{bio,medical} informatics
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Genomeweb
Should Bioterror Fear Make Sequences Secret? For TIGR's Fraser
It's a Qualified No
"Despite fears that bioterrorists will use DNA sequence data to create 21st century superpathogens, genomic science should remain public, The Institute for Genomic Research head Claire Fraser said at a special National Academies meeting on national security and the life sciences last week.
Her explanation: genomics just isn't good enough yet to provide the kind of tools terrorists need."
redux [12.01.02]
[requires 'free' registration]
"Scientific information that the US government wants to keep mum, but which can't officially be labeled "classified," has been designated "sensitive but unclassified." One example is the National Academy of Science's recent report on agricultural bioterrorism. Its chapter on bioterror case studies is available only on a need-to-know basis. Other professional groups may find themselves in the same boat, but the rules governing the category are anything but clear.
Reference: Enserink, M. 2002. Entering the twilight zone of what material to censor. Science 298(5598):1548."
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The Scientist
Metaphors and Dreams
[requires 'free' registration]
"To reread James Watson's The Double Helix is to see once again the power of the scientific method: Reduce the problem to little solvable bits and attack them serially. The book shares the exhilaration of the discovery of why DNA must be the secret of life.
But "must be" is a prediction, not an explanation. The secrets are still there. How could DNA inside the cell make trillions of cells behave as one? What is it about DNA and the cell that makes a protein, that triggers a process, that ends in a firing of electrical signals and discharge of transmitters that assembles a thought, like this one, in these 40 words? What flickering community of a spin doctor's genes set in motion the thought expressed by President Clinton upon the completion of the first drafts of the human genome, on June 26, 2000? He said (and compared to some other things people said, it seemed quite modest), "This is the most important, the most wondrous map ever produced by mankind. It will revolutionize the diagnosis, prevention, and treatment of most, if not all, human diseases." And could there have been a genetic basis for the response of 100,000 clinicians, biomedical researchers, health managers, and patients: "Yes, but how? And when?""
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Genomeweb
Systems Biology at MIT: It's All Over the Place
"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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Bio-IT World
Grids: When Concepts Collide
"Clearly, grid computing means different things to different people, often at different times. To its most visionary pundits, grids symbolize the penultimate step in the evolution of computing architecture into a universal source of pervasive, utility-like computing power that companies can purchase as needed, much as they purchase electricity today. Most stalwart advocates believe that grids not only represent the IT environment of the future but also will ultimately eclipse in significance what the Internet is today."
"All hype aside, it is unlikely that grids will fundamentally change the way that scientific and technical computing is done in the near term, particularly in the private sector."
redux [09.13.02]
"A final obstacle that Stuart pointed out is of the self-inflicted variety: Grid, distributed, peer-to-peer, and other similar incarnations have become victims of their own hype. Increasing media coverage of these technologies has led to confusion in the marketplace, Stuart posited, "and when a prospect becomes confused, the easiest thing is not to do anything.""
"However, he added, there is a bright side to the publicity deluge. Citing the Gartner Group's annual "Hype Cycle of Emerging Technologies" report, which tracks new methods from the initial "tech trigger" period through the "peak of inflated expectations," the "trough of disillusionment," the "slope of enlightenment," and onto the final "plateau of productivity," Stuart noted that desktop grid computing might be working its way from the trough to the slope phase right now, largely because users are discovering which applications work best with the architecture."
redux [09.11.02]
"Platform Computing recently announced Bristol-Myers Squibb (BMS) has selected Platform ActiveCluster to build one of the largest enterprise desktop grids in production for pharmaceutical research to date. BMS, after an extensive competitive evaluation and pilot stage, is currently deploying Platform ActiveCluster to several thousand desktop computers housed in its research sites across the northeast United States."
