{bio,medical} informatics
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MacDevCenter.Com
Bioinformatics and Comparative Genomics
"Why this drive to sequence every animal in the zoo? Do we really care about the genetics of pufferfish? In isolation, not so much, but comparisons with the other genomes yield tremendous insights into the genes that are essential for life and those that define the species. They reveal the mechanisms of evolution and the hidden mechanisms of gene regulation.
This article will give a brief introduction to comparative genomics and will show you how to start exploring this treasure trove of data."
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Wired News
Better Science Through Gaming
"The success of various DNA-sequencing projects promises to make genomic research an exciting new frontier. But studying the data has proved so tedious that some scientists have been tempted to quit.
"It wasn't fun," said Al Aplin, a research scientist at the University of Washington in Seattle who crunched information by cramming data on 20,000 genes into an Excel spreadsheet augmented with custom macros. "I was going blind looking at the stuff."
He wasn't the only one not having fun."
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The Scientist
Bioinformatics awarded
[requires 'free' registration]
"Two bioinformatics scientists have been awarded the Max Planck Research Prize for International Cooperation, each of which carries a cash award of €750,000 (USD $915,900) to be spent over a period of 5 years."
""I have been doing it almost 20 years," Vingron said. "For me, it came of age almost 20 years ago. But in society, [this year's prize] does mean that bioinformatics has now found widespread acceptance.""
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The New York Times
A Quiet Revolt Puts Costly Journals on Web
[requires 'free' registration]
"More than money and success is at stake. Free and widespread distribution of new research has the potential to redefine the way scientific and intellectual developments are recorded, circulated and preserved for years to come.
"Society pays for science," said Dr. Nicolelis, whose article in the October issue of PLoS got worldwide attention. "We have the technology, we have the expertise. Why is it that the only thing that has remained the same for 50 years is the way we publish our results? The whole system needs overhaul.""
redux [11.22.03]
"Science's Rocky-style publishing battle starts its second round Monday when a groundbreaking journal releases its latest issue.
The challenger, the upstart Public Library of Science: Biology, packed a strong punch last month with its first issue, which featured a headline-grabbing report of monkeys getting brain implants to control robot arms. The upcoming issue spotlights newly discovered genes for obesity and osteoporosis."
redux [10.14.03]
"There are lots of scientific journals, and the debut of another one normally would not raise many eyebrows.
But yesterday's online launch of Public Library of Science Biology drew so many curious browsers -- half-a-million Web hits in the first eight hours -- that the swamped site had to divert many to a backup site."
"Led by heavyweights such as Nobel laureate Harold Varmus, former director of the National Institutes of Health, the PLoS project aims to shake up the world of scholarly publishing by freely sharing its monthly contents."
redux [10.10.03]
"In the highly lucrative world of cutting-edge scientific research, it is nothing short of a revolution. A group of leading scientists are to mount an unprecedented challenge to the publishers that lock away the valuable findings of research in expensive, subscription-only electronic databases by launching their own journal to give away results for free.
The control of information on everything from new cancer treatments to space exploration is at stake, while caught in the crossfire are the world's publicly funded scientists, some of whom will soon face a choice between their career and their conscience."
redux [08.22.03]
[requires 'free' registration]
"Debate over open access to scientific articles is steadily moving into the mainstream, with the publication this month of an editorial in The New York Times, a recently introduced Congressional bill to promote open access publishing, and a television commercial sponsored by the Public Library of Science (PLoS), a California-based group that plans to launch an open-access journal in October.
As enthusiasm grows, however, some skeptics wonder whether open-access journals will succeed financially, since they charge relatively small "article processing fees," paid upfront by the researcher, instead of substantial fees for institutional library subscriptions."
redux [07.01.03]
""It's ridiculous," Eisen said in this voice during a recent phone interview from Washington. "All these things we're so used to doing with information on the Internet, we're preventing clever entrepreneurial people from doing with works of science. The idea that a narrow profit motive would prevent the dissemination of this information -- it's insane!"
Eisen was in Washington to lend his support to a congressional effort he believes will make scientific publishing less insane and less ridiculous. Most scientific journals -- such as Science, Nature or the New England Journal of Medicine -- require researchers to turn over all rights to the reports selected for publication; the publications then charge institutions and individuals subscription fees to view these reports, a model that Eisen believes inhibits scientific progress. The approach is especially galling, Eisen says, when you consider that a great deal of the money that funds the research published in these journals comes from the federal government. The public is paying for science that it never gets to see, he says."
redux [12.16.02]
[requires 'free' registration]
"A group of prominent scientists is mounting an electronic challenge to the leading scientific journals, accusing them of holding back the progress of science by restricting online access to their articles so they can reap higher profits.
