genes Is It Necessary and Is It Evil?
[requires 'free' registration]
"Last October, biologists' neck hair rose when J. Craig Venter announced his company, Celera, had filed 6,500 provisional patent applications for human genes. Henry Ford mass-produced automobiles - it seems evident we are now entering an era in which intellectual property is rolling off the assembly lines. Is this really the ultimate legacy of Watson and Crick's elegant double helix? And what does it portend for the future of biology?"
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"Will genomics kill the insurance industry? It's a credible scenario. And even biotechnology executives are beginning to buy into it.
Last week, during an industry conference held here in Boston, senior executives from several of the world's leading genomics concerns agreed that genomics, with its promise of being able to show who will be predisposed to what disease, would eventually give rise to universal healthcare in the United States.
"This could happen especially if the defects in our genomes make us all uninsurable,'' said panelist Craig Venter, uber-geneticist of human genome renown."
redux [06.08.00]
Yahoo! News Researcher Calls for Laws to Protect Genetic Information
"As researchers race to complete mapping the human set of genes, one of the project's leaders sounded an alarm Tuesday about the practical implications of this knowledge, and called for legislation to protect individuals from misuse of genetic information. ``We cannot wait until we have finished sequencing the human genome to pass important legislation that protects a person from being discriminated against--by health insurance companies or by employers. We do not need hundreds to thousands of casualties before acting on this important issue,'' Dr. Francis Collins, director of the National Human Genome Project said here Tuesday."
redux [03.21.00]
BBC News Tests spark fears of genetic underclass
"The UK Government is considering allowing insurance companies to use genetic testing to assess a person's risk of inheriting a serious illness."
"One opponent of the wider use of genetic testing said it was part of a "terrifying trend" that would lead to a culture of "cherry picking"."
redux [06.08.00]
GeneLetter Managed care needs to prepare for biotech revolution
"Unless they begin preparing now, health plan executives and medical directors could be blindsided by the revolution in medicine that will come with the mapping of the human genome, members of a managed care conference keynote panel warned on Monday."
"You think the genetic revolution is still 3-to-5 years off for your health plans," said Dr. Billings, who also serves as deputy director and chief medical officer of the Heart of Texas Veterans Health Care System. "I have to tell you, you better wake up. The tsunami is on the horizon," he warned.
For example, Schering-Plough's Dr. Haverty predicted that gene-based information could lead to the identification of many different types of asthma. As a result, health plans will need to develop many new codes and to upgrade their information systems, he said."redux [03.30.00]
JAMIA Integration and Beyond: Panel Discussion
"I think one of the toughest things we all have to deal with is updating our dictionaries. In the simplest cases, the name of an organism is changed and we just have to do the maintenance. It is tougher, when, as with Citrobacter, they do genetic studies and say, "Oh, it's really six different organisms, not one." We have the human genome project coming very quickly. Even that is just the tip of the iceberg. We're not only going to see all the genes; we're then going to see clinical tests based on gene expression. Essentially, you'll be able to look at something on the order of 180,000 gene products and whether they're up or down regulated. How are we going to integrate such an incredible amount of data at a time when we're going to also be changing how we think about these processes? Classification and simple mapping are not going to work, because the lumpers and splitters are going to be arguing furiously on a daily basis."
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"The company also announced that Scott is forming a new online health company that will use the genetic information supplied by Incyte's technology and databases for public, procedural and research applications.
The company will link individuals to genomic information regarding their disease in order to reach understanding of a particular condition and enable individual participation in the search for remedy."
redux [08.14.00]
Bioinform DNA Sciences Develops Two New Bioinformatics Tools for Genotyping
"LAST WEEK DNA Sciences announced plans to become a major force in the genomics sector by establishing a facility that will eventually identify one million genotypes a day. The company, which is backed by such industry icons and financiers as James Watson, Jim Clark, and George Soros, plans to use the information it generates from the 50,000 to 100,000 DNA donors it hopes to enlist to create better diagnostic methodologies.
But the Mountain View, Calif., upstart won’t be doing any of this with prepackaged bioinformatics tools. Instead, DNA Sciences will store, manage, and mine SNP data using software the company has developed in-house.
