{bio,medical} informatics
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"A group of plant scientists are calling for a project to understand the biological machinery of a plant in enough detail so that they could construct a 'virtual' plant. "
"The effort is called Project 2010 because by 2010 plant researchers hope to construct a complete "wiring diagram" of all the biological pathways of Arabidopsis.
Dr Chory said, "Ultimately, we hope to create a 'clickable plant.' We want to be able to go to our computers and click on a cell type and understand all the protein-protein interactions."
redux [05.07.00]
Bioinform Academic-Industry Initiative Will Develop Bioinformatics Tools to Model Living Cell
"A team of researchers led by Bob Franza of the University of Washington here is developing bioinformatics tools to create a quantitative model of the living cell.The Cell Systems Initiative was launched late last year, and thus far has attracted the support of two corporate backers who would like to mine the data it generates to identify new drug targets."
"The goal, according to Franza, is to understand the stages of a cell's development. "How does one stage know when it's supposed to start and stop?" Franza asked. "How do we reconstruct the temporal process?" A complete model of the living cell will need to be understood not as parts, but as components of a continuous system, he said. To that end, the initiative also aims to build a computational infrastructure that can manage the entire dynamic system of data collection and integration."
redux [02.24.00]
HMS Beagle Virtual Cures
[requires 'free' registration]
"For a brief period, supplying the data was enough. More genes meant more potential drug targets. But now the victims of the data flood are crying for help. Companies like Entelos, Inc. (Menlo Park, California) are coming to the rescue by building models that integrate all those data into a single, homeostatic, interconnected whole. The models allow researchers to run virtual drug trials to determine the best drug targets, treatment regimens, and patient populations."
Modelers feel that their time has come. "Leaders in the genomics field are all coming to this realization that model building is becoming the rate-limiting step," says Palsson. "There's a major shift taking place in the biological sciences." Math is back, he says, and "biology is going to become quantitative."Biospace Virtual Drug Development: Start-ups Put Biology in Motionredux [04.05.00]
"One way of animating our growing store of static information is through computer simulation. It is an area that is beginning to emerge slowly in the life sciences, with only a handful of academic and commercial players active in the area. But for a fledging discipline, there is a great variety in the scope of work being undertaken. While academic labs try to create accurate simulations of red blood cells and simple bacteria, the private companies are taking on bolder projects--simulating human organs and even human diseases in their entirety."
Science Revealing Uncertainties in Computer Models
[summary - can be viewed for free once registered]
"Computer simulations give the impression of precision, but they are founded on a raft of assumptions, simplifications, and outright errors. New tools are needed, scientists say, to quantify the uncertainties inherent in calculations and to evaluate the validity of the models. But making uncertainties evident is a tough challenge, as evidenced by several recent workshops.”
HMS Beagle Are Computers Evolving in Biology?
[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."
The Institute for Systems Biology What is Systems Biology?
"Systems biology is a unique approach to the study of genes and proteins which has only recently been made possible by rapid advances in computer technology. Unlike traditional science which examines single genes or proteins, systems biology studies the complex interaction of all levels of biological information: genomic DNA, mRNA, proteins, functional proteins, informational pathways and informational networks to understand how they work together."
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"SeWeR is an acronym, stands for SEquence analysis using WEb Resources. In addition to its common *dirty* use, the word SeWeR also has two meanings- first, "a medieval servant or household officer of high rank in charge of serving the dishes at table and sometimes of seating and tasting" and the second one, "one who sews". SeWeR fits all of these definitions. First, it is *dirty* at the code level. Second, it serves. It serves you a single door to all the common web-based services for sequence analysis. And it sews. It sews all these services together. For refined mind, SeWeR is an integrated portal to common web-based services in bioinformatics." [via bioinformatics.org]
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"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 [03.08.00]
New Scientist A gene profiling system threatens to reveal your innermost secrets
"WILL "DNA chips" that reveal your genetic makeup within minutes prove to be awesome medical tools or the means of genetic discrimination? We could find out sooner than anyone expected. A British biotech start-up has filed for a patent on a device that can detect variants of over 2500 genes--including genes that affect behaviour and intelligence."
