{bio,medical} informatics
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The Journal of Open Source Medical Computing
First Call for Papers"The Journal of Open Source Medical Computing (JOSMC) is open and issuing its first call for papers. The Journal was started after the success of Linux Medical News indicated the need for a more scholarly publication. The Journal '...is an electronic forum for disseminating information on free and open source medical computing. Scholarly work on any aspect of free and open source medical computing will be considered for peer-reviewed publication...' Read the editorial guidelines for information on submitting articles, editorials or features."
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Building Team
HARVARD RECEIVES $25M GIFT TO BUILD GENOMICS CENTER"Harvard University has received a $25 million gift from an alumnus to build a Center for Genomics Research, whose director says it will focus on "the last and most exciting frontier of human knowledge.""
"Other universities are also establishing genome centers. Murray said that what will make Harvard's different "is that the center will be mostly populated by [post-doctoral and more senior] fellows who we will recruit to come to spend five years with a research team. We're taking extremely seriously the notion of giving young people freedom" in scientific inquiry.
The center's resources will also be used to teach undergraduates about the science of genomics but also its social, ethical, and legal implications, Murray said. "This will enable people who aren't necessarily biology majors to go off and think seriously about these issues, which will play a bigger and bigger part in peoples' lives.""
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Scientific Computing World
THE BEATING HEART OF VIRTUAL ENGINEERING"As the human genome project nears completion, the problem of how to use genomic information in clinical medicine imposes new demands on computational hardware and software. For the beating heart, and some potentially lethal arrhythmias, it is already possible to create a computational pathway from genetic abnormalities to clinical outcome. Using virtual reality techniques, it may soon be possible to 'hold' a beating heart in your hands and feel the irregular writhing and squirming as it begins to fibrillate.
A major problem for computational molecular biology is to work out how the three-dimensional structure of a protein emerges, for the sequence of bases in DNA encodes only the linear sequence of the protein's amino acids. However, the practical problems are not with how genetic information determines molecular structures but with how it determines functional behaviour: of cells; tissues; organs; and systems within the organism."
"The PHYSIOME is the quantitative description of the physiological dynamics or functions of the intact organism. The name comes from "physio-" (life) and "-ome" (as a whole).
The PHYSIOME PROJECT is an integrated multi-centric program to design, develop, implement, test and document, archive and disseminate quantitative information and integrative models of the functional behavior of organelles, cells, tissues, organs, and organisms. The long-range goal is to understand and describe the human organism, its physiology and pathophysiology, and to use this understanding in improving human health. but much or most of what must be learned will come from other species. The project aims toward providing models that summarize information on physiological systems, integrating the observations from many laboratories into quantitative, self-consistent, comprehensive descriptions. The goal is to provide to the community of scientists, physicians, teachers, and to medical health professional and industrial communities, functional descriptions of human biological systems in health and disease. A fundamental and major feature of the program is the databasing of the basic observations for retrieval and evaluation.
A network of Physiome Centers could comprise an adaptable international resource for databasing data on the functional aspects of biological systems covering the genome, molecular form and kinetics, cell biology, up to intact functioning organisms. These many databases would provide the raw information that might be integrated via physiological systems models, and should be structured hierarchically for accessibility and utility. The centers would maintain databases of information and models for retrieval over the Internet. The databases and models will have to accommodate data from many species. "
"The biomedical sciences are generating vast amounts of experimental data at an unprecedented rate. Genomes of entire organisms are now being sequenced at a rate of several per year. The databases of three-dimensional molecular structure are growing exponentially and currently contain over 6,000 macromolecular structures. Data on cell and tissue structures and physiological functions is growing at similar rates, aided by technical advances such as improved biological imaging modalities.
The last two decades have been a spectacular success for reductionist biological science. Many molecular mechanisms, such as the action of molecular motors, ligand-receptor interactions, and regulation of protein expression have been elucidated in detail to the level of the primary DNA sequence or the three-dimensional protein structure. With the end-point of the Human Genome Project already in sight, biological science is beginning to define the challenges of a future where extensive and even complete databases will be readily available. The demand for the development of what is becoming known as functional genomics is one such example. The emerging field of genetic circuits is another.
With this explosion of experimental information at the molecular and cellular levels there is an increasing need to re-integrate this detail into an understanding of how these mechanisms interact in a regulated way to produce normal and pathological functions."
"It was within the context of these developments that the BioNOME Resource has been created. It has to provided a service to those in the biological modeling community who share the desire to integrate their models and see them used more widely by experimental biologists and physiologists, physicians and bioengineers."
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BioMedNet
EU boosts genomics spending[requires 'free' registration]
"The European Union's research commission says that it will boost support for genomics resource centers and large-scale genomics research. In response to complaints by scientists, the agency has pledged an extra $21 million for "genomic and proteomic databases and repositories of suitable animal models." That is likely to mean more money for centers such as the European Bioinformatics Institute near Cambridge and the European Mouse Mutant Archive in Rome. The commission has also set aside nearly $25 million for large integrated projects that incorporate research, networks, and training. It is hoping for initiatives employing functional genomics in the service of human health.