“You cannot buy off-the-shelf software that solves these problems and I think every company that does genetics has built their own software,” said DNA Sciences’ CEO Hugh Rienhoff."redux [08.01.00]
The New York Times Company Seeking Donors of DNA for a 'Gene Trust'
[requires 'free' registration]
"Wanted: your genes.
A California start-up called DNA Sciences is introducing a Web site today that will recruit people to donate their DNA to help find genes that cause disease. The company, which has James D. Watson, a discoverer of the DNA double helix, as a director and James H. Clark, Netscape's founder, as an investor, hopes to get 50,000 to 100,000 people to contribute to its "gene trust" by appealing to their altruism."
"Under DNA Sciences' program, volunteers answer on-line questionnaires about their medical history, and their family's. The company will then send someone to their homes or offices to collect blood samples. Healtheon/WebMD, the medical Web site, owns a stake in DNA Sciences and will be used to help recruit patients.
Donors will not be paid, as is true with the other companies as well."redux [07.19.00]
Individual.Com Healtheon/WebMD (HLTH) and Netscape (NSCP) Founder Clark
"Clark is the only person in history to have guided three companies from inception to becoming public companies with more than one billion in market cap each. In addition to privately held Shutterfly and Mycfo.com, Jim is currently hard at work on his sixth startup: DNA Sciences."
"DNA Sciences is focused on exploiting the genome information and specifically finding the genotypes variations in genes that give rise to the genes that are associated with certain diseases. The variations in those genes that give rise to variance of that disease and treatment for that disease so the company is heavily focused on gene applications in the genome area."
"Healtheon was driven four or five years ago when I started the company in attempt to try to bring the internet to what I thought was the most inefficient industry in the world, the U.S. Healthcare system. I am still positive and bullish about the company's future. In the case of DNA Sciences it was more because I think it is more immediate. It has a tremendous potential. I put the two companies together and WebMD has a lot of disease affinity groups, if you will. People with breast cancer, prostate cancer, hepatitis, a variety of ailments and we can collect blood samples from people in the groups and identify genes and put them in a specific category to see what the best treatment is."
redux [06.17.00]
Stanford Medical Informatics Preprint Archive Bioinformatics in Support of Molecular Medicine
"Basic biological science has always had an impact on clinical medicine (and clinical medical information systems), and is creating a new generation of epidemiologic, diagnostic, prognostic, and treatment modalities. Bioinformatics efforts that appear to be wholly geared towards basic science are likely to become relevant to clinical informatics in the coming decade. For example, DNA sequence information and sequence annotations will appear in the medical chart with increasing frequency. The algorithms developed for research in bioinformatics will soon become part of clinical information systems. In this paper, I briefly review the intellectual roots of bioinformatics and how the field has evolved in the last few years. Fortunately, a core set of scientific paradigms have provided a focus to the field. Even in this short period, however, there has been a change in the nature of the questions being asked and the types of experiments being attempted. These changes are consistently leading bioinformatics towards problems of clinical relevance. Some molecular biology information systems already have important clinical implications. I will discuss the differences in the culture and approach to science of clinical informatics and bioinformatics, but will argue that the two disciplines share important intellectual challenges which make them very closely allied fields (despite the cultural differences). Finally, I will identify a few areas common to both disciplines where developments in one field may help catalyze faster progress in the other. For example, useful database integration technologies have (arguably) matured more rapidly within bioinformatics than in clinical informatics. At the same time, clinical informatics embraced the idea of controlled terminologies relatively early, and offers lessons to those in bioinformatics attempting similar tasks."
redux [05.15.00]
The New York Times Who Owns Your Genes?
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""I just wanted to do something good," Mr. Fuchs said. "But once money came into the picture, why not have it be shared with me?"These days more and more patients are asking the same question. Laboratories offer tests for more than 700 human genes, with more being discovered almost daily. And, for almost every gene, some medical institution or some company owns a patent on its use.
"The value of patients' tissues has potentially gone up enormously," said Dr. Barry Eisenstein, the vice president for science and technology at the Beth Israel Deaconess Medical Center in Boston. But, Dr. Eisenstein said, patients whose cells provided the genes that have been patented are almost never compensated. "
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[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.""
