{bio,medical} informatics
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"The flood of knowledge that will follow the human genome map will answer many questions, but experts pointed out that some questions just can't be answered, even by unraveling each of the 3.2 billion chemical letters that make us human."
"Nonetheless, [Incyte's CEO Randy] Scott said answers in medicine will come fast. Both Moore's Law and Metcalfe's Law will accelerate the speed of progress in the biotech industry, replicating the growth of the computer and Internet industries.
"The effect of Moore's Law is pretty straightforward," Scott said. Moore's Law, conceived by Gordon Moore, the founder of Intel, maintains that computer power doubles every 18 months. In biology, DNA sequencing rates are doubling every year.
"While you may recognize that the Human Genome Project has been going on for the past ten years, you may not realize that all of the sequencing for the human genome has happened in the last year, and over 50 percent of that just within the last four months," said Scott."
"Metcalfe's Law, Scott said, will help researchers waste less and make discoveries faster. Conceived by Robert Metcalfe who invented the ethernet, the law states that the power of a network increases exponentially with the number of computers connected to it."
Right now up to 80 percent of research is wasted, because graduate students and postdocs repeat past experiments as part of their training, and scientists refuse to share their research until it's published, which can be up to two years after the results are compiled.
"Metcalfe's Law is going to do to biology what the Internet has done to e-commerce," he said. "It's going to connect vast groups of people who previously didn't talk."
"Instead of putzing around in the lab for weeks or months, scientists will search Web-based databases to quickly narrow their ideas and devise experiments that they know they are unique and relevant."
redux [03.29.00]
UIUC Collaboratory for Structural Biology
"The Theoretical Biophysics Group at the University of Illinois is proud to announce the initial public release of BioCoRE, a collaborative research environment. BioCoRE software is freely available for use at the Theoretical Biophysics Group website. BioCoRE development is supported by the NIH National Center for Research Resources.
Modern computational structural biology requires scientists to employ a wide range of tools and techniques to solve complex problems while keeping accurate and complete records of research activities. Additional complications are introduced by the need to effectively engage in interdisciplinary collaborations with geographically dispersed colleagues. The software BioCoRE, a collaborative research environment for molecular modeling and simulations, addresses these challenges."
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"A day after Monday's announcement that it had sequenced the entire human genome, Celera Genomics said on Tuesday that it will turn its attention to other, potentially more profitable, endeavors.
"Speaking to investors during a conference call, Tony L. White, chairman of the PE Corporation, Celera's parent company, said that ``all of the energy'' of the genomics unit will be directed toward discovery efforts "that are subject to intellectual property protection.''"
"The move toward discovery efforts represents ``a shift from what we've been doing,'' White acknowledged. "Our focus from the formation of the company 2 years ago was to build a significant bioinformatics presence,'' he said, "but we have the money to pursue a much more grandiose strategy now and we intend to do that.''"
Forbes Celera's Worth Still Up In The Air
"Great discoveries do not necessarily make great businesses. Businesses have to sell something. Celera Genomics doesn't sell or make anything tangible. It hawks service and information. It sells access to lists of genes and computers that can sort through those messy lists. Samuel Broder, the company's executive vice president and chief medical officer, makes Celera sound like some kind of consulting company, or perhaps a library."
"Venter's quest could be a fable, with all sorts of morals about the power of capitalism and the importance of a single, brilliant, willful individual who used the market to shake the ivory towers of science. But those morals only hold if Celera succeeds, if business and science blend to propel the company into the future with breathtaking speed without rocketing it into the realities of the marketplace. Celera could become one of the great business success stories. It could also be a financial train wreck."
Right now, that makes it a very volatile stock."
The New York Times U.S. Hopes to Stem Rush Toward Patenting of Genes
[requires 'free' registration]
"Long before scientists had completed the task of reading the human genome, parts of it had already been claimed for commerce. In what has often been compared to a land grab, companies and universities have filed for patents on hundreds of thousands of genes and gene fragments. "
"Indeed, genes have been patented for years. Many of the first were for drugs. For example, erythropoietin, for anemia, was found by cloning genes that coded for particular proteins. In those early days, scientists knew the function of the protein and worked backwards, taking years to isolate a single gene.
