{bio,medical} informatics
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GenomeWeb
Current Genomics Job Market Shuts Some Doors As Others Swing Open
"While hard data on the number of jobs for genomics, proteomics, and bioinformatics specialists are notoriously difficult to come by (and those that are available are subject to a variety of interpretations) a consensus in the biotech jobs-placement community points to three trends: 1) greater consolidation in biotech may translate into fewer jobs; 2) opportunities abound for scientists with a taste for business development; and 3) bioinformatics, bioinformatics, bioinformatics."
redux [05.20.02]
"The fusion of biology and computer science is the hottest of the hot in science right now, and it's going to heat up even more. Bioinformaticians, also known as computational bi- ologists, use computer modeling to predict which drugs will work on which illnesses, shaving the time and cost of getting new products to market. No wonder drugmakers are salivating over these professionals, especially in the wake of human-genome mapping. Chris Smith, who works as a bioinformatician at the San Diego Supercomputer Center, predicts that "there will be a 100 percent increase per year in the field for the next five years at least." Even now a bioinformatician with three to five years of experience can command $120,000."
redux [10.05.01]
"Almost all companies say they're having trouble finding people with expertise in bioinformatics, the use of computers to solve complex biological problems. The human genome's mapping has ushered in a new era of genetic medicine, but to capitalize on this knowledge, researchers need to know how to use powerful computers to translate raw biological data into information useful for developing new therapies.
"There's a struggle to have people that are well educated in both computer science as well as biology," said David Pot , InforMax's director of application sciences. "We recognize we need super scientists, but those super scientists don't have the training to write super software.""
redux [03.05.01]
"Move over Information Age. Make room for the age of bioinformation.
Experts have already dubbed bioinformatics - a hybrid profession pairing biology and computer science - the career choice of the decade.
"There is a crying need for experts in bioinformatics and this is not something that will just fade away," said Dr. Leena Peltonen, chairwoman of the Department of Human Genetics at UCLA."
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BioMedNet
Yeast genome sheds 500 genes
[requires 'free' registration]
"Thanks to the power of comparative genomics, yeast researchers will have "10% less work to do," according to Eric Lander, one of the leaders of the Human Genome Project. Aligning the genomes of four species of yeast, Lander and his colleagues have unpublished data indicating the genome has approximately 5,600 genes, nearly 500 less than previously thought."
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Kurtzweil AI
Predictive Human Genomics Is Here
"Thanks to breakthroughs in genomics testing, physicians now have tools for true preventive medicine. Gene chips and genomics test panels can predict one’s predisposition towards many serious -- and often preventable -- genetic diseases and allow doctors to modify gene expression through precise, targeted, individualized interventions."
redux [05.17.02]
"An unprecedented wealth of biological data has been generated by the human genome project and sequencing projects in other organisms. The huge demand for analysis and interpretation of these data is being managed by the evolving science of bioinformatics. Bioinformatics is defined as the application of tools of computation and analysis to the capture and interpretation of biological data. It is an interdisciplinary field, which harnesses computer science, mathematics, physics, and biology. Bioinformatics is essential for management of data in modern biology and medicine. This paper describes the main tools of the bioinformatician and discusses how they are being used to interpret biological data and to further understanding of disease. The potential clinical applications of these data in drug discovery and development are also discussed."
"Complex diseases have complex phenotypes, and proper diagnosis requires that the analysis take into account the patient's history and exposure to environmental factors, as well as genetic information. Signaling information is one aspect of a grander "biomedical informatics" approach advocated for a better understanding of a patient's medically relevant disease phenotype."
redux [04.17.02]
"Research into human genetics is being limited by a lack of knowledge in other areas of science, say delegates at the Seventh International Human Genome Meeting (HUGO) in China.
Professor Lap-Chee Tsui, HUGO's outgoing president, says that our poor understanding of even basic human anatomy means that the human genome project is not delivering cures for genetic diseases as was hoped."
redux [12.08.01]
"The goal now is to redefine disease based on the underlying biological mechanisms, Lander said. By that token, diseases are going to surprise us. Reclassifying them means that some diseases will get split in half and other diseases will get lumped together because they have the same mechanism, although they may look different to us, he said.