"BMS will use the Platform technology, Rozenman said, to link a large number of desktop PCs and existing dedicated computer clusters. The resulting grid initially will be utilized to run both cheminformatic applications, such as Dock, Autodock, Think and GOLD. Ultimately, the grid also will be used to run a variety of bioinformatics applications. "
redux [08.30.02]
"A research team at the San Diego Supercomputer Center is using a grid-based computer system from Entropia to build a set of protein structure databases."
"With the help of 250 desktop computers with processing power ranging from 180 MHz to 2.2 GHz, the platform has so far completed calculations on almost 1,000 proteins, said Elbert."
""What they've done in principle they could have done on one of their supercomputers, but those machines are heavily used for other projects," he said. "This is a way of expanding capacity. And it's a whole lot cheaper.""
redux [11.28.01]
"IBM will supply the University of Pennsylvania and four hospitals with computers that will link into a computing "grid" to check for breast cancer, the company will announce Wednesday.
The grid will be used to detect breast cancer in patients, store mammograms in digital form and identify populations that are particularly susceptible, the company said in a statement. The system can be used, for example, to compare a new mammogram to a previous year's image to detect changes.
IBM, along with rivals such as Sun Microsystems and Compaq Computer, have been backing grid computing, which joins computers and storage systems into a large pool of computing power.
redux [11.21.01]
"The US National Science Foundation has announced a $12 million programme - called the NSF Middleware Initiative (NMI) - to develop middleware: software that allows scientists to share applications, scientific instruments and data, and collaborate with their colleagues across high-performance networks.
The effort will build on the success of the Globus project in developing middleware tools for grid computing, and will integrate Globus and other emerging middleware components into a well-tested, comprehensive, commercial-quality, middleware distribution package that runs on multiple platforms. These middleware distributions will be disseminated to research labs and universities worldwide."
redux [11.12.01]
"Platform Computing, a company that tries to harness the collective computing power on computer networks, has signed a deal to commercialize an open-source supercomputing project.
Platform is working with the Globus Project to commercialize the Globus Toolkit for governing the use of computers and storage systems joined into a large computing "grid," Platform said Wednesday."
"Grid computing, though, often uses higher-powered computers than mere desktop PCs, and has attracted the interest of IBM, which thinks corporate customers as well as academics will use grid methods. IBM is working with Globus to boost this expansion.
Grid computing has long held potential for some types of computing tasks--typically those that don't require as much communication between one computing task and another. For this reason, they don't replace single mammoth supercomputers such as those from Cray. However, grid computing is popular among pharmaceutical companies and others."
"Computational Grids are emerging as a popular paradigm for solving large-scale compute and data intensive problems in science, engineering, and commerce. However, application composition, resource management and scheduling in these environments is a complex undertaking. In this paper, we illustrate the creation of a virtual laboratory environment by leveraging existing Grid technologies to enable molecular modeling for drug design on distributed resources. It involves screening millions of molecules of chemical compounds against a protein target, chemical database (CDB) to identify those with potential use for drug design. We have grid-enabled the molecular docking process by composing it as a parameter sweep application using the Nimrod-G tools. We then developed new tools for remote access to molecules in CDB small molecule database. The Nimrod-G resource broker along with molecule CDB data broker is used for scheduling and on-demand processing of jobs on distributed grid resources. The results demonstrate the ease of use and suitability of the Nimrod-G and virtual laboratory tools."
redux [10.09.00]
"The SETI@Home problem can be thought of as a special case of the distributed computation verification problem: "given a large amount of computation divided among many computers, how can malicious participating computers be prevented from doing damage?" This is not a new problem. Distributed computation is a venerable research topic, and the idea of "selling spare CPU cycles" has been a science fiction fixture for years."
"The Internet makes it possible for computation to be distributed to many more machines. However, distributing computing around the internet requires developers to consider the possibility of malicious clients."
"The general study of secure multiparty computation has produced much interesting work over the last two decades. Less well studied, unfortunately, are the tools and techniques required to move the theoretical results to the real world. The old dream of massively distributed computations is finally coming true, and yet our tools for building and analysing real systems still seem primitive. The challenge of the next few years will be to bridge this gap."