But now high-speed gene sequencing and other techniques are allowing genes or fragments of genes to be discovered en masse, without knowing the functions of the proteins produced by the genes. These genes, rather than representing a product in themselves, are now guides to future product discovery. And there is concern that if these genes are patented it would discourage other scientists from doing research using the same genes. Some compare it to trying to gain ownership of the alphabet, rather than of a novel or play."
redux [04.26.00]
SF Gate Call It the Gene Rush -- Patent Stakes Run High
"After years of bickering, the patent office has proposed adding three simple words to its guidelines. To win a patent, applicants will have to describe a "substantial, specific and credible'' use for their gene."John Doll, who heads the patent office's biotech division, said the guidelines essentially group the huge backlog of 30,000 patent applications into three classes.
The first are genes isolated in a laboratory, whose purpose is likely to be known. Doll calls this ``wet biology.'' Government and academic scientists have used wet biology to patent genes for 20 years. These are not controversial.
Another class of applications cover ``naked DNA sequences.'' These were the sort of early, machine-generated gene discoveries that provoked alarm in the first place. The new guidelines rule them out.
The battleground is the large number of applications that fall in the middle. These are machine-discovered genes, but they aren't "naked sequences.'' ."
"As the controversy over "naked sequences'' festered, biotech companies got smarter about using their machines. When they discovered a new gene, they employed software that analyzed its structure and deduced its purpose. Doll called these "in silico'' applications -- a reference to the fact that the gene's purpose was deduced through a computer analysis."
""It's not important that you understand the function of the gene (to get a patent), it's only important that it have a commercial utility,'' Incyte's Scott said. "
redux [03.18.00]
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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"At the intersection of biology, information technology, computer science, and genetic engineering is a revolutionary industry and the career advancement opportunity of a lifetime . . .
In a world where data is being amassed faster than it can be analyzed and utilized, there is a tremendous demand for professionals who can use technology to digest the ever-growing mass of genetic information. We are answering that demand with our bioinformatics programs at Rensselaer. Bioinformatics is the science of storing, extracting, organizing, analyzing, interpreting, and utilizing biological information. It is the backbone of leading research laboratories, hospitals, and pharmaceutical companies, and the driving force of biotechnology and genetic engineering. We offer you this one-of-a-kind, breakthrough workshop . . . in a high growth industry . . . from a university on the leading edge of science, information technology, and interdisciplinary learning.
Join other key scientists and managers in this 4-day exploration of key topics in bioinformatics and drug discovery. You'll learn from leading researchers and educators of the drug industry, gain hands-on experience in this growing field, and advance your knowledge base.
Discover the benefits bioinformatics and related technologies can bring to your organization, your job, and your career."
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"A slew of new genetic methods, tests, and knowledge promises to revolutionize medicine now that scientists have cracked the human genome map. But those same advances could land health-care providers and insurance companies in a quagmire of sticky issues, including conflicts with patient privacy."
"Yet in order to proceed with SNP research, scientists need to know identifying characteristics of populations, such as whether they smoke, their exposure to chemicals, infectious diseases they may have encountered, and what drugs they take.
"You must have ways to link those very different data sets or the whole thing comes crashing down with very little understanding and very little advancement from all this fabulous genetics," said Gilbert S. Omenn, executive vice president for medical affairs at the University of Michigan and CEO of the University of Michigan Health System.
"The information in the aggregate form of patient databases will probably be one of the most powerful tools for the medical industry in the future," said Randy Scott, president and CEO of Incyte Genomics. "Protecting the freedom of the individual" while using that information stored in patient databases for the good of all is the goal "in terms of value for society."
MIT Technology Review Medical Records, Inc.