Reference: Abbot, A. 2000. Europe boosts genome resource centres . . . Nature 408(6811):393."
redux [07.24.00]
"With the announcement of the completion of the Human Genome Project, comes the end of the sequencing stage of the genomic revolution and the start of the post-genomic era. The 3 billion letters of DNA coding the human genome have been fully sequenced, well before the initial target date of 2005. This is an important milestone in the efforts to translate this knowledge into practical uses to benefit humankind. For all of its importance, however, the sequencing of the genome is but a humble first step into the Genomic Era. It provides the letters of a new alphabet and a tantalizing glimpse of the future, but the ultimate payoff will be the successful application of genomics to improve human health and quality of life. Knowledge of the sequence of the human genome is virtually useless in and of itself, much as pages in a foreign script are of little value without a way to decipher the meaning and the intelligence to evaluate that meaning. There exists a tremendous opportunity for companies to intercede at multiple levels in this process with technologies and information that will catalyze the realization of the genomics promise in its ultimate incarnation: novel approaches to improving human health."
redux [10.17.00]
[requires 'free' registration]
"What can people expect from biotechnology and genomics? Ten luminaries from the biomedical arena, law, and journalism grappled with issues related to that question at the City University of New York's Graduate Center on Sept. 20. In attendance was an audience of 350 whose research, medical, and counseling careers could hinge on how such issues are resolved. Syracuse University's Gene Media Forum (www.genemedia.org) sponsored the event.
The recurring theme was biological predictability. Eric Lander, director of the Whitehead Institute Center for Genome Research, in Cambridge, Mass., noted that in the past century, biologists "worked out a disease by being clever enough to figure out what was wrong." The systematic approach of genomics, he continued, would render research largely predictable.
Panelists stressed, nevertheless, that genomics would not yield answers easily. Harold Varmus, president of Memorial Sloan-Kettering Cancer Center in New York, said that biologists were used to studying one gene at a time. Now, he added, "you've got all the parts of the clock dumped on the table, and you can look at them. But, you know, it's a lot harder to put back together, too."
A consensus emerged that much of the public--including many journalists, behavioral scientists, and physicians--either were unaware of this newfound complexity or twisted it into misguided support for genetic determinism. "
redux [06.26.00]
""How it's going to help me develop drugs or do anything, I really don't have a clue," said Craig Rosen, executive vice president for research and development at Human Genome Sciences."
""It's like being given the best book in the world, but it's in Russian, and it's incredibly boring to read," said Ewan Birney, a team leader at the European Bioinformatics Research Institute, part of the Sanger Centre, one of the major labs working on the Human Genome Project."
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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BusinessWeek
A Software Model That Fathoms the Human Heart? "What do a Boeing 777 and the human body have in common? Both are complex systems, dependent on millions of complex parts, whether they be a jet-propelled engine or a pumping organ such as the heart. The big difference: Engineers can design and build highly accurate computer models of the way a Boeing 777 will behave in flight. The human heart? Its complexity has long stymied efforts by researchers intent on turning drug development into a predictive science, much like building airplanes.
But that's changing. A handful of companies are developing software that can model single cells, whole organs, cellular metabolism and toxicology, diseases throughout a patient's body, and even an entire clinical trial."
redux [02.24.00]
[requires 'free' registration]
"For a brief period, supplying the data was enough. More genes meant more potential drug targets. But now the victims of the data flood are crying for help. Companies like Entelos, Inc. (Menlo Park, California) are coming to the rescue by building models that integrate all those data into a single, homeostatic, interconnected whole. The models allow researchers to run virtual drug trials to determine the best drug targets, treatment regimens, and patient populations."
Modelers feel that their time has come. "Leaders in the genomics field are all coming to this realization that model building is becoming the rate-limiting step," says Palsson. "There's a major shift taking place in the biological sciences." Math is back, he says, and "biology is going to become quantitative."redux [09.06.00]
"One way of animating our growing store of static information is through computer simulation. It is an area that is beginning to emerge slowly in the life sciences, with only a handful of academic and commercial players active in the area. But for a fledging discipline, there is a great variety in the scope of work being undertaken. While academic labs try to create accurate simulations of red blood cells and simple bacteria, the private companies are taking on bolder projects--simulating human organs and even human diseases in their entirety."
"Nobel laureate Dr. Alfred Gilman, chairman of pharmacology at UT Southwestern Medical Center at Dallas, will lead a $10 million-per-year project allowing researchers around the world to pool their efforts in studying one of the biggest unsolved problems in biomedicine -- how cells interact with, or signal, each other."
"Work of these Alliance for Cellular Signaling (AFCS) researchers in the post-genome era ultimately could lead to the development of a "virtual cell" that could be used to test new drugs.”
"When we have a complete virtual cell, it can be used as a drug discovery engine to test drugs on the computer, rather than on cells or animals. It would be a wonderful way to understand what the optimal point would be to place a drug to achieve a specific goal in a specific patient in a specific kind of disease," Gilman said."
"NIGMS has called the AFCS funding "glue grants -- grants to glue together different sorts of people for a common goal," Gilman said. "We actually are gluing together people's brains and their ideas, but the research is not going to be done in their individual labs."
Instead, the researchers will use the Internet as their joint laboratory."redux [08.12.00]
"The current and pending availability of complete genomic sequences inspires confidence that complex biological phenomena and systems can be understood completely. These feelings are heightened by rapidly expanding capabilities to manipulate gene content and expression in mammalian cells and organisms, detect protein-protein interactions, and quantify the activities of macromolecules in vivo. Such understanding implies the capacity to predict quantitatively the altered behavior of these systems that results from their genetic or environmental (including pharmacological) perturbation. We can envision, rather than simply imagine, the construction of a virtual cell."
The overall goal of the Alliance for Cellular Signaling is to understand as completely as possible the relationships between sets of inputs and outputs in signaling cells that vary both temporally and spatially. The same goal, stated from a slightly different perspective, is to understand fully how cells interpret signals in a context-dependent manner. This will involve identification of all the proteins that comprise the various signaling systems, the assessment of time-dependent information flow through the systems in both normal and pathological states, and finally the reduction of the mass of detailed data into a set of interacting theoretical models that describe cellular signaling."