""Where Genostic comes up with thousands of gene variants to put on their chip is a mystery to me," says Francis Collins, director of the US National Human Genome Research Institute near Washington DC. Daniel Cohen, chief genomics officer at Genset of Paris, agrees. "There haven't been enough population studies, as far as I know, to assess with enough precision the risk or predisposition for any of the diseases mentioned in the patent," he says.
redux [04.25.00]
UniSci Selfish Gene Theory Of Evolution Called Fatally Flawed
"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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"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."
British Medical Journal Genetic epidemiology
"Research in disease aetiology has shifted towards investigating genetic causes, powered by the human genome project. 1 2 Successful identification of genes for monogenic disease has led to interest in investigating the genetic component of diseases that are often termed complexthat 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. "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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"First came germ theory with antibiotics. Then came replacement theory with insulin and growth factors. Now the paradigm for drug development has shifted once again: We have entered the era of genomics-based medicine.
In less than a decade a new genomics industry has taken hold. Gemomics companies now ferret through miles of genetic code to identify the genetic causes of disease, select potential target genes, and help big pharma find the next blockbuster.
But the face of genomics—or at least its role in drug discovery—is about to change, due largely to its own success. “We’re knee deep in potential targets,” says Nicholas Dracopoli, executive director of pharmacogenomics with Bristol-Myers Squibb. “Prioritising the targets is the rate limiting step.”"
"Leaders in the genomics field, as in any other industry, will be companies that offer a value-added service. Large pharmaceutical companies agree on what that service should be: integration of all the genomics information available. With more information readily accessible, companies can easily decide on whether to continue investigating potential targets.
So the future of genomics companies may rest in their IT and software capabilities, a view held by Celera Genomics, a newcomer to genomics. “We are entering an era of ‘cyberpharmaceutical’ drug development,” says Samual Broder, executive VP and chief medical officer. “Pharmaceutical corporations will use genomic databases, and other relational databases involving gene expression, proteomics etc. as the foundation of their drug discovery pipelines. One of the immediate goals... is to produce appropriate databases and software to link biologic and genomic information.” "
Medscape Conference Report : Genomics and Proteomics in Drug Discovery and Development
[requires 'free' registration]
"As efforts to sequence the human genome are nearing completion, there is an increased interest in the application of genomic and proteomic approaches to aid in the discovery, development, and rational use of drugs. Much of this effort is focused on understanding the significance of genetic variation in drug-response genes in determining drug efficacy and toxicity. In parallel, biologists and computer scientists are teaming up to develop global technologies that will allow us to decipher the complex nature of physiological and pathophysiological functions. The impact of genomics and proteomics on the pharmaceutical sciences is yet to be fully realized but will no doubt enhance the traditional approaches to drug discovery, development, and rational use."Biospace Biotech Productivity: Myth or Method?
""The data suggest that the biotechnology industry used to be more productive than Big Pharma, but not any longer," said Rebecca Henderson, a professor at MIT's Sloan School of Management whose been studying the question for six years. "The public biotechs have declining productivity… and look as if they are running into the same problems as Big Pharma."On every metric that Henderson has studied---number of scientific papers and patents per R&D dollar, cost per new drug--she found that biotech and Pharma productivity were quickly converging, and both were getting worse. After spending six years of studying the question, Henderson says she has found "no systematic evidence that small firms are more productive.""
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"Garage.com, an online venture capital company that helps entrepreneurs and investors create, build, and fund promising early-stage technology companies, announced that Quicksilver Genomics, a team from the University of California, San Francisco, won the $150,000 Grand Prize at the PLANedu Final Pitch-off and Awards Ceremony that took place last night."
"Quicksilver's mission is to accelerate post-genomic drug discovery. The team's licensable technology enables pharmaceutical, biotechnology, and academic researchers to rapidly discover patentable lead compounds from unclassified gene sequences."
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[requires 'free' registration]
"The selective estrogen receptor (ER) modulators (SERMs) tamoxifen and raloxifene act primarily as estrogen antagonists in the mammary glands, and are therefore used in the treatment of estrogen-responsive breast cancer. They also act as agonists in the bone and cardiovascular systems, making them candidates for estrogen replacement therapy. The authors sought to identify additional SERMs by using a method of differential gene expression modulation. They analyzed 24 combinations of genes and cells to come up with an assay that could discriminate between estrogen, tamoxifen, raloxifene, and the pure ER antagonist ICI164384. They then used it to measure the activity of 38 compounds. Next, they obtained fingerprint gene expression profiles (GEFs) and used them to classify each into one of eight categories. Most compounds with similar GEFs produced similar effects, which demonstrated the utility of GEF-based screens in predicting the pharmacological profile of a compound.