"The United States’ most famous epidemiological study, the Framingham Heart Study, is about to take a medically promising step that could help in the effort to discover genes responsible for common diseases. But the move is also likely to raise questions about the commercial exploitation of patients’ medical records."
"The demand for so-called “phenotype” data (measurements of an individual’s actual physical characteristics) from well-studied populations like Framingham is rising dramatically thanks to rapid advances in genetic technology. “Genetic analysis can be done with an arbitrarily great degree of precision. But you are limited by patient data,” says Ledley. “This is the missing link.”
"In fact, genomic researchers expect they will eventually need medical data on hundreds of thousands, even millions, of people. For that reason, some European governments with centralized health care systems are now casting hungry eyes on their citizenry’s medical records. The U.K. Medical Research Council, for instance, is planning a massive study involving more than 500,000 volunteers, and scientists have lobbied the U.K.’s National Health Service to create a genetic database encompassing the entire British population. Similar national databases are under consideration in Italy and Estonia."
redux [06.15.00]
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]redux [05.26.00]
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."
Yahoo! News Partners HealthCare and DeCODE Genetics Join Forces Against Disease
"Through a better understanding of the genetic components of disease, the alliance aims to pioneer new diagnostic and therapeutic approaches to common illnesses and to develop leading-edge bio- informatics that can improve the quality of healthcare.The three-year agreement includes research and business collaborations in three distinct areas. First, the alliance will enable Partners and deCODE scientists to form joint research teams to identify and compare disease- causing genes or loci responsible for diseases in both the Icelandic and Massachusetts populations. Second, the two entities will be able to collaborate on basic research related to these new genes and on the discovery of novel approaches to preventing and treating common diseases. Third, deCODE will provide Partners with healthcare informatics systems resulting from deCODE's development of the Icelandic Health Sector Database (IHD). These technologies will strengthen Partners' existing information system infrastructure, enabling a more comprehensive population-based approach for its genetics research and facilitating collaborations between the two parties. deCODE has the right to develop and market products and services resulting from the collaborative research programs."
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"A fast-growing field known as bioinformatics uses computing to analyze the vast amount of biological, genomic, and related research to make sense of things too complex for the human brain to fathom.
But bioinformatics is also a bottleneck for many drug and biotech companies that can't find enough talented software engineers who combine sophisticated analysis tools with an understanding of genomics.
''We resolve the bioinformatics issue [by hiring] two people: one who understands computer science and the biologist or researcher,'' said Kenneth Fasman, vice president and global head of informatics of AstraZeneca LLC in Waltham."
"...according to Dr. Donald Johnson, a pathologist at the Nebraska University Medical Center. He estimated there are about 60,000 jobs available to scientists and managers versed in bioinformatics."
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""How it's going to help me develop drugs or do anything, I really don't have a clue," said Craig Rosen, executive vice president for research and development at Human Genome Sciences."
""It's like being given the best book in the world, but it's in Russian, and it's incredibly boring to read," said Ewan Birney, a team leader at the European Bioinformatics Research Institute, part of the Sanger Centre, one of the major labs working on the Human Genome Project."
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"A new synthesis linking the large and increasing amount of biological information at the molecular level with what we know about the structure of cells and organisms must be attempted. Post-genome Informatics sets out the starting point for a study of the gap between these two levels, i.e. how genes and proteins are networked to create a biological system.
"Researchers in the biomedical sciences and the computer scientists who create genome databases, the stated audience for the book, may feel a little cheated. The first hundred or so pages are, as the genesis of the book shows, undergraduate level material.
In the final 30-page chapter does the book begin to do justice to its title. Even then, as the author acknowledges, the most up-to-date information must be sought on the Internet. Considered as a text for advanced undergraduates, however, the book should be welcomed as a concise introduction to genome informatics and beyond. "
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""Plastics." When a family friend whispered this word to Dustin Hoffman's character in the 1967 film The Graduate, he was advocating not just a novel career choice but an entirely different way of life. If that movie were made today, in the age of the deciphering of the human genome, the magic word might well be "bioinformatics.""
