{bio,medical} informatics
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Washington Post
J. Craig Venter's Next Little Thing
"Five years after antagonizing government scientists while racing them to map the human genome, Venter is back, making the typically bold statements that have long polarized opinion about him. Either he is one of this era's most electrifying scientists, or he's one of the most maddening. He is apt in conversation to compare himself to Robin Hood. Or Darwin.
"Yes, Craig confronts," said Alfonso Romo Garza, a Mexican billionaire, controller of a decent chunk of the world's commercial vegetable seeds and a backer of Venter's latest undertaking. "Of course, he's antagonistic. He's controversial. But I love controversial people because those are the people who change the world.""
redux [06.26.05]
"During the dash to sequence the human genome, Craig Venter's adversaries called him "Hitler", "an asshole", and "an opportunistic maniac and leech". Collins sometimes ended presentations with a slide of a double helix made entirely of money, preaching against those who would sell the human genome as a commodity. The publicly funded scientists often vilified Venter when talking to reporters, which had its intended effect in the media as newspapers and magazines ran stories about Venter cashing in on human DNA. It was Time magazine that dubbed him the "bad boy of science", leading Venter to tell his wife: "I don't mind being bad boy. I just don't want to be evil boy.""
redux [05.30.03]
"Craig Venter is trapped - in a comfy white armchair overlooking the spring leaves and water of Cold Spring Harbor Laboratory in New York.
Artist Lewis Miller is sketching his portrait and the human genome pioneer has to sit still for half an hour. It's not something Venter is used to."
redux [01.31.03]
"J. Craig Venter's company, Celera Genomics, decoded the human genome faster and more cheaply than a large federally-funded effort. Join host Iraq Flatow and Venter for a discussion about his philosophy and vision for genomics. Who should own the human genome?"
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."
redux [10.15.02]
"But we're asking the philanthropic community to say, 'How about funding 100 genomes for patients with these diseases? Diseases that you care about or ethnogeographic groups to make sure there's sufficient diversity in the population or in some cases you yourself or your family as part of a legacy,' and everybody would have their data be part of a database that would be used for genome analysis in comparing clinical records, genotype/phenotype correlations, obviously in an anonymous fashion."
"It was misrepresented the first time in the press that this was the millionaires' genome project. Hopefully, it would not just be millionaires' genomes, although I think that would be an interesting study. I think we would find them to be remarkably similar to all the other genomes, but I think what we'd expect to happen is that there would be groups that support diseases that they really care about getting solved that they know are not going to get solved with the current paradigm..."
redux [10.03.02]
"Mapping and reading J. Craig Venter's genome took 15 years, $5 billion and some of the world's most sophisticated computers.
Wouldn't you, too, like your genome decoded?
Venter says he plans to offer the service, with the goal of burning individual human's entire DNA sequences onto shiny compact discs."
redux [05.03.02]
"Coming from a man whose life revolves around the study of genes, this might sound surprising: People are not the sum total of their genes.
But J. Craig Venter, former president of Celera Genomics and genome mapper extraordinaire, wants the American public to know that genes are not fate and he's launched a nonprofit organization to prove it. "
redux [01.28.02]
"As all that was happening, people who know him say, White, Venter's boss, was getting grumpy. He well knew that Celera, under its original business plan, could not deliver long-range earnings growth that would justify what the market was paying for Celera shares. One top genetic scientist said White snapped to him in the midst of the publicity barrage, "'This is all nice, but we need a business plan.'"
They quickly came to the same conclusion as many minds before them: In biology and medicine, the only business plan that offers the potential of extraordinary profits is drug development. All the biotechnology superstars have been companies with hit drugs."
redux [01.22.01]
"Dr Craig Venter, the US scientist who led the private effort to decode the human genome, has quit as boss of his company Celera Genomics."