Reference: Zajchowski, D.A., Kauser, K., Zhu, D. et al. 2000. Identification of selective estrogen receptor modulators by their gene expression fingerprints. J. Biol. Chem. 275(21):15885-15894."
Weinstein Genomics and Bioinformatics Group A cDNA microarray gene expression database for the molecular pharmacology of cancer
[requires 'free' registration]
"We used cDNA microarrays to assess gene expression profiles in 60 human cancer cell lines of the National Cancer Institute's drug discovery program...we link the bioinformatics with chemoinformatics by correlating gene expression and drug activity patterns in the 60 cell types. Clustering the cells on the basis of gene expression yields a picture very different from that obtained when the cells are clustered on the basis of their response to drugs. Gene-drug relationships for the important clinical agents 5-fluorouracil and L-asparaginase exemplify how variations in the transcript levels of particular genes can relate to mechanisms of drug sensitivity and resistance. This is the first study to integrate large databases on gene expression and molecular pharmacology. "Nature One-stop shop for microarray data
"With the advent of DNA microarray and 'chip' technologies...gene expression in an organism can be examined on a genomic scale, allowing the transcription levels of many genes to be measured simultaneously2. For instance, we can study the effects of a compound (such as a drug) on the level of expression of many genes...With gene expression, context is everything: without it, the information is meaningless. For example, the precise stage of a tumour sample could have a crucial bearing on the interpretation of expression measurements. This context can be infinitely detailed, and it is this detail that must be captured in gene-expression studies.The bioinformatics underlying the management of these huge volumes of data are crucial if any sense is to be made of gene-expression experiments. A single microarray experiment looking at 40,000 genes from 10 different samples, under 20 different conditions, produces at least 8,000,000 pieces of information."
"It is time to create a public repository for microarray data, with standardized annotation (see Box 2, overleaf). But this is a complex and ambitious project, and is one of the biggest challenges that bioinformatics has yet faced. Major difficulties stem from the detail required to describe the conditions of an experiment, and the relative and imprecise nature of measurements of expression levels. The potentially huge volume of data only adds to these difficulties. However, it is this very complexity that makes an organized repository necessary.
Important tasks to be undertaken include: (1) agreement on the essential information that should be reported for a microarray experiment; (2) definition of ontologies and an extensible, structured document format to capture these data and their semantics; (3) production of a database to store these documents; and (4) development of tools for searching documents in a database and using the semantic context to allow comparisons and sophisticated queries."
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[requires 'free' registration]
"How many human genes are there? Recent estimates have ranged from 60,000 to 140,000 and might be expected to narrow sharply as the human genome nears completion. In fact, the range has widened, suggesting that gene-counting remains at least as much art as science."
"Faced with estimates that are all over the lot, genome scientists have contrived a simpler way of settling the question, at least for the present. At a meeting this month at the Cold Spring Harbor Laboratory on Long Island they opened a sweepstakes for bets on the number of human genes. The winner will be chosen based on the most likely number decreed at the same annual meeting in 2003."
The Ensembl Project Gene Sweepstake ("Genesweep")
"Genesweep was organised by Ewan Birney, from the EBI, one of the technical leaders of the Ensembl project to provide an current and consistent annotation of the human genome free to everyone. The betting book stays at Cold Spring Harbor under the care of David Stewart. Anyone can make a bet as long as they physically sign the book."redux [05.13.00]
Wired News Amped Geneticists Bet on Genome
"Well, they weren't all men, but mostly. The betting in the pub continued, the lowest bet being 29,800 genes placed by Pat Tome and the highest number coming from John Quackenbush at 118,259.The pool was organized by Erwin Birney, a team leader at the European Bioinformatics Institute. He tried to convince the bartender to oversee the betting, but was told in no uncertain terms that no gambling was allowed in the Cold Spring bar.
Guesses on the number of genes in the human genome have lowered considerably since the mapping of chromosome 21, which researchers found to contain only 225 genes, far fewer than previously predicted. The researchers on the chromosome 21 study predicted their results could mean that there are as few as 40,000 genes in the entire human genome.