What this portends commercially is up to smart companies to figure out, he said. Companies will need the ability to integrate scale and informatics; they'll need what he called a "fleetness" with technologies—not just one favored technology, but many kinds. They shouldn't worry too much about hoarding intellectual property rights nor depend on one technology platform. It is more important to understand the big picture in the first place in order to choose the right target, Lander said."
redux [08.01.01]
"Pharmacogenomics requires the integration and analysis of genomic, molecular, cellular, and clinical data, and thus offers a remarkable set of challenges to biomedical informatics. These include infrastructural challenges such as the creation of data models and data bases for storing this data, the integration of these data with external databases, the extraction of information from natural language text, and the protection of databases with sensitive information. There are also scientific challenge in creating tools to support gene expression analysis, three-dimensional structural analysis, and comparative genomic analysis. In this review, we summarize the current uses of informatics within pharmacogenomics, and show how the technical challenges that remain for biomedical informatics are typical of those that will be confronted in the post-genomic era."
redux [11.16.00]
"Neither we nor our critics defined a revolution in medicine. We mean a paradigm shift in theory or practice. Sotos and Rienhoff's plea for "precise diagnosis" epitomizes the current paradigm. In most of those who will have common disorders, the interaction of genetic, environmental, and behavioral factors makes the quest for precise diagnosis illusive."
"The revolution in medicine will come with the recognition, based in part on genetic research, that the quest for single causes for common diseases will seldom be fruitful and that a new paradigm of a causal web must be adopted. Interventions must be directed at the most vulnerable points in the web. Sometimes this will involve biomedical interventions. At other times, it will involve modifying aspects of our social structure, lifestyle, or environment that increase the risk of disease."
redux [08.06.01]
[ summary can be viewed for free once registered ]
"The human genome sequence will dramatically alter how we define, prevent, and treat disease. As more and more genetic variations among individuals are discovered, there will be a rush to label many of these variations as disease-associated. We need to define the term disease so that it incorporates our expanding genetic knowledge, taking into account the possible risks and adverse consequences associated with certain genetic variations, while acknowledging that a definition of disease cannot be based solely on one genetic abnormality."
"In thinking about how clinicians use the term disease, we think that three elements should be considered: disease is a state that places individuals at increased risk of adverse consequences . Treatment is given to those with a disease to prevent or ameliorate adverse consequences. The key element in this definition is risk: deviations from normal that are not associated with risk should not be considered synonymous with disease. Our definition has three definable elements and should serve clinicians well. Of course, its success will depend on whether it becomes clinically useful."
redux [07.11.00]
"For most of us, formal biology education begins with complex systems--the traditional dissection of a frog in high school biology class is virtually a rite of passage in the U.S.
But the way many people learn about and invest in biotechnology is at the smallest end of the spectrum--the genome, now often described as the "periodic table" of biology. Genomics and all its related buzzwords have been responsible for much of the media attention, government grants, and investment capital heaped on the biotech industry over the past decade.
But just as there is a whole lot of chemistry that happens in between the periodic table and a birthday cake, there is a lot of biology in between the genome and a living organism. With the completion of biology's periodic table within sight, academics and industry players alike are pondering the best way to apply our hard won knowledge.
The only problem is, the path from genome to system seems to get harder the more we learn."
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Wired News
A Map That Maps Gene Functions
"The genetics revolution is generating such a gigantic glut of information that artificial intelligence may be the only way scientists will ever put it to practical use.
Inspired by an AI effort to record all of the common-sense knowledge shared among humans called Cyc, scientists have come up with a technology that can gather all of the information scientists know about an organism."
redux [09.19.01]
"Future understanding of genomic data may be severely limited unless bioinformaticists gain a better understanding of knowledge representation, according to Peter Karp, director of SRI International's Bioinformatics Research Group."