""We are now at a critical juncture where my best contributions can be made in a scientific advisory role, allowing the rest of the organisation to continue Celera's progress toward becoming a successful pharmaceutical business.""
redux [06.09.00]
"Great discoveries do not necessarily make great businesses. Businesses have to sell something. Celera Genomics doesn't sell or make anything tangible. It hawks service and information. It sells access to lists of genes and computers that can sort through those messy lists. Samuel Broder, the company's executive vice president and chief medical officer, makes Celera sound like some kind of consulting company, or perhaps a library."
"Venter's quest could be a fable, with all sorts of morals about the power of capitalism and the importance of a single, brilliant, willful individual who used the market to shake the ivory towers of science. But those morals only hold if Celera succeeds, if business and science blend to propel the company into the future with breathtaking speed without rocketing it into the realities of the marketplace. Celera could become one of the great business success stories. It could also be a financial train wreck."
Right now, that makes it a very volatile stock."
redux [07.17.00]
"Craig Venter, head of Celera Genomics which last month completed the map of the human genome, has outlined his next goal.
Speaking at a conference he said his new task was to map the proteins which drive all chemical reactions in the body."
""A big part of the business is the straightforward providing of information, but I'm not complacent just to do that," Venter said."
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Forbes
Protein Interactions Offer Up Clues to Disease
"Researchers at Johns Hopkins University and the Institute of Bioinformatics in Bangalore, India, analyzed a database of more than 25,000 protein-protein interactions and developed what's believed to be the most detailed human "interactome" -- the interplay of proteins that occurs in cells when people are healthy or when they have disease.
The researchers found that proteins encoded by mutated genes involved in inherited disorders were likely to interact with proteins already known to cause similar disorders. The study also disputes the long-held belief that a specific protein's relative importance is always indicated by the number of other proteins it interacts with in a cell."
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InfoWorld Nederland
Notes from the Lab: Multicore and more
"The BioTeam recently had the opportunity to perform a set of benchmarks on one of the new quad-chip, dual-core Xeon systems from Intel. Our complete analysis is available online at bioteam.net/intel_benchmarks.
The most interesting thing to me about multicore systems is that they represent a significant push back in the ever-present single system image versus compute farm debate. For the past several years, the most cost-effective way to build a personal compute server at the 8 or 16 CPU level was to build a small cluster out of dual CPU systems. The Intel system that we evaluated contained four physical chips, each of which contained two cores. This made it an 8 CPU system before even counting any virtual CPUs. In terms of performance, administrative overhead, and cost per CPU, a single system is clearly a win over a cluster."
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Bio-IT World
Guerilla Informatics – Genzyme Style
"The great sucking sound of bioinformatics groups being shrunk or swept away after disappointing results has never been heard at Genzyme. It would have been a soft whoosh anyway. Genzyme’s core bioinformatics team has only seven members, including one recent hire. For the first few years, it was pretty much Partha Manavalan working alone at the bench and computer doing protein engineering.
This slowness — perhaps prudence is a better word — to jump on the bioinformatics bandwagon hasn’t hurt Genzyme."
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Business Intelligence Network
Federated Databases in Bioinformatics and Translational Medical Research
"In my last article, I described federated database architectures and their use in bioinformatics research. This month I would like to review some real-world examples of federated systems and describe how they are currently being used in the bioinformatics community and in medical research. Translational medical research, which seeks to integrate basic academic medical research with clinical trials research, will especially benefit from federated systems."
"With the ever-increasing complexity of biological data sets, geographically distributed data sources and cross-functional collaborative research teams, the federation approach to bioinformatics data management has a bright future."
redux [01.10.06]
"“Find 3-D structure of hypothetical protein UPF0301 in V. cholerae, SWISS-PROT homology models, PFAM/SCOP classifications, and recent PUBMED entries.”
These are difficult tasks posed by biomedical researchers.
