{bio,medical} informatics
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BBC
Anthrax gene code unravelled
""Scientists have the technology now which allows them to see exactly which genes are switched on or off. Having this information may reveal chinks in the armour of anthrax."
Another bacterial specialist, Professor Chris Wilmott, from the University of Leicester, warned that the genome data would not bear fruit for patients for some time - and doctors would have to be careful not to over-use effective drugs in the meantime."
"Scientists say they've found potential new targets for drugs and vaccines against the anthrax germ by deciphering and analyzing the bacterium's complete genetic makeup."
"For vaccines, the leads come from the study's indications that certain proteins are displayed on the bacterium's surface, he said."
"The research confirmed that the Bacillus anthracis isolated from a terror attack in Florida was different from closely related anthrax strains, the scientists reported. Researchers, using a comparison of the whole-genome sequence of the Florida sample with other strains, also confirmed that the anthrax discovered in Florida was derived from the Ames strain.
The scientists found 60 new genomic markers that include four "high quality" SNPs that were found to divide a collection of anthrax isolates into distinct families, according to the paper's authors."
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Nature: Science Update
Chimps expose humanness
"By studying chimpanzees, scientists are honing their genetic view of humanity, researchers told this week's meeting of the Human Genome Organisation in Cancun, Mexico."
"The data call for some revision of the estimated genetic similarity between us and our closest relatives. Previously, human and chimp genetic sequences were quoted as being nearly 99% identical, with a difference of only a few DNA's letters. In fact, the similarity may be as low as 94-95%, says Todd Taylor of the RIKEN Genomic Sciences Center in Yokohama, Japan.
redux [03.04.03]
"Chimpanzees seem almost human, and scientists have maintained for decades that chimps are, in fact, 98.5 percent genetically identical to humans.
But the results of a new study call that figure into question, with a finding that there are actually large chunks of the human and chimp genomes that are vastly different."
"It involves sampling data from select regions of many different related species, and then comparing them within the context of their phylogenetic relationships. In the research described in the Science paper, Rubin and colleagues sampled 17 primate species closely related to human and spanning 40 million years of evolution -- insufficient time for significant genetic divergence to have taken place.
According to Rubin, phylogenetic shadowing compensates for the failure of traditional comparative genomics techniques, which "invariably miss recent changes in DNA sequence that account for primate-specific biological traits." The approach overcomes the primary challenge of comparing genomes of closely related species: the difficulty in distinguishing functional from nonfunctional sequences."
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Mass High Tech
Bioinformatics’ promise meets with plenty of resistance at local biotechnology companies
"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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Slashdot
Distributed Computing Attacking SARS
"D2OL has added a SARS Target to it's distributed computing project which locates potential drug candidates for several viruses. At this point, I've replaced SETI@Home at least temporarily on all of my Boxen. There are clients available for Linux, Solaris, Mac OS X, and of course Windows."
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The Economist
Back to bases
"As a scientific model, the double helix opened the way to answering many lingering questions in genetics: how hereditary information is stored, how it is copied and passed on from one generation to another, how genetic damage is repaired and how information flows from the level of the gene to the marvellous structures of nature. But the double helix has invaded the wider world, too, and has become a symbol of the hopes and fears that people have about where biological knowledge might lead. When a movie about a genetically engineered future was dubbed "GATTACA" by its creator, he did not need to spell out the fact that the four letters used in the title are the abbreviations for the nucleotide bases--in other words, the letters of the genetic code.
In scientific terms, the model of the double helix, combined with the notion that DNA is a code, has transformed biology. But it has also given people a powerful visual and verbal means to communicate their concerns about the fruits of this new science--gene prospecting, DNA patenting, genetic testing, designer babies, cloning--and their social consequences."
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Wired News
Biotech Inventor Wins Big Bucks
"Leroy Hood has the kind demeanor of a kindergarten teacher. But his vocabulary belies his real identity: the most important inventor in modern biology.
