{bio,medical} informatics
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eWeek
Virtual Databases Make Sense of Varied Data
"Separately, IBM last week announced it is working with a Canadian bioresearch center to create an information system that uses a virtual database to integrate data from a variety of databases, flat-file formats and file types. The iQ Engine, being developed with iCapture Center, of Vancouver, British Columbia, uses IBM's DB2 database and DiscoveryLink integration technology.
The goal is to create a system that will assist researchers in correlating genetic susceptibility of patients with cardiovascular and respiratory diseases to environment influences such as culture, socioeconomic status, educational background, inhaled cigarette smoke, pollutants, viruses, allergens, diet and obesity."
redux [03.17.02]
[requires 'free' registration]
"The great challenge in biological research today is how to turn data into knowledge. I have met people who think data is knowledge but these people are then striving for a means of turning knowledge into understanding. Knowledge and science are related words and to know, I believe, is to understand. Before rushing to convert genomics to 'genamics' and finding that it is another dead end, we should consider evacuating the Tower of Babel. We need a theoretical framework in which to embed biological data so that the endless stream of data, filled with the flotsam and jetsam of evolution, can be sifted and abstracted.
Very simply, the network we should be interested is not the network of names but the network of the objects themselves. The language of these objects is not the Oxford Dictionary of Molecular Biology--the Ontology Consortium's main source--but that of molecular recognition, the language of molecular biology itself."
redux [01.08.02]
"Research directed toward discovering how genetic factors influence a patient's response to drugs requires coordination of data produced from laboratory experiments, computational methods, and clinical studies. A public respository of pharmacogenetic data to which investigators from different centers can contribute will facilitate hypothesis generation for further research. We are developing a pharmacogenetics knowledge base (PharmGKB) that will support storage and retrieval of experimental data and conceptual knowledge. We are confronted with the challenge of designing an Internet-based resource that integrates complex biological, pharmacological, and clinical data in such a way that researchers can submit their data and users can retrieve information that supports genotype phenotype correlations. Successful management of the names, meaning, and organization of concepts used within the system is crucial. We have selected a frame-based knowledge-representation system for development of an ontology of concepts and relationships that represent the domain and that will permit storage of experimental data. Preliminary experience shows that the ontology we have developed for gene-sequence data submissions is appropriate for experimental data that researchers will enter."
"Ontologies are specifications of the concepts in a given field and the relationships among those concepts. The development of ontologies for molecular-biology information and the sharing of those ontologies within the bioinformatics community are central problems in bioinformatics. If the bioinformatics community is to share ontologies effectively, ontologies must be exchanged in a form that uses standardized syntax and semantics. This paper reports on an effort among the authors to evaluate a number of alternative ontology-exchange languages, and to recommend one or more languages for use within the larger bioinformatics community. The study selected a set of candidate languages, and defined a set of capabilities that the ideal ontology-exchange language should satisfy. The study scored the languages according to the degree to which they provided each capability. In addition, the authors performed several ontology-exchange experiments with the two languages that received the highest scores: OML and Ontolingua. The result of those experiments, and the main conclusions of this study, was that the frame-based semantic model of Ontolingua is preferable to the conceptual graph model of OML, but that the XML-based syntax of OML is preferable to the Lisp-based syntax of Ontolingua."
redux [05.10.00]
"There is an increasing demand for formalized knowledge on the Web. Several communities (e.g. in bioinformatics and educational media) are getting ready to offer semiformal or formal Web content. XML-based markup languages provide a 'universal' storage and interchange format for such Web-distributed knowledge representation. This tutorial introduces techniques for knowledge markup: we show how to map AI representations (e.g., logics and frames) to XML (incl. RDF and RDF Schema), discuss how to specify XML DTDs and RDF (Schema) descriptions for various representations, survey existing XML extensions for knowledge bases/ontologies, deal with the acquisition and processing of such representations, and detail selected applications. After the tutorial, participants will have absorbed the theoretical foundation and practical use of knowledge markup and will be able to assess XML applications and extensions for AI. Besides bringing to bear existing AI techniques for a Web-based knowledge markup scenario, the tutorial will identify new AI research directions for further developing this scenario."