Supported by a $9 million grant from the Gordon and Betty Moore Foundation, the scientists say that this week they will announce the creation of two peer-reviewed online journals on biology and medicine, with the goal of cornering the best scientific papers and immediately depositing them in the public domain."
redux [11.15.02]
"Having persuaded the Energy Department to pull the plug on PubScience, a Web site that offered free access to scientific and technical articles, commercial publishers are taking aim at government-funded information services offering free legal and agricultural data.
"We're delighted with the decision [to shut down PubScience]," LeDuc said. "The administration has done a tremendous job of hearing our concerns and responding to what we've always considered to be our legitimate concern."
redux [09.24.02]
[requires 'free' registration]
"The UK's Office of Fair Trading says that the prices for scientific, technical, and medical (STM) journals are too high because normal competitive forces have been suspended. Libraries are paying too much. The prices of STMs are rising faster than inflation, and the disparity between for-profit and not-for-profit journals is obvious. Part of the problem is that the journals compete on quality, not price, so libraries are prone to skip the cheaper journals for the better, more expensive ones. Bundling journals also skews the market.
Goodman, S. 2002. "Unusual forces" are pushing journal market off course. Nature 419(6904):239.
redux [09.05.01]
[requires 'free' registration]
"Publishers of established scientific journals have thus far resisted demands for freer access. In its campaign to make biomedical research literature available free online, Public Library of Science is now taking a new tack: It hopes to publish peer-reviewed, electronic journals.
"If we really want to change the publication of scientific research, we must do the publishing ourselves," says an announcement posted Sept. 1 on the group's Web site. "It is time for us to work together to create the journals we have called for."
redux [04.24.01]
"When a molecular biologist or a biochemist has made a discovery - often after many months or even years of tedious experiments - they tell the rest of the world by publishing their results in a scientific journal. So far, these journals have controlled who can read them and who cannot - but maybe not for much longer.
E-mail, Internet discussion groups, electronic databases and pre- or e-print servers have already transformed the way scientists openly exchange their results. And in the life sciences, researchers are now demanding that their work be included in at least one free central electronic archive of published literature, challenging the traditional ownership of publishers. The demand has sparked widespread discussions among scientists, publishers, scientific societies and librarians about the future of scientific publishing. The outcome may be nothing short of a revolution in the scientific publishing world."
redux [09.20.00]
"How should biomedical research be communicated? How should research be assessed and validated?"
"Below are abstracts, transcripts, and biographies from the conference. Some presentations did not lend themselves to transcription. Where possible we have supplemented them with editorials from the speakers.
We have also commissioned editorial articles from several speakers and delagates at the meeting."
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Linux Journal
A Secure Bioinformatics Linux Lab in an Educational Research Environment
"In delivering a new bioinformatics curriculum in the Graduate School at the University of Medicine and Dentistry of New Jersey, we undertook the challenge of incorporating new computational resources over an existing research support infrastructure, adding new services and platforms and reacting to an increasingly burdensome responsibility to protect ourselves from network threats. Our new environment spans two cities and links Linux workstations, Linux servers, Silicon Graphics workstations, a Sun 6800 Enterprise Server and the Internet. Open-source solutions combined with selective use of commercial resources integrate in a cost-effective, service-friendly, bioinformatics research environment. In this report, we describe solutions to a set of challenges in our core, Linux-driven server/client environment."
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Genomeweb
At Beyond Genome, Naylor Identifies 10 Challenges Facing Proteomic Scientists
[requires 'free' registration]
"Kicking off the proteomics track at the Beyond Genome conference here today, Stephen Naylor from MIT's CSBi program introduced a number of challenges he sees facing proteomics scientists.
The good news, he noted, is that proteomics is getting more attention from more researchers, noting that the majority of talks and papers at this year's ASMS meeting last month involved proteomics. He also assured conference attendees that there have been plenty of advances moving the field forward.
But there's some bad news too, he said, including what he called the "graveyard" of embattled or completely failed proteomics companies."
redux [12.26.02]
" Proteomics is the study of human proteins, the building blocks of life -- and the culprits behind diseases. Oxford was arguably the first to tackle proteomics on a large scale."
" Now, the former chief of one of the world's largest pharmaceutical companies is trying to resurrect Oxford. Some six months ago, the board hired a new CEO, Dr. David Ebsworth, who used to run the worldwide pharmaceuticals operations of Bayer (BAY ), the German drug and chemical giant. Ebsworth has wasted no time in implementing changes. He has hired new management and broadened Oxford's focus to proteomics, cancer research, and a niche drug market known as "glyco-lipid storage disorders." The goal: profitability within three years."
redux [12.06.02]
"In the twilight of 2002, the proteomics flame is a mere glimmer. The term has devolved from buzzword to dirty word, and VCs have grown skeptical of p-word business models."