Not that he's unconcerned about school kids. Hood has worked to make the science curriculum in Seattle-area K through 12 schools one of the best in the country. But the focus of his career, and the reason MIT has awarded him the $500,000 Lemelson-MIT Prize, is the invention of technologies that are the backbone of the life sciences today."
redux [04.26.03]
"When Dr. Leroy Hood sits down to talk about his latest ambition, he takes all of 10 seconds to warm up.
"I think we'll lead the way toward revolutionizing new ways of understanding biology," he said."
"But Hood's enthusiasm these days has been limited by finances. More than two years after an unceremonious exit from the University of Washington, he has been scrounging for money. And his newest vision -- using high-speed computers to turn the DNA jumble into something useful for predicting and preventing disease -- requires lots of money."
redux [01.19.02]
"The integration of bioinformatics with these systems approaches is an integral, essential feature. One of the things that we stress is that in the future it's going to be increasingly important for people in bioinformatics to be intimately associated with data producers, because no matter how smart you are you can't model biological complexity--it's just too complex. The only way we're going to understand it is through the integration of these global experimental observations, together with powerful computational tools for analysis, and ultimately, for modeling.
A mistake that a lot of people in bioinformatics have tended to make is thinking that you can set up a bioinformatics center and it can work in isolation from the biology, and it can study all these great databases and learn lots and lots about biology. In vitro biology and in silico biology are all popular terms, but it isn't true, and it isn't going to be true in the future."
redux [04.18.01]
[requires 'free' registration]
"Systems biology is a loosely defined term, but the main idea is that biology is an information science, with genes a sort of digital code. Moreover, while much of molecular biology has involved studying a single gene or protein in depth, systems biology looks at the bigger picture, how all the genes and proteins interact. Ultimately the goal is to develop computer models that can predict the behavior of cells or organisms, much as Boeing can simulate how a plane will fly before it is built.
But such a task requires biologists to team up with computer scientists, engineers, physicists and mathematicians. The structure of universities makes that difficult, Dr. Hood said."
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News.Com
IBM gives away tool for DNA searches
"IBM is giving away free Web services technology to help scientists track down DNA, as the company continues its push into the promising life sciences arena."
"IBM said its Web services technology allows scientists to do such things as narrow the search for useful genes related to a particular diagnosis in PubMed and retrieve the nucleotide sequences in GenBank."
redux [02.21.03]
"Web Services for the Life Sciences are illustrated in this application targeted for Bio-informatics researchers using the National Center for Biotechnology Information (NCBI) databases, PubMed, GenBank, and BLAST. The Rochester Life Sciences Framework team developed Web Services wrappers around each of the applications and provides example programs that use each of the three Web services as well as an example program that combines all three as sequential searches. Each of these programs are downloadable and include both the Java sources and compiled codes to show developers how these Web services can be constructed."
[ via bioinformatics.org ]
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."
"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 [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)."
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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Bio-IT World
In Silico Models with Many More Variables
"One of the critical priorities now is to take all the components we can detect, and reconstruct the interaction networks inside cells that underlie biological processes. This type of reconstruction is very tricky: People call it 'integration of heterogeneous databases.' Collating these data files is like stacking playing cards -- each piece of data stands upon, and influences, the reliability of other pieces.
The next priority is then to generate computer models that can be used for simulations -- in silico biology. There are three categories of models we need to build: models for metabolism, DNA regulation, and cell signaling."
redux [02.2.03]
[requires 'free' registration]
"Systems biology, a siren in a sea of dark prospects, has lured investors frustrated with low returns in biotechnology and anxious to set a new course of drug discovery. Institutions have also geared up training programs, but the excitement in the new field has failed to arrest downsizing in the biotech industry."
"Despite the interest of the pharmaceutical industry, prospective systems biologists should think carefully before investing in training in hopes of landing a job in the new field."
redux [01.10.03]
"At last count, 103 of the 341 faculty in MIT's engineering school-and we're talking aeronautic, astronautic, chemical, civil, electrical, environmental, materials science, mechanical, and nuclear engineering--were using the term "bio" to describe the nature of their research.