redux [03.22.01]
"To realize the full potential of biological databases requires more than the interactive, hypertext flavor of database interoperation that is now so popular in the bioinformatics community. Interoperation based on declarative queries to multiple network-accessible databases will support analyses and investigations that are orders of magnitude faster and more powerful than what can be accomplished through interactive navigation. I present a vision of the capabilities that a query-based interoperation infrastructure should provide, and identify assumptions behind, and requirements of, this vision. I then propose an architecture for query-based interoperation that identifies a number of novel components of an information infrastructure for molecular biology. Those components include: A knowledge base that describes relationships among the conceptualizations used in different biological databases; a module that can determine what known DBs are relevant to a particular query; a module that can translate a query, or the results of a query, from one conceptualization to another; a family of DB drivers that provide uniform physical access to different DBMSs; a family of translators that can interconvert among different database schema languages; and a database that describes the network location and access methods for biological databases. A number of the components are translators because biological databases exhibit heterogeneity at several different levels, including the conceptual level, the data model, the query language, and data formats."
redux [02.28.01]
"The integration of heterogeneous data sources and software systems is a major issue in the biomedical community and several approaches have been explored: linking databases, "on-the-fly" integration through views, and integration through warehousing. In this paper we report on our experiences with two systems that were developed at the University of Pennsylvania: an integration system called K2, which has primarily been used to provide views over multiple external data sources and software systems; and a data warehouse called GUS which downloads, cleans, integrates and annotates data from multiple external data sources. Although the view and warehouse approaches each have their advantages, there is no clear "winner". Therefore, users must consider how the data is to be used, what the performance guarantees must be, and how much programmer time and expertise is available to choose the best strategy for a particular application. Our experiences also point to some practical tips on how updates should be published by the community, and how XML can be used to facilitate the processing of updates in a warehousing environment."
redux [01.17.01]
"Personal bibliography on query mediation, database integration, database interoperability and related topics, concentrating on projects in genomic research."
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Bio-IT World
Xserve and iPod simplify cluster setup
"iNquiry combines the technology The BioTeam developed for Texas A&M into a system that other bioscientists can use to create their own Xserve clusters in a matter of minutes instead of weeks, according to Van Etten. The secret is another Apple product -- the iPod.
Wholly self-contained in about 2GB of storage space on the iPod, iNquiry uses a Perl-based script that's controlled through a simple graphical configuration utility. The user tells the configuration utility how to configure the Xserve cluster, how many nodes it has, how the network is configured, and how to use the individual drive bays in each Xserve."
redux [01.16.03]
"LIFE SCIENCE TECHNOLOGY is about as cutting-edge as it gets, but now it's apparently also hip. At least that's the image projected by University of New Hampshire researcher Will Gilbert, who has taken to carrying around the human genome on his Apple Computer iPod."
"Gilbert recalls the story of Nobel Prize winner Walter Gilbert -- no relation -- who, during a speech at Harvard in the late '80s, held up a CD-ROM and said, "One day you will be carrying the genome around on this." Actually, the iPod-touting Gilbert notes, it turned out to be an MP3 player."
redux [11.06.02]
"While it sounds neat to put the human genome on a hip-looking device people more commonly use to crank out Mos Def tunes, some researchers say using it to store the blueprint for humankind is not entirely practical."
""If you're walking back and forth (to transfer data) that's not good," said Richard Gibbs, director of the human genome sequencing center at Baylor College of Medicine. "It's often tempting to do that because of bandwidth, but the smart thing to do is make sure you have the proper infrastructure to (transfer data).""
redux [10.29.02]
"Dr. Will Gilbert likes to carry the human genome around on his iPod. It's the easiest way, he says, to transfer the genome -- 3 billion chemical "letters" that make up a person's genetic code, or DNA -- to the computers of other researchers at the Hubbard Center for Genome Studies at the University of New Hampshire.
Gilbert had set up a research project involving the human genome on his Power Mac, using the Apple/Genentech version of BLAST. A breakthrough implementation of the popular bioinformatics tool from the National Center for Biotechnology Information (NCBI), A/G BLAST conducts high-speed DNA searches in biomedical research and drug discovery. "But," says Gilbert, "I wanted to run the project down the hall on another Mac. Rather than copy it across the network, I'd pull out my iPod. Plug it in, drag, drop, zip, boom, bang and walk it down the hall.""
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Bio-IT World
Extracting Jewels, Even from the Junk
"Besides the obvious big issue -- the small number of genes in the human genome - one of the most interesting recent developments regards "junk" DNA. Initially, there was a lot of concern about sequencing so much "junk" DNA (the regions that don't code for genes). But it turns out that junk DNA has a lot of important stuff in it, and now we are seeing a great deal of emphasis on how functional RNA, which is not protein-coding, works as a mechanism for controlling gene expression. It's going to be very important to be able to study this on a genome level - comparing across species and finding conserved sites."
redux [11.21.02]
"In a provisional patent application filed July 31, Pellionisz claims to have unlocked a key to the hidden role junk DNA plays in growth -- and in life itself.