"Corporate and government-led scientists have already compiled the three gigabytes of paired A's, C's, T's and G's that spell out the human genetic code--a quantity of information that could fill more than 2,000 standard computer diskettes. But that is just the initial trickle of the flood of information to be tapped from the human genome. Researchers are generating gigantic databases containing the details of when and in which tissues of the body various genes are turned on, the shapes of the proteins the genes encode, how the proteins interact with one another and the role those interactions play in disease. Add to the mix the data pouring in about the genomes of so-called model organisms such as fruit flies and mice, and you have what Gene Myers, Jr., vice president of informatics research at Celera Genomics in Rockville, Md., calls "a tsunami of information." The new discipline of bioinformatics--a marriage between computer science and biology--seeks to make sense of it all. In so doing, it is destined to change the face of biomedicine.
"For the next two to three years, the amount of information will be phenomenal, and everyone will be overwhelmed by it," Myers predicts. "The race and competition will be who can mine it best. There will be such a wealth of riches.""
Oscar Gruss & Son Trends in Commercial Bioinformatics
""The purpose of this document is to provide an overview of the rpidly emerging field of "commercial bioinformatics."
"For the purposes of this review, we define bioinformatics as the backbone computational tools and databases that support genomic and related research, which broadly encompasses the study of DNA structure/function, gene expression and protein production/structure/function.""
redux [05.10.00]
Alfred P. Sloan Foundation Hiring Patterns Experienced by Students Enrolled in Bioinformatics/Computational Biology Programs
"As expected, salaries for the most part climb as the level of training rises, starting in the $40,000-$50,000 range for BAs and reaching over $100,000 for one post doc. But there are exceptions. For example, two of the three undergraduates who were placed received salaries between $50,0000 to $60,000. This is higher than that earned by seven of the masters students, although ten of the nineteen masters students for whom we have salary information earn more than $60,000. One masters student received a starting salary of over $100,000. Reported salaries for five hires at the doctorate level are over $70,000. One is between $80,000 to $90,000; another is over $100,000; yet another is between $60,000 to $70,000. Three post docs received placements with a salary between $80,000 to $90,000. One post doc was placed at a salary of over $100,000. One institution reported that one or more masters student(s) received a signing bonus.""The results of our current survey make it clear that the majority of these jobs are not being filled by graduates of formal programs—who by our count represent about 15 percent of the positions advertised in 1997. And, we believe the 15 percent figure to be an overestimate given that ads have been growing over time and our most recent ad count is for 1997, a year earlier than our hiring data. This leads us to infer that most of the advertised positions are being filled by individuals trained in informal programs and by individuals who change jobs. The distinct possibility exists that a number of these jobs remain vacant for a period of time, an issue not studied here. Furthermore, our pipeline estimates (see Table 2) lead us to conclude that the number of individuals currently enrolled in formal programs falls far short of the number of positions that have recently been advertised."
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"For insiders in genome research, the name Eric Lander evokes a palpable image of the trends sweeping biology—automation, computers, entrepreneurialism, big science and big ideas.
A mathematician turned Harvard Business School professor turned gene scientist, the 42-year-old Lander is director of the Whitehead Institute for Biomedical Research/MIT Center for Genome Research. Lander has built the lab into the world’s most productive academic gene sequencing facility and the flagship of the international Human Genome Project. "
"TR Senior Associate Editor Antonio Regalado managed to catch up with Lander by phone early on a recent Sunday morning."
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"In a major step toward a new era of gene-based medicine and disease treatment, two research centers are expected to announce on Monday that they separately have sketched a map detailing the secrets of human genetic structure."
"Francis Collins, director of the Human Genome Project at the National Institutes of Health, said "it's hard to overstate the importance of reading our own instruction book and that's what the human genome project is all about.""
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"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."
Tools The Ensembl Project
"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."