At a luncheon for 175 invited guests in the MIT faculty club here today, Vest gave a plug for the institute's nascent Computational and Systems Biology Initiative, an interdisciplinary program that will facilitate cross-fertilization among all of MIT's bio-interested faculty and students, whether they be engineers or in the departments of biology, chemistry, computer science, or physics."
redux [03.08.02]
[ summary can be viewed for free once registered ]
"To understand biology at the system level, we must examine the structure and dynamics of cellular and organismal function, rather than the characteristics of isolated parts of a cell or organism. Properties of systems, such as robustness, emerge as central issues, and understanding these properties may have an impact on the future of medicine. However, many breakthroughs in experimental devices, advanced software, and analytical methods are required before the achievements of systems biology can live up to their much-touted potential."
redux [02.26.02]
"Over the last few years, there's been an explosion of information in biology. The mapping of the human genome gave biologists unprecedented detail about some 30,000 to 40,000 genes. Efforts are also under way to identify the thousands--and potentially millions--of proteins encoded by those genes. Researchers are now pursuing the next logical step in integrating all this data: systems biology.
The goal is to understand not just the functions of individual genes, proteins and smaller molecules like hormones, but to learn how all of these molecules interact within, say, a cell. Biologists hope to then use this information to generate more accurate computer models that will help unravel the complexities of human physiology and the underlying mechanisms of disease. The biggest payoff: faster development of more-effective drugs."
redux [04.05.00]
[requires 'free' registration]
"I suspect that although the new enthusiasm for computers in biology is genuine, it overlooks some basic problems in implementation. The basic difficulty, as I see it, is that although biologists use computers, they do not trust everything that comes out of them. It is one thing to use them to print up nice-looking graphs, but it is an entirely different matter to use them to think better."
"Francis Crick was once quoted as saying that no biologist had ever made a discovery using a mathematical model. I would reply that no biologist has ever made a discovery by running an electrophoretic gel. They make discoveries by using their brains. Computers, like all scientific tools, are only as good as the person who uses them. If biologists don't understand how computer models are constructed, they won't know their strengths and limitations. Without some foundation of trust, biologists will be unlikely to utilize or accept this powerful method of data analysis."
redux [02.05.02]
"The project has been a pet of Gov. Gray Davis, who helped seed QB3 with $75 million in state funding. Intel co-founder Gordon Moore has quietly pledged an additional $10 million to launch this novel high-tech/biotech collaboration."
"Kelly said the future will involve figuring out how millions upon millions of interactions between inanimate genes and proteins somehow give rise to life at the cellular level -- a field called systems biology."
redux [01.19.02]
"The integration of bioinformatics with these systems approaches is an integral, essential feature. One of the things that we stress is that in the future it's going to be increasingly important for people in bioinformatics to be intimately associated with data producers, because no matter how smart you are you can't model biological complexity--it's just too complex. The only way we're going to understand it is through the integration of these global experimental observations, together with powerful computational tools for analysis, and ultimately, for modeling.
A mistake that a lot of people in bioinformatics have tended to make is thinking that you can set up a bioinformatics center and it can work in isolation from the biology, and it can study all these great databases and learn lots and lots about biology. In vitro biology and in silico biology are all popular terms, but it isn't true, and it isn't going to be true in the future."
redux [04.18.01]
[requires 'free' registration]
"Systems biology is a loosely defined term, but the main idea is that biology is an information science, with genes a sort of digital code. Moreover, while much of molecular biology has involved studying a single gene or protein in depth, systems biology looks at the bigger picture, how all the genes and proteins interact. Ultimately the goal is to develop computer models that can predict the behavior of cells or organisms, much as Boeing can simulate how a plane will fly before it is built.
But such a task requires biologists to team up with computer scientists, engineers, physicists and mathematicians. The structure of universities makes that difficult, Dr. Hood said."
redux [03.17.01]
"When Lee Hood started the Institute for Systems Biology, a project to build an integrated research supercenter for the biological sciences, few doubted the validity of the concept, but many wondered whether the technology existed to make it work.
Now, in a sign that others are also willing to gamble on the idea, systems biology is attracting commercial attention. Beyond Genomics (BG), a startup based in Cambridge, Mass., is attempting to glean medically-relevant information from multiple systems simultaneously, from genes to metabolites, by using software that identifies patterns in these systems caused by disease."
redux [07.13.00]
"A new mathematical biology is emerging. Building on experimental data from developing organisms, it uses the power of computational methods to explore the properties of real gene networks."