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The Standard: China
Bio-IT sector `set to boom'
"Growth of biotechnological and information technology spending in the mainland's life sciences industry will rise at a five-year compound annual growth rate of 42 per cent to US$344 million (HK$2.68 billion) by 2006, according to IDC Asia-Pacific."
""The academic [34 per cent] and government [19 per cent] sectors are currently most prevalent in Bio-IT adoption,'' IDC said. However, it forecasts China's biotech firms will overtake the government sector in Bio-IT spending by 2006."
"Expenditure is currently fuelled by infrastructure ramp-up in the form of servers/clusters and software. Professional and IT services are expected to dominate by 2006 with a forecast compound annual growth rate of 64 per cent to 2006, accounting for revenues of US$105.2 million."
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Journal of the American Medical Association
John Quackenbush Talks About the Clinical Promise of Genetic
Microarrays
"Much like the giant Homer Simpson Pez dispenser in his office, John Quackenbush, PhD, dispenses tasty tidbits when he opens his mouth."
" I think if you review the microarray literature, everybody in the early days was saying, oh, we're going to find out what all the pathways are. And now I think everyone is realizing that what comes out of the arrays are associations. It's the whole link, the disjunction between correlation and causality. I may discover that mass murderers drink more milk than anybody else but that doesn't mean drinking milk makes you a mass murderer."
redux [12.17.02]
"Investors may have stopped watching, but drug companies are finally beginning to wrench tangible benefits from the human genome. Two years after a boom fed by hype, a revolution finally is starting to take hold not in how drugs are invented, but in how they are tested.
Merck (nyse: MRK - news - people ), the world's third-largest drug company, is using gene expression arrays, also known as DNA chips, to keep clinical duds from reaching expensive animal or human trials. Separately, Millennium Pharmaceuticals (nasdaq: MLNM - news - people ) used similar chips in its late-stage clinical studies of its cancer drug, Velcade. Millennium's work is a big step toward so-called personalized medicine, in which treatment would be tailored toward individual patients based on genetic makeup."
redux [10.07.02]
"Perlegen has spent upwards of $50 million on the chemistry, instruments, computers and brain power needed to pull off this hellish job of proofreading.
Yet there was only a muted celebration a few weeks ago, when Perlegen's scientists decided they'd found the last of the 1,717,015 SNPs that biotech firms have been seeking since the human genome was sequenced in 2000.
[requires 'free' registration]
"Pharmacogenomics holds the promise of delivering safer, better designer drugs--and profits--to pharmaceutical manufacturers. But the technology also poses a challenge to the industry's current, highly successful business model that relies on one-size-fits-all blockbuster drugs.
For small biotech companies and large drug manufacturers alike, pharmacogenomics remains only one component of genome-based research and consumes only a small part of the $30 billion (US) in annual pharmaceutical research and development funding, according to the Pharmaceutical Research and Manufacturers of America (PhRMA). "It's an area where we are seeing movement, but it's not there yet," says Gillian Woollett, associate vice president for biologics and biotechnology at PhRMA."
redux [09.10.02]
"Collins is unimpressed by the hubbub that has shaken the industry lately. "In some quarters there was a misunderstanding, or naivete, about how having the sequence was going to solve everything. And there were some business models built solely upon the notion of quick profits, particularly selling subscription databases."
He dismisses talk about a foundering industry. "I think that every pharmaceutical company is still expecting that genomics will be the platform upon which they will build the next generation of drugs," says Collins. Others echo Collins' perspective. "We will change the treatment of cancer," says Variagenics' Adams. And there is no hint of doubt in his voice."
redux [08.08.01]
"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."
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Wired News
A
Name for Clone Babies: 'Hoax'
"The independent scientist and journalist brought in by Clonaid to verify its successful cloning of a human denounced its claim on Monday as a possible "elaborate hoax" and halted his review."