"Someone from Incyte will probably show up and bet 150,000," one gambler said."
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"The race to read the three billion DNA letters that encode the instructions for human life entered the final lap on Wednesday, with a UK Genome Campus researcher saying a "working draft" will be revealed on 15 June. "
"Dr Ewan Birney, one of the lead researchers at the publicly-funded European Bio-informatics Institute (EBI) in Cambridge, UK, told the BBC: "The public project decided last year to accelerate its rate of discovery to match the private project and on 15 June we will say that we're effectively 90% done - 90% of the interesting bits."
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"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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"The number of genes encoded in human DNA may be far fewer than thought.
Until now, the main estimates have ranged from 65,000 to 120,000. But two research teams, using independent methods, estimate there may be as few as 30,000 or 34,000 genes."
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"Genomix has licensed components of its genefinding and annotation technology to Celera Genomics, a company that it also plans eventually to compete with as a provider of value-added genomic data. Genomix was established two-and-a-half years ago as Genome Informatics to commercialize genomic analysis tools developed by the public Genome Annotation Consortium, whose members include Oak Ridge National Laboratory, and nine other laboratories, institutes, and universities."
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"Knowledge-based systems have become ubiquitous in recent years. The World-Wide Web consortium is developing the Resource Description Framework (RDF) - a system for annotating even Web pages with knowledge elements. Knowledge-base developers need to be able to share and reuse knowledge bases that they build. Therefore, interoperability among different knowledge-representation systems is essential. The Open Knowledge-Base Connectivity protocol (OKBC) is a common query and construction interface for frame-based systems that facilitates this interoperability. Protege-2000 is an OKBC-compatible knowledge-base–editing environment developed in our laboratory. Protege-2000 has an easy-to-use and configurable interface. We describe its OKBC-compatible knowledge model that makes the import and export of knowledge bases from and to other knowledge-base servers easy. We discuss how the requirements of being usable and configurable knowledge-acquisition tool affected our decisions in the knowledge-model design. Protege-2000 also has a flexible metaclass architecture which provides configurable templates for new classes in the knowledge base. The use of metaclasses makes Protege-2000 easily extensible and enables its use with other knowledge models. For example, we demonstrate that we can resolve many of the differences between the knowledge models of Protege-2000 and RDF by defining a new metaclass set. Resolving the differences between the knowledge models in declarative way enables easy adaptation of Protege-2000 as an editor for other knowledge-representation systems."
The Protege Project
"Protégé allows domain experts to build knowledge-based systems by creating and modifying reusable ontologies and problem-solving methods."Protégé-2000 source code is available under the open-source license."
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"We are pleased to inform you that Release 2.15 of GeneCards has been published at our site.
What's New: -----------
* 10,286 genes, 10,047 of them have gene symbols approved by the HUGO gene nomenclature committee.
* Information on protein families from BLOCKS.
* Information on assemblies of sequences from MIPS.
* Additional links to OMIM.
* Improved display of sequences: definition of Unigene clusters, Unigene reresentative sequence, REFSEQ mRNAs, REFSEQ constructed genomic contigs, MIPS assemblies and Additional Gene/cDNA sequences.
* Improved display of GeneCard Disorder Information. "
"The mission of GeneCards is to integrate data related to human genes and make it available to the scientific community world wide.
GeneCards is a database of human genes, their products and their involvement in diseases. It offers concise information about the functions of all human genes that have an approved symbol, as well as selected others. It is especially useful for those who are searching for scientists working in functional genomics and proteomics."
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"Both Collins and Venter acknowledge that the job of ''annotation'' -- adding to the map of the genes and their sequence all relevant information about gene function -- will take decades and is necessary for battling disease. In that sense, the Human Genome Project may never be finished. In other words, by the time the fat lady sings at this (soap) opera, the audience will probably be asleep.
'In five or 10 years, all of this focus on a competition won't seem very interesting to the public,'' Collins says. ''What matters is whether we did this right and ended up with a quality product.''
New Scientist The genome has landed
"Next month, after a decade of work by thousands of researchers across the globe, we will have a rough draft of the human genome: the blueprint for a human being.""A century from now, few will remember who won the race. But in the meantime, there are still plenty of questions to answer. Who controls this genetic information? Will researchers scanning our chromosomes for genes linked to inherited diseases be prevented by rival commercial interests from developing new tests and therapies? Will knowledge of what is encoded in the DNA of our own cells allow us to alter our behaviour and avoid disease, or simply inform us about our inevitable, and possibly early, demise? Will omens in our genes be used against us, by insurers, employers or governments?