"Proteome players are also fighting a backlash. "There's a lot of singed hair and burnt fingers from some of the genomic endeavors, and big pharma is being more careful," says Affinium CEO John Mendlein."
redux [11.22.02]
[requires 'free' registration]
"The Human Proteome Organization (HUPO), which will tomorrow launch its first world congress, faces the unique challenge of bringing together the public and private sectors in a coordinated global research effort aimed at mining the human proteome, says HUPO president Sam Hanash.
Contributing to that effort are researchers in Europe, Asia-Oceania, and North America. "We are witnessing a tremendous interest in proteomics on the part of countries that a decade ago were not active in genomics and that may well become leaders in proteomics in a short time," said Hanash, an oncologist at the University of Michigan in Ann Arbor."
redux [10.10.02]
"The Institute for Systems Biology, a Seattle nonprofit research center led by gene-sequencing pioneer Dr. Leroy Hood, said yesterday it has landed a $19.8 million contract from the National Institutes of Health to advance understanding of proteomics, the study of how proteins interact in the body."
In the wake of recent breakthroughs unraveling the human genetic code, proteomics is increasingly being viewed by scientists as the next step. Scientists say genes provide the instructions for making proteins, and proteins carry out the real action inside the cell."
redux [12.20.01]
[requires 'free' registration]
""Just because you use a protein doesn't make you a proteomics researcher," Joshua LaBaer, director of the Institute of Proteomics at Harvard Medical School, told BioMedNet News.
After the success of genomics, "everyone wants to think of proteomics as the next great science," but calling themselves proteomics researchers "is not really fair," LaBaer said. "A lot of people who claim to do genomics aren't genomic researchers either," he added. "They are just studying gene sequences.""
redux [12.12.01]
[ summary can be viewed for free once registered ]
"Proteomics aims to chart the ebb and flow of tens of thousands of proteins at once to produce snapshots of life inside cells. The technology to pull it off doesn't exist yet, however, and the competition is stiff for those proteins that can be nabbed using current methods. But this young field is growing up fast. This special News Focus looks at the promise and roadblocks of biology's latest wellspring. The package includes profiles of GeneProt, the biggest proteomics test-bed to date, and Stephen Burley , a crystallographer who is leaving academia to direct research at a small start-up company. Other stories discuss the potential of protein chips for new diagnostics and research tools and the problems faced by companies attempting to patent proteins."
redux [08.15.01]
"A new study of the proteomics market forecast that the proteomics market would grow nearly six-fold to $5.6 billion by 2006 from $963 million in 2000.
In its report, consultancy firm Frost & Sullivan said the increase would be driven by a shift towards the analysis of proteomes following the discovery that the human genome contains fewer genes than originally predicted.
"Proteomics adds value to drug discovery by charting the distribution of proteins, identifying and characterizing proteins of interest, and elucidating the participation of proteins in biochemical pathways boosting the number of potential targets around which lead compounds can be designed and screened," Eric Gay, a Frost & Sullivan analyst, said in a statement."
redux [07.11.01]
"Their bold proclamation has raised a few eyebrows in the scientific community. "It's easy to say that you'll complete a comprehensive proteome map," notes Marc Vidal of the Dana-Farber Cancer Institute in Boston. "But none of us knows what that means." There may be only one genome, but when it comes to the proteome, different proteins can be more or less active in different cells at different times during development, under different physiological conditions or in different disease states. The proteome's nature "makes it hard to define what we're doing--not just Myriad, but all of us," remarks Joshua LaBaer, director of the Institute of Proteomics at Harvard Medical School. "There's no such thing as a human proteome," adds Keith L. Williams, CEO of Proteome Systems, headquartered in Sydney, Australia. Look at the liver, for example, he says: "After a glass of red wine, you'll have a different proteome."
redux [06.20.01]
"Scientists thought about trying to catalogue all the proteins in the body a decade ago.
But it seemed impossible, and was therefore impossible to fund. Researchers moved on to the much simpler job of sequencing the human genome.
They were right to do so. Cataloguing proteins turns out to be downright confusing. Lately, more and more biotech companies are entering a field they call "proteomics," an ugly word searching for a focus group."
redux [03.13.01]
[requires 'free' registration]
"A commonly expressed opinion is that a single Human Proteome Project can never match HGP's success. Eric S. Lander , director of the Whitehead Center for Genome Research in Cambridge, Mass., notes that biologists simply don't know how to characterize the proteome "from end to end, nailing every protein. The tools are not ready. And it's not clear that [such a project] makes sense." He contrasts proteomics to HGP where "there is a certain fixed number of base pairs--about three billion--and we were going to get them all. And so it had a beginning and an end to it."
redux [01.31.01]
"Can sequencing do for the proteome what it did for the genome?