"As biological research grows more and more dependent on information technology to make sense of increasing amounts of genomic data, Karp wrote, it will be crucial for bioinformaticists to keep up with new developments in symbolic computing. "The genome revolution is increasing the need for pathway databases in the biological sciences, and similar developments will occur in other sciences. However, effective implementation of this paradigm is hampered because most biologists (and most other scientists) receive essentially no education in databases or knowledge representation."
redux [08.19.01]
"Biomedical researchers are decoding the human genome with astonishing speed, but the clinical significance of the massive volumes of data collected remains largely undiscovered. Progress requires communication and data sharing among scientists. These data may be in the form of (1) raw data, derived data, and inferences that result from computational analyses, or (2) text documents published by experts who present their conclusions in natural language. The World Wide Web provides a valuable infrastructure for enabling researchers to share the rapidly growing knowledge about biology and medicine, and a fully functional Semantic Web is necessary to support data submission and retrieval, the sharing of knowledge, and interoperation of related resources."
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."
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Nature: Science Update
New word in life's lexicon
"The scientists who cracked life's genetic code in the 1950s said that it writes a mere 20 'words' - the amino acids from which the myriad proteins in all life are built. But in 1986 another amino acid was discovered in bacteria.
"We thought the 21st was an aberration, but here we see another one," says biochemist Michael Chan of Ohio State University, Columbus. "Perhaps 23 and 24 are just around the corner.""
""The implication is that the genetic code itself can be modified through evolution to encode more stuff -- new amino acids," Gesteland said."
"Gesteland said discovery of the 22nd genetically encoded amino acid raises the bigger question of how life's genetic code is reprogrammed to do new things, and also suggests "there may be other surprises out there. Are there yet other amino acids?""
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The Washington Post
More Species Chosen for Genome Project
"The nominees were a varied lot. A monkey. A cow. A hairy, single-celled organism called Oxytricha trifallax. Each was backed by a group of scientists with a singular goal: convince a panel of experts that their creature was worthy of having its entire genetic code spelled out.
The judging wasn't televised and Whoopi Goldberg wasn't there. But yesterday, in a contest tracked closely by scientists around the world, a committee of the National Institutes of Health awarded what amounts to the Oscar of comparative genomics to six winning "model organisms.""
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The Nando Times
American Indians concerned about mapping of wild rice genome
"As University of Minnesota researchers map the wild rice genome, they are hoping the information could lead to more nutritious, disease-resistant crops that help feed the world.
But decoding the genome has upset many American Indians, who say they have been shut out of the research and warn that manmade alteration of the plant is "cultural and spiritual genocide.""
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Wired News
A Good Sequence, Easy to Dance To
"Companies doing genomic research, like Redwood City's Maxygen, have a problem. To make money, the companies feel they need to control the rights to the DNA sequences they uncover. But patenting these sequences is ethically and legally tricky.
So, Maxygen's scientists and lawyers are proposing a downright odd solution to this pickle: Encode the DNA sequences as MP3s or other music files and then copyright these genetic "tunes.""
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SmartMoney
The Next Hot Jobs
"The fusion of biology and computer science is the hottest of the hot in science right now, and it's going to heat up even more. Bioinformaticians, also known as computational bi- ologists, use computer modeling to predict which drugs will work on which illnesses, shaving the time and cost of getting new products to market. No wonder drugmakers are salivating over these professionals, especially in the wake of human-genome mapping. Chris Smith, who works as a bioinformatician at the San Diego Supercomputer Center, predicts that "there will be a 100 percent increase per year in the field for the next five years at least." Even now a bioinformatician with three to five years of experience can command $120,000."
redux [10.05.01]
"Almost all companies say they're having trouble finding people with expertise in bioinformatics, the use of computers to solve complex biological problems. The human genome's mapping has ushered in a new era of genetic medicine, but to capitalize on this knowledge, researchers need to know how to use powerful computers to translate raw biological data into information useful for developing new therapies.
"There's a struggle to have people that are well educated in both computer science as well as biology," said David Pot , InforMax's director of application sciences. "We recognize we need super scientists, but those super scientists don't have the training to write super software.""
redux [03.05.01]
"Move over Information Age. Make room for the age of bioinformation.
Experts have already dubbed bioinformatics - a hybrid profession pairing biology and computer science - the career choice of the decade.
"There is a crying need for experts in bioinformatics and this is not something that will just fade away," said Dr. Leena Peltonen, chairwoman of the Department of Human Genetics at UCLA."
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Grid Computing Planet
Mac OS X Gets A Grid Solution
"Platform Computing plans to make its flagship Platform LSF software available for Apple's new Xserve, extending support for Mac OS X and Apple's new server, storage and systems management offerings.