"The flood of data from genome-wide analysis is transforming biology. We need to develop new, interdisciplinary approaches to convert these data into information about the components and structures of individual biological pathways and to use the resulting information to yield knowledge about general principles that explain the functions and evolution of life."
"Genomics increases the chance that biology will experience a split like the one in physics, between those who collect and those who analyze data. This will challenge the majority of biologists who believe that modeling, simulation, and theory have little to contribute to biology. This prejudice rests on insecurity engendered by most biologists' weakness in mathematics (including my own) and previous efforts to model systems using more variables than there were data points. If we keep clinging to this prejudice, we will drown in a sea of data."
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 [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 [02.24.00]
[summary - can be viewed for free once registered]
"Computer simulations give the impression of precision, but they are founded on a raft of assumptions, simplifications, and outright errors. New tools are needed, scientists say, to quantify the uncertainties inherent in calculations and to evaluate the validity of the models. But making uncertainties evident is a tough challenge, as evidenced by several recent workshops.”
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Infoworld
IT firms compete to compute the genome"The gene machines at the Sanger Centre near Cambridge, responsible for mapping a third of the human genome, are still whirring night and day.
Never mind that a working draft of the 3.1 billion letters in the "book of life" was completed on June 26. That is just the start of a coming tidal wave of genetic information.
Managing and interpreting the trillions of bits of data, or terabytes, generated by the genomics revolution is now the biggest task facing biologists -- and a major business opportunity for computer companies."
redux [09.14.00]
"IBM is pushing hard against the boundaries of data processing andintegration in a way that ultimately could affect everyone'shealth and well-being.
Through a technology license with Incyte Genomics Inc., IBM is applying its DiscoveryLink technology to the challenge of sifting mountains of genetic data to better identify the causes of diseases and aid in developing cures. DiscoveryLink's data- integration technology will be integrated with Incyte's Genomic Knowledge Platform."
"IBM says it has earmarked $100 million to develop advanced research technology for biotechnology, genomic, E-health, pharmaceutical, and agri-science industries."
"Compaq Computer said it plans to invest $100 million in early-stage companies that focus on genomics, tapping into a growing market of biotech start-ups involved in gene discovery, analysis, and information.
The company said its goal is to help promote development of biotech companies through a combination of financial support and access to its AlphaServers and StorageWork computing systems for use in gene sequencing, gene discovery, and other related activities.
Compaq said it would make its first investment in the Applied Genomics Technology Capital Fund, a Cambridge, Mass.-based venture capital fund that invests in companies specializing in genomics and bioinformatics, a new field that develops systems for analyzing, processing, and storing genetic information."
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BBC
Company acquires island gene pool"A biotechnology company has acquired the exclusive rights to research the genetic make-up of people living on the South Pacific island of Tonga.
Researchers at Melbourne-based Autogen want to study the remote community to trace the genes that cause particular diseases."
"The biotechnology wing of the Australian company will take DNA and blood samples from among Tonga's 108,000 inhabitants.
"It is not known how much, if anything, Autogen has paid the authorities in Tonga for the right to carry out the tests."
redux [09.22.00]
"Leading geneticists scrutinized plans for a national gene bank Thursday, with advocates saying it could dramatically improve understanding of diseases and critics saying it's a waste of money in a country still struggling with basic health needs.
The government in this former Soviet republic recently OK'd the dlrs 200 million proposal to digitally store the genetic codes of at least two-thirds of the 1.4 million population and sent it to parliament, where it's expected to win easy approval."
""Estonia can be a follower of knowledge in the world or it can a leader,'' said Jaanus Pikani, chairman of the Genome Foundation, which drafted the project. "I want it to be one of the leaders.''"
"KUCHING: The Chemistry Department will complete building the DNA (deoxyribonucleic acid) database for the Iban, Bidayuh and Melanau communities in Sarawak by December or early next year, said Science, Technology and Environment Minister Datuk Law Hieng Ding.
He said a similar database for Sarawak's other minority sub-groups, like the Penans, Kayans and Bisaya, would be established next year.
The department relies on hospitals for the supply of blood from the various ethnic groups to build up the DNA database.”
"Law said the first to be established were the DNA database for the Malay, Chinese and Indian communities in the peninsula, which could also be used for Sabah and Sarawak.
Taib said the state government would set up a research council next year to coordinate research actitivities in the state."
[requires 'free' registration]
"Should genetic material be collected from individuals for the purpose of studying human disease in specific populations? The native genome of Iceland offers a powerful and rare resource in genomic research -- a relatively homogeneous population. In this setting, the proposed Icelandic Healthcare Database, which would integrate medical information with genealogy and molecular genetic data, has driven a number of issues -- both ethical and scientific -- to the fore."
redux [06.15.00]
"DNA molecules are entirely separate from medical records. In the future, however, the DNA molecule and the medical record are likely to merge into one when it becomes possible to sequence a person's entire genome and put that information on a computer chip or disk. This is not deCODE's current project, but we should not wait until this step is taken to explore its implications. The most important questions would then be who has the authority to make such a disk in the first place; who owns the disk; who controls the use of the disk; and whether the disk containing the genome should be treated as specially protected medical information, as is the case for psychiatric and drug-dependency records? In clinical settings, it seems reasonable to treat such a disk as containing particularly private and sensitive medical information. It also seems reasonable to permit patients to agree to have their entire genome scanned without detailing the tens of thousands of tests that would be run. This is akin to consent to a battery of tests during an annual physical examination.