On Wednesday, a number of world-renowned researchers in the field of proteomics issued a resounding " no."
"When a company has phenomenal success with strategy A, you want to do strategy A on the next subject," said John Richards, a professor of organic and biochemistry at California Institute of Technology, referring to current corporate attempts to map the proteome.
"This doesn't work," he said."
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Federal Computer Weekly
Bugs in the system
"The Bush administration has proposed $6.98 billion in fiscal 2005 for biodefense-related programs across the federal government. That includes $274 million for a Bio-Surveillance Program Initiative. According to Homeland Security Department officials, the initiative will, among other things, require DHS to create a system that will integrate a broad variety of bioinformatics data from across the government."
"The National Institute of General Medical Sciences (NIGMS) — a component of the National Institutes of Health, which spends almost $30 billion a year on research — founded the Center for Bioinformatics and Computational Biology last year. NIGMS officials are creating eight NIH National Centers for Biological Computing. Among other activities, the centers will develop a national software engineering system and computer simulations of everything from molecular biology to infectious diseases and bioterrorism threats."
redux [04.09.04]
"Government analysts have begun scanning the U.S. daily for the first signs of a bioterror attack by monitoring enormous databases that include over-the-counter drug sales and common ailments reported in hospital emergency rooms."
"Although supporters of the effort, including top Bush administration officials, believe stepped-up surveillance is crucial, critics say the concept is largely untested and likely to impose new burdens on an already over-stretched public health system."
redux [10.28.04]
"Prompted by the US anthrax attacks of October 2001, most of the new surveillance systems are designed to pick up early warning signs of a bioterror attack, such as a hike in fevers or rashes. They use sophisticated algorithms to filter computerized health data for unusual peaks.
But the systems are untested as yet by bioterror agents - so researchers are teasing other information from them. "These data have all sorts of uses," says Julie Paulin, an expert in preventive medicine at the Walter Reed Army Institute of Research in Silver Spring, Maryland."
redux [04.17.03]
"Public health surveillance is changing in response to concerns about bioterrorism, which have increased the pressure for early detection of epidemics. Rapid detection necessitates following multiple non-specific indicators, accounting for spatial structure, and quickly characterizing aberrancies. A single analytic method cannot meet these requirements, but there is no existing framework for the interoperation of surveillance methods. In this paper, we present such a framework and report on a preliminary implementation. Our framework consists of a decomposition of the surveillance analysis task into sub-tasks, and an ontology of surveillance analysis methods, which automate the sub-tasks. As an initial implementation, we use methods developed according to this framework to analyze 911 dispatch data from San Francisco."
redux [01.22.03]
[requires 'free' registration]
"To help protect against the threat of bioterrorism, the Bush administration on Wednesday will start deploying a national system of environmental monitors that is intended to tell within 24 hours whether anthrax, smallpox and other deadly germs have been released into the air, senior administration officials said today.
The system uses advanced data analysis that officials said had been quietly adapted since the Sept. 11 attacks and tested over the past nine months. It will adapt many of the Environmental Protection Agency's 3,000 air quality monitoring stations throughout the country to register unusual quantities of a wide range of pathogens that cause diseases that incapacitate and kill."
redux [11.25.02]
"The Albuquerque physician-turned-researcher just returned from a trip to the NATO Summit in Prague, where he hoped to persuade President Bush and the other 19 member nations that a global health surveillance network is the best way to protect people from manufactured disease."
""The current system is exquisitely designed to fail," Zelicoff said."
redux [10.31.02]
"An epidemic resulting from an act of bioterrorism could be catastrophic. However, if an epidemic can be detected and characterized early on, prompt public health intervention may mitigate its impact. Current surveillance approaches do not perform well in terms of rapid epidemic detection or epidemic monitoring. One reason for this shortcoming is their failure to bring existing knowledge and data to bear on the problem in a coherent manner. Knowledge-based methods can integrate surveillance data and knowledge, and allow for careful evaluation of problem-solving methods. This paper presents an argument for knowledge-based surveillance, describes a prototype of BioSTORM, a system for real-time epidemic surveillance, and shows an initial evaluation of this system applied to a simulated epidemic from a bioterrorism attack."
redux [02.18.02]
"President George W. Bush, the National Homeland Defense Secretary, Tom Ridge, and Health and Human Services Secretary, Tommy Thompson visited the University of Pittsburgh (UP) yesterday to review one of the advanced developments in medical informatics - a collaboration of the University's Center for Biomedical Informatics and Carnegie Mellon University. The project, known as the Real-Time Outbreak and Disease Surveillance system (RODS), is an early warning system for outbreaks of disease designed to obtain and analyze existing sources of data in real time."