"Our understanding of gene networks is at an early stage. We perceive their complexity only after it has been filtered by the limitations of the techniques used to study them. Genome databases and DNA-chip technology, which enables huge numbers of genes to be screened for activity, will undoubtedly provide more, and much more complicated, data than anything produced by Drosophila genetics. If a relatively simple gene network such as the segment-polarity system is hard to understand intuitively, we can be certain that modelling will be essential to make sense of the flood of new data.
But this will not be elegant theoretical modelling: rather, it will be rooted in the arbitrary complexity of evolved organisms. The task will require a breed of biologist-mathematician as familiar with handling differential equations as with the limitations of messy experimental data. There will be plenty of vacancies, and, on present showing, not many qualified applicants."
redux [05.15.01]
"Our Mission is to develop an integrated, easy-to-use environment, the workbench , which will enable biologists to create, manipulate, display and analyze biological models at molecular, cellular and multicellular levels. We are focusing on biochemical networks including mass action kinetics, metabolic pathways, stochastic simulation, gene expression and regulation."
"One of the key aspects of out project is to facilitate collaboration among existing developers and users of system biology software. We aim to do this by providing an open-source software infrastructure which will enable collaborators to freely use and share each other's computational resources."
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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Canada.Com
Nova on PBS pays tribute to Rosalind Franklin, the unsung
heroine of DNA
"The 50th anniversary of the discovery of DNA's double helix structure is being observed this year.
Perhaps heightening the celebration is the fact that James Watson, Francis Crick and Maurice Wilkins, who shared a Nobel Prize for this scientific revolution, are around for the occasion. But the birthday party has a dark side and a tragic absentee, as this week's Nova documentary explains. The missing person is Rosalind Franklin, who, despite her extraordinary accomplishments, was kept an outsider in the men's world of science. She is the unsung heroine of DNA, just as she has been for a half-century."
"Fifty years later, Watson anticipates the one question that critics always ask: Why didn't he give Rosalind Franklin more credit for her role in the discovery?
"And the answer, though we saw a lot of her -- you know, when she was dying she went and stayed with the Cricks -- the only answer I can give -- and it sounds sort of gratuitous, but -- was, she sort of flubbed it, and we didn't want to say, 'Rosalind, why didn't you find the answer?'""
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The Scientist
The Behaviorome Mental Map Project
[requires 'free' registration]
"If we define an idea as the mental conceptualization of something, including physical objects, an action, or sensory experience, either now or in the future, then the number of objects in a living being's universe is finite. If we apply the methodologies used in genetics, psychology, animal behavior, sociology, history, and other disciplines to those ideas, it would provide us with the basis of a mental mapping project with the goal of describing the diversity of human ideas in any given situation or dilemma. This is not a diagram of a physical structure, like a genome or proteome, but a map of ideas.
The project stages will include verification and expansion of my initial proposal for nine separate classes of ideas, including: conceptualization of physical objects; memories; sensory states such as pain, pleasure, libido; and interactive conceptualization of ideas in a community-based response."
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BBC
Most
ancient DNA ever?
"The oldest ever DNA has been found preserved in ice in Siberia.
The record-breaking samples are from plants which lived there 400,000 years ago."
"The approach gives archaeologists a new window into the past, creating a vivid picture of plant and animal diversity at the time."
"For instance, the plant DNA from Siberia suggests that tundra was once an area rich in plants that would have been able to support large herds of mammoths and other big animals. But about 11,000 years ago, the once plentiful grasses began to disappear, perhaps helping to cause the extinction of some of the large plant eaters that once roamed parts of Siberia and Alaska.
Linking the soil DNA with specific times in the past may "have major implications for many fields," including the study of ancient peoples, the authors said in the study."