"Through transglobal sampling of neutral genetic markers -- stretches of genetic material that do not help create the body's functioning proteins but instead are composed of so-called junk DNA -- researchers have found that, on average, 88 percent to 90 percent of the differences between people occur within their local populations, while only about 10 percent to 12 percent of the differences distinguish one population, or race, from another.
To put it another way, the citizens of any given village in the world, whether in Scotland or Tanzania, hold 90 percent of the genetic variability that humanity has to offer."
""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."
redux [08.01.00]
GeneLetter Inequalities and individualized medicine
"Over the next few years a number of competing groups - my own company, Sequenom, among them -- will sort through the diverse genetic material of the human species to find those variations called single nucleotide polymorphisms (SNPs, pronounced SNIPS) that predispose individuals to major clinical disorders."
“At present the overwhelming bulk of the effort to identify these natural variations is in the private sector. This is inevitable because SNPs that associate with major diseases are patentable, by traditional standards."
"Whatever ensues, it is clear that the rate of discovery of medically important SNPs and their conversion into clinically useful tools will not progress equally fast or uniformly for all segments of mankind."
"It will be easier to discover medically important SNPs in geographically isolated and inbred populations in which good familial records and where migration has not introduced confounding genetic variation. Iceland and Finland are strong early candidates."redux [07.17.00]
Orchid Biosciences The SNP Consortium and Orchid Announce Collaboration to Determine Frequency of SNPs in Diverse Populations
"Orchid BioSciences, Inc. (Nasdaq: ORCH) and The SNP Consortium Ltd. today announced that they have entered into an agreement under which Orchid will determine the allelic frequency of 60,000 single nucleotide polymorphism (SNP) genomic markers in diverse populations. This work will be undertaken in Orchid's MegaSNPatron(TM) service facility in Princeton using its SNP-IT(TM) primer extension technology."GeneLetter Drawing DNA lines of ethnicityredux [06.15.00]
"The idea of using genetics to determine ethnic heritage has been growing in popularity over recent years. When Rick Kittles, a geneticist at Howard University, offered to trace tribal roots via a $350 DNA test, African Americans flooded his telephone line with requests.
"Even if an identifying marker shows up, the result isn't necessarily definitive. While certain markers may be more common to one ethnic group, most also can be found in other populations as well.
"Because of the tremendous genetic variation within populations, it would be biologically impossible to settle on a limited number of genetic markers that could define "Native Americans," says Morris Foster, an anthropologist at the University of Oklahoma who has wrestled with the risks faced by Indian tribes interested in genetic research.
Furthermore, Foster added in an e-mail interview with GeneLetter, "it is absurd to try to define what is essentially a social identity by using biological characteristics. This, though, is how racism has historically worked.""
New England Journal Of Medicine Rules for Research on Human Genetic Variation -- Lessons from Iceland
"DNA molecules are entirely separate from medical records. In the future, however, the DNA molecule and the medical record are likely to merge into one when it becomes possible to sequence a person's entire genome and put that information on a computer chip or disk. This is not deCODE's current project, but we should not wait until this step is taken to explore its implications. The most important questions would then be who has the authority to make such a disk in the first place; who owns the disk; who controls the use of the disk; and whether the disk containing the genome should be treated as specially protected medical information, as is the case for psychiatric and drug-dependency records? In clinical settings, it seems reasonable to treat such a disk as containing particularly private and sensitive medical information. It also seems reasonable to permit patients to agree to have their entire genome scanned without detailing the tens of thousands of tests that would be run. This is akin to consent to a battery of tests during an annual physical examination.
On the other hand, in a research setting, or when a specific genetic disorder is suspected, the creation and use of an individual patient's genome disk should be subject to the informed consent of the patient. And since they can be both separated from the medical record and readily recreated, research subjects should retain the right to have the files containing their genetic information destroyed at any time.