Rather than being useless evolutionary debris, he says, the mysteriously repetitive but not identical strands of genetic material are in reality building instructions organized in a special type of pattern known as a fractal. It's this pattern of fractal instructions, he says, that tells genes what they must do in order to form living tissue, everything from the wings of a fly to the entire body of a full-grown human."
redux [08.28.02]
"In a new study in the August 29 issue of Nature, researchers at The Wistar Institute identify a cohesin-containing protein complex that reshapes chromatin to allow cohesins to bind to DNA. In doing so, they also identified the locations on the human genome where the cohesins bind. Somewhat to their surprise, the binding sites were found to be a repetitive DNA sequence found throughout the human genome for which no previous role had ever been identified. These bits of DNA, known as Alu sequences, are liberally represented along those vast stretches of the human genome not known to directly control genetic activity, sometimes referred to as junk DNA."
redux [08.09.02]
"Results of a new University of Michigan study suggest that junk DNA - dismissed by many scientists as mere strings of meaningless genetic code - could have a darker side.
In a paper published in the Aug. 9 issue of Cell, scientists from the U-M Medical School report that, in cultured human cancer cells, segments of junk DNA called LINE-1 elements can delete DNA when they jump to a new location - possibly knocking out genes or creating devastating mutations in the process."
"Scientists in the past decade have discovered that remnants of ancient germ line infections called human endogenous retroviruses make up a substantial part of the human genome. Once thought to be merely "junk" DNA and inactive, many of these elements, in fact, perform functions in human cells.
Now, a new study by John McDonald of the University of Georgia and King Jordan at the National Center for Biotechnology Information at the National Institutes of Health, suggests for the first time that a burst of transpositional activity occurred at the same time humans and chimps are believed to have diverged from a common ancestor - 6 million years ago."
redux [01.20.01]
[requires 'free' registration]
"Speaking at a National Institutes of Health conference on ethical and social issues in genetics, Dr. Francis Collins said that a "spate of papers in public journals'' due out within a month will signify the incredibly rapid pace of scientific discovery seen since the announcement of the nearly complete sequencing of the human genome last summer.
The first, Collins said, will be a paper that puts the total count of human genes at between 30,000 and 35,000. "That's less than half the number most people have been predicting.'' The second is a study ascribing previously unknown biological missions to genes scientists thought were inactive, or so-called "junk genes."
"There is now clear evidence that (the junk genes) have been performing a number of functions for tens or hundreds of thousands of years,'' he said."
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Genomeweb
Mayo Clinic, U. Minnesota Plan to Build New Statewide Genomics
Centers
""We are exploring concepts to established some sort of Minnesota initiative in the area of biotechnology and genomics," said Chris Gade, a spokesman for the Mayo Clinic in Rochester. "We still have to work out ... the specifics of that proposal.
Before they can determine when the centers can be created--or even what the research logistics between them might be--the partners must first secure some capital. So far, they have approached the Minnesota governor for financial help, Gade told GenomeWeb. He added the Mayo Clinic also has been "exploring a variety of funding options to make it happen," and stressed that philanthropy is "for sure" one of the options."
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itNews Australia
Computers cluster for genes research
"Computer cluster technology will be used to speed up gene analysis at CSIRO's newly launched bioinformatics facility in Canberra.
Australia's Commonwealth Scientific and Industrial Research Organisation (CSIRO) claims it has created the country's largest dedicated bioinformatics computer cluster in its Bioinformatics Facility (CBF) which opened its doors last week."
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MIT Technology Review
Life Made to Order
"But now a small group of researchers are looking to a far more ambitious goal than simply reading the sequence of genetic material: they are attempting to write entirely new genomes from scratch. In essence, they hope to create new synthetic forms of life, the likes of which have never before existed, by painstakingly spelling out exact sequences of DNA that hold all the instructions for the new organisms.
It is biotech's most brazen attempt, so far, to play God. So the fact that Craig Venter, the legendary self-aggrandizing visionary of genomics, is leading the charge should come as no surprise."
redux [11.26.02]
[requires 'free' registration]
"Craig Venter's "minimal genome" project announced Wednesday is not about creating a new life form and probably doesn't pose much of a biowarfare threat, researchers say. The high-profile project was just funded by the US Department of Energy (DOE) with $3 million going to the Institute for Biological Energy Alternatives (IBEA), one of the non-profit research institutes Venter founded after leaving the newly profit-minded Celera Genomics early this year.