In the Human Genome Special, New Scientist explores the new world that the human genome will bring."
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"The two companies will collaborate on the development and creation of genomics education programs linked to Incyte's on-line database products.
During the first phase of the collaboration, GeneEd will create a customized training course on the use of Incyte's LifeSeq(R) Gold database, the world's largest collection of human gene information. The initial course will teach Incyte customers about bioinformatics and the best way to utilize Incyte's flagship product.
"Teaming GeneEd with Incyte puts us at the forefront of educating people about the role of genomics in understanding the molecular basis of disease," said GeneEd CEO Sunil Maulik. "GeneEd is looking forward to working with Incyte to explain genomics in a clear, comprehensive manner.""
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"When the history of the just-dawning genetic revolution is finally written, a clunky-looking machine the size of a sidewalk trash can will play a starring role. The automated DNA sequencer is letting researchers quickly crack the biochemical code of life, an achievement that could one day turn incurable diseases into treatable ones. But the machine is at the vortex of a struggle over wealth, fame and, quite possibly, control of the genetic code itself.
The sequencer's developers say they invented the device without a penny from the federal government, the usual source of funds for such endeavors. Their act of entrepreneurial wizardry, they say, entitles them to sweeping rights over their invention. But The Times has turned up a paper trail that suggests a quite different story: one in which the developers collected millions in federal funds and failed to provide the government with certain key rights, such as discounts on purchases of the sequencers. Federal officials are now investigating.
The difference between these two versions of events could have a big financial effect on the inventors of the sequencer, the machine's manufacturer and the California Institute of Technology, where the device was developed. It could also affect the fortunes of investors who are wagering billions of dollars on claims made by the manufacturer, PE Corp., which has gained widespread recognition in both financial and scientific circles for its pioneering work.
Most important, the dispute could influence who gains control of the human genetic blueprint and all the medical miracles that it is expected to generate: the public or a few drug and biotech companies. "
redux [02.20.00]
Wired News Science + Business: A Bad Mix?
"Despite the conflict-of-issue problems, there are those who insist the status quo is the only practical way to go. If scientists were prevented from straddling the fence between research and profit, they reason, there would be few of them left to do the work. "Leroy Hood, faces scrutiny on a different sort of conflict-of-interest issue. Hood, one-time director of the genetics lab at Caltech, is being investigated by the Department of Health and Human Services for allegedly scamming the government back in the 1980s.
According to Wednesday's editions of the Los Angeles Times, Hood may have overcharged the government for machines developed by his lab that are critical to genetic research today.
Hood, who later headed up the molecular research department at the University of Washington, played a role in founding seven biotechnology companies while at UW and Caltech, including Amgen, Applied Biosystems, Systemix, Darwin, and Rosetta. "
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[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. "
HMS Beagle Caught in secret tests
[requires 'free' registration]
"Lawrence Berkeley National Laboratory in California has settled a class-action suit over genetic and medical testing for more than $2 million. The suit was brought by employees who charged that they were discriminated against and that their privacy was invaded when they were tested for pregnancy, syphilis, and genetic traits without their knowledge. Each of the plaintiffs will get $25,000, and other employees may get $2,000 each. The settlement also covers legal fees estimated at $440,000.Reference: Lehrman, S. 2000. Medical tests cost Lawrence Berkeley $2.2 million. Nature 405(6783):110."
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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"This week's web feature highlights a commentary article in which Maurer et al review the main databases of science and discuss the maintenance and funding of these increasingly important resources.
Databases underpin most endeavours of scientific research, but they tend not to be given high priority by funders. Some have been kept going by committed individuals or small groups, but in too many cases vital information has been lost completely. Not so long ago databases were relatively small, but now large, electronically searchable, complex databases have become essential to progress in many fields. Maurer et al suggest ways by which the scientific community should act so that essential information can be captured and used for future research and development.
The web feature is enhanced with related content from Nature's own online database of past content. This includes a briefing by Tony Reichhardt which looks at how databases are helping scientists deal with the flood of data that many current research projects are producing."