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"We would like to invite you to the Third Annual Bio-Ontologies Meeting (Bio-Ontologies 2000), on August 24th in La Jolla, California, USA. This is immediately after ISMB-00 August 20-23 in La Jolla.
The goal of this consortium is the identification and promotion of a practical set of technologies that will aid in the knowledge management and exchange of concepts and representations in the life sciences. The first meeting took place in Montreal in 1998, and made clear the general interest and support people had for ontologies in the life sciences. The following year in Heidelberg we discussed ontology exchange and presented ontologies currently under development.
Many in the group have been active since our last meeting. The community now has considerable experience in the development and deployment of ontologies in the life sciences, so it is appropriate for us to take stock and reflect. So the theme for this year's meeting is Sharing Experiences and Spreading Best Practice. The idea is that we share not only the results of our labours but how we got there, and what we wished we had known while we did it."
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."
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"Scientists in the government and for-profit sectors are keeping the public guessing as to how and when they will announce they've finished mapping all of the genetic material that makes up a human.
Reports are conflicting. On Tuesday The Wall Street Journal said that the White House would be hosting a joint announcement on Monday, but a White House spokesman later denied the report. Researchers also say the report was premature."
""I think this is a great time in biology. I would describe it as the beginning of thousands of races," [Incyte's] Whitfield said. "If you have colon cancer, the race is about curing colon cancer. If you have arthritis, it's a race to cure arthritis. It's the start of a really long race to have a tremendous impact on human health."
BioInform As Celera Nears Finish Line, Myers Prepares for Post-Assembly
"Gene Myers, who gained notoriety in the pages of The New Yorker last week as a perpetually chilled, Nerf gun-shooting, emerald earring-wearing computer scientist, is the brain behind Celera’s assembly project. But assembling the human genome sequence, a task Myers and his team are expected to complete any day now, is just the first stage in his career at Celera, where he is director of informatics research.
After assembly, computational biologists will have their work cut out for them, Myers told BioInform. “I don’t think that our tools and capabilities in assisting biologists to investigate whole genomes at systemic levels are up to par. The right tools and right infrastructures have not been built.”
While existing tools are good, lack of integration is the weak link, Myers asserted. “What you are striving for is to allow a biologically focused investigator to sit down at a machine and generate conjectures for experiments,” he said. “I don’t think anyone’s gotten near the right formula for that.”"
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"The Linux operating system has helped scientists in Cambridge to decode the 34 million chemical 'letters' that constitute a human chomosome."
"Over three hundred Alpha-based Compaq TRU64 Unix systems as well as 60 Intel-powered Linux machines contributed to the huge number-crunching effort required to interpret the chemical make-up of a chromosome. The centre combined all the Linux machines into one giant 'virtual computer' in order to maximise their computational power. " [via bioinformatics.org]
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[requires 'free' registration]
"In what some call a taste of the future of genetic medicine, Boston University has created a company to analyze a valuable cache of medical data from a federally financed study that has lasted 52 years. The university expects that companies will want to use the data to facilitate the search for new drugs."
"... new company, Framingham Genomic Medicine, supported by $21 million from venture capitalists, will assemble the study's data in ways useful to companies or scientists. For example, researchers seeking clues to genes and environments that protect against heart disease will be able to sift through participants' medical histories and genetic data to home in on the information they want."
""This is the beginning of a new era," said Dr. Arthur Holden, chairman and chief executive of the SNP Consortium, a collaboration of 14 companies, mostly drug makers, that are creating a publicly available map of the human genome, concentrating on individual places on DNA where people differ. "The demand for genetic databases is beginning to increase, and many of the leading university centers are beginning to think about how they can commercialize their samples and data sets.""
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."
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"Patient data from the world-famous Framingham Heart Study - the pioneering research into heart attacks and strokes that has been available free of charge for 50 years - for the first time will be sold for a profit under a new venture started by the study's sponsor, Boston University.
The university has struck a deal with a group of venture capitalists, who have committed $21 million to form Framingham Genomic Medicine Inc.