On the other hand, in a research setting, or when a specific genetic disorder is suspected, the creation and use of an individual patient's genome disk should be subject to the informed consent of the patient. And since they can be both separated from the medical record and readily recreated, research subjects should retain the right to have the files containing their genetic information destroyed at any time.
Iceland's experience with deCODE provides a useful catalyst for formulating fair and ethical rules for research on genetic variation. The Icelandic experience demonstrates that people are concerned about how genetic research is done, that medical-records research and DNA-based research are not the same, that community consultation is necessary but not sufficient to justify DNA-based research ethically, that the probable benefits of such research should be spelled out as clearly as possible, and that international standards for consent to and withdrawal from research should apply directly to research on human genetic variation. Rules for such research will retain their relevance even after it becomes possible to transfer all the genetic-sequence information in a DNA molecule to a computer disk."
Science When an Entire Country Is a Cohort
[summary - can be viewed for free once registered]
"Denmark has gathered more data on its citizens than any other country. Now scientists are pushing to make this vast array of statistics even more useful by easing restrictions on the use of data coded by personal identification numbers. But government officials are reluctant to do so, citing privacy concerns."
redux [02.25.00]
[summary - can be viewed for free once registered]
"Following the examples of Iceland, Sweden, and Estonia, the United Kingdom is drawing up plans to create a national database linking the DNA of 500,000 of its citizens to their medical records and lifestyle details. Its main goal is to tease apart the genetic and environmental components of conditions such as cardiovascular disease and cancer and, eventually, to come up with new drugs to treat--or even prevent--these conditions. An expert panel is currently hammering out a strategy for setting up the database and is due to report its recommendations next month.”
redux [02.13.00]
"By the spring of this year, the first draft of the human genome -- the sequence of all the genetic instructions needed to make up a human being -- will be published on the Web. But that is only the end of the beginning. Scientists still have very little idea of what most of the 100,000 or so human genes actually do, and finding out will take them into a very different area of research.
The raw material of the genome program has been anonymous samples of DNA, manipulated by complex laboratory machines that turn out information like a production line turns out widgets. But the new era of post-genome research involves analysing real people and their confidential medical records. The records are needed to match the genes that people carry with the diseases they may develop. Only then will gigabytes of genetic data into new treatments for cancer or heart disease. And that is why socialised healthcare is a vital part of post-genome research.
Countries such as the U.S., which provide healthcare through private enterprise, are useless for this sort of genetic inquiry. Only those countries which have organized the delivery of healthcare to their population in a way that is independent of the marketplace have built up the universal medical records necessary to make sense of the patterns of disease."
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The Scientist
The State of Bioinformatics[requires 'free' registration]
"In the wake of last June's near completion of the Human Genome Project,1 some scientists are now calling for new agendas and tools for next-phase bioinformatics--the science of understanding the structure and function of genes and proteins through advanced, computer-aided statistical analysis and pattern discovery. Wade Rogers, senior research associate for the Corporate Center of Engineering Research, DuPont Corp., puts it this way: "The human genome is an enormously rich source of fundamental data, but the data's availability is both a blessing and curse. The more data we have to work with, [the more challenging it is] to find fundamental nuggets of useful information buried in that data." He is among those who argue that software, processing, and computational algorithms more powerful than today's will be needed to decipher the functional interactions of multiple genes and proteins--the driving agenda of structural genomics in the near future. "Even though you can never hope to find all the patterns, we need more efficient algorithms that scale polynomially--clever algorithms that enable us to solve problems that are otherwise not solvable," Rogers continues."
[requires 'free' registration]
"Much of the promise of bioinformatics likely lies with the big money and novel approaches of the private sector. At a late October symposium titled "Biosilico 2000," several bioinformatics company executives came together at the Trump Plaza in New York City to discuss the state of the immensely expansive and increasingly heterogeneous field of bioinformatics. Not surprisingly, many touted their products and business plans; but they also discussed and compared philosophies for engaging in the daunting task of applying information technology to biology, chemistry, and medicine.
Sponsored by Scientific American magazine, the symposium, the first of a series to be held annually, addressed the crucial dilemma faced by these companies, many of them only a few years old: How will they and their customers keep from drowning in an ever-increasing sea of raw genomics data that, largely a result of the Human Genome Project, has inundated biology and chemistry? "
[requires 'free' registration]
"Last year, the U.S. Patent and Trademark Office (PTO) routinely assigned patent applications for bioinformatics inventions to examiners in diverse departments. Then the office made a projection, based on input from companies, that it would receive more than 300 such applications in the fiscal year that ended Sept. 30. To ensure consistent treatment for the predicted flood of filings, PTO created Art Unit 1631 (AU1631) last December. This unit now consists of 10 examiners holding degrees, sometimes joint ones, in disciplines ranging from biology to physics to electrical engineering.
The deluge, however, never materialized."
[requires 'free' registration]
"To retool for a job in bioinformatics first requires some considerations. You need to ask yourself: "What kind of job do I want? Research at a pharmaceutical firm or genomics start-up? Teaching and research in academia? Or, do I really want to learn the latest tools to enhance my molecular biology research?"
The most flexibility for jobseekers, says Hunter, is in pharmaceutical firms and biotech companies because the demand is the greatest there. At the very least when looking for a position in bioinformatics you'll need to exhibit an interest and basic skills, which can be picked up through mini-courses, summer courses, and other venues, to land an entry-level job at a larger company. It also helps if your biological expertise is in an area in which the firm is interested, such as G-coupled receptor proteins. But, he cautions, "funding issues alone are not enough of a motivation," to move into bioinformatics.