"The Real-time Outbreak and Disease Surveillance (RODS) system is a prototype public health surveillance system. RODS collects and analyzes relevant data automatically and in real-time, including emergency room registration data, microbiology culture results, reports of radiographs, and laboratory orders. RODS provides tools that (1) help detect the presence of a disease outbreak, and (2) support the characterization of that outbreak by a public health official. These tools include case definitions, automatic detection algorithms that can be attached to specific data streams, and data analytic tools that support temporal and spatial data analysis and visualization."
redux [06.29.01]
"The merits of linking two fields seemingly as disparate as geographic information systems (GIS) and bioinformatics might not seem obvious, but Virginia Tech's recent symposium linking the twoaeand its roster of renowned participants from both fieldsaehas raised expectations "Applications of GIS to Bioinformatics" was the first major public forum to cross-pollinate the disciplines, helping to fortify a relatively new, yet highly promising investigative area."
""As a result of new dialog between the fields, as we've had at this conference, we are gaining an important mechanistic link between individual-level processes tracked by genomics and proteomics and population-level outcomes tracked by GIS and epidemiology. This will allow us to do a far better job of monitoring, quantifying, and predicting human-health consequences associated with the environment. The potential payoff in related fields such as those looking at climate change, emerging and resurgent infectious diseases, and environmental health is enormous.""
"The meeting brings together researchers in two of the most dynamic analytical technologies-GIS and bioinformatics. The value of GIS analytical systems and data structures to bioinformatics are only now being recognized. Similarly, the methodologies used in bioinformatics can inform GIS scholars of new approaches to pattern recognition and analysis. The purpose of the symposium is to explore the potentials for using GIS as an analytical methodology in bioinformatics and to understand the opportunities bioinformatics presents to the GIS research community. The symposium, the first to focus on the interface between these two research areas, will afford scholars the opportunity to establish new research directions in both fields of investigation."
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Bio-IT World
IBM plans second Blue Gene supercomputer
"The latest list of the top 500 performing supercomputers in the world was released today and it shows IBM has placed two Blue Gene/L prototype systems in the top 10. Additionally, clusters are now the most common supercomputer architecture."
"Coming in at number four and eight were the Blue Gene/L DD1 and DD2 Prototype systems. The systems’ performance benchmarks were 11.68 teraFLOPS sustained speed and 16 teraFLOPS peak performance for the DD1 and 8.66 teraFLOPS sustained, 11.47 tearFLOPS peak for the DD2."
redux [02.20.04]
"IBM will install a second Blue Gene/L supercomputer as part of a radio telescope project in the Netherlands, the company plans to announce Monday.
The supercomputer will be used for a new radio telescope project called Lofar, short for low frequency array, run by a Dutch organization called Astron. The system, which is expected to be complete in 2005, will run the Linux operating system, use about 12,000 processors and perform more than 30 trillion calculations per second, sources familiar with the plan said."
redux [11.15.03]
"IBM on Friday talked up its Blue Gene/L supercomputer, the first module of which is a relatively small, dishwasher-size machine that can perform 1.4 trillion calculations per second.
The performance is enough to make the machine the world's 73rd fastest supercomputer, according to a ranking of the top 500 to be released Sunday. By the time IBM has upgraded the box's 512 chips, each with two processors, and linked it with another 127 identical systems in 2005, Big Blue hopes to take the top spot."
redux [09.19.03]
"WHATEVER happened to Blue Gene, IBM's ambitious attempt to build the world's fastest computer? The project, launched in 1999, called for the construction of a "massively parallel" computer with over 36,000 processing chips, each containing 32 processing cores roughly equivalent in power to a desktop PC. Harnessing all that computing horsepower--more than one petaflop, or 1,000 trillion floating-point calculations per second--would, it was hoped, allow scientists to simulate the folding of a protein, an extraordinarily demanding task which might help to streamline the discovery of new drugs. The idea was to achieve all of this within five years--something that even enthusiasts thought ambitious.
Four years on, the chips that will power the first Blue Gene computer are now being manufactured and tested. But the plans have changed somewhat."
redux [05.08.03]
""Blue Gene is a completely oddball, you've-never-seen-anything-like-this-before design," said Illuminata analyst Jonathan Eunice. "It is not custom everything, (but) it is still very exotic compared to anything you can buy.""