""It's very clear everyone has, rightfully so, proven these people to be the kooks that they are," said Kevin Wilson, director of public policy for the American Society for Cell Biology. "The problem is, I worry that their kookiness is going to be visited upon research," he added."
redux [12.27.02]
"A cult which believes that humans were first created by aliens claimed yesterday that it had won the clandestine and increasingly bizarre race to produce a human clone. It said a baby girl was born on Thursday from an egg fertilised by a skin cell from her mother.
Brigitte Boisselier, who calls herself a bishop of the Raelian sect, offered no proof to back her claim at a press conference in Florida, but said an independent panel of scientists would be allowed to verify it with DNA tests in the next eight or nine days."
"A former ABC News science editor, Michael Guillen, said during the news conference that he was arranging "independent, world-class experts" to run DNA tests needed to verify successful cloning. Guillen said he was not being paid by Clonaid."
"Guillen, who said he would find experts to perform DNA testing, is not wholly trusted by scientists. In a recent book on "Voodoo Science," physicist Robert Park -- an outspoken critic of pseudo-science and fakery who is a professor of physics at the University of Maryland and director of the Washington office of the American Physical Society -- said of Guillen: "Although uniquely positioned to help millions of scientifically unsophisticated viewers understand how the natural world behaves, Guillen chose instead to portray the darkest superstitions that beset our species as open scientific questions.""
"Less than six years after the cloning of a sheep named Dolly, a group claims to have engineered the first cloning of a human being."
"Here are key facts about the chronology of cloning."
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USA Today
Educators working to create comprehensive digital library
"More than 100 teams of educators nationwide are working with the National Science Foundation to develop what they hope will be the nation's most comprehensive digital library for the sciences."
"Developers note that while tons of information is already available on the Internet, it can be difficult for teachers to find what they need and then gauge its quality."
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MSNBC
Could fear of
terror muzzle science?
"The Massachusetts Institute of Technology walked away from a $404,000 study because the government wanted to restrict participation by foreign students. Other universities are balking at demands that the government check research in the name of national security before scientists can publish or even talk about it.
WHILE MOST FEDERAL financing still comes free from such strings, attempts to impose restrictions on research have increased since Sept. 11, 2001, out of fear that some information could help terrorists."
" The Massachusetts Insitute of Technology turns down a $400,000 contract for a federal research study. The government ordered limits on participation by foreign students. The case highlights new restrictions on research since the Sept. 11 attacks. NPR's Renee Montagne talks with MIT aeronautics professor Sheila Widnall."
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British Medical Journal
Papyrus
to PowerPoint (P 2 P): metamorphosis of scientific
communication
"Journals do not have an exclusive "right" to science. A publication and a scientific presentation do virtually the same thing---they share scientific knowledge. Publication and presentation have been separate but could "morph" into a single entity. This metamorphosis is taking place and is driven by a juggernaut called PowerPoint, Microsoft's graphics and slide presentation software."
"Over 95% of presentations use PowerPoint. It is the lingua franca of science. Each day 30 million PowerPoint presentations are produced. PowerPoint is on 250 million computers worldwide. There are four million PowerPoint lectures on the web, and the number is increasing logarithmically (Google search). Reasons for the rapid spread are obvious. PowerPoint is easy, relatively inexpensive, and fast, and scientists control production."
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The Financial Express
Pharma Players To Invest More In Bio-IT, Govt To Chip In Less,
Says IDC Report
"The 'Economist' wrote sometime ago, "If Indian biotechnology has a cover girl, it is Kiran Mazumdar Shaw...." Ms Shaw, chairperson and managing director of Biocon India Ltd, the country's biggest biotechnology company, has definitely contributed lots to bring India under the spotlight, where bioscience is concerned. But, how is India tipped to fare in Bio-IT or bioinformatics, which is hyped to be the next big thing after information technology?