If there is any hope of providing answers for them, bioinformaticians will have to provide coherent access to a wide variety of data and information sources. Database federations are one promising solution. These federations act as integration points to bring together biological and biomedical information from widely distributed sources. Let’s briefly examine database federations and their benefits for biomedical research."
redux [08.16.05]
"The need for data integration is widely acknowledged in the bioinformatics community. Bioinformatics data is currently spread across the Internet and throughout organizations in a wide variety of formats. Success in most bioinformatics-related activities, from functional characterization of genomic sequences to prioritization of drug targets, requires an integrated view of all relevant data in a drug discovery R&D program. The challenges of data integration may be addressed using a wide variety of approaches, and integration systems abound in both the academic and commercial sectors. While each approach has strengths and weaknesses, it can be difficult to evaluate which approach suits a particular need best without fully understanding the data integration landscape."
redux [11.05.03]
"The scientists spending two days at the National Institutes of Health (NIH) in Bethesda this week want to integrate the reams of information spewed out from sequencing machines and computer models.
At the moment, it is a struggle to link a patient's genetic profile with their brain scans and the latest clinical studies. It's like a primitive PC running incompatible word-processing, e-mail and spreadsheet programs, says Erik Jakobsson of the National Institute of General Medical Sciences, who helped to convene the meeting. "We're way behind in making it all work together," he says."
redux [03.31.03]
"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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ITWorld
Bioinformatics brain drain helps consultancies
"One analyst refers to bioinformatics having become a "base technology." Others say it has evolved into a commodity. But whatever it's called, that evolution -- a natural process in a maturing industry -- has led increasing numbers of biopharmas and biotechs to slash in-house bioinformatics or to shutter such departments entirely.
Outsourcing and offshoring have contributed to changes under way in bioinformatics. As biology and IT have converged, "the need for specialization goes away," says Alan Louie of IDC's Health Industry Insights.
As the heady days of cracking the human genome gave way to day-to-day work on a plethora of new drug targets, many bioinformaticians have reached a career crossroads, going to work for major consultancies, starting their own such small firms, or switching to academia."
redux [10.04.05]
[requires 'free' registration]
"The lessons of bioinformatics' recent boom and bust cycle have not been lost on Rainer Fuchs, vice president of research informatics and operations at Biogen Idec.
Fuchs, who spoke at Cambridge Healthtech Institute's inaugural Bridging Discovery and IT conference here last week, said that he's "seeing a shift from lofty expectations" about what bioinformatics can accomplish "to more realistic, smaller projects with a better [return on investment]."
Fuchs asked for a show of hands from those attendees who saw "significant cost savings" in drug discovery from their investment in informatics over the last several years.
Not one hand was raised."
redux [08.13.03]
"Those charged with hearing pitches from software vendors who want to sell wares to biotechnology companies don't like these words: "enterprise-wide solution." They don't want to hear the generic wonders of the "solution" being pitched, they don't want to hear marketing buzzwords or that the software will revolutionize the pharmaceutical business. They won't believe that kind of approach and they will show the software vendor the door, perhaps within minutes, without an invitation back."
"But perhaps the largest issue has little to do with technology, but with getting recalcitrant scientists excited about tools available to them."
redux [04.28.03]
"Leading executives speaking at several recent seminars, however, suggested that this cross-tech hybrid is not generating the gains that proponents initially projected.
One challenge to the effectiveness of bioinformatics is that independent software developers have not been able to develop useful products for life sciences companies looking to save time and money.
“Very few companies, if any, can give us a turnkey solution,” said Mark Murcko, chief technical officer at Vertex Pharmaceuticals, at a recent panel discussion."
redux [03.08.03]
""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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Genomics and Proteomics
Computer Tutoring for Protein Origami
"In a climate-controlled room at the IBM Thomas J. Watson Research Center in Yorktown Heights, N.Y., one of IBM's newest supercomputers quietly cogitates. Blue Gene/W, or BGW, unveiled last June, boasts a processing speed of 91.29 teraflops (one teraflop is a quadrillion operations per second) and comes in second on the 25th annual Top 500 list of supercomputers compiled by the University of Tennessee. Number one on the list is Blue Gene/L, the famous massively parallel supercomputer located at Lawrence Livermore National Laboratory in Livermore, Calif. As its name implies, a Blue Gene computer is a bioinformatics machine. When the full power of those 91 teraflops are focused on a biological problem, its use is much like a telescope searching the skies as it probes the microscopic biological world."
redux [10.28.05]
"Lawrence Livermore National Laboratory and IBM unveiled the Blue Gene/L supercomputer Thursday and announced it's broken its own record again for the world's fastest supercomputer.