"IBM already has spent more than the original $100 million budgeted for the project and won't meet its 2004 goal for the ultimate machine, but the company has made progress bringing its ideas to fruition."
redux [02.11.03]
"THE first version of IBM's revolutionary Blue Gene chip will roll off the production line this quarter, Ajay Royyuru, head of IBM's Computational Biology Centre, has revealed."
""We plan to build a 512-node prototype Blue Gene machine in our Watson Research Centre, in New York, where I am located, hopefully before the end of the year.
Then we will build a 64,000- node Blue Gene machine and deliver it to the Lawrence Livermore laboratory by late 2004, or early 2005."
redux [10.24.02]
"Linux will be the main operating system for IBM's upcoming family of "Blue Gene" supercomputers--a major endorsement for the OS and the open-source computing model it represents."
""We had two choices of operating systems for the Blue Gene family, either use a special purpose system or Linux," Bill Pulleyblank, director of Exploratory Server Systems at IBM Research, said in a statement. "We chose Linux because it's open and because we believed it could be extended to run a computer the size of Blue Gene. We saw considerable advantage in using an operating system supported by the open-source community so that we can get their input and feedback.""
redux [07.13.01]
""Ambuj Goyal, IBM Research's general manager for software, solutions, and strategy, was more ambitious than that. Why not build a machine to model molecular dynamics using general-purpose chips rather than specialized ones? That way you'd produce a prototype for a whole new family of supercomputers. Not only would it be great technology development, it would be great marketing, too. Whereas the Department of Energy has the greatest interest in top-end supercomputing - with its need to understand how nuclear weapons work - focusing on the life sciences rather than the death sciences could make supercomputing more widely appealing. What's more, a biology program would be a way of telling one of the newest markets for big iron - the post-genome biotech world - that IBM took its interests seriously. "We believe that the life sciences are going to be a rapidly growing area," says Blue Gene project manager Bill Pulleyblank, "a huge growth area for IBM.""
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American Scientist
The Accidental Scientist
"A paradox lies close to the heart of scientific discovery. If you know just what you are looking for, finding it can hardly count as a discovery, since it was fully anticipated. But if, on the other hand, you have no notion of what you are looking for, you cannot know when you have found it, and discovery, as such, is out of the question. In the philosophy of science, these extremes map onto the purist forms of deductivism and inductivism: In the former, the outcome is supposed to be logically contained in the premises you start with; in the latter, you are recommended to start with no expectations whatsoever and see what turns up.
As in so many things, the ideal position is widely supposed to reside somewhere in between these two impossible-to-realize extremes. You want to have a good enough idea of what you are looking for to be surprised when you find something else of value, and you want to be ignorant enough of your end point that you can entertain alternative outcomes. Scientific discovery should, therefore, have an accidental aspect, but not too much of one."
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Nature: Science Update
Lotharios tamed by brain protein
"Want to tame the eye of a philandering love rat? Then help is at hand. New research shows that gene therapy can turn promiscuous male voles into faithful bedfellows."
"Whether or not the technique could work in humans is not known. Promiscuous and monogamous monkey species have different patterns of vasopressin receptor expression that closely match those seen in the voles. So it is possible that philandering and faithful humans may share similar brain chemistry, says Lim."
""Part of the reason we are doing this research is that we are trying to understand the social brain," explained Professor Young. "Why do we interact with other people, and what could be wrong in diseases like autism?
"In autism, people are very aloof - they don't want to interact with others. It could be that vasopressin plays a role in normal human social interactions."
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The Independent
Scientist says pioneering human cloning experiment is vital for future of medicine
"The scientist planning Britain's first human embryo cloning experiment has insisted it must be allowed for the sake of "the future of modern medicine"."
"If granted, the licence would allow a team led by Dr Miodrag Stojkovic from the Institute of Human Genetics at Newcastle University to grow specially-created embryos, using eggs donated by couples undergoing fertility treatment and skin cells from adults. It would produce stem cells that would be used to make insulin-producing cells for a new class of treatment for diabetes."
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The Scientist
Integrating plant 'omics'
[requires 'free' registration]
"Although the Arabidopsis and rice genomes have been sequenced, the complex gene-to-metabolite networks that produce what we know as these plants have been difficult to discern. In the June 15 PNAS, Masami Hirai and colleagues report a solution that involves mathematically combining transcriptomics and metabolomics, thus allowing the analysis of sulfur and nitrogen gene-to-metabolite networks in Arabidopsis.