Already scientists have dismissed the boom as a hype, but India's involvement in the sector is set to grow, if IDC's latest research is to be believed. According to the report, the growth of Bio-IT spending in the domestic life sciences industry is expected at a five-year compounded annual rate of 65 per cent."
redux [12.13.02]
[requires 'free' registration]
"India is set to reap substantial rewards in the field of functional genomics, thanks to an invaluable genetic resource and highly advanced IT expertise, predicts Samir Brahmachari, director of the country's Institute of Genomics and Integrative Biology in Delhi."
"Brahmachari sees India's genetic resource - not the biological samples themselves, but the associated information - as a tradable commodity. Data can be processed using India's unparalleled IT expertise, he says: The country's IT industry generated about $10 billion in revenues this year, and has continued to grow by 50% each year over the past decade. The information, once processed, represents an "intellectual-property protectable" commodity, he says."
redux [06.23.02]
"Also, India's success in information technology provides excellent opportunities in the field of bioinformatics.
"Traditional IT companies are translating their strong capabilities in data mining and warehousing to business models based on biological data," says the report, citing examples of IBM's India Research Lab and Satyam's five-year agreement with the Center for Cellular and Molecular Biology, Hyderabad."
redux [02.13.02]
"India's biotech boom could even dwarf software in coming years if you trust the most optimistic projections. Much of our $2.5-billion biotech market relies on low-end products like vaccines, but experts predict that as more start-ups come up, that could change dramatically."
"The need to dive into this ocean of genetic data for hidden treasures has created a whole new discipline--bio-informatics, the science of using information technology (IT) to decipher the genomic jumble. Thanks to a flourishing IT industry, bioinformatics is today the darling of venture capitalists, drug firms, and, of course, IT majors. So, Satyam Computers has signed a five-year alliance with CCMB to create, store, and annotate genetic databases, and it is angling for contracts from global bigpharma to sequence genes and build protein catalogs. Strand Genomics, a Bangalore-based bio-informatics start-up, is designing tools to accelerate drug discovery."
redux [09.17.01]
"India has the potential to garner 8-10 per cent of the global software market in the next few years from the current levels of just 1.5 per cent, but the country?s planners need to focus on improving computer penetration and use of Indian made software in the industry.
This was the view of FC Kohli, chairman, Tata Consultancy Services, while speaking at Connect 2001, an international conference and exhibition on information technology, communication technologies and bioinformatics, which opened on Thursday. Currently, India's IT exports are about $8.7 billion."
redux [08.27.01]
"THE mood is one of caution as far as bioinformatics is concerned. The beginning of the year saw hype building up around the fledgling industry as the next big gold rush for India.
But six months after the first bioinformatics seminar in the country, with the IT industry's lesson on hype fresh in mind, things are moving at a more sedate pace."
"In India, bioinformatics training institutes have already begun to mushroom. Bangalore and Hyderabad have around five private training institutes between them. However, the industry is sceptical about the quality of manpower these centres can supply because most of them have short-term courses offering basic skills, says Dr. Sabharwal. In all fairness to them she adds, "We need to wait for a few months to see the outcome of it all.""
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The New York Times
To Study Disease, Britain Plans a Genetic Census
[requires 'free' registration]
"In 2003, Britain plans to undertake the world's most ambitious study of the origins of disease.
Looking forward to the day when people will know their genetic makeups and request a precise picture of their risks of developing various diseases, the study organizers plan to assemble a database of medical information about 500,000 Britons, including their DNA."
redux [11.08.00]
"For the past decade, Stanford Medical Informatics has combined clinical informatics and bioinformatics research and training in an explicit way. The interest in applying informatics techniques to both clinical problems and problems in basic science can be traced to the Dendral project in the 1960s. Having bioinformatics and clinical informatics in the same academic unit is still somewhat unusual and can lead to clashes of clinical and basic science cultures. Nevertheless, the benefits of this organization have recently become clear, as the landscape of academic medicine in the next decades has begun to emerge. The author provides examples of technology transfer between clinical informatics and bioinformatics that illustrate how they complement each other."