"The combination of the Mac Xserve with Platform Computing's technology will enhance the quality and speed of work for Mac applications in life sciences, education and business," Ron Okamoto, Apple's vice president of Worldwide Developer Relations, said in a statement."
" Genentech -- Guy Kraines, vice president, Corporate IT. We got to use them, and we've got some observations. First, this is not a desktop box with rack-mount ears. From the physical design, the hot-swap capabilities, the remote monitoring -- this is a data center box. My guys in the data center are fully accepting of it. They did it right, right down to cable management. Second, performance. The G4 itself is a heck of a processor, especially with what we do. Velocity Engine doesn't just do Photoshop rendering well -- it does matching of genetic code really well too. The single most common application in bioinformatics is Blast. I'm not going to give you numbers today in terms of what we've done, but let's just say that this is not just a measurable improvement, but a meaningful improvement in helping us do what we need to do."
redux [12.16.01]
"Scientists are porting bioinformatics tools to the Macintosh platform because often they are already Macintosh users, and they want the convenience of being able to perform their research on their primary desktop computers. Traditionally scientific researchers have needed a desktop computer for all of their productivity applications, and a separate platform for the compute engine to support their research. "The tremendous benefit of Mac OS X is it gives you both," says Van Etten. "The only thing that comes close is Linux, but for most bioinformaticists, the Linux desktop user experience is a little sophisticated.""
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British Medical Journal
Science, medicine, and the future: Bioinformatics
"An unprecedented wealth of biological data has been generated by the human genome project and sequencing projects in other organisms. The huge demand for analysis and interpretation of these data is being managed by the evolving science of bioinformatics. Bioinformatics is defined as the application of tools of computation and analysis to the capture and interpretation of biological data. It is an interdisciplinary field, which harnesses computer science, mathematics, physics, and biology. Bioinformatics is essential for management of data in modern biology and medicine. This paper describes the main tools of the bioinformatician and discusses how they are being used to interpret biological data and to further understanding of disease. The potential clinical applications of these data in drug discovery and development are also discussed."
"Complex diseases have complex phenotypes, and proper diagnosis requires that the analysis take into account the patient's history and exposure to environmental factors, as well as genetic information. Signaling information is one aspect of a grander "biomedical informatics" approach advocated for a better understanding of a patient's medically relevant disease phenotype."
redux [04.17.02]
"Research into human genetics is being limited by a lack of knowledge in other areas of science, say delegates at the Seventh International Human Genome Meeting (HUGO) in China.
Professor Lap-Chee Tsui, HUGO's outgoing president, says that our poor understanding of even basic human anatomy means that the human genome project is not delivering cures for genetic diseases as was hoped."
redux [12.08.01]
"The goal now is to redefine disease based on the underlying biological mechanisms, Lander said. By that token, diseases are going to surprise us. Reclassifying them means that some diseases will get split in half and other diseases will get lumped together because they have the same mechanism, although they may look different to us, he said.
What this portends commercially is up to smart companies to figure out, he said. Companies will need the ability to integrate scale and informatics; they'll need what he called a "fleetness" with technologies—not just one favored technology, but many kinds. They shouldn't worry too much about hoarding intellectual property rights nor depend on one technology platform. It is more important to understand the big picture in the first place in order to choose the right target, Lander said."
redux [08.01.01]
"Pharmacogenomics requires the integration and analysis of genomic, molecular, cellular, and clinical data, and thus offers a remarkable set of challenges to biomedical informatics. These include infrastructural challenges such as the creation of data models and data bases for storing this data, the integration of these data with external databases, the extraction of information from natural language text, and the protection of databases with sensitive information. There are also scientific challenge in creating tools to support gene expression analysis, three-dimensional structural analysis, and comparative genomic analysis. In this review, we summarize the current uses of informatics within pharmacogenomics, and show how the technical challenges that remain for biomedical informatics are typical of those that will be confronted in the post-genomic era."
redux [11.16.00]
"Neither we nor our critics defined a revolution in medicine. We mean a paradigm shift in theory or practice. Sotos and Rienhoff's plea for "precise diagnosis" epitomizes the current paradigm. In most of those who will have common disorders, the interaction of genetic, environmental, and behavioral factors makes the quest for precise diagnosis illusive."