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"nature.com today publishes the DNA sequence of human chromosome 21 as a special and freely available web pre-publication. The article will appear in print in the May 18 issue of Nature and this print version should be referred to in citations.
A striking feature of the chromosome is that it contains less than 300 discernible genes, each likely to encode a protein with a specific role in our biochemical production line. Extrapolation of this observation implies that the whole human genome may contain no more than 40,000 genes, many fewer than previously thought."
Wired News Amped Geneticists Bet on Genome
"Well, they weren't all men, but mostly. The betting in the pub continued, the lowest bet being 29,800 genes placed by Pat Tome and the highest number coming from John Quackenbush at 118,259.The pool was organized by Erwin Birney, a team leader at the European Bioinformatics Institute. He tried to convince the bartender to oversee the betting, but was told in no uncertain terms that no gambling was allowed in the Cold Spring bar.
Guesses on the number of genes in the human genome have lowered considerably since the mapping of chromosome 21, which researchers found to contain only 225 genes, far fewer than previously predicted. The researchers on the chromosome 21 study predicted their results could mean that there are as few as 40,000 genes in the entire human genome.
"Someone from Incyte will probably show up and bet 150,000," one gambler said."
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"Significant change and progress is apparent between the first and second issues of the BITS project.
The first issue has established BITS as the main web portal for bioinformatics business and technology issues; the project has taken a regular 20 000+ visitors every month over the past year. This second issue of BITS now includes a vastly expanded range of subjects covering all informatics related technologies, systems and tools within the life sciences (bio) market.
We will now also cover an array of highly relevant and inter-related disciplines in the life sciences, all of which are technology lead. New subject areas range from computational and conformational analysis to modelling, QSAR and semiempirical chemistry software systems (quantum chemistry). We are opening areas for computer server technology, programming, visualisation and following up with new methodologies which will re-shape science; not just robotics and HTS, but miniaturisation and EDA (Electronic Design Automation) and other important progress areas in the last year i.e. fluorescence techniques, “lab-on-a-chip” systems.....and more!"
We have also cross-linked informatics in a general sense. Subjects ranging from artificial intelligence (AI), new algorithms through to pattern recognition and electronic data capture are all covered and given their rightful place in the research and development framework. Other interactive links include LIMS (Laboratory Information Management Systems), Data Automation, contracted research and clinical trials (where the first fruits of BITS relevant projects and techniques are beginning to appear and are showing high success rates)."
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"The Human Genome Project (HGP) international consortium announced on Tuesday the official launch of the final phase of the human genome sequencing project, today's China Daily reported. "
"The first phase of HGP began in the United States in 1990 and will finish by mid-June and produce a working draft -- 90 per cent of human genome with an accuracy of 99.9 per cent.
HGP international consortium announced early this week that international collaboration is now being directed to the second phase to sequence the remaining DNA, fill the gaps in the sequence and increase the overall sequence accuracy to 99.99 per cent."
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"A publicly funded scientific consortium -- intended to ultimately provide drug makers with tools to create custom medications -- has not lived up to promises to publicly disclose all of its research. Patent issues are at the heart of the dilemma.
Laurence Stein, a member of the SNP Consortium comprised of 10 major pharmaceutical companies and five academic institutions, Wednesday said only fully "mapped" SNPs are released into the public database. About 30 percent of SNP discoveries remain private."
redux [05.02.00]
Individual.com The SNP Consortium Exceeds First-Year Goals To Identify and Map Set of Gene Markers
"The SNP Consortium Ltd., a collaborative effort to create a genome-wide map of genetic markers called single nucleotide polymorphisms (SNPs), today released into the public domain approximately 60,000 newly identified SNPs. The total number of SNPs the consortium has contributed is now 102,719 -- more than twice what had been projected for the first year of the two-year program. These data are available for the free and unrestricted use of biomedical researchers worldwide."redux [02.18.00]
Science SNP Mappers Confront Reality and Find It Daunting
[summary - can be viewed for free once registered]
"The genetic markers called SNPs have been widely touted as the key to personalized medicine, with drugs tailored to an individual's genotype and simple tests to determine one's risk of specific diseases. But a closed meeting held last week, sponsored by the SNP Consortium and the U.S. National Human Genome Research Institute, concluded that those promises may be harder to achieve than expected, and that more SNPs may be required to track down a particular disease gene than previously estimated.”