Iceland's experience with deCODE provides a useful catalyst for formulating fair and ethical rules for research on genetic variation. The Icelandic experience demonstrates that people are concerned about how genetic research is done, that medical-records research and DNA-based research are not the same, that community consultation is necessary but not sufficient to justify DNA-based research ethically, that the probable benefits of such research should be spelled out as clearly as possible, and that international standards for consent to and withdrawal from research should apply directly to research on human genetic variation. Rules for such research will retain their relevance even after it becomes possible to transfer all the genetic-sequence information in a DNA molecule to a computer disk."redux [02.13.00]
The Daily Davos Beyond the Genome
"By the spring of this year, the first draft of the human genome -- the sequence of all the genetic instructions needed to make up a human being -- will be published on the Web. But that is only the end of the beginning. Scientists still have very little idea of what most of the 100,000 or so human genes actually do, and finding out will take them into a very different area of research.
The raw material of the genome program has been anonymous samples of DNA, manipulated by complex laboratory machines that turn out information like a production line turns out widgets. But the new era of post-genome research involves analysing real people and their confidential medical records. The records are needed to match the genes that people carry with the diseases they may develop. Only then will gigabytes of genetic data into new treatments for cancer or heart disease. And that is why socialised healthcare is a vital part of post-genome research.
Countries such as the U.S., which provide healthcare through private enterprise, are useless for this sort of genetic inquiry. Only those countries which have organized the delivery of healthcare to their population in a way that is independent of the marketplace have built up the universal medical records necessary to make sense of the patterns of disease."
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"THE COMPARISON IS IRRESISTIBLE: The search for the sequence of the human genome, the substance that transmutes a single fertilized cell into bodies of astonishing variety, remarkably resembles the mythical Philosopher's Stone, the object of alchemical fascination that would unlock the secrets of the physical world. Now that the human genome, the object of the biggest Big Science project in the history of biology, has finally been sequenced (more or less), we seem to be on the verge of the biological equivalent of turning lead into gold. By recording the essential instructions for human life, the sequenced genome clearly marks a new scientific era."
"In fact, what the bioinformaticists (scientists who use computers to explore biological information) in San Diego are talking about are the ways in which this neat view of the world -- dominant since Mendel's genetic experiments were rediscovered at the turn of the last century -- is a vast oversimplification.
"These questions will gradually move out of the genetics labs, and as we better understand the network of relations between genes, bodies, and environments, the boundaries between biology and medicine, medicine and psychiatry, psychiatry and sociology, sociology and environmental studies, environmental studies and biology will continue to blur. If the lesson of the Philosopher's Stone has any relevance for the monumental achievement of a sequenced genome, it is the way the search for the Stone marked not the completion of alchemy but its replacement -- by something altogether more rigorous and useful."
Yahoo! News Genomics Research to Be Boosted by New International Data Consortium Launched At Major Biocomputing Meeting
"A multinational group of biotechnology and pharmaceutical companies is being formed to establish common computing standards for data and information analyses related to gene-based drug development. The lack of a single information standard worldwide prevents intelligent linking and sharing of information developed by different companies, public databases and academic institutions, and is considered to be a major obstacle for more rapid development of gene-based pharmaceutical and other products. "
""The design of models for bioprocess representation and simulation are very open,'' said Dr. Neumann. "The Consortium will need to examine and discuss relationships between all pathway information, protein interaction data, and biological and disease processes so that we can generate informatics specifications for any combination of these types of data.''"The BioPathways Consortium Why the Need for a BioPathways Consortium?redux [07.25.00]
"With the completion of several genomics initiatives, including the Human Genome Project, researchers are poised to begin the next phase of elucidating how living systems function. This involves the identifcation of genes and their functions, followed by their organization according to their roles and interactions within the more global context of cellular mechanisms. Constructing representations of the latter will involve not only structural information, but more dynamic and causal forms relevant to biochemical processes.
To ensure the success of capturing, organizing, and utilizing this information, there is an urgent need to discuss and develop new informatics technologies that will support such new forms of biological information. Data regarding pathways and interactions is already being accumulated in dozens of different formats, but no standard way of representing or exchanging them exists to date. In order to prevent the confusion that has occurred in bioinformatics due to the lack of early standards, we plan to be preemptive in considering specifications while this field is in its early stages. On a more fundamental level, representations of biological processes should provide the foundation for and thus may have an important bearing on the definition(s) of biological function."