"The revolution in medicine will come with the recognition, based in part on genetic research, that the quest for single causes for common diseases will seldom be fruitful and that a new paradigm of a causal web must be adopted. Interventions must be directed at the most vulnerable points in the web. Sometimes this will involve biomedical interventions. At other times, it will involve modifying aspects of our social structure, lifestyle, or environment that increase the risk of disease."
redux [08.06.01]
[ summary can be viewed for free once registered ]
"The human genome sequence will dramatically alter how we define, prevent, and treat disease. As more and more genetic variations among individuals are discovered, there will be a rush to label many of these variations as disease-associated. We need to define the term disease so that it incorporates our expanding genetic knowledge, taking into account the possible risks and adverse consequences associated with certain genetic variations, while acknowledging that a definition of disease cannot be based solely on one genetic abnormality."
"In thinking about how clinicians use the term disease, we think that three elements should be considered: disease is a state that places individuals at increased risk of adverse consequences . Treatment is given to those with a disease to prevent or ameliorate adverse consequences. The key element in this definition is risk: deviations from normal that are not associated with risk should not be considered synonymous with disease. Our definition has three definable elements and should serve clinicians well. Of course, its success will depend on whether it becomes clinically useful."
redux [07.11.00]
"For most of us, formal biology education begins with complex systems--the traditional dissection of a frog in high school biology class is virtually a rite of passage in the U.S.
But the way many people learn about and invest in biotechnology is at the smallest end of the spectrum--the genome, now often described as the "periodic table" of biology. Genomics and all its related buzzwords have been responsible for much of the media attention, government grants, and investment capital heaped on the biotech industry over the past decade.
But just as there is a whole lot of chemistry that happens in between the periodic table and a birthday cake, there is a lot of biology in between the genome and a living organism. With the completion of biology's periodic table within sight, academics and industry players alike are pondering the best way to apply our hard won knowledge.
The only problem is, the path from genome to system seems to get harder the more we learn."
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Wired Magazine
Hacking the Genome
"Eric Engelhard is bioengineering a honeybee. In his garage. He's part of a new generation of bioinformatics brainiacs - people improvising with computers and molecular biology - who are making it possible to move genomics out of the lab and into your spare room.
To hack a genome at home, you need a roll-your-own supercomputer cluster: a collection of standard PCs running blazingly fast on the power of many inexpensive CPUs. In cheap-but-kick-ass Linux tradition, Engelhard uses a cluster of salvaged "reject boxes" to putter around with insect genomes. He wants to design a venomless honeybee. "The idea is to deconstruct an insect for whatever use you like," he says. "You could even create a receptor on the honeybee's antennae that finds bombs."" [ via bioinformatics.org ]
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The O'Reilly Network
Web Services for Bioinformatics
"At the January 2002 O'Reilly Bioinformatics conference, Lincoln Stein delivered a keynote address on "Building a Bioinformatics Nation." In this talk, Lincoln argued that current biological databases are islands unto themselves, much like the Italian city states of the Middle Ages. He also proposed that a more formalized Web Service model could link disparate systems, and thereby create a more unified set of bioinformatics tools and databases."
"This article follows up on Lincoln's talk and explores two bioinformatic services you can try out today. By examining these specific services, we get a bird's eye view of the Web Service protocol stack, including WSDL and SOAP."
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Bio-IT World
When “off-the-shelf” works just fine
"For small cash-strapped biotechs, off-the-shelf computers and databases represent an attractive five-figure option versus millions for supercomputers and Unix solutions that easily rocket into six figures.
“Off-the-shelf” — also known as commodity components — usually means the Windows operating system and applications running on Intel servers or workstations. Rosetta Genomics, a two-year-old Israeli company, is using 8-processor Dell servers, Microsoft SQL Server 2000, Windows 200 Data Center, and a finely tuned EMC CLARiiON storage system to mine two terabytes of genomic data, searching for patterns relevant to drug discovery and disease. Before the year is out, Rosetta promises that its database will grow to 10 TB."
redux [03.26.01]
"The conjunction of hacker interest in science, the enormous commercial potential of genomics, proteomics and other bioinformatics disciplines, and the availability of cheaper supercomputing via distributed computation, seem to me to be an explosive mix."