Specialists emphasize that there's a big difference between using informatics tools and inventing new ones. If you're serious about inventing new tools or about a more senior-level position, then you'll need some formal training in computer science, says Hunter. He adds that this is not just about programming. "You'll need to know about data structures, computational complexity, and numeric methods."
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BioMedNet
Genomic junk[requires 'free' registration]
"Nearly 97% of the DNA in the human genome is believed to be junk DNA. It may seem wasteful, but most of the DNA in all higher organisms appears to be junk. Whatever information is contained in junk DNA is never translated into proteins. Intron DNA is transcribed into RNA but does not appear after maturation, and it is never translated into protein. To determine if much of the junk DNA is intron DNA, researchers used a new approach to analyze all of the complete or nearly complete genomes on record. They conclude that most junk DNA in animals is intron DNA. Their conclusion, however, does not apply to plant DNA.
Reference: Wong, G.K.-S., Passey, D.A., Huang, Y.-z. et al. 2000. Is "junk" DNA mostly intron DNA? Genome Res. 10(11):1672-1678."
"A hypothesis formulated by Adam Heller, who holds the Ernest Cockrell Sr. Chair in Engineering at The University of Texas at Austin, suggests that genes are cathodically protected against oxidation by long stretches of non-coding DNA, sometimes referred to as junk DNA. Cathodic protection, first described in 1824 by the English chemist Sir Humphrey Davy, involves the transfer of electrons from one conducting material to an adjacent one, and is used to prevent corrosion on ships, pipelines, and other metal structures. Heller is proposing a similar mechanism is at work in DNA, and may be important to the understanding of aging, mutations, and cancer."
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Individual.Com
Moves aim to bring supercomputer clout to
desktop"Innovations like high-speed data portals and software that taps idle time on PC networks promise to bring networked supercomputing power to the desktop.
The National Science Foundation's Partnerships for Advanced Computational Infrastructure has announced a "grid portal" to a Web-based net of supercomputers. Separately, the foundation announced that it will fund a next-generation project called Web100 that looks to boost desktop access to networked supercomputers. The government-backed programs complement the recently formed New Productivity Initiative (NPi), a consortium of commercial companies trying to harness the desktop PC in a distributed network to harvest unused cycles on idle computers."
redux [09.14.00]
"With the completion of a "rough draft" of the entire human genome in June, government and corporate scientists have assembled enough genetic code to fill 2,000 computer diskettes.
Now, the scientific footrace shifts from spelling out the seemingly endless string of "A's," "C's," "T's," and "G's" that make up our DNA, to actually understanding what it means.
That's where a new field of "bioinformatics" comes in."
"Researchers at the University of Idaho are building their own "super" computer using parts from 40 to 100 desktop PCs. The hardware will cost only about $44,000, but with the proper connections, the system will be sophisticated enough to run experiments on "jumping genes," bits of genetic material that migrate along the DNA double helix like microscopic hitchhikers.
James Foster, the computer scientist at the University of Idaho directing the project, said that building better programs called algorithms is more important to understanding biological data than just building bigger computers.
"Nature can always defeat brute-force approaches," says James Limpan, director of the National Center for Biotechnology Information in Rockville, Md.
"We need the most clever ways of measuring things and not more CPU power," he says."redux [09.07.00]
"Despite the existence now of a rough draft of the human genome, the story it tells is still full of holes. Just one of them: the mystery of how human proteins get molded into the functional building blocks of life. What's stood in the way of researchers unraveling this puzzle has been the enormous complexity of the chemistry, and inadequate computing power to decipher those intricate workings. That may all change in five years when IBM (NYSE: IBM) researchers enlist the company's newest water-cooled silicon circuits to model the way in which a human protein folds into a specific shape, thus determining its biological function. Called Blue Gene, the supercomputer project will cost $100 million and will be 1,000 times more powerful than Deep Blue, which defeated legendary chess master Garry Kasparov three years ago. It will need all the extra circuitry it can muster, because simulating the behavior of a sinuous strand of protein is no simple task. It involves applying basic principles of physics and chemistry to instruct Blue Gene to calculate the atomic forces at work along a single strand of the human protein. Paul Horn, senior vice president of IBM Research, says this unlocking of protein folding is a milestone in the future of medicine and health care.
Blue Gene is so powerful that even the terminology used to describe its processing abilities is beyond today's computing lexicon. Researchers say it will be able to harness a petaflop of processing power, which is 5 million times faster than a PC. IBM's researchers say the best way to envision that is by imagining a picture one inch tall (representing a single PC processor's capability), while Blue Gene's processing prowess would stretch 30 miles into the sky."
"The mapping of the human genome is the tip of the iceberg that is the biological information revolution.
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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GeneLetter
Genome project leader says clinicians are unprepared for gene-based medicine"A decade from now, predictive genetic tests will be available for some 10 to 12 conditions, and interventions will be available for several of these, yet the medical profession is far from ready to practice this kind of medicine, Dr. Francis S. Collins, director of the National Human Genome Research Institute, told healthcare leaders at a conference this morning."
"By 2010, many physicians will find themselves practicing genetic medicine, yet such individualized gene-based treatment is now a foreign concept in the examining room. "I think that most physicians are not really ready for this phase, through no fault of their own," he said.
redux [06.08.00]
"Unless they begin preparing now, health plan executives and medical directors could be blindsided by the revolution in medicine that will come with the mapping of the human genome, members of a managed care conference keynote panel warned on Monday."