According to some scientists, the new project won't even define the minimal genomethe basic gene set required for lifebecause there can be no single minimal genome."
"Several years ago, Venter first looked at this mycoplasma as the best such model, because the organism is a record-holder of sorts: the self-replicating life form with the smallest known complement of genetic material. Unlike the human genome with its 30,000 to 50,000 genes, M. genitalium gets by with only 517. But remarkably, nearly half of even that minimal set is extra baggage. Under some laboratory conditions, as few as 300 of the genes can fulfill its definition as a lifeform that feeds and divides.
As it turns out, what is the definition of life itself? and also exactly what is its minimal genetic set? have been hotly contested. Gene size is one of the main limits to what could be the final and minimal cell size, and thus may set a limit on possible targets for creating life from scratch.
But what structures are too small or too simple to be considered "life"?"
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Bio-IT World
Startups explore ways to 'live another day'
"The buzzwords are gone, replaced by talk of how "gloomy," "bleak," and "grim" the prospects are for biotech startups. At the Sachs-Bloomberg Global Biotech Investor Forum in Boston this week, both big pharmas and venture capitalists (VCs) warned early-stage companies that the price would have to be right before they would put any money in a company."
"Genomics and proteomics tool companies weren't even on the menu at this Forum. Anvil was the lone bioinformatics company presenting."
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KDNuggets
New
clustering method for gene expressions using KL similarity
measure
"A new approach to identifying patterns in gene expression analysis has been shown to be more effective than the most popular method in a joint Penn State and University at Buffalo study. Using two published gene expression data sets as test cases, the research team found that the KL clustering method, which uses a novel measure of similarity (Kullback-Leibler) not previously used for gene expression analysis, was superior to the most popular method, hierarchical clustering, in separating the data into dense clusters with similar patterns."
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BioMedNet
Biotechnology: which way now?
[requires 'free' registration]
"Which approach is more likely to make a biotechnology company successful: a focus on novel technologies or on development of novel compounds?
Getting into clinical compounds has been portrayed as the route out of tough times like those the biotech industry is suffering through now, according to Mark G. Edwards, founder of Recombinant Capital, a California consulting firm and purveyor of biotech financial databases. But the data show, he says, that there doesn't seem to be any sure route out; companies specializing in compounds have fallen just like those specializing in technology."
redux [04.19.02]
[requires 'free' registration]
"This should be the golden age for pharmaceutical scientists. The deciphering of the human genome is laying bare the blueprint of human life. Medical research has increased understanding of disease. Robots and computers are turning drug discovery from a mixing of chemicals in a test tube to an industrialized, automated process."
"Instead of narrowing the list of compounds that might be useful in drugs, automation has broadened it -- greatly increasing the number of formulas tested without yet delivering commensurate growth in safe and effective drugs."
redux [12.14.01]
"And although the drug industry remains the most profitable worldwide--it generated profits as a percentage of revenues four times the median rate for all Fortune 500 firms during the end of the last decade, according to a Kaiser Family Foundation report released that day--an editorial in this month's Nature Biotechnology by David Horrobin, CEO of Laxdale Research, in Stirling, Scotland, had this to say: "With rare exceptions, most of the top 20 multinational pharmaceutical companies are not generating in-house the new products needed to sustain the rates of growth they have enjoyed in the past.
"No serious industry onlooker could dispute this depressing picture," the commentary continues. "Although a few pharmaceutical companies may survive in their present form, most cannot.... A few brave companies are recognizing the obvious: large companies excel at sales and marketing but are hopeless at innovative research.""
redux [05.26.00]
""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.""
redux [11.29.01]
[requires 'free' registration]
"Glenn Giovanetti at Ernst & Young Life Sciences Industry Services, comments "You could really compare [today's situation] to a large degree with the first biotech boom in the late eighties and early nineties where the thought was, 'Hey, this is going to lead to better drugs faster,' and clearly that hasn't been the case." Having the genome in hand has brought about more drug targets, but, explains Ma, "People are getting more concerned that novel targets are going to have a higher rate of failures because there is less information on them." And when working in 10-year drug-development cycles, failures are costly.