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Stanford Medical Informatics Preprint Archive
A Modular Framework for Automated Space-Time Surveillance
Analysis of Public Health Data
"Public health surveillance is changing in response to concerns about bioterrorism, which have increased the pressure for early detection of epidemics. Rapid detection necessitates following multiple non-specific indicators, accounting for spatial structure, and quickly characterizing aberrancies. A single analytic method cannot meet these requirements, but there is no existing framework for the interoperation of surveillance methods. In this paper, we present such a framework and report on a preliminary implementation. Our framework consists of a decomposition of the surveillance analysis task into sub-tasks, and an ontology of surveillance analysis methods, which automate the sub-tasks. As an initial implementation, we use methods developed according to this framework to analyze 911 dispatch data from San Francisco."
redux [01.22.03]
[requires 'free' registration]
"To help protect against the threat of bioterrorism, the Bush administration on Wednesday will start deploying a national system of environmental monitors that is intended to tell within 24 hours whether anthrax, smallpox and other deadly germs have been released into the air, senior administration officials said today.
The system uses advanced data analysis that officials said had been quietly adapted since the Sept. 11 attacks and tested over the past nine months. It will adapt many of the Environmental Protection Agency's 3,000 air quality monitoring stations throughout the country to register unusual quantities of a wide range of pathogens that cause diseases that incapacitate and kill."
redux [11.25.02]
"The Albuquerque physician-turned-researcher just returned from a trip to the NATO Summit in Prague, where he hoped to persuade President Bush and the other 19 member nations that a global health surveillance network is the best way to protect people from manufactured disease."
""The current system is exquisitely designed to fail," Zelicoff said."
redux [10.31.02]
"An epidemic resulting from an act of bioterrorism could be catastrophic. However, if an epidemic can be detected and characterized early on, prompt public health intervention may mitigate its impact. Current surveillance approaches do not perform well in terms of rapid epidemic detection or epidemic monitoring. One reason for this shortcoming is their failure to bring existing knowledge and data to bear on the problem in a coherent manner. Knowledge-based methods can integrate surveillance data and knowledge, and allow for careful evaluation of problem-solving methods. This paper presents an argument for knowledge-based surveillance, describes a prototype of BioSTORM, a system for real-time epidemic surveillance, and shows an initial evaluation of this system applied to a simulated epidemic from a bioterrorism attack."
redux [02.18.02]
"President George W. Bush, the National Homeland Defense Secretary, Tom Ridge, and Health and Human Services Secretary, Tommy Thompson visited the University of Pittsburgh (UP) yesterday to review one of the advanced developments in medical informatics - a collaboration of the University's Center for Biomedical Informatics and Carnegie Mellon University. The project, known as the Real-Time Outbreak and Disease Surveillance system (RODS), is an early warning system for outbreaks of disease designed to obtain and analyze existing sources of data in real time."
"The Real-time Outbreak and Disease Surveillance (RODS) system is a prototype public health surveillance system. RODS collects and analyzes relevant data automatically and in real-time, including emergency room registration data, microbiology culture results, reports of radiographs, and laboratory orders. RODS provides tools that (1) help detect the presence of a disease outbreak, and (2) support the characterization of that outbreak by a public health official. These tools include case definitions, automatic detection algorithms that can be attached to specific data streams, and data analytic tools that support temporal and spatial data analysis and visualization."
redux [06.29.01]
"The merits of linking two fields seemingly as disparate as geographic information systems (GIS) and bioinformatics might not seem obvious, but Virginia Tech's recent symposium linking the twoaeand its roster of renowned participants from both fieldsaehas raised expectations "Applications of GIS to Bioinformatics" was the first major public forum to cross-pollinate the disciplines, helping to fortify a relatively new, yet highly promising investigative area."
""As a result of new dialog between the fields, as we've had at this conference, we are gaining an important mechanistic link between individual-level processes tracked by genomics and proteomics and population-level outcomes tracked by GIS and epidemiology. This will allow us to do a far better job of monitoring, quantifying, and predicting human-health consequences associated with the environment. The potential payoff in related fields such as those looking at climate change, emerging and resurgent infectious diseases, and environmental health is enormous.""