"Understanding… network behavior through a combination of analytical and mathematical approaches has great potential for deepening our understanding of metabolic regulation," said Alisdair Fernie, from the Max Planck Institute, Golm, Germany, who was not involved the study."
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National Geographic News
Rat DNA Offers Clues to Pacific Colonization, Study Says
"Wherever people go, rats go too. Now researchers are making use of this fact to help understand patterns of human migration. A new genetic comparison of rats from various Pacific islands presents clues about the origins of Polynesian people.
The study, published this week in the science journal Proceedings of the National Academy of Sciences, strikes a blow against one popular theory of how remote Pacific islands were colonized, and argues that the migration was a slow and complex process."
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MacDevCenter.Com
Introduction to Bioinformatics
"Bioinformatics is the intersection of molecular biology and computer science. For software developers, it's a fascinating and challenging area in which to work. During the coming months, the Mac DevCenter will touch on different areas of bioinformatics; what the hot topics are right now, how Mac OS X and open source software are playing a role, and how you can get involved.
In this article I want to introduce this exciting field and set the scene for the articles that will follow."
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The Economist
An open-source shot in the arm?
"The open-source model is a good way to produce software, as the example of Linux shows. Could the same collaborative approach now revitalise medical research too?"
"In fact, open-source approaches have emerged in biotechnology already. The international effort to sequence the human genome, for instance, resembled an open-source initiative. It placed all the resulting data into the public domain rather than allow any participant to patent any of the results. Open source is also flourishing in bioinformatics, the field in which biology meets information technology. "
redux [05.13.04]
"Typical open source project development strategies work well for free software but don't flourish in commercial settings, according to one expert."
"Specifically, [Professor Jim Herbsleb of Carnegie Mellon University's International School of Computer Science] looked at cases where many developers from all over the world would successfully collaborate and coordinate to work on one piece of software. While looking at this, he also examined why this distributed development model has not thrived in industry. In fact, Herbsleb found that it takes companies more than twice as long to develop software in disparate locations than in one location."
redux [03.31.04]
"Australia's bioinformatics industry will increasingly rely on open source software as researchers look for inexpensive point solutions that are not just a "black box", according to delegates at an Australian Technology Park Innovations bioinformatics symposium in Sydney.
Sydney University senior lecturer in bioinformatics, Dr Bret Church, said open source is undoubtedly the founding stone of bioinformatics.
"We love it," Dr Church said. "It is made for research, and there was plenty out there when bioinformatics came along. On the way to solutions, and while exploring possibilities and avenues, open source code tends to play a leading role.""
redux [12.18.03]
"3rd Millennium wants to cash in on the software it spent seven years developing for various government and commercial clients - by giving it away free.
The Waltham, Mass.-based informatics consultancy and services firm has released its Data Centric Knowledge Management System for biotech and drug R&D under a GNU general public license (GPL)."
"The company is betting that, of those life science organizations deploying the software, some will want to buy support and maintenance contracts."
redux [11.20.02]
"Until recently, open source has often appeared to bioscientists as some sort of novelty, or, worse, a threat to IP protection. In the last few years, though, solid achievements in clustering, genomic data management, Web publication, and scores of specific "vertical" applications have established open source as a serious technical alternative.
Big Pharma and other biosciences are just starting to realize how open source can systematically cut costs, improve security, allow their own workers to shift attention back to their "core competences" from proprietary IT expertise, and even promote better science. We're in the midst of a dramatic evangelical movement that teaches better ways for open source IT to support bioscientific goals. Perhaps the most consequential shift is that participants have begun to understand that standards-based open source can enhance biosciences' fundamental values. These are exciting times for open source bioinformatics."
redux [09.30.02]
"Brenner, for example, stressed that while open sourcing "has potential in a generic sort of way," success depends on the operational and business models of specific companies.
Even considering a move to open sourcing can meet with resistance. "All of the instrument companies were brought up in closed-source shops, so they would have to change this fundamental attitude," explained Hood."
"THE OPEN SOURCE MOVEMENT has gained significant momentum of late, particularly within the bioinformatics field. While open source licenses vary widely, distribution of open source software typically requires delivery of both the object code and the source code. Most commercial software is delivered only in object code form, which is not easily read and modified by programmers.
The decision of whether to use open source software requires a careful analysis of various factors. In the right situations, open source software can be an excellent choice. In other cases, it can be disastrous."
redux [08.21.02]
"Want to make money from open-source bioinformatics? As long as it's not too much you might be OK.
This was the verdict of a panel of academics and business executives who had convened last week to talk broadly about open-source bioinformatics. But the discussion, which took place at the IEEE Computer Society bioinformatics conference at Stanford University, frequently veered to whether one could, or even should, make money from it.