The Scientist The Language of Bioinformatics
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"Once the world had a single language and not too many words, but then clarity deteriorated into clamor. Today in the small but prolific world of bioinformatics, another Tower of Babel is rising up, with the miscommunication due as much to the rapid expansion of information as to basic changes in how it is processed. "Horrible problems" crop up as more information is computed on instead of read by a human researcher, according to Ewan Birney, a group leader in the Ensembl genome annotation project at the European Bioinformatics Institute (EBI) in Cambridge, England.
In the early days of bioinformatics, human-readable data exchange formats such as ASN.1, the format adopted for GenBank by the National Center for Biotechnology Information (NCBI) 10 years ago, were the norm. Easily editable with a text utility, ASN.1's syntactic looseness makes it congenial to the human user, but not to the machine, which likes its inputs defined with dictatorial rigidity."
redux [05.10.00]redux [03.30.00]
The XML Cover Pages XML and Semantic Transparency
"We may rehearse this fundamental axiom of descriptive markup in terms of a classical SGML polemic: the doubly-delimited information objects in an SGML/XML document are described by markup in a meaningful, self-documenting way through the use of names which are carefully selected by domain experts for element type names, attribute names, and attribute values. This is true of XML in 1998, was true of SGML in 1986, and was true of Brian Reid's Scribe system in 1976. However, of itself, descriptive markup proves to be of limited relevance as a mechanism to enable information interchange at the level of the machine.As enchanting as it is to contemplate the apparent 'semantic' clarity, flexibility, and extensibility of XML vis-à-vis HTML (e.g., how wonderfully perspicuous XML <bookTitle> seems when compared to HTML <i>), we must reckon with the cold fact that XML does not of itself enable blind interchange or information reuse. XML may help humans predict what information might lie "between the tags" in the case of <trunk> </trunk>, but XML can only help. For an XML processor, <trunk> and <i> and <booktitle> are all equally (and totally) meaningless. Yes, meaningless.
Just like its parent metalanguage (SGML), XML has no formal mechanism to support the declaration of semantic integrity constraints, and XML processors have no means of validating object semantics even if these are declared informally in an XML DTD. XML processors will have no inherent understanding of document object semantics because XML (meta-)markup languages have no predefined application-level processing semantics. XML thus formally governs syntax only - not semantics."
redux [05.01.00]
Stanford Medical Informatics Preprint Archive Ontology-Oriented Design and Programming
"In the construction of both conventional software and intelligent systems, developers continue to seek higher level abstractions that both can aid in conceptual modeling and can assist in implementation and maintenance. In recent years, the artificial intelligence community has placed considerable attention on the notion of explicit ontologies -- shared conceptualizations of application areas that define the salient concepts and relationships among concepts. Such ontologies, when joined with well defined problem-solving methods, provide convenient formalisms for modeling and for implementing solutions to application tasks. This chapter reviews the motivation for seeking such high-level abstractions, and summarizes recent successes in building systems from reusable domain ontologies and problem-solving methods. As the environment for software execution moves from individual workstations to the Internet at large, casting new software applications in terms of these high-level abstractions may make complex systems both easier to build and easier to maintain. "Gene Ontology Consortium
"This is the home of the Gene Ontology Consortium. The goal of the Gene Ontology consortium is to produce a dynamic controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.""The three organising principles of GO are molecular function, biological process and cellular component. A gene product has one or more molecular functions and is used in one or more biological processes; it may be, or may be associated with, one or more cellular components."