The company will use the heart study's vast collection of genetic, clinical, and behavioral data from the 10,000 participants, all families from Framingham, to create a huge electronic database. Pharmaceutical and biotechnology companies are expected to pay annual fees to access the treasure trove of medical information."
"The Framingham Heart Study, which has been collecting data from families who live in its namesake city west of Boston for 52 years, has accumulated vast amounts of information, including 500,0000 chest X-rays and electrocardiograms, 5,000 blood samples, and truckloads of paper medical records that include diet diaries and early studies of male balding patterns. The heart study also owns 160 computer databases."
redux [02.25.00]
Science U.K. Plans Major Medical DNA Database
[summary - can be viewed for free once registered]
"Following the examples of Iceland, Sweden, and Estonia, the United Kingdom is drawing up plans to create a national database linking the DNA of 500,000 of its citizens to their medical records and lifestyle details. Its main goal is to tease apart the genetic and environmental components of conditions such as cardiovascular disease and cancer and, eventually, to come up with new drugs to treat--or even prevent--these conditions. An expert panel is currently hammering out a strategy for setting up the database and is due to report its recommendations next month.”
redux [05.26.00]
British Medical Journal Genetic epidemiology
"Research in disease aetiology has shifted towards investigating genetic causes, powered by the human genome project. Successful identification of genes for monogenic disease has led to interest in investigating the genetic component of diseases that are often termed complex, that is, they are known to aggregate in families but do not segregate in a mendelian fashion. Genetic epidemiology has permitted identification of genes affecting people's susceptibility to disease, although progress has been much slower than many people expected. While the role of genetic factors in diseases such as hypertension, asthma, and depression is being intensively studied, family studies and the large geographical and temporal variation in the occurrence of many diseases indicate a major role of the environment. Thus, it is necessary to consider findings about susceptibility genes in the context of a population and evaluate the role of genetic factors in relation to other aetiological factors. This article discusses some approaches used to resolve the genetic architecture of disease and to study the relation of genes to environmental factors in the population. "
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"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."
redux [05.15.00]
The New York Times Who Owns Your Genes?
[requires 'free' registration]
""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. "
redux [05.26.00]
Yahoo! News Partners HealthCare and DeCODE Genetics Join Forces Against Disease
"Through a better understanding of the genetic components of disease, the alliance aims to pioneer new diagnostic and therapeutic approaches to common illnesses and to develop leading-edge bio- informatics that can improve the quality of healthcare.The three-year agreement includes research and business collaborations in three distinct areas. First, the alliance will enable Partners and deCODE scientists to form joint research teams to identify and compare disease- causing genes or loci responsible for diseases in both the Icelandic and Massachusetts populations. Second, the two entities will be able to collaborate on basic research related to these new genes and on the discovery of novel approaches to preventing and treating common diseases. Third, deCODE will provide Partners with healthcare informatics systems resulting from deCODE's development of the Icelandic Health Sector Database (IHD). These technologies will strengthen Partners' existing information system infrastructure, enabling a more comprehensive population-based approach for its genetics research and facilitating collaborations between the two parties. deCODE has the right to develop and market products and services resulting from the collaborative research programs."
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"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]
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 [03.29.00]
LinuxWorld Farming, Linux-Style
"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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"The two sides in one of the fiercest competitions of modern science--the effort to crack the human genetic code--are quietly trying to negotiate a compromise that could let each declare victory. Intermediaries, fearful that the race between the publicly led Human Genome Project and upstart biotech firm Celera Genomics could taint science's public reputation for objectivity, are trying to broker a deal under which the rivals would simultaneously publish separate scientific articles about their findings as early as September.
If successful--and previous such efforts have failed--the arrangement could help defuse what has turned into a raucous struggle for scientific credit and commercial control of a body of knowledge that many believe will fundamentally alter science and medicine in the coming century."
redux [06.06.00]
SiliconValley.Com Researchers deny they're in a race to complete human genome map
"Leaders of two groups mapping the human genes said they are not in a race, but are trying to reach the same goal using different methods and the results will be "complementary.''