"You think the genetic revolution is still 3-to-5 years off for your health plans," said Dr. Billings, who also serves as deputy director and chief medical officer of the Heart of Texas Veterans Health Care System. "I have to tell you, you better wake up. The tsunami is on the horizon," he warned.
For example, Schering-Plough's Dr. Haverty predicted that gene-based information could lead to the identification of many different types of asthma. As a result, health plans will need to develop many new codes and to upgrade their information systems, he said."redux [03.30.00]redux [04.19.00]
"I think one of the toughest things we all have to deal with is updating our dictionaries. In the simplest cases, the name of an organism is changed and we just have to do the maintenance. It is tougher, when, as with Citrobacter, they do genetic studies and say, "Oh, it's really six different organisms, not one." We have the human genome project coming very quickly. Even that is just the tip of the iceberg. We're not only going to see all the genes; we're then going to see clinical tests based on gene expression. Essentially, you'll be able to look at something on the order of 180,000 gene products and whether they're up or down regulated. How are we going to integrate such an incredible amount of data at a time when we're going to also be changing how we think about these processes? Classification and simple mapping are not going to work, because the lumpers and splitters are going to be arguing furiously on a daily basis."
"Scientists should quit fretting about how to classify organisms and start figuring out how to make biology a unifying influence for researchers, doctors and their patients, biology pioneer Dr. Leroy Hood said Tuesday."
""I think we can revolutionize and transform the teaching of biology if we look at it as an informational science," said Hood, who began his career at Caltech, where he developed some of the first DNA sequencing machines."
"He said the most important place for that shift to take place is in medical schools."
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GenomeWeb
Waterman to Work with Celera as Company's First Fellow"Michael Waterman, considered by many to be the father of computational biology, will begin working with Celera Genomics as the company’s first fellow.
Speaking Thursday at an event honoring his appointment, Waterman said he would likely work on SNPs as well as on the “coverage process” to determine whether whole genes were in fact cloned. He is planning to work with Gene Myers, Celera’s vice president of informatics research."
"“His work really is the underpinning of the whole-genome shotgun strategy,” said Celera’s resident Nobel laureate Hamilton Smith."
"Description: Introduces computational methods for understanding biological systems at the molecular level. Problem areas such as mapping and sequencing, sequence analysis, structure prediction, phylogenic inference, regulatory analysis. Techniques such as dynamic programming, Markov models, expectation-maximization, local search. "
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The New England Journal Of Medicine: Correspondence
Will Genetics Revolutionize Medicine?"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."
"On both sides of the Atlantic, revolutionary claims have been made about the ultimate impact of genetics on clinical medicine. John Bell at Oxford has asserted that "within the next decade genetic testing will be used widely for predictive testing in healthy people and for diagnosis and management of patients.... The excitement in the field has shifted to the elucidation of the genetic basis of the common diseases." (1) And in the United States the director of the National Human Genome Research Institute, Francis Collins, has stated that the good that would come from mapping the human genetic terrain "would include a new understanding of genetic contributions to human disease and the development of rational strategies for minimizing or preventing disease phenotypes altogether." (2)
Statements like these clothe medicine in a genetic mantle. The result of efforts to identify genes that have a role in common diseases suggests a different picture: the genetic mantle may prove to be like the emperor's new clothes. In this article we argue that the new genetics will not revolutionize the way in which common diseases are identified or prevented. Mapping and sequencing the human genome will lead to the identification of more genes causing mendelian disorders and to the development of diagnostic and predictive tests for them. The development of safe and effective treatments, however, will usually lag behind, (3) although occasionally a treatment does precede the discovery of the disease-causing allele, as was the case for hemochromatosis. (4) Furthermore, only a small proportion of the population has mendelian disorders, and this will limit the ultimate impact of the Human Genome Project.
Our doubts stem from the incomplete penetrance of genotypes for common diseases, the limited ability to tailor treatment to genotypes, and the low magnitude of risks conferred by various genotypes for the population at large. Consequently, most people will have little interest in learning their genotypes."
"With advances in the human genome project and the increasing availability of DNA markers scattered throughout the genome such as simple sequence polymorphisms, variable number tandem repeats, and short sequence repeat polymorphisms, it has become increasingly possible to search for the genetic basis of complex human diseases using genomic wide screening methods. Linkage analysis using LOD score analysis in large pedigrees has been the traditional tool to identify gene loci for human disorders both for single gene disorders (e.g. Huntington) and for complex chronic diseases (e.g. bipolar disease). Recently, Risch and Merikangas have argued that the future of genetic studies of complex human disease may depend, to a large extent, on applications of new "association" type methods to family-based data. The main method of interest is the transmission disequilibrium test (TDT) in which alleles at a given locus for a person with a specific disease are compared with parental non transmitted alleles, to look for evidence of deviation from expectations in the absence of linkage. The TDT has been shown to be a valid test of linkage in the presence of linkage disequilibrium (which creates associations with specific alleles). They showed that the TDT has more power than traditional linkage analysis for disease genes with weak to moderate effects on disease risks.
In this paper, we argue that the future of the genetic study of complex disorders will rely increasingly on the classical epidemiologic "association" paradigm. We show that on the long run, improvements in study designs and in adjusting for population stratification using interviews and genetics markers will lead to a new era of population-based incident case-control studies that could have more power and lead to more detailed information not only on the presence or absence of a disease susceptibility gene but define the magnitude of risks and gene-environment interaction- a crucial first step to disease prevention and health promotion."