JAMIA Integration and Beyond: Linking Information from Disparate Sources and into Workflow
"The vision of integrating information—from a variety of sources, into the way people work, to improve decisions and process—is one of the cornerstones of biomedical informatics. Thoughts on how this vision might be realized have evolved as improvements in information and communication technologies, together with discoveries in biomedical informatics, and have changed the art of the possible. This review identified three distinct generations of "integration" projects. First-generation projects create a database and use it for multiple purposes. Second-generation projects integrate by bringing information from various sources together through enterprise information architecture. Third-generation projects inter-relate disparate but accessible information sources to provide the appearance of integration. The review suggests that the ideas developed in the earlier generations have not been supplanted by ideas from subsequent generations. Instead, the ideas represent a continuum of progress along the three dimensions of workflow, structure, and extraction. "JAMIA Integration and Beyond: Panel Discussionredux [07.11.00]
"I think one of the toughest things we all have to deal with is updating our dictionaries. In the simplest cases, the name of an organism is changed and we just have to do the maintenance. It is tougher, when, as with Citrobacter, they do genetic studies and say, "Oh, it's really six different organisms, not one." We have the human genome project coming very quickly. Even that is just the tip of the iceberg. We're not only going to see all the genes; we're then going to see clinical tests based on gene expression. Essentially, you'll be able to look at something on the order of 180,000 gene products and whether they're up or down regulated. How are we going to integrate such an incredible amount of data at a time when we're going to also be changing how we think about these processes? Classification and simple mapping are not going to work, because the lumpers and splitters are going to be arguing furiously on a daily basis."
Biospace.Com Big Picture Biology
"For most of us, formal biology education begins with complex systems--the traditional dissection of a frog in high school biology class is virtually a rite of passage in the U.S.
But the way many people learn about and invest in biotechnology is at the smallest end of the spectrum--the genome, now often described as the "periodic table" of biology. Genomics and all its related buzzwords have been responsible for much of the media attention, government grants, and investment capital heaped on the biotech industry over the past decade.
But just as there is a whole lot of chemistry that happens in between the periodic table and a birthday cake, there is a lot of biology in between the genome and a living organism. With the completion of biology's periodic table within sight, academics and industry players alike are pondering the best way to apply our hard won knowledge.
The only problem is, the path from genome to system seems to get harder the more we learn."
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[requires 'free' registration]
"The National Cancer Institute is collaborating with a Virginia company to enlist people to use their computers to help fight cancer. Parabon Computation, Inc., divides large computations into chunks and distributes them among some 5,000 volunteers. The data track how gene expression is affected by anticancer drugs. The volunteers' computers use idle time to process the data before sending it back to Parabon. The company says that it's conducting the experimental demonstration project for free.
Reference: 2000. Fighting cancer at the keyboard. Science 289(5482)."
redux [08.09.00]
BBC Screensavers could save lives
"Your computer could be helping to save lives when you are not using it to play games or surf the internet.
Instead of it sitting idle, it could be taking part in scientific experiments being distributed across thousands of computers on the internet.
Drugs to beat cancer and flu are starting to be tested in simulations split up and run on personal computers that would otherwise be doing nothing useful." [via slashdot.org]PC Magazine New Apps Exploit Connectivity
"A natural complement to distributed file-sharing capabilities is distributed computation. The idea behind distributed computation is that a really big problem gets split into discrete, independent chunks, which are then parceled out to individual computers whose owners have volunteered their idle processor time to the cause. In aggregate, the users' computers form a sort of distributed supercomputer. The concept was first popularized by U.C. Berkeley's SETI@Home project, a 1999 PC Magazine Technical Excellence finalist that's now been downloaded by more than 2 million users. Though SETI@Home is a single-purpose tool designed solely to scour radio-telescope signals for signs of extraterrestrial transmissions, you can expect to see general-purpose mechanisms for distributing all kinds of massive computations. United Devices, for example, is a company that will use distributed computing for projects in areas such as bioinformatics research, drug design, and climate studies."
redux [07.22.00]
The Standard Distributed Computing Goes Commercial
"The distributed-computing model could be one of those rare cases where capitalism and pure scientific research mesh. Not every lab can afford to pay $200,000 for an eight-processor Origin 2000 SGI supercomputer, much less $1 million for a 40-processor machine, says David Fenstermacher, director of scientific computing for the medical school at the University of North Carolina at Chapel Hill. (Fenstermacher is also acting director of the campus' Center for Bioinformatics and a United Devices adviser.) And even the most powerful supercomputers need time to process data.
A project that would take several months on a supercomputer – creating a 3D model of a protein's linear be accomplished in much less time using thousands of distributed computers"redux [04.05.00]
Wired Researcher Borrows from Napster
"A researcher working on the Human Genome Project is using Napster technology, and he's not looking for T3 connections to download Moby.