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"Well, we see today that DoubleTwist is claiming to be a competitor to Celera Genomics. In one aspect they are a competitor to Celera in the same way that an aftermarket sunroof installer is competition for General Motors."
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"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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"Bioinformatics is the systematic development and application of computing systems and solutions to enhance biological research but mostly to analyze gene and genomic data through experimentation, modeling, database searches, and instrumentation. Gene identification has become a priority as the human genome is decoded. Users are presently restricted by having to analyze multiple sequence databases, compare results from different algorithms, and compute and analyze alignments or linkage results at database level. The present study evaluates current genetic terms, Extended Markup language (XML), Document Type Declaration (DTD) genomic files, and genetic databases for the purpose of developing a wider electronic access platform. XML files were generated with Python and parsed against their DTD's. Many of the current genomic DTDs consisted of general access, formatting, reference and genetic elements in one XML file. Genetic databases had different terms for the same item. The authors propose the use of informative terms and the separation of elements. A unified platform to access the domain is proposed. "
bioperl XML Project
"The purpose of this web site is to coordinate information dissemination and discussion on the use of XML in bioinformatics, and to serve as a repository for metadata describing the relationships between biological XML data resources.""Biology is a complex discipline and a wide variety of data resources and repositories have been developed to support biological research. Many of these are interrelated, but it is currently difficult to identify or use these in relationships computationally because the different data sources use incompatible formats and semantics. XML offers a way to serve and describe data in a uniform and automatically parseable format."
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."
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"With increasing numbers of academics jumping ship to reap the rewards of IPO-filing biotech companies, universities could be left in the dust instead of heading the charge in genetic research.
That's why Vanderbilt University has recently become the first academic institution to purchase a genomics database subscription. The move is intended to give the university a leg up in bioinformatics, a discipline the private sector has already mastered.
Vanderbilt doesn't have a bioinformatics department per se, which is one reason the university decided to purchase the database, Magnuson said.
Critics say the database subscription is a quick fix -- essentially a Band-Aid for a larger problem.
"In my view the answer is not to go out and buy a genomics database. The answer is to recruit and retain people in the schools of bioinformatics," said Richard Gibbs, director of the human genome sequencing center at Baylor College of Medicine in Houston.
"I personally think the critical issue is building a bioinformatics infrastructure. It's the lifeblood of biology now and will be for the next unknown number of years," Gibbs added."
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"Incyte Genomics, Inc. (Nasdaq: INCY - news), the leading genomic information company, announced today a contract with the National Institutes of Health (NIH) to sequence DNA for the Mammalian Gene Collection. The agreement is part of an effort by the NIH to create a public domain set of full-length expressed human and mouse genes, a resource that will be vital in unraveling how genes influence health and disease. All of the gene sequence data and clones from this project will be publicly available to the entire scientific research community.
The Mammalian Gene Collection (MGC) project is an ambitious new effort by the NIH. Coordinated by the National Cancer Institute and the National Human Genome Research Institute, the MGC will generate a comprehensive catalogue and clone library of full-length expressed human and mouse genes. Currently, for example, only about 6,000 full-length gene sequences from the more than 100,000 human genes are in the public domain. Incyte will play a critical role in the project by providing customized sequencing services."
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"Researchers in Japan and Germany announced today a breakthrough in the human genome project -- Chromosome 21, the smallest chromosome in the human genome, has become only the second human chromosome to be fully sequenced.
The genetic information on Chromosome 21 has been linked to Down Syndrome, one form of Alzheimer's, and several types of cancer including Lou Gehrig's disease."
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"A "dark horse" private company in the US is claiming to have won the race to produce a complete gene map of humans.
The private company Doubletwist is a relative newcomer in the genome race and claim to have obtained the first "working draft" of the entire human genome.
They say they did this by analysing publicly-available data using Sun workstation computers. The human genetic blueprint."
Wired Dot-Comming the Genome Race
""DoubleTwist and Sun have dot-commed the human genome," said Steve McKay, vice president of architecture and technology at Sun.DoubleTwist, however, does not plan to patent any genes. Its intentions are strictly to provide tools to help the research community make discoveries sooner by using its Internet tools, according to company CEO John Couch. "
"In order to do this, DoubleTwist has skipped the sequencing phase of the Genome. HGP is already doing the sequencing and providing that information for free to researchers. Instead, DoubleTwist will provide the sequencing annotation -- the phase that begins to identify what human functions and diseases particular genes are associated with."