Ma points to a trend of growth in clinical informatics that would effectively garner more information from expensive clinical trials instead of simply treating them as regulatory hurdles. "People are beginning to think through to how ... to take greater advantage of that information," he adds. But increasingly, the suppliers of genomic information have been looking to do the same thing.
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The Hindu
Biotech industry fails to take quantum jump - Chamber
"Despite several strengths inherent, India's biotechnology industry is not able to take a quantum jump mainly due to lack of capital and low R&D spending, absence of industry-academic partnership and the mismatch between strategic research, product planning and effective collaboration.
The Associated Chambers of Commerce and Industry of India (Assocham) paper on Business of Biotechnology has pointed out that India has several options with the main focus on informatics. Bioinformatics is crucial for the advancement of the biotech industry by cutting the timeframe and costs in developing a product tremendously."
"Everyone in the room, from Sen. Hillary Rodham Clinton to Buffalo Mayor Anthony Masiello, was beaming at last week's announcement.
The news was that Asia's largest computer consultant has become a deep-pocket partner of the University at Buffalo. Under an agreement signed Monday, Tata Consultancy Services of India will partner with local researchers and help transform their discoveries into money-making products."
"But some in the tech community voiced concern that the state's $100 million-plus bioinformatics investment will wind up boosting the economy in Bombay instead of Buffalo."
redux [12.13.02]
[requires 'free' registration]
"India is set to reap substantial rewards in the field of functional genomics, thanks to an invaluable genetic resource and highly advanced IT expertise, predicts Samir Brahmachari, director of the country's Institute of Genomics and Integrative Biology in Delhi."
"Brahmachari sees India's genetic resource - not the biological samples themselves, but the associated information - as a tradable commodity. Data can be processed using India's unparalleled IT expertise, he says: The country's IT industry generated about $10 billion in revenues this year, and has continued to grow by 50% each year over the past decade. The information, once processed, represents an "intellectual-property protectable" commodity, he says."
redux [06.23.02]
"Also, India's success in information technology provides excellent opportunities in the field of bioinformatics.
"Traditional IT companies are translating their strong capabilities in data mining and warehousing to business models based on biological data," says the report, citing examples of IBM's India Research Lab and Satyam's five-year agreement with the Center for Cellular and Molecular Biology, Hyderabad."
redux [02.13.02]
"India's biotech boom could even dwarf software in coming years if you trust the most optimistic projections. Much of our $2.5-billion biotech market relies on low-end products like vaccines, but experts predict that as more start-ups come up, that could change dramatically."
"The need to dive into this ocean of genetic data for hidden treasures has created a whole new discipline--bio-informatics, the science of using information technology (IT) to decipher the genomic jumble. Thanks to a flourishing IT industry, bioinformatics is today the darling of venture capitalists, drug firms, and, of course, IT majors. So, Satyam Computers has signed a five-year alliance with CCMB to create, store, and annotate genetic databases, and it is angling for contracts from global bigpharma to sequence genes and build protein catalogs. Strand Genomics, a Bangalore-based bio-informatics start-up, is designing tools to accelerate drug discovery."
redux [09.17.01]
"India has the potential to garner 8-10 per cent of the global software market in the next few years from the current levels of just 1.5 per cent, but the country?s planners need to focus on improving computer penetration and use of Indian made software in the industry.
This was the view of FC Kohli, chairman, Tata Consultancy Services, while speaking at Connect 2001, an international conference and exhibition on information technology, communication technologies and bioinformatics, which opened on Thursday. Currently, India's IT exports are about $8.7 billion."
redux [08.27.01]
"THE mood is one of caution as far as bioinformatics is concerned. The beginning of the year saw hype building up around the fledgling industry as the next big gold rush for India.
But six months after the first bioinformatics seminar in the country, with the IT industry's lesson on hype fresh in mind, things are moving at a more sedate pace."
"In India, bioinformatics training institutes have already begun to mushroom. Bangalore and Hyderabad have around five private training institutes between them. However, the industry is sceptical about the quality of manpower these centres can supply because most of them have short-term courses offering basic skills, says Dr. Sabharwal. In all fairness to them she adds, "We need to wait for a few months to see the outcome of it all.""
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Informatics Review
The Open Source Movement
"I am a practicing ophthalmologist in Los Angeles, and a medical informatics student at UC Davis. I have followed the conversations about open source software with interest. Recently I have been reviewing the literature on the topic. One thing is not clear to me. I see lots of software available, but IS ANYBODY ACTUALLY DOING THIS? I can see that there are bits and pieces being used here and there. Has anybody set up a whole health care institution using open source software, and if so, is it working in real life? How does the quality/cost compare IN REAL LIFE to commercial software? Does hiring commercial groups to support the products, if you don't have the staffing in house, actually work?""