The answer was a resounding maybe."
redux [01.16.02]
"A debate is heating up in the academic community over whether software that is generated by publicly funded research must be released with an open source license. The Internet is one example of how releasing research code benefited the public, but the trend seems to be changing now, and universities are more likely to consider the profit opportunity. The Bayh-Dole Act paved the way for the privatization of publicly funded resources, but not everyone is happy with the results.
Against the tide of privatization comes a group of bioinformatics researchers and programmers with an online petition to require that all software created by publicly funded research projects be licensed as open source. They have founded a group and a Web site, OpenInformatics.org, to further this cause.
Here we present two opposing viewpoints on this issue."
redux [01.07.01]
"The Open Source movement is infectious, it seems. It has bubbled up in the field of bioinformatics - gene research software. Gene research is already a burgeoning area of activity, which is predicted to deliver numerous benefits to the health industry. It is also an area where software counts and where universities have managed to prosper from their activities. US universities lodge about 2000 patents each year, many in bioinformatics, and these patents contribute a good deal of revenue - an amount estimated at about $5 billion per annum, or ten percent of their total budgets. Thus Open Source activities in this area are not universally welcomed."
"Over the past several years, open-source software development has won high-profile adherents in the business world -- including the likes of IBM and Sun Microsystems. But it has always had its strongest fans in the academic world, where open-source software is seen as a natural extension of the idea that the fruits of academic research should be shared with everyone.
But now some academic programmers on the cutting edge have found that the licensing office is proving a more formidable obstacle to progress than the limits of their imagination and skill."
redux [11.26.01]
"Before computer whiz Steven E. Brenner accepted his tenure-track research post at the University of California-Berkeley last year, he demanded that the school's intellectual property police leave him alone.
Brenner prevailed. He's now one of the few experts in the emerging field of bioinformatics with the freedom to distribute his work, software used in gene research.
``It's vital to what we do,'' says Brenner, who supports a movement to force universities to allow ``open source'' publishing of gene research software code."
redux [08.18.01]
"Steve Brenner, assistant professor and leader of a computational genomics research group at the University of California, Berkeley, said he fears that many academic bioinformaticists are unaware of a legal risk they face on a daily basis: contributing to open source software projects without explicit permission from their institutions.
While many employers have clauses in their employment contracts that restrict the creation and use of open source software, bioinformatics programmers at universities are often not as attuned to copyright issues as their industry counterparts. This fact, Brenner said, raises the possibility that a good portion of biological open source software is currently being produced illegally."
"The issue seems to be coming to a head in the academic world now, as more universities are exploiting the revenue stream made possible by their copyright and patent holdings. ?If you?re a software developer, the university holds rights to your software, but if you?re an English professor or Law professor and publish a book, they?re not the least bit interested in copyright,? said Thomas Field, an attorney at the Franklin Pierce Law Center affiliated with the Association of University Technology Managers."
redux [11.05.01]
"Computers are supposed to help biotechnology, right? Isn't bioinformatics all the rage right now? Well, it is, but with popularity comes legal questions that many companies don't address until it's too late."
"It seems that many biotech companies don't realize that a computer vendor may have the rights to the software, and ultimately, the work that the biotech companies do.
For example, if a biotech company orders a computer network to help it sequence the genome of yeast, the company may ask the vendor to customize the software it will use to do the sequencing. However, the question is, who owns the right to that customized software--the biotech company or the software programmer?"
redux [08.23.01]
"This report outlines recent activity in open source software development within the discipline of bioinformatics. I present the relevant highlights of two bioinformatics meetings held in July 2001 in Copenhagen, Denmark: the Bioinformatics Open Source Conference and the Intelligent Systems for Molecular Biology Conference. The report also describes a large number of projects and groups important to bioinformatics open source software development. The appendices include meeting programs, the currently accepted definition of open source software, and descriptions of important online biological data sources."
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Science Daily
Scientists Find Cancer's Genetic Core: 67 Genes Universally Activated In Human Cancer
"Of the approximately 35,000 genes in the human genome, scientists at the University of Michigan’s Comprehensive Cancer Center have found that activity from just 67 is required to change normal human cells into cancer.
These 67 genes constitute what U-M scientists call cancer’s meta-signature – a core set of essential genes, which somehow triggers the transformation from normal cells to cells that are neoplastic, or growing abnormally."
"“We used a statistical analysis method called comparative meta-profiling to examine 40 datasets from other investigators showing specific patterns of genetic activity associated with one of 12 types of cancer,” says Daniel Rhodes, the paper’s first author and a student in the U-M Medical School’s Medical Scientist Training Program and Bioinformatics Graduate Program."