"The classic tool of molecular genetics is linkage analysis, in which highly polymorphic markers distributed throughout the genome are used to identify chromosomal regions that segregate with disease susceptibility within families. This is the preferred method for identifying genes that exert a major effect on disease susceptibility, but it is less likely to be successful if disease susceptibility is determined by several genetic determinants with small individual effects. With most infectious diseases, a more practicable approach is to analyse genetic association by comparing allele frequencies in diseased individuals with those of controls recruited from exactly the same ethnic group. Because of the difficulty of ensuring exact ethnic matching, an alternative is to study intrafamilial association, in which the distribution of genotypes among index cases is compared with that predicted from the parental genotypes.28 As the number of polymorphisms grows, sample size requirements also escalate, since a P value of 0.05 may be of little significance if this is for only one of 100 polymorphisms that are being assessed in a study. With a long term prospect of screening diseases for association with polymorphic markers in every known human gene, sample sizes in the order of 2000 will be required to validate genetic associations that give a doubling or a halving of relative risk.29
Discovering a genetic association is not the end of the story. Every polymorphism shows a greater or lesser degree of association with neighbouring polymorphisms (linkage disequilibrium). So when we find a disease association with a polymorphism in gene X, the next step is to search for other polymorphisms in the region of X and then to compare the strength of disease association with different combinations of linked polymorphisms (known as haplotypes) in order to dissect the causative polymorphism from linked markers that are functionally irrelevant. If gene X is just one of several environmental and genetic factors that determine disease susceptibility then the process of fine mapping may be extremely complex (thus, it is much more difficult for diabetes than for cystic fibrosis), and this is the area where the most questions remain about the feasibility of the new genetic approach to the analysis of common human diseases. "
redux [11.02.00]
"As a result of the revolution in the biological sciences following the development of recombinant DNA technology and the sequencing of most of the human genome, the role of genetics in the pathogenesis of human disease now dominates biomedical research. There is every sign that the rapidly evolving technology of the post genome era will unravel the function of the human genome and explain how the 50 000 to 100 000 genes interact with one another and the environment to make us what we are.
The central question for the medical sciences is the extent to which it will be possible to relate events at the molecular level with the clinical findings or phenotypes of patients with particular diseases. This problem will permeate every aspect of medical research and practice in the future. It will dominate predictive genetics and genetic counselling. It will also be of major importance for clinical decision making as new and novel approaches to the treatment of disease become available, particularly those involving genetic manipulation. Further exploration of the genome may also provide information on some of the common killers of Western society, such as heart disease, stroke, diabetes, and psychiatric disease, leading to a new form of pharmacology in which drugs are tailored to an individual's genetic make up. Even more important, and certainly more complex, will be relating genotype to phenotype. Many of our most important diseases almost certainly reflect varying susceptibility, due to the action of many different genes and a wide variety of environmental factors and to the ill understood biology of ageing."
"Is there any way of guessing the likely levels of complexity that will be encountered as the genetic basis of disease is explored with the new technology?"
redux [07.13.00]
[requires 'free' registration]
"Genes may cause more than one-quarter of three major types of cancer, more than previously thought, a group of researchers says.
Scandinavian researchers concluded that genes account for 42 percent of the risk for prostate cancer, 35 percent for colorectal cancer and 27 percent for breast cancer.
The rest of the cases are caused by what people do, such as smoking and diet, or what happens to them, such as on-the-job hazards or viral infections, the researchers said."
"...the conclusion runs contrary to the widespread belief that scientists "will find solutions or cures to all diseases in the genes," Dr. Lichtenstein said. "That won't be the case."
redux [10.05.00]
"Simple genetic diseases, such as cystic fibrosis and thalassaemia are just that — simple. A single gene underlies them. Finding it is like climbing a steep hill — hard work but straightforward. Complex disorders, such as asthma and type 2 diabetes, by contrast, have many components, which makes finding a cause more like scaling Everest — far harder, requiring more specialist equipment and the strong possibility of failure.
In work published in the October issue of Nature Genetics, University of Chicago researchers have cleared a path to studying the genetic foundation of type 2, or non-insulin-dependent diabetes mellitus (NIDDM). In a study of a Mexican-American population and two white populations (Finns and Germans) they have found that small genetic variations, called single-nucleotide polymorphisms (SNPs), in a particular gene tend to occur more often in diabetics than in healthy relatives. Although finding a common genetic variation in family groups affected by simple genetic disorders is implicit, a gene implicated in a population with a complex disease could provide a potential new target for gene therapy. "Variation in this gene is associated with a threefold increased risk in the groups studied," explains lead researcher Graeme Bell. "
"The research does represent a shift in the landscape of genetic diseases. "Studies are not going to be easy," says Bell "but they are not impossible and each locus will present its own challenges." Kruglyak feels the path is clearer, if only because of the 'psychological factor' of showing it can succeed. How important it will be in the overall problem of diabetes, or how often this kind of success will occur in other diseases, will emerge in time. "
redux [08.31.00]
""Like any large construction project in the public domain, sequencing the human genome has been a subject of discussion and controversy. Major issues have been the cost of the project, its scientific merit, and the effects of the knowledge gained on human affairs. The concern about cost subsided as the project proved viable and attracted private funding. That leaves the other two questions: What will we learn from this sequence, and how will it affect our lives? With fame and fortune to be made in the genome business, one can only be skeptical of the wondrous claims made by the project's protagonists. The Triple Helix examines these questions from a critical and biologically informed angle."