"Every time we've had a radical lowering of the barriers of entry into a computing market, that market has exploded. The industry-standard IBM PC architecture liberated software developers from the need to work for hardware vendors; the open standards of the internet, plus the simplicity of HTML, and the power of scripting languages, allowed content providers to build the information applications that we now take for granted on the web. Now, hackers and scientists are working together to break down the barriers to discovery."
"Scientific computing is going to be where the action is."
redux [09.07.00]
"University of Idaho computer scientists and mathematicians are joining biologists to explore new ways to interpret the complex genetic information that describes all living things and their relationships.
Along the way, UI students returning to school this fall will find a new course few schools could hope to offer: building a new supercomputer."
"The students will work on every step of the project, from determining the requirements the supercomputer must meet, though the purchase, assembly, software selection and installation. "They are involved from start to finish. It should be a great experience for them," Heckendorn added." ""It's commodity computing. If you can only buy commodity computers and hook them together with the right stuff in the right way, you can get supercomputing power," he said. Although multi-million dollar specialty supercomputers still dominate the high end of the market, Beowulf-style supercomputers are gaining."
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The Scientist
A Scrap over Sequences, Take Two
[requires 'free' registration]
"Science magazine's controversial decision to publish the Syngenta draft rice genome sequence without requiring the company to deposit its data in a public database is getting less than rave reviews from scientists who need to use the genome map in their work. Over the objections of leading scientists who warn that scientific publishing principles have been sacrificed to commercial gain, Science allowed the agrochemical giant based in Basel, Switzerland, to maintain control of its data when it unveiled its draft blueprint of the japonica strain of rice in the journal's April 5 edition."
redux [04.12.02]
"In the United States, innovators have traditionally relied on copyright and confidential-information rights to protect their databases. In Europe, however, database owners have a novel weapon in their IP armamentarium: the database right.
But there's a catch: Database innovators must have sufficient nexus with Europe--actually, the European Economic Area, or EEA--in order for their databases to qualify for protection. Perhaps it's time for US database makers to consider how they might create sufficient ties with Europe to benefit from this powerful new IP right."
redux [02.27.02]
"For the scientists working on the Human Genome Project, the data defining who we are is too important to be left to Celera -- or any other company. David Haussler, a team leader at the University of California at Santa Cruz who helped Kent and others put the genome online, expresses the credo of a data liberator succinctly: "Information about the human genome is better in public hands than secretly locked up somewhere."
"But it's not just the research data itself that is at the center of the tug of war between corporations and scientists. When working with data as complex and vast as the human genome, the software tools necessary to manipulate that data are as important as the genetic code itself."
"Analysts tend to value drug companies more favorably than those that sell information, and their response to Confirmant's announcement has been lukewarm.
Other biotech company officials with experience in selling database information said that large, general databases such as the protein atlas might have a challenge in finding a market.
"What we have found out is that people ... want technologies that apply to their specific research," said Lior Ma'ayan, executive vice president of corporate development at Compugen, a biotech company based in Tel Aviv."
redux [03.10.01]
"With information on the genome now rapidly becoming available, the business models for companies that sell information about the genome, such as Celera and Incyte, may soon be outmoded. Biotech companies will then have to earn their stripes the old-fashioned way: by developing blockbuster drugs. Of course, proteomics companies could arise to sell information about proteins to other drug companies, but Strosberg thinks this is a flawed approach. Given his history, he should know. "Incyte's business model," he recalls, "was originally to be an information provider. That period is over. People will not pay as much for information as they used to because so much of it is now publicly available. Information is becoming a commodity." Instead of selling information about proteins, he is focusing Hybrigenics on using its proteomics information to develop drugs, either alone or in partnership with larger pharmaceutical companies."
redux [03.20.02]
[requires 'free' registration]
"The genomics revolution and the Internet have changed science in ways impossible to imagine 20 years ago. Among other advances, these forces have allowed the latest research to be routinely gathered, organized, and disseminated, typically at little or cost, through online biological information databases.