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Genomeweb
Human Genome Project vs. Celera: The Rematch
"The human genome debate teams recently lined up for another round of point-counterpoint, with the Human Genome Project's Robert Waterston, Eric Lander, and John Sulston on one side, and Celera genome sequencers Mark Adams, Granger Sutton, Hamilton Smith, Eugene Myers, and Craig Venter on the other.
In the latest salvo in the debate over the use of publicly-available data in Celera's sequencing of the human genome, both groups have once again argued the merits of their positions in articles published in the March 18, 2003 edition of Proceedings of the National Academy of Sciences."
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SignOnSanDiego.Com
Biotech firms seek to corral data overload
"The ability to run tests "in silico" has increased the rate of data flowing out of these companies from 10 mph to about 100 mph. And it's expected to move faster.
How to store this data, so companies are not continually reinventing the wheel, is a major topic on the minds of biotechnology executives as they gather today at the San Diego Convention Center for CalBiosummit, the annual gathering of San Diego County's biotech industry.
It's a daunting task."
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Salon
National Genes, Inc.
"The newest resources "discovered" in Estonia are the genes of its 1.4 million citizens. The country's government and a Silicon Valley start-up called EGeen International are treating the Estonian gene pool as a commodity to be exploited for medical research and profit.
EGeen owns the exclusive commercial rights to data from the Estonian Gene Bank Project. In March the bank will begin a full-scale effort to collect blood samples and medical histories that will help scientists understand Estonians from the inside out."
redux [02.17.01]
[requires 'free' registration]
"A good gene pool, like love, is where you find it. Now genomics researchers have two new ones to swoon over: one from Estonia, a crossroads of Scandinavian cultures and the northernmost of the former Soviet Union's Baltic republics; and from Tonga, an island kingdom half a world away where a Polynesian people has lived in near-perfect isolation for close to 3,500 years. Tonga and Estonia laid final plans last November and December, respectively, for national gene pool exploration programs aimed at discovering disease-associated genes and developing therapies based on the discoveries.
They follow the trail blazed by Iceland, where for several years the gene pool of 275,000 Icelanders has been the fishing preserve of Reykjavik-based deCODE Genetics which is hunting for gene variants that affect serious, often chronic diseases by finding statistical links between Icelanders' genotypes and their inherited illnesses."
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The Kingston Whig-Standard
High-tech darling suddenly closes its doors
""We have great technology - perhaps ahead of its time," Molecular Mining president and CEO Evan Steeg said yesterday.
Steeg refused to go into details about the company's demise, citing legal reasons. He said it was hard to make things work for the biotechnology and information technology hybrid in an economy where corporations in both sectors have tightened their belts."
"The market for bioinformatics firms like Molecular Mining is "brutal," Molloy said."
redux [02.24.03]
"To some extent, the life sciences market, which relies heavily on computational biology, has lived up to the promise. Research centers in both the private and public sectors placed orders last year for thousands of servers and storage systems capable of handling terabytes of the new genomic, proteomic, drug, and health care data generated hourly.
That's the good news. The bad news is that, during the past year, companies that develop software tools for managing and exploiting all of the new data struggled mightily. Red ink, consolidation, and layoffs were the norm. Welcome to the tumultuous world of ''bioinformatics,'' the underachieving wonder child of a genomics revolution-in-waiting."
redux [12.12.02]
"Bioinformatics: In life-sciences establishments around the world, the laboratory rat is giving way to the computer mouse--as computing joins forces with biology to create a bioinformatics market that is expected to be worth nearly $40 billion within three years."
"Welcome to the world of bioinformatics--a branch of computing concerned with the acquisition, storage and analysis of biological data. Once an obscure part of computer science, bioinformatics has become a linchpin of biotechnology's progress. In the struggle for speed and agility, bioinformatics offers unparalleled efficiency through mathematical modelling. In the quest for new drugs, it promises new ways to look at biology through data mining. And it is the only practical way of making sense of the ensuing deluge of data."
redux [11.30.02]
"Bioinformatics as a business, not to be confused with bioinformatics as a field of study, is at an interesting crossroads. As an academic branch of learning, bioinformatics remains mostly what it always was -- a cross-disciplinary endeavor between computer science and molecular biology. But bioinformatics as a money-making proposition has different criteria for success, and it has received a lot of bad press lately, some of it deserved."