"In Lewontin's triple helix, the genes are placed in their natural context, where history and geography shape the nature of organisms and the genes they contain. His differences with the most modern of molecular and cellular biologists are irreconcilable and reflect the ever-widening gulf between biologists who have an affinity for what goes on outside the laboratory and those for whom the differences between individuals and between species represent "an annoyance [to be] ignored whenever possible." In many laboratories, organisms are now studied under conditions in which genetic variation is eliminated and the environment held constant. It is only under these special conditions, where neither variation nor natural selection is tolerated, that the triple helix collapses into the double helix and genes appear to be paramount.""
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The Guardian Unlimited
The race to buy life"The race for commercial control over the essence of life is threatening to spiral out of control with private firms, universities and charities claiming exclusive development rights over natural processes in the human body at the rate of 34,500 a month.
For the first time, research commissioned by the Guardian reveals the awesome scale of the gene rush, as investors, scientists, entrepreneurs and lawyers use powerful new technology and obscure new laws to isolate and patent the genes which make us what we are - before they even understand what the genes do."
[requires 'free' registration]
"Public opinion of biotechnology has little, if any, impact on the future business plans of pharmaceuticals and biotechnology companies, admit industry representatives. Their view contrasts sharply with that of academics.
Results of confidential keypad voting yesterday at a conference in Germany covering genomics, proteomics, bioinformatics and business strategies revealed that 38% of representatives of pharmaceuticals companies take no account of public opinion whatsoever when they draw up business plans.
Employees of the biotechnology industry revealed themselves to be even more immune, with 56% from large biotech companies (defined as more than 7 years old and employing more than 40 people) and 40% from smaller biotech companies unswayed in their business judgements by public concerns."
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BioMedNet
Genetic screening promises 14 disease databanks in UK[requires 'free' registration]
"Geneticists in the UK today saw at last the fruits of a hard-won campaign to secure more funding for genomic research to aid public health, with over £8 million going toward DNA databases to study the causes of common diseases.
The government's Medical Research Council (MRC) confirmed awards totalling £8.3 million to 14 groups around the territory that specialise in conditions such as heart disease, breast cancer, hypertension, leukemia, kidney failure, degeneration of the retina, and multiple sclerosis."
"Conscious that its latest awards raise the sensitive issues behind genetic screening, the MRC emphasizes that this current work is very different from the proposed study of DNA samples from much larger numbers of people, the Population Biomedical Collection (PBC). This controversial program, which would allow research on the interactions between genes, environment and lifestyle, only recently completed a public consultation exercise. It is backed by the MRC in association with the Wellcome Trust, the UK's biggest provider of funds for science research, and the National Health Service.
The PBC and the DNA collections are different but complementary pieces of research, says Porteous, who is a member of the working party advising the Wellcome Trust on the large-scale study. The PBC is concerned with "environmental and genetic effects on health risks later in life rather than on individuals [with diseases]," he said."
"Britain's largest ever DNA collection project has been announced by the Medical Research Council. Genetic material from thousands of sick people will be collected and stored in databases across Britain."
""Perhaps the most ambitious is the colorectal cancer project in Scotland," says Rawle. "They're planning on taking samples from every person with colorectal cancer in Britain - that's a tremendous challenge."
Ellen Solomon at King's College London will lead a DNA breast cancer project. Mutations in single genes cause some cases of breast cancer, but most probably involve mutations in many genes, says Solomon.
Her team will take DNA samples from families with only slightly more cases of breast cancer than most. This suggests that they have a genetic predisposition to breast cancer, but that predisposition involves mutations in more than just one or two genes."
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"In 1993, a researcher at the Miami Children's Hospital, with the encouragement and help of families of victims, discovered the genetic basis for Canavan disease, a disease of the central nervous system that affects 1 in 6,400 Ashkenazi Jews. The mutation, on chromosome 17, was patented, and the researcher developed a genetic test. Four parents and three nonprofit groups filed a lawsuit in a Chicago federal court claiming "misappropriation of trade secrets," because they used children's blood and tissue without consent to file the patent.
Reference: Marshall, E. 2000. Families sue hospital, scientist for control of Canavan gene. Science 290(5494):1062."
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GenomeBiology
Senior scientists promise to boycott journals"A group of leading American scientists is promising to boycott scientific journals that refuse to make research articles available free of charge. The scientists have joined a campaign to promote the unfettered exchange of scientific information and establish a web-based public library for science."
"The supporters of the initiative believe that it will "vastly increase the accessibility and utility of the scientific literature, enhance scientific productivity, and catalyze integration of the disparate communities of knowledge and ideas in biomedical sciences." Campaigners aim to prevent the published record of scientific research, much of it paid for with public funds amounting to tens of billions of dollars a year, from being "permanently controlled and monopolized by publishers."
"publiclibraryofscience.org was established to promote the unfettered exchange of scientific information and to organize community support for an international online public library of science. We are asking all scientists of all nations to sign the following letter, which we plan to publish as an open letter in May 2001. Your support will help us to persuade the publishers of scientific journals to commit to giving their archival material to the public domain for distribution through online public libraries. More information about this effort, and a list of journals that are currently compliant is available in our FAQ. Click here if you would like to sign the open letter. We welcome your questions and comments at feedback@publiclibraryofscience.org.
This website is intended to provide information about the open letter and the "public library" initiative to interested scientists, and to provide a convenient mechanism for scientists to sign the letter. Because the open letter is not intended to be "published" until May 2001, we ask that neither the letter nor the list of scientists who have signed the letter be reported elsewhere befor