The 65,536-processor machine can sustain 280.6 trillion calculations per second, called 280.6 teraflops, IBM said Thursday. That's the top end of the range IBM forecast and more than twice the previous Blue Gene/L record of 136.8 teraflops, set when only half the machine was installed."
redux [09.07.05]
"Researchers at IBM’s Thomas J. Watson Research Center and Columbia University have used a small (single-rack) Blue Gene system from IBM to discover a new phenomenon having to do with the folding of a melittin protein in water.
Specifically, the Blue Gene system’s processing power allowed the researchers to perform simulations that were impractical to run on previously available high-performance computing systems."
""It's a big game changer," says Ajay Royyuru, a computational biologist in charge of IBM's life science research. "We now have the ability to think about the whole system, not just parts. We can start to build a robust model of how a system is behaving or misbehaving and ask, 'How can I correct it?' If I knock a gene out, how will the whole system behave?"
The ability to simulate how an entire system behaves is the modus operandi of Blue Gene, which ties the brute strength of tens of thousands of processors with a sophisticated architecture that lets processors share information on the fly. The record-breaking versions are running in elite institutions such as the Lawrence Livermore Lab--its behemoth consists of 32 e-Servers lashed together--and Japan's Advanced Institute of Science and Technology, but the basic 5.7-teraflop "e-Server" system is available for roughly $2 million. IBM is also renting space on Blue Gene systems for about $10,000 a week."
redux [08.19.05]
"IBM and Argonne have agreed to augment Argonne's Innovative and Novel Computational Impact on Theory and Experiment (INCITE) computer capacity with compute cycles on IBM's Blue Gene "BGW" supercomputer system at IBM T.J. Watson Research Center in Yorktown Heights, N.Y."
""What we're really talking about about is over 1 million CPU hours over the course of a year, running 24 x 7, minus maintenance and upgrades," Herb Schultz, a Blue Gene manager at IBM, told internetnews.com. "Depending on the project, the workload could take 10 racks at a time. We're trying to learn what these kinds of applications are all about, so it's a good exercise for us." Each of the twenty racks at the IBM facility has 2,048 CPUs."
redux [06.21.04]
"The latest list of the top 500 performing supercomputers in the world was released today and it shows IBM has placed two Blue Gene/L prototype systems in the top 10. Additionally, clusters are now the most common supercomputer architecture."
"Coming in at number four and eight were the Blue Gene/L DD1 and DD2 Prototype systems. The systems’ performance benchmarks were 11.68 teraFLOPS sustained speed and 16 teraFLOPS peak performance for the DD1 and 8.66 teraFLOPS sustained, 11.47 tearFLOPS peak for the DD2."
redux [02.20.04]
"IBM will install a second Blue Gene/L supercomputer as part of a radio telescope project in the Netherlands, the company plans to announce Monday.
The supercomputer will be used for a new radio telescope project called Lofar, short for low frequency array, run by a Dutch organization called Astron. The system, which is expected to be complete in 2005, will run the Linux operating system, use about 12,000 processors and perform more than 30 trillion calculations per second, sources familiar with the plan said."
redux [11.15.03]
"IBM on Friday talked up its Blue Gene/L supercomputer, the first module of which is a relatively small, dishwasher-size machine that can perform 1.4 trillion calculations per second.
The performance is enough to make the machine the world's 73rd fastest supercomputer, according to a ranking of the top 500 to be released Sunday. By the time IBM has upgraded the box's 512 chips, each with two processors, and linked it with another 127 identical systems in 2005, Big Blue hopes to take the top spot."
redux [09.19.03]
"WHATEVER happened to Blue Gene, IBM's ambitious attempt to build the world's fastest computer? The project, launched in 1999, called for the construction of a "massively parallel" computer with over 36,000 processing chips, each containing 32 processing cores roughly equivalent in power to a desktop PC. Harnessing all that computing horsepower--more than one petaflop, or 1,000 trillion floating-point calculations per second--would, it was hoped, allow scientists to simulate the folding of a protein, an extraordinarily demanding task which might help to streamline the discovery of new drugs. The idea was to achieve all of this within five years--something that even enthusiasts thought ambitious.