Asked about their competition, [Francis] Collins told reporters, "racing is the wrong metaphor. I wish you would stop using it.''"
"Venter hinted that Collins' group and his company may be in discussions about a joint announcement, but declined to be specific."
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[requires 'free' registration]
"Australian postdoctoral fellow Marc Wilkins coined the term "proteome" in the mid-'90s, referring to the total set of proteins expressed in a given cell at a given time. The term took hold, and a new scientific discipline was born. In proteomic studies, all the proteins from a given cell, organelle, or tissue are analyzed simultaneously with respect to properties such as expression levels, posttranslational modifications, and interactions with other molecules. Proteomics is a young discipline but is rapidly growing due to the development, integration, and automation of requisite large-scale analytical tools and the emergence of sophisticated bioinformatic techniques. The push is on to obtain global, integrated views of disease states and cellular processes at the proteome level."
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"WHEN HUMAN GENOME Project (HGP) statisticians were looking for a way to mine billions of bases on the human genetic code and find out which ones cause certain diseases, they turned to SAS Institute and its Enterprise Miner for help."
"In particular, scientists are using features such as SEMMA (Sample, Explore, Modify, Model, Assess), a built-in guide to help extract data, and decision-tree analysis of SNPs (single nucleotide polymorphisms), genetic markers on the human genome. The data must be managed in a way to keep it logically structured and capable of being easily matched and organized. Enterprise Miner's decision-tree analysis creates a graphical representation of the data, making it easier to see where all the data fits phenotypically.
To further aid HGP scientists, SAS Institute has developed several features specifically for mining genomic data, providing a filter for false alarms, or "noise" of SNPs that may look like they are markers signaling an abnormality but really aren't. The company also has provided a tool that looks at how different markers relate to each other, and a tool that helps factor in family history patterns. "
iBiomatics SAS Spins Off New B2B Internet Company for Biomedical Research
""Packaging and delivering research information over the Internet changes the structure of biotechnology and drug development," says Lee Evans, president of iBiomatics and previous executive director of SAS PharmaHealth Technologies. "For the first time, research organizations of all sizes will have access to biomedical information through a Web browser. They can focus on scientific research, and iBiomatics will deliver, leverage and add value to their information."
""Since information is now the primary catalyst and currency of any marketplace, we believe that the growth of other markets will pale in comparison to that of bioinformatics over the next decade," says Doug Laney, vice president of the META Group, an IT advisory services firm. "The forthcoming deluge of information from unraveling the genome, matched with the accessible analytic output from collaborative biomedical research ventures like iBiomatics, will enable unfathomable advances in life sciences and spawn countless ancillary industries." "
redux [05.23.00]
The Standard DNA Detectives
"For all the "brave new world" rhetoric surrounding the recent rapid advances in genetics, scientists are only on the threshold of understanding how genes work and their role in health and disease.So too are the DNA dot-coms in their search for success. By combining strains of Wall Street's two favorite industries of the moment – biotech and the Internet – online genomics companies have reaped valuations last seen by Net companies circa 1999. "You take the two great buzzwords, 'genome' and 'Internet,' put them together and someone will throw money at them..."
"But the rush to go public has made the DNA dot-coms vulnerable to the volatility that seems to strike biotech and Net startups particularly hard. "
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"The public-private race to get the first complete map of the human genome is nearing the finish line, with both groups expected to announce a working draft sometime this month. Then the real work begins: finding the genes along those long stretches of DNA and determining their function. This hour, we'll get an update on the latest genetics news. "
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"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 [02.25.00]
Science U.K. Plans Major Medical DNA Database
[summary - can be viewed for free once registered]
"Following the examples of Iceland, Sweden, and Estonia, the United Kingdom is drawing up plans to create a national database linking the DNA of 500,000 of its citizens to their medical records and lifestyle details. Its main goal is to tease apart the genetic and environmental components of conditions such as cardiovascular disease and cancer and, eventually, to come up with new drugs to treat--or even prevent--these conditions. An expert panel is currently hammering out a strategy for setting up the database and is due to report its recommendations next month.”