Arduous to use and filled with mostly unanalyzed data early on, these computer databases are now packed with valuable, up-to-date information made easily accessible with improved search engines. They have become so ubiquitous and integral to science today that almost every molecular biologist consults one when initiating research projects. "It would be impossible to do molecular biology properly these days without access to them."
redux [05.09.01]
"It may seem surprising, considering the amount of publicity the Human Genome Project has garnered over the past year, but a recent Wellcome Trust survey indicates that only half of biomedical researchers using genome databases are familiar with the services provided by Ensembl and other freely available options.
Although the number of hits on the Ensembl website has doubled since the publication of the Human Genome Project’s findings in Nature in February, a questionnaire sent to 777 individuals funded by the Wellcome Trust found that only 82 used Ensembl regularly, 189 used it occasionally, and only 50 percent of those who used DNA databases regularly used Ensembl at all.
Even more surprising was the finding that of those who didn’t use Ensembl, 50 percent had never heard of it.""
redux [02.27.01]
"ONCE upon a time, pure and applied science were the same. Sir Humphry Davy discovered seven chemical elements, and invented the miner's safety lamp. Louis Pasteur investigated the properties of molecules, and worked out how to stop milk spoiling. Everybody thought that was admirable. Somehow, things have changed. Today the feeling is widespread that science and commerce should not - must not - mix. There is a queasy suspicion that the process of discovery is in some way corrupted if it is driven by profit."
"Far from compromising science, profit in both these cases - the development of new medicines and the elucidation of the genome - has animated it, and directed it towards meeting pressing human needs. It is a happy marriage. Davy and Pasteur would surely have approved."
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Red Herring
New strategies for the post-genomic era
"A detective is called in one morning to his captain's office and is informed that he must locate a dangerous felon living in Manhattan. The captain tells the detective, "It should be no problem locating him, we have a phone book!"
With the February 2001 completion of the first rough draft of the human genome, a similar scenario could unfold in biotech: a venture capitalist provides funds to an upstart biotech firm attempting to identify novel disease-causing genes and tells its chief scientific officer, "It shouldn't be that hard, you have access to the human genome database.""
redux [04.19.02]
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"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]
"Leaders in the genomics field, as in any other industry, will be companies that offer a value-added service. Large pharmaceutical companies agree on what that service should be: integration of all the genomics information available. With more information readily accessible, companies can easily decide on whether to continue investigating potential targets.
So the future of genomics companies may rest in their IT and software capabilities, a view held by Celera Genomics, a newcomer to genomics. “We are entering an era of ‘cyberpharmaceutical’ drug development,” says Samual Broder, executive VP and chief medical officer. “Pharmaceutical corporations will use genomic databases, and other relational databases involving gene expression, proteomics etc. as the foundation of their drug discovery pipelines. One of the immediate goals... is to produce appropriate databases and software to link biologic and genomic information.”"
""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]
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"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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Nature
Bioinformatics: Online organization
"The field of bioinformatics is dominated by rival groups, each promoting its own websites, services and data formats, and thus hindering researchers who typically need to integrate data from many online sources. So argues Lincoln Stein. He suggests that the emerging technology of web services is the best way to allow full exploitation of biological data, providing online databases with a consistent and familiar user interface. Implementation of web services is some years away so, in the meantime, Stein proposes a bioinformatics data-provider's code of conduct to maximize the usefulness and reusability of biological data."
redux [01.31.02]
"Lincoln then summarized efforts to unify the bioinformatics data services. These efforts started 12 years ago with the Meetings of the Molecular Biology Databases (MMBD), which essentially ended in argument. Every member thought his or her way of doing things was the best way. Next came the federated models like Gaea and Kleisli , and then the data warehouses of Ensembl, UCSC, and others. This brings us to the ad hoc Web services that are currently in place. These allow programmatic access to data, as in the GenBank/EMBL example. To truly unify the services of bioinformatics data providers we need to move beyond this to a more formal Web services model.
In this Web services model, the data providers would register their services in a formalized service registry, and researchers' scripts would no longer need to be concerned with the interface details of the different databases. This model represents the unification that Lincoln, and judging by the response, apparently everyone in the audience, hopes to see in bioinformatics."
redux [09.27.01]
"As you might be aware of, flat-files have severe limitations, and we have been asked various times if we are going to distribute the EMBL data in different formats as well, XML being the one most prominently mentioned. In short, the XEMBL project will bring to the user several alternative formats of EMBL data."