"In his article "The promises of health care" J.H. Bemmel writes that "some 25 years ago, there was no shortage of optimism about expert systems in health care...it becomes clear that perhaps the early researchers were overenthusiastic, many challenges lie ahead, much fundamental research still has to be done."
Is therefore only wise not to look too far ahead, not to be too overenthusiastic again. 10 years ahead seems to be a good pick. A white paper by the American College of Informatics published recently made predictions for the year 2008, a year "not so far in the future as to be ungrounded in current realities""
"The future brings not only new innovations and applications: It will also affect Medical Informatics as a discipline:
- Its imminent merger with bioinformatics
- the emergence of sub-disciplines in medical informatics."
redux [06.07.00]
"Basic biological science has always had an impact on clinical medicine (and clinical medical information systems), and is creating a new generation of epidemiologic, diagnostic, prognostic, and treatment modalities. Bioinformatics efforts that appear to be wholly geared towards basic science are likely to become relevant to clinical informatics in the coming decade. For example, DNA sequence information and sequence annotations will appear in the medical chart with increasing frequency. The algorithms developed for research in bioinformatics will soon become part of clinical information systems. In this paper, I briefly review the intellectual roots of bioinformatics and how the field has evolved in the last few years. Fortunately, a core set of scientific paradigms have provided a focus to the field. Even in this short period, however, there has been a change in the nature of the questions being asked and the types of experiments being attempted. These changes are consistently leading bioinformatics towards problems of clinical relevance. Some molecular biology information systems already have important clinical implications. I will discuss the differences in the culture and approach to science of clinical informatics and bioinformatics, but will argue that the two disciplines share important intellectual challenges which make them very closely allied fields (despite the cultural differences). Finally, I will identify a few areas common to both disciplines where developments in one field may help catalyze faster progress in the other. For example, useful database integration technologies have (arguably) matured more rapidly within bioinformatics than in clinical informatics. At the same time, clinical informatics embraced the idea of controlled terminologies relatively early, and offers lessons to those in bioinformatics attempting similar tasks."
redux [05.15.00]
[requires 'free' registration]
""I just wanted to do something good," Mr. Fuchs said. "But once money came into the picture, why not have it be shared with me?"
These days more and more patients are asking the same question. Laboratories offer tests for more than 700 human genes, with more being discovered almost daily. And, for almost every gene, some medical institution or some company owns a patent on its use.
"The value of patients' tissues has potentially gone up enormously," said Dr. Barry Eisenstein, the vice president for science and technology at the Beth Israel Deaconess Medical Center in Boston. But, Dr. Eisenstein said, patients whose cells provided the genes that have been patented are almost never compensated."
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NHGRI
50 Years of DNA: From Double Helix to Health
"April 2003 will witness the historic culmination of one of the most important scientific projects in history: the sequencing of the human genome. In addition, April 2003 will mark the 50th anniversary of another momentous achievement in biology: James Watson and Francis Crick's Nobel Prize winning description of the DNA double helix.
Furthermore, the April 2003 publication of a landmark scientific report will describe the future of the field of genomics, and the role that the National Human Genome Research Institute (NHGRI) and the National Institutes of Health (NIH) will play in enabling that future."
[ via bioinformatics.org ]
[ rhetoric ]
“Bioinformatics will be at the core of biology in the 21st century. In fields ranging from structural biology to genomics to biomedical imaging, ready access to data and analytical tools are fundamentally changing the way investigators in the life sciences conduct research and approach problems. Complex, computationally intensive biological problems are now being addressed and promise to significantly advance our understanding of biology and medicine. No biological discipline will be unaffected by these technological breakthroughs.”
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