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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"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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"To be sure, many industry insiders are skeptical of the bioinformatics internet portal business model. Even among vendors of the 220-plus software products available at the BioNavigator site, some told BioInform they wondered how companies such as eBioinformatics and DoubleTwist will make money. A product manager at one of eBioinformatics’ partner com-panies said, “I don’t see how either company will make the sort of money necessary to cover these costs. Scientists are used to free stuff. I’m not sure they will pay money for the not-free stuff.”"
redux [05.23.00]
The Standard DNA Detectives
"For all the "brave new world" rhetoric surrounding the recent rapid advances in genetics, scientists are only on the threshold of understanding how genes work and their role in health and disease.So too are the DNA dot-coms in their search for success. By combining strains of Wall Street's two favorite industries of the moment – biotech and the Internet – online genomics companies have reaped valuations last seen by Net companies circa 1999. "You take the two great buzzwords, 'genome' and 'Internet,' put them together and someone will throw money at them..."
"But the rush to go public has made the DNA dot-coms vulnerable to the volatility that seems to strike biotech and Net startups particularly hard. "
Chemical & Engineering News Bioinformatics for the Masses
"As computing and biology have converged, software tools for data capture, management, analysis, mining, and dissemination have emerged. More than 40 companies, most of them small, are trying to capitalize on the development and marketing of new bioinformatics tools. Whereas the market for generated data or "content" is very lucrative, bioinformatics sales are expected to reach about $160 million this year, according to market research firm Frost & Sullivan""Who I really want as customers are the scientists themselves," says John Couch, chief executive officer of DoubleTwist , Oakland, Calif. "We're challenged in this field to deliver something to the scientists so that they can do their science."
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"Leaders of two groups mapping the human genes said they are not in a race, but are trying to reach the same goal using different methods and the results will be "complementary.''
Asked about their competition, [Francis] Collins told reporters, "racing is the wrong metaphor. I wish you would stop using it.''"
"Venter hinted that Collins' group and his company may be in discussions about a joint announcement, but declined to be specific."
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"The US company racing to produce the first "working draft" of the human genome is understood to have finished its task.
Over the past few weeks, powerful computers at Celera Genomics have been trying to determine the exact order of the 3bn or so individual chemical building blocks, or bases, that make up our genetic code.
A source has informed BBC News Online that this goal was finally achieved at the weekend. An official announcement is expected any day from the company - perhaps as soon as Tuesday or Wednesday."
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.''"
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"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."
Conference: The Bioinformatics Industrialization Workshop : Bioinformatics Comes of Age
"Pilot Workshop Co-sponsored by IBM, The Task Force on Bioinformatics of the International Union for Pure and Applied Biophysics, and The Whitehead Institute for Biomedical Research"
"The underlying theme throughout the workshop will be the identification and exploration of process bottlenecks, the scientific factors that influence the quality of data, and the choice of software and data standards.Potential areas of interest for discussion groups include 'New Scientific Challenges', 'Urgently Required Tools', 'Analyzing hundreds of new genes per day', 'Data Management: Storage and Incrementing on Flatfiles and Relational Data Bases', 'Federalization and Data Mining', 'Linkage to Expression and Metabolic Simulation', 'Linkage to Chemoinformatics' 'Linkage to Biblioinformatics' 'The Data Flow Network', 'The Fully Electronic Life Science Company' 'Integration and Automation','Automated Drug Design', 'Simulation and Deep Computing', 'Specialized Hardware', 'The Blue Gene Project'. Informal discussions will be encouraged to address the Expertise Shortage in Bioinformatics, including the shortage of qualified job candidates and will explore methods of increasing the pool of expertise along with associated discussions on the possible relevance and potential impact of Expert Systems."
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