"The meeting brings together researchers in two of the most dynamic analytical technologies-GIS and bioinformatics. The value of GIS analytical systems and data structures to bioinformatics are only now being recognized. Similarly, the methodologies used in bioinformatics can inform GIS scholars of new approaches to pattern recognition and analysis. The purpose of the symposium is to explore the potentials for using GIS as an analytical methodology in bioinformatics and to understand the opportunities bioinformatics presents to the GIS research community. The symposium, the first to focus on the interface between these two research areas, will afford scholars the opportunity to establish new research directions in both fields of investigation."
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Bio-IT World
The Complete Gene Set as the Key Data Connector
"The real surprise, of course, was this issue about the number of genes. At first, we weren't so sure about the new, lower estimate [~30,0000], but there is an increasing degree of confidence in it. People are still finding genes, and some people have reported finding very many. But there is more than one explanation for that. For example, there are clearly a lot of pseudogenes in the genome -- sequences derived from a functional gene but that are no longer functional.
Part of this uncertainty about the number of genes is because of the state of gene prediction."
redux [06.05.02]
"Re-analyzing the same chromosome through a different technique, researchers at the University of Geneva and the Ludwig Institute for Cancer Research found that chromosome 21 contains roughly 10% more genes than were either confirmed or predicted.
"This demonstrates why we cannot rely on gene prediction alone to identify all human genes," said the study's lead author, Dr. Stylianos Antonarakis, of the Division of Medical Genetics at the University of Geneva Medical School. "Getting the right number of genes is crucial if we hope to use this information to fight disease.""
redux [10.11.01]
[requires 'free' registration]
"Counting human genes ought to be straightforward. Tracking telltale signs--motifs for promoters, translation start sites, splice sites, CpG islands--gene counters must by now be mopping up, finalizing chromosomal locations of every human gene already known, and predicting whereabouts of all the rest. Insert one human genome sequence, turn the bioinformatics crank, and genes gush out like a slot machine jackpot, right?
"No, no, no," says Bo Yuan, of Ohio State University, having a laugh over the idea that computation is all you need to tally genes. To the contrary, states the director of the bioinformatics group in the division of Human Cancer Genetics at Ohio State, trawling for genes is so labor-intensive that several years may pass before researchers possess a highly accurate count."
redux [08.24.01]
[requires 'free' registration]
"After a humiliating deflation this February, human dignity is on the recovery path, at least as measured by the number of genes in the human genome.
Two new estimates put the likely number of human genes at around 40,000, up by a third from the estimate of about 30,000 in February by the two teams of scientists who decoded the human genome. The low estimate still has its defenders."
"Recent estimates that the human genome consists of only about 30,000 genes may be way off the mark, according to a study published today in the journal Cell. NPR's Richard Harris has the story. (3:45)"
redux [01.18.01]
"Two rival teams that cracked the human genome may have underestimated the number of human genes, according to a new computer analysis."
Scientists in the United States claim humans are built from 66,000 genes, nearly twice as many as the current consensus."
"But the new analysis, published on the website of the journal Genome Biology, has been dismissed by the Sanger Centre, in Cambridgeshire, UK, which was responsible for about a third of the human genome sequencing effort."
""The experimental evidence actually points to 30-40,000 genes," Dr Hubbard told BBC News Online. "I don't believe the argument in this paper that there are a lot more genes. This is an entirely computational paper and I don't think it's very credible.""
redux [11.13.00]
[requires 'free' registration]
"If James Watson, co-discoverer of DNA's structure, says we don't know how many genes there are, you're inclined to believe him. So it was a great surprise to hear the legend denounced, albeit with due deference. At the last count, insisted Kay Davies, professor of anatomy at the University of Oxford, humans are reckoned to have 40,944 tiny protein factories.
She was drawing on statistics that define the proteome, the protein equivalent of the genome, as the set of all expressed proteins in humans, for which 40,944 genes are individually responsible. Not a huge figure, she noted, barely the equivalent of three flies or a couple of worms. "Apologies Jim, let's talk over tea," she added."
redux [05.13.00]
"Well, they weren't all men, but mostly. The betting in the pub continued, the lowest bet being 29,800 genes placed by Pat Tome and the highest number coming from John Quackenbush at 118,259.