Four years on, the chips that will power the first Blue Gene computer are now being manufactured and tested. But the plans have changed somewhat."
redux [05.08.03]
""Blue Gene is a completely oddball, you've-never-seen-anything-like-this-before design," said Illuminata analyst Jonathan Eunice. "It is not custom everything, (but) it is still very exotic compared to anything you can buy.""
"IBM already has spent more than the original $100 million budgeted for the project and won't meet its 2004 goal for the ultimate machine, but the company has made progress bringing its ideas to fruition."
redux [02.11.03]
"THE first version of IBM's revolutionary Blue Gene chip will roll off the production line this quarter, Ajay Royyuru, head of IBM's Computational Biology Centre, has revealed."
""We plan to build a 512-node prototype Blue Gene machine in our Watson Research Centre, in New York, where I am located, hopefully before the end of the year.
Then we will build a 64,000- node Blue Gene machine and deliver it to the Lawrence Livermore laboratory by late 2004, or early 2005."
redux [10.24.02]
"Linux will be the main operating system for IBM's upcoming family of "Blue Gene" supercomputers--a major endorsement for the OS and the open-source computing model it represents."
""We had two choices of operating systems for the Blue Gene family, either use a special purpose system or Linux," Bill Pulleyblank, director of Exploratory Server Systems at IBM Research, said in a statement. "We chose Linux because it's open and because we believed it could be extended to run a computer the size of Blue Gene. We saw considerable advantage in using an operating system supported by the open-source community so that we can get their input and feedback.""
redux [07.13.01]
""Ambuj Goyal, IBM Research's general manager for software, solutions, and strategy, was more ambitious than that. Why not build a machine to model molecular dynamics using general-purpose chips rather than specialized ones? That way you'd produce a prototype for a whole new family of supercomputers. Not only would it be great technology development, it would be great marketing, too. Whereas the Department of Energy has the greatest interest in top-end supercomputing - with its need to understand how nuclear weapons work - focusing on the life sciences rather than the death sciences could make supercomputing more widely appealing. What's more, a biology program would be a way of telling one of the newest markets for big iron - the post-genome biotech world - that IBM took its interests seriously. "We believe that the life sciences are going to be a rapidly growing area," says Blue Gene project manager Bill Pulleyblank, "a huge growth area for IBM.""
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PressZoom
Microsoft funds a new high-performance computing institute for computational biology at Cornell
"Microsoft is funding a Microsoft Institute for High-Performance Computing at Cornell with annual funding of $400,000, renewable each year for an indefinite period. The new institute will greatly expand the ability of researchers to work with huge databases of DNA sequences and protein composition and shapes, and explore new software and applications for the analysis of biological information."
"Ron Elber, professor of computer science and director of CBSU, also will be director of the new institute, and it will be managed by CTC senior research associate Jaroslaw Pillardy, who manages CBSU. "The support of Microsoft is very much appreciated," Elber said. "They have supported us before, but this increased support makes it possible for the CBSU to expand and to do more interesting things and larger things based on new software technology from Microsoft.""
redux [10.29.05]
"In all, bioinformatics is a field of research that has undergone a rapid explosion in terms of the numbers of tools and techniques that it has produced. While much of this progress can be attributed to the adaptability and flexibility of open source technologies such as Linux and Perl, it is important for bioinformatics professionals to consider that disseminating their bioinformatics tools to users can be as critical to scientific progress as developing new tools. A key way to facilitate the widespread dissemination of bioinformatics applications to biologists will likely be the development of an open sourced .NET class library to serve as framework for Windows-based bioinformatics applications."
redux [05.27.04]
"The Cornell Theory Center currently operates a cluster consisting of more than 900 processors based on Intel chips housed in Dell computers operating on Microsoft's Windows software. It represents the first steps in the development of Windows for a wide range of supercomputing applications.