Dr. Lincoln Stein, an associate professor of bioinformatics at the Cold Spring Harbor Lab in New York, is investigating ways to use Napster-type technology to allow scientists to share their discoveries of the genome.
"I was very interested when I saw Napster," Stein said. "It has a similar architecture (to what we use now), but it allows for 'peer-to-peer' data exchange and it dawned on me that it would be marvelous for our annotation system.""
Stein Laboratory Distributed Sequence Annotation System (DAS)
"The pace of human genomic sequencing has outstripped the ability of sequencing centers to annotate and understand the sequence prior to submitting it to the archival databases. Multiple third-party groups have stepped into the breach and are currently annotating the human sequence with a combination of computational and experimental methods. Their analytic tools, data models, and visualization methods are diverse, and it is self-evident that this diversity enhances, rather than diminishes, the value of their work."
"The solution that we advocate allows sequence annotation to be decentralized among multiple third-party annotators and integrated on an as-needed basis by client-side software. A single server is designated the "reference server." It serves essential structural information about the genome: the physical map which relates one entry to another (where an "entry" is an arbitrary segment of the sequence, such as a sequenced BAC or a contig), the DNA sequence for each entry, and the standard authorship information. Multiple sites then act as third-party "annotation servers." Using a web browser-like application, researchers can interrogate one or more annotation servers to retrieve features in a region of interest. The servers return the results using a standard data format, allowing the sequence browser to integrate the annotations and display them in graphical or tabular form. No attempt is made to automatically resolve contradictions between different third-party annotations. Indeed, it is the ability to facilitate comparison among different centers' annotations that distinguish this proposal. We currently have a working prototype of this system based on ACeDB servers and CGI scripts, and are now generalizing this architecture to support other client and server combinations."
egroups : Decentralization Description
"* Is decentralization ever a good idea? If so, when? Is there non-anecdotal evidence on costs and benefits?
* What protocol issues are there? Can we begin assembling a good protocol for decentralized messaging? To what degree do the protocols for Freenet, Gnutella or WorldOS meet the need? Do we need an application protocol or something lower level? Can HTTP do the job? Can we implement peer routing as an add-on to existing protocols? Is there a call to develop an IETF working group?
* Given that authoring and versioning are critical but hard in a decentralized environment, how can we approach the job? Is it possible to integrate WebDAV with peer networking?
* What are the business issues? Who are the players? Who else stands to win or lose, and why?
At present many people and groups are working on the issues in isolation, some for competitive reasons and some for lack of an alternative. My belief is that a communal approach will be more productive."
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"IBM will join the life sciences love train by investing $100 million to develop technologies for the burgeoning field."
""One of the areas where IBM has always been lacking, from a business point of view, was really an effort in the life science area. And in fact they could dominate, given their strength," said Trevor Hawkins, co-director of the Department of Energy Joint Genome Sequencing Center in Walnut Creek, California.
In the post-human genome map era, the biggest challenge is bioinformatics -- which basically means figuring out how to use mountains of biological information to cure, diagnose, and prevent disease."
redux [07.31.00]
BioInform IBM to Invest $100M in Life Sciences; Unit to Link Computing and Biology
"IBM HAS announced plans to invest $100 million in its new life sciences unit, marking a major step in the company’s efforts to bridge the divide between biology and computational science.
“We see this as an important emerging growth market,” Caroline Kovac, vice president of IBM’s Life Science Solutions Software Group, said. “Over the next two and a half years we are going to put $100 million in business development in life sciences.”"
"IBM’s life science unit, which currently employs 40 people, will focus on four main areas: supercomputing, databases, knowledge management, and e-business for the life sciences. In 2000 at least, the unit expects to dedicate the lion’s share of its resources to bioinformatics."redux [06.03.00]
Washinton Post IBM to Put Genetics on Fast Track
"Here is the plan: IBM scientists intend to spend five years building the fastest computer in the world, 500 times faster than anything in existence today. It will suck down every spare watt of electricity and throw off so much heat that engineers have bought a gas turbine the size of a jet engine to cool it.