The pool was organized by Erwin Birney, a team leader at the European Bioinformatics Institute. He tried to convince the bartender to oversee the betting, but was told in no uncertain terms that no gambling was allowed in the Cold Spring bar.
Guesses on the number of genes in the human genome have lowered considerably since the mapping of chromosome 21, which researchers found to contain only 225 genes, far fewer than previously predicted. The researchers on the chromosome 21 study predicted their results could mean that there are as few as 40,000 genes in the entire human genome.
"Someone from Incyte will probably show up and bet 150,000," one gambler said."
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Genomeweb
Canadian Team Leader: SARS Coronavirus Genome Has 11 Novel
ORFs
"The sequenced coronavirus believed to cause Severe Acute Respiratory Syndrome has eleven open reading frames, and these predicted coding regions lack homology to sequence in existing gene databases, Steven Jones, director of bioinformatics at the British Columbia Cancer Center, said today.
"People were thinking that [the SARS virus] was some kind of hybrid virus between a fairly well studied human virus, recombined with a non-human virus," he said. "A lot of those Asian flus have been associated with avian viruses." But the ORFs that Jones' group is finding all have consistent phylogeny. "They all look like they have been in the same organism for a long period of time," he said. And they are "only modestly similar to [ORFs in] other coronaviruses.""
"After accomplishing what no other group of scientists has done, they celebrated with a round of doughnuts and a sigh of relief.
It was 4 a.m. Sunday, and the scientists at the Michael Smith Genome Sciences Centre in Vancouver had published the draft sequence of what is suspected to be the SARS virus."
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UC Santa Cruz Currents
UCSC Genome Browser provides portal to finished human genome
sequence
"As leaders of the Human Genome Project announced the project's successful completion at a press conference today in Bethesda, Md., UCSC bioinformatics researchers made the completed reference sequence of the human genome publicly available on the web-based UCSC Genome Browser."
""We have now built the browser on top of the finished genome sequence. That sequence will serve as a new foundation for medicine and human biology, and our browser will form the most popular portal to explore our shared genetic heritage," said Haussler, who directs UCSC's Center for Biomolecular Science and Engineering (CBSE)."
redux [06.13.02]
"But Celera's rival published its version free of charge on the internet, a move which damaged Celera's commercial prospects. "That has had an impact," says Bennett. "Any stand-alone information business will be challenged because the value of information degrades," he adds.
But he denies that the venture has been a failure. "We have 250 subscribers, both commercial and non-commercial," says Bennett. The business even makes a profit, but the company will not discuss the impact of the free genome data on profits."
redux [04.08.02]
"Jim Kent was a graduate student in biology at the University of California, Santa Cruz (UCSC), when he wrote the program that allowed the public human genome team to assemble its fragments just before Celera's private, commercial effort. His program ensured that the human genome data would remain in the public domain. Kent wrote the 10,000-line program in a month, because he didn't want to see the genome data locked up by commercial patents."
"Kent's work illustrates the need to think about more than just open source code; in the scientific community there is a growing awareness of the importance of open data."
redux [03.07.02]
"''I humbly have to admit that between only 15 to 20 percent of my requests are fulfilled. I cannot afford to do anything else,'' said Tak Mak, a leading genetics researcher at the University of Toronto.
"In fact, according to a recent study published in the Journal of the American Medical Association and led by doctors at Massachusetts General Hospital, nearly 50 percent of surveyed geneticists at major US academic institutions said that another faculty member had denied them at least one request for information in the past three years. The study also found that geneticists are vastly more likely to believe that sharing has decreased in their field over the past decade than that it has increased - a startling figure given how much easier the Internet has made the transfer of information."
redux [01.23.02]
[requires 'free' registration]
"Nearly half the academic geneticists who asked for additional information, data, or materials related to a published research report were denied their requests, a new survey reports today. Are geneticists being unfairly pilloried?"
"Because they were denied access to data, 28% of geneticists reported that they had been unable to confirm published research. Other reported consequences were delays in publications, abandonment of a promising line of research, and the collapse of collaborations."