Microsoft Research says its workshop brings together about 75 scientists to discuss data-intensive scientific computing as it pertains to Windows and .NET . The participants represent such fields as astronomy, material sciences, physics, archeology, oceanography, and bio-informatics and computational biology."
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Flags and Lollipops
Postgenomic
"I've been pretty quiet over the last week or so because... well, because I just got an Xbox 360 as an anniversary present (King Kong rocks). My talk of putting off any new video game related purchases for a while in favour of flash based biology games made Mrs Stew take pity on me, I think.
But it's also (and mainly) because I've been working on a new site at postgenomic.com.
Postgenomic aggregates the feeds from life science blogs in order to do useful and interesting things with them. It's kind of like Technorati crossed with a really big hot papers meeting."
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The New York Times
Scientists Sort Through 'Junk' to Unravel a Genetic Mystery
[requires 'free' registration]
"More broadly, however, the team's findings suggest a new approach to teasing out the genetic basis of innate disorders that cannot be traced to simple protein-coding defects.
"There are about 30,000 genes in the human genome, but there are at least 150,000 different genetic disorders," Dr. Thakker said. "You can't just look at the genes that code for proteins, you've got to look at the surrounding regulatory regions, as well — the 'junk.' ""
redux [06.03.04]
"In a region of DNA long considered a genetic wasteland, Harvard Medical School researchers have discovered a new class of gene. Most genes carry out their tasks by making a product-a protein or enzyme. This is true of those that provide the body's raw materials, the structural genes, and those that control other genes' activities, the regulatory genes. The new one, found in yeast, does not produce a protein. It performs its function, in this case to regulate a nearby gene, simply by being turned on."
"Like many researchers, Winston and his colleagues may have known in the back of their minds that someday they would have to contend with junk DNA, but it was not their intention to map a new gene in those wild and relatively uncharted regions of the chromosome."
redux [05.07.04]
"If you thought we had explored all the important parts of our genome, think again."
"The segments, dubbed 'ultraconserved elements', lie in the large parts of the genome that do not code for any protein. Their presence adds to growing evidence that the importance of these areas, often dismissed as junk DNA, could be much more fundamental than anyone suspected."
redux [02.21.04]
"Genetic Technologies (GTG), the Australian biotech company at the heart of a controversy surrounding its patents on the genetic mapping applications of noncoding (junk) DNA, has added another large company to its tally of licensees -- Laboratory Corporation of America Holdings (LabCorp)."
"Last year, GTG granted licenses to Sequenom, Perlegen Sciences, Myriad Genetics, and Pyrosequencing, among others."
redux [11.18.03]
"Investors piled into Genetic Technologies yesterday after the biotech company announced that two US groups it was suing for patent infringement had settled out of court."
"The Melbourne-based Genetic Technologies has consistently warned it would sue any company, research institution or university that infringed its patent over the so-called junk DNA."
redux [08.18.03]
"An Australian biotech company, Genetic Technologies Ltd. (GTG), is stirring up controversy over its decision to enforce a series of patents, granted in the 1990s by the US Patent and Trademark Office, over the genetic diagnostic and mapping applications of non-coding, or junk, DNA."
"Scientists, including NHGRI chief Francis Collins and Sir John Sulston, are also upset over GTG's recent decision to ask academic institutions to sign research licenses."
redux [05.19.03]
[requires 'free' registration]
The dark side of the moon is a misnomer. Light reaches la luna's entire surface, but one half is unviewable from Earth. The human genome, the now essentially decoded map of life, likewise has a light side--the genes encoding mRNA and protein--and a dark side, which is coming into view for the first time. The dark side encompasses more than its opposite: The majority of the genome comprises intronic regions, stretches of repeat sequence, and other assorted gibberish that has attained the ignoble dubbing, "junk."
The first exploratory missions to the human genome's faceted surface are turning up traces regarding the extent of the junk."
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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