"During this golden age, bioinformaticists developed software that computational biologists could use to make biological discoveries based on genomic data. But the industry swerved off course by selling expensive systems that focused on the individual pieces of a solution, without heeding downstream processes that were the actual bread-and-butter of our customers. Bioinformatics has always been about integrating data and converting it into information. When it loses that focus, it loses its value to the customer."
redux [11.05.02]
[requires 'free' registration]
"The biotechnology industry is facing one of its worst financial squeezes ever. The prices of many biotechnology stocks have plummeted, and Wall Street's vaults have snapped nearly shut, making it almost impossible for capital-hungry companies to finance themselves."
"Another sector that has suffered is bioinformatics, which uses computers to analyze masses of genetic data. Several young companies have gone out of business or been acquired for a pittance after sales did not meet expectations."
redux [07.09.02]
"Most agree that venture money is there for companies -- but the pressure must seem insurmountable for entrepreneurs, who probably feel like they have to give the perfect business pitch to venture capitalists just to get a foot in the door.
"If people aren't rethinking their models, they're nuts; if they were waiting for Viaken to be their wake-up call, they're nuts," Nelson says."
redux [04.18.02]
""Bioinformatics is heterogeneous, but many bioinformatics [tools] fulfill a narrow niche," said Williamson. "There is room for someone to consolidate, but I don't know if that is needed or necessary. Plus there's always an academic coming up with the next thing. So it's a hard business to sustain."
Bioinformatics "is great for smaller companies," he went on. And there are "people who can tie the islands of analysis together, and who have the resources to pull it off, but is that a business? That's the million dollar question. And will anyone buy it if you can pull it together? Everybody wants to be the Microsoft Office of bioinformatics, but I'm not sure that's going to happen.""
redux [03.11.02]
"The emerging field of bioinformatics, the use of computers to analyze the inner workings of biology, is transforming an industry that just a decade ago relied on the manual labor of chemists and biologists. But even as it does so, bioinformatics is floundering as a business.
Shares of public companies that sell biological data or software are trading at a fraction of what they did two years ago. Dozens of companies have crowded into the field. Some have folded; others have survived only by morphing into drug-discovery companies.
''It's a hard market to build a business around,'' said Oliver Fetzer, a vice president at Boston Consulting Group."
redux [02.11.02]
"LIKE EVERY BUBBLE, this one had to burst. Stock prices of many bioinformatics firms have fallen sharply in recent years. LION Biosciences of Germany went public at $40 a share and now trades at about $13. Iceland's DeCode is worth a fourth of its former high. Even Celera, the U.S. firm that helped decode the human genome, is off its peak.
Falling stock prices are a symptom of a greater disappointment in bioinformatics. A few years ago the laborious and quirky process of drug discovery seemed on the verge of giving way to new streamlined, data-driven methods. Some firms organized the blizzard of genetic data into databases that researchers could mine with search engines from still other firms. Software companies built computer programs that modeled what goes on in human cells and even whole organs. Many investors came to believe that bioinformatics would open a new avenue to the discovery of drugs. But this avenue simply hasn't materialized. Says biotech analyst Earling Refsum at Nomura Bank in London: "Bioinformatics has not helped Big Pharma get more drugs into the pipeline.""
redux [01.03.02]
"Inside the laboratories of the world's major pharmaceutical companies and biotechnology start-ups, an emerging science is quietly transforming the drug industry. Bioinformatics -- the use of computers to analyze the inner workings of biology -- is helping researchers pinpoint the roots of diseases and design sophisticated medicines to treat them.
But even as it becomes a vital part of drug research, bioinformatics as a business is losing favor with investors. Shares of publicly traded firms that sell biological data and software tools are slumping, and venture capitalists are increasingly wary of investing in such companies.
redux [12.18.01]
"There comes a point in the life cycle of every organism when it must change or perish. For bioinformatics, the time for metamorphosis is now. Though computational biology is already an intrinsic part of the drug discovery process, the business models adopted by most bioinformatics firms have failed to produce profits. Competition -- from the IT industry and big pharma itself -- is growing and investors, both public and private, are unimpressed. While some companies are hoping persistence pays off, many are pursuing new business models that should allow them to retain a bigger share of the profits they are helping to create."
redux [03.14.01]
"The story proclaimed in its lead, "Move over Information Age. Make room for the age of bioinformation." You could picture bleary eyes opening all over the Bay Area. The story went on to note that a San Jose consulting firm was predicting a 10 percent annual growth in the bioinformatics market for years to come; and that the National Science Foundation estimated that 20,000 new jobs in the field would be created in the field in just the next four years.