The machine, dubbed Blue Gene, will be turned loose on a single problem. The computer will try to model the way a human protein folds into a particular shape that gives it unique biological properties. Obscure as it may sound, that kind of puzzle is at the heart of mankind's efforts to understand the nature of consciousness, the origins of sex, the causes of disease and many other mysteries."
redux [06.05.00]
BusinessWeek The Genome Gold Rush
"But for all the drama behind the unveiling of humanity's genetic code, the race marks a beginning, not an end. In fact, the pharmaceutical and biotech industries are already drowning in a flood of genetic information, says Mihael Polymeropolous, vice-president for pharmacogenetics at Novartis. ''That's why this race for me is a little silly,'' he says. ''The real race is who will develop the tools to analyze the genome first.''"
"Another consequence of this flood of information is that the computer has become one of the most important tools in biology. Consider these experiments. You want to measure how each of tens of thousands of drugs affects every one of humanity's 34,000 to 120,000 genes and its 1 million proteins. Or you want to compare the sequences of thousands of unknown proteins with the 3 billion bits of DNA in the human genome. In each case, the amount of data to analyze is mind-boggling. ''We have reached a point where processing information is one of the major bottlenecks,'' says Sharon L. Nunes, senior researcher at the computational biology center at IBM's T.J. Watson Research Center.
Once the information problem has been solved, scientists will be left with a wealth of possibilities. Having the full human genome sequence and all these new tools ''will keep researchers busy for a long time,'' says Vincent Dauciunas, head of strategic planning in the chemical analysis group at toolmaker Agilent. ''I call it the Full-Employment Act for the millennium.''"
redux [02.07.00]
IBM.com IBM Joins Group to Create Library of Genetic Markers
"IBM has pledged to contribute about $3 million to the SNP Consortium, a group dedicated to creating a public database of single nucleotide polymorphisms (SNPs) patterns, which can indicate whether individuals are predisposed to certain diseases. IBM will also develop software, computers, and services to be sold to pharmaceutical companies engaged in the study of SNP patterns."
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"LAST WEEK DNA Sciences announced plans to become a major force in the genomics sector by establishing a facility that will eventually identify one million genotypes a day. The company, which is backed by such industry icons and financiers as James Watson, Jim Clark, and George Soros, plans to use the information it generates from the 50,000 to 100,000 DNA donors it hopes to enlist to create better diagnostic methodologies.
But the Mountain View, Calif., upstart won’t be doing any of this with prepackaged bioinformatics tools. Instead, DNA Sciences will store, manage, and mine SNP data using software the company has developed in-house.
“You cannot buy off-the-shelf software that solves these problems and I think every company that does genetics has built their own software,” said DNA Sciences’ CEO Hugh Rienhoff."
redux [08.01.00]
The New York Times Company Seeking Donors of DNA for a 'Gene Trust'
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"Wanted: your genes.
A California start-up called DNA Sciences is introducing a Web site today that will recruit people to donate their DNA to help find genes that cause disease. The company, which has James D. Watson, a discoverer of the DNA double helix, as a director and James H. Clark, Netscape's founder, as an investor, hopes to get 50,000 to 100,000 people to contribute to its "gene trust" by appealing to their altruism."
"Under DNA Sciences' program, volunteers answer on-line questionnaires about their medical history, and their family's. The company will then send someone to their homes or offices to collect blood samples. Healtheon/WebMD, the medical Web site, owns a stake in DNA Sciences and will be used to help recruit patients.
Donors will not be paid, as is true with the other companies as well."redux [07.19.00]
Individual.Com Healtheon/WebMD (HLTH) and Netscape (NSCP) Founder Clark
"Clark is the only person in history to have guided three companies from inception to becoming public companies with more than one billion in market cap each. In addition to privately held Shutterfly and Mycfo.com, Jim is currently hard at work on his sixth startup: DNA Sciences."
"DNA Sciences is focused on exploiting the genome information and specifically finding the genotypes variations in genes that give rise to the genes that are associated with certain diseases. The variations in those genes that give rise to variance of that disease and treatment for that disease so the company is heavily focused on gene applications in the genome area."
"Healtheon was driven four or five years ago when I started the company in attempt to try to bring