"We have XEMBL running as a web service using SOAP (Simple Object Access Protocol) and WSDL (Web Service Definition Language)."
"Web Services can't create a framework in which any two arbitrary applications can interact because XML doesn't provide shared languages, merely shared alphabets. The Web Services stack pushes this shared semantics problem into higher and higher layers without solving it. Humans often cannot create perfectly transparent descriptions even when they are trying to, and they simply won't try when there's an economic incentive to stretch the truth."
redux [11.06.00]
"The semantics of services -- what they do and what data elements they manipulate mean -- is the key issue. Business value results from B2B collaborations that do the right thing. If they do something else, the damage may be dramatic. How, then, do we trust that a service does the right thing before it is used? And how do we make that determination at Internet speeds?
In small-scale OO systems, interface compatibility usually implies semantic compatibility. That is, an object that implements the right set of messages with the right types of arguments probably does "the right thing." This is true, in part, because small-scale systems tend to be built by a small team of programmers with shared understanding of how the system operates and, in part, because small systems offer little opportunity for ambiguity. However, in large-scale OO systems, the semantics provided by a given class cannot be reliably deduced from the message interface alone. Clearly, in an Internet populated with many thousands of services offered by thousands of different companies with very different agendas, compliance with some specified message set will not be sufficient to deduce the semantics of the service."
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Nature: Science Update
Antibiotic maker mapped
"Medicine's favourite bacterium has disclosed its DNA sequence. Researchers hope that the newly completed genome of Streptomyces coelicolor will lead the way to more effective antibiotics.
The bacterium and its relatives produce most of the natural antibiotics in current use, including tetracycline and erythromycin. They also generate compounds that are used to treat cancer and suppress the immune system."
"Professor Sir David Hopwood, of the John Innes Centre, in Norwich, UK, who led the £2m research project, said: "We knew four antibiotics were made by this strain, but we found 17 or 18 other clusters which make other active compounds that are possibly only produced under very special soil conditions.
"This organism has twice as many genes as typical free-living bacteria. You could say it's a boy scout - it's prepared. You've got the core of the chromosome, and then there are arms which are not essential but do useful things, like making antibiotics.""
"Streptomyces coelicolor A3(2) is the model representative of a group of soil-dwelling organism with a complex lifecycle involving mycelial growth and spore formation. These microbes are notable for their production of pharmaceutically useful compound including anti-tumour agents, immunosupressants and over two-thirds of all natural antibiotics currently available. The sequence was generated using a clone-by-clone approach, initially using cosmids generated and mapped by David Hopwood's group at the John Innes Centre, and latterly using a BAC library to fill gaps and confirm the map."
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The Washington Post
Scientists Compile Map of Mouse's Genome
"Passing yet another milestone in the rapidly advancing science of genetics, biologists said yesterday that they had compiled a map of the hereditary instructions of the laboratory mouse, the single most important test organism in medical research."
"At a blistering pace, scientists are gaining the tools they need for a deep inquiry into the nature of life."
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"Leaders of the public consortium of academic centers that decoded the human genome announced yesterday that they had also decoded the mouse's genome, a tool of great value in interpreting that of people. But the consortium directors' news release neglects to mention that their rival, Dr. J. Craig Venter, the former president of Celera Genomics, decoded the mouse genome more than a year ago."
"In interviews, Dr. Collins and Dr. Waterston said they did not dispute that Dr. Venter had indeed decoded the mouse genome earlier, but both said they had not seen the data. "There's a rumor it exists," Dr. Collins said, adding that Celera's mouse genome was available only to subscribers."
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The New York Times
Citing RNA, Studies Suggest a Much Deeper Gene Pool
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"Two scientific papers published this week suggest that there might be many more human genes than thought, or at least that the human genome has hidden levels of complexity that are only starting to be revealed.
Both papers report that human cells make far more RNA, a counterpart of the genetic material DNA, than can be accounted for by the estimated 30,000 to 40,000 human genes."