If that wasn't enough, the rest of the section was filled with page after page of biotech firms listing job openings - in powerful juxtaposition to the endless lists of dot-com layoffs just a few pages earlier. Picture Starbucks spit-takes from Marin to Santa Cruz.
Wow! Rewrite that resume to emphasize that biology course you took in college. Roll your Aeron chair down to the nearest lab. Trade that black turtleneck for a white lab coat..."
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Perl.Com
Genomic Perl
"This is a book I have been looking forward to for a long time. Back when James Tisdall had just finished his Beginning Perl for Bioinformatics, I asked him to write an article about how to get into bioinf from a Perl programmer's perspective. With bioinformatics being a recently booming sphere and many scientists finding themselves in need of computer programmers to help them process their data, I thought it would be good if there was more information for programmers about the genomic side of things.
Rex Dwyer has produced a book, Genomic Perl, which bridges the gap."
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The New York Times
University's Drug Patent Is Invalidated by a Judge
[requires 'free' registration]
"A federal judge yesterday invalidated a broad patent held by the University of Rochester on a popular class of painkillers and dismissed the school's lawsuit seeking royalties from Pharmacia and Pfizer on sales of their big-selling drug Celebrex.
The decision is a big blow to the university, which had envisioned billions of dollars in royalties that would have helped turn its medical school into a research powerhouse. When the patent was granted and the patent infringement lawsuit was filed in April 2000, school officials predicted the patent might become the most lucrative ever held by a university."
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BBC
Gene
clue to secrets of the fall
"Dozens of genes may help tell trees when it is time to shed their leaves for winter, say scientists from Sweden."
"They found more than 2,400 expressed in the leaves at various times of the year - but only 35 expressed in huge quantities in leaves as they changed colour ready to drop in Autumn."
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Wired News
You Can't Make a Monkey Out of Us
"Chimpanzees seem almost human, and scientists have maintained for decades that chimps are, in fact, 98.5 percent genetically identical to humans.
But the results of a new study call that figure into question, with a finding that there are actually large chunks of the human and chimp genomes that are vastly different."
"It involves sampling data from select regions of many different related species, and then comparing them within the context of their phylogenetic relationships. In the research described in the Science paper, Rubin and colleagues sampled 17 primate species closely related to human and spanning 40 million years of evolution -- insufficient time for significant genetic divergence to have taken place.
According to Rubin, phylogenetic shadowing compensates for the failure of traditional comparative genomics techniques, which "invariably miss recent changes in DNA sequence that account for primate-specific biological traits." The approach overcomes the primary challenge of comparing genomes of closely related species: the difficulty in distinguishing functional from nonfunctional sequences."
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Financial Times
The biotech dilemma: cash-rich, product-poor
"I'm an absolute idiot," says David Ebsworth, chief executive of Oxford Glycosciences. "I'm destroying value and it would be better if we closed the company and put our money in the bank. That's what the market's telling me. Of course, I don't think that's true."
For companies like Oxford Glycosciences (OGS), trading for less than the cash they have on hand, that is indeed the message."
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The Buffalo News
JEFFREY SKOLNICK SUPERSTAR
"Jeff Skolnick didn't sign up for all this hype.
He did not apply to the following posting:
Savior wanted: A wunderkind in cutting-edge technology who can help build a new economy and carry the hopes of a Rust Belt region of 1.2 million people.
He just took a job heading a new academic program, the University at Buffalo's Center of Excellence in Bioinformatics."
[ rhetoric ]
“Bioinformatics will be at the core of biology in the 21st century. In fields ranging from structural biology to genomics to biomedical imaging, ready access to data and analytical tools are fundamentally changing the way investigators in the life sciences conduct research and approach problems. Complex, computationally intensive biological problems are now being addressed and promise to significantly advance our understanding of biology and medicine. No biological discipline will be unaffected by these technological breakthroughs.”
BIOINFORMATICS IN THE 21st CENTURY[ search ]
[ outbound ]
biospace
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genomeweb
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bio-it world
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scitechdaily
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biomedcentral
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the panda's thumb
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bioinformatics.org
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nodalpoint
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flags and lollipops
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on genetics
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a bioinformatics blog
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andrew dalke
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the struggling grad student
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