"DoubleTwist's initial analysis located about 6,500 genes, and reaffirmed the theory that there are about 100,000 genes in the human genome. But the company's director of research Nick Tsinoremas emphasized that locating genes is not DoubleTwist's main goal.
"We're not here today to make a scientific statement of how many genes there are; We're here to say we have achieved a major milestone," Tsinoremas said."
SF Gate New Player In Race to Track Genome DoubleTwist.com says it has partial draft
"We've been doing a very quantitative analysis, and the public database is missing about 25 percent of the genome that's in our sequences,'' [Celera's CEO] Venter said. ``Any list of genes produced from it would be incomplete at best.''Indeed, DoubleTwist's chief computer scientist, Nick Tsinoremas was reluctant to issue any gene count, knowing that subsequent computer analyses will change the number, purpose and location of many genes."
"Tsinoremas said 65,000 of the genes in DoubleTwist's rough draft passed through three sets of software programs designed to identify genes. He assigned these genes a 90 percent probability of accuracy. The other 40,000 genes only passed one or two sets of tests, giving them accuracy rates of 50 percent or 75 percent, respectively."
LA Times An Unfolding Gene Map at 'Finish Line'
"The mapping of the human genome is one of the most significant and widely trumpeted achievements in modern science. The research it enables promises new treatments for disease, new drugs to promote healthy growth and delay aging, and new ways to detect disorders early while there is still time to do something about them.""Yet many of the participants on the public side say that it isn't the time to shoot off fireworks in celebration. This is a meaningful milestone that has come much faster than expected, they say, but the work is far from done. "
"Everyone agrees that deciphering the human genome, even in a working-draft stage, has opened up new worlds to explore, even if the health gains that are promised will not come immediately. It will take years of research to understand how human genes interact, and it can take eight to 10 years to bring any new medications to market."
The British Medical Journal Waiting for the working draft from the human genome project
"However, while the draft will be valuable for identifying gene and polymorphism, the relaxed error rate means that much work will be needed before the most basic sequence information can be put to practical use. For example, novel cytochrome P450 enzymes involved in drug metabolism are likely to emerge in the working draft, giving new targets for pharmacogenetics research. However, the new genes will need to be verified first, so that accurate assays can be developed to assess the genotype composition of patients with specific disorders or undergoing trials of different treatments. The working draft provides a framework but remains just a map, one that is still too crude for clinical use. As with any map, its utility lies in specific applications to specific circumstances. For the human genome project, this specificity requires application at the level of the patient or research participant, rather than the abstract level of consensus. While not wanting to begrudge a historic scientific achievement, it is best to acknowledge that we will have to wait for more than the working draft to see a real impact on medicine."
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"Celera Genomics (NYSE:CRA), a PE Corporation business, announced today it signed an agreement with Vanderbilt University that provides a five-year, comprehensive subscription to certain Celera database products. Vanderbilt will become the first subscriber to access Celera's database information through its Celera Discovery System(TM) on the World Wide Web."
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"A team of researchers led by Bob Franza of the University of Washington here is developing bioinformatics tools to create a quantitative model of the living cell.
The Cell Systems Initiative was launched late last year, and thus far has attracted the support of two corporate backers who would like to mine the data it generates to identify new drug targets."
"The goal, according to Franza, is to understand the stages of a cell's development. "How does one stage know when it's supposed to start and stop?" Franza asked. "How do we reconstruct the temporal process?" A complete model of the living cell will need to be understood not as parts, but as components of a continuous system, he said. To that end, the initiative also aims to build a computational infrastructure that can manage the entire dynamic system of data collection and integration."
Cellworks Project Information management and data analysis systems for the research biologist
"The Cellworks Project [referred to as CWP throughout this section] is a multifaceted design, research and development effort located in the Department of Molecular Biotechnology at the University of Washington. CWP is a combined basic biology research program and information systems research and development program focused on bringing the power and technologies available in today's computer industry to the biology research laboratory environment. The primary goal of the information systems research component of CWP is to develop an optimal networked environment for collaborating, distributed groups of biologists."
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"The National Center for