{bio,medical} informatics
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ZDNet
Google accused of bio-piracy
"Search giant Google has been accused of being the "biggest threat to genetic privacy" for its alleged plan to create a searchable database of genetic information.
Google was presented with an award as part of the Captain Hook Awards for Biopiracy in Curitiba, Brazil, this week. The organisers allege that Google's collaboration with genomic research institute J. Craig Venter, to create a searchable online database of all the genes on the planet, is a clear example of biopiracy."
redux [01.09.06]
"For all the benefits technology provides, it does provoke anxiety. In a recent letter in the New England Journal of Medicine, a New York rheumatologist describes a scene at rounds where a professor asked the presenting fellow to explain how he arrived at his diagnosis. Matter of factly, the reply came: "I entered the salient features into Google, and [the diagnosis] popped right up." The attending doctor was taken aback by the Google diagnosis. "Are we physicians no longer needed? Is an observer who can accurately select the findings to be entered in a Google search all we need for a diagnosis to appear—as if by magic?" In a post-Google world, where evidence based education is headed is anyone's guess.5 Googling your diagnosis; Googling your treatment—where is all this leading us?"
redux [12.26.05]
"Google’s IPO has also made big news this year as their current stock position places the net worth of the company at an amazing USD 130 billion. This brings them close to the giants of the industry IBM and is only trailed by biggest like Intel and Microsoft. However, the Google guys are not resting on their laurels, as they believe that there is much more to be done and achieved.
"Brin said in a statement: “It’s clear there’s a lot of room for improvement, there’s no inherent ceiling we’re hitting up on. Google has a large computational infrastructure – that could be very useful for microbiology or computational biology. I don’t think we particularly restrict ourselves or have a 20-year vision or anything like that. I don’t think we’re averse to doing something new.”"
redux [11.29.05]
"SERGEY BRIN and Larry Page have ambitious long-term plans for Google’s expansion into biology and genetics through the fusion of science, medicine and technology."
"Over dinner and plenty of wine in February, Brin discussed the prospects for genetics with Craig Venter, the maverick biologist who decoded the human genome.
Despite millions of dollars in funding and thousands of hours of computing time from America’s federal Department of Energy, Venter needed more help to unlock the molecular mysteries of life. It seemed to him that Google’s mathematicians, scientists, technologists, and computing power had the potential to vault his research forward. He pressed Brin hard to get Google involved."
"Not long after the dinner, Brin and Page teamed up with Venter."
redux [11.08.05]
"By the end of next year, Google intends to open an engineering center in the Valley that will employ 600. The company has said it wants to be in a place with a strong quality of life for its employees, with access to public transportation and amenities."
"Downtown Phoenix offers perfect geography, housing and the public transit amenities that Google wants, said John Chan, deputy director of the downtown development office."
"Downtown is the Valley’s financial center and it also has a growing cluster of biotechnology companies. That may interest Google, since the company is said to be intrigued by bioinformatics, the use of computers to characterize the molecular components of living things."
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B-EYE-Network
Bioinformatics in Structure-Based Drug Design
"Bioinformatics plays an important role in the design of new drug compounds. In this month’s article, we’ll explore one approach in drug design that benefits from the availability of bioinformatics applications in the cancer research community."
"In a future article I’ll review additional bioinformatics applications that assist scientific researchers in structure-based drug design."
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myDNA
"Junk" science is a real turn-on
"Researchers at the McKusick-Nathans Institute of Genetic Medicine at The Johns Hopkins Medical Institutions in Baltimore, Md., have invented a cost-effective and highly efficient way of analyzing what many have termed "junk" DNA and identified regions critical for controlling gene function.
And they have found that these control regions from different species don't have to look alike to work alike."
redux [01.14.06]
[requires 'free' registration]
"More broadly, however, the team's findings suggest a new approach to teasing out the genetic basis of innate disorders that cannot be traced to simple protein-coding defects.
"There are about 30,000 genes in the human genome, but there are at least 150,000 different genetic disorders," Dr. Thakker said. "You can't just look at the genes that code for proteins, you've got to look at the surrounding regulatory regions, as well — the 'junk.' ""
redux [06.03.04]
"In a region of DNA long considered a genetic wasteland, Harvard Medical School researchers have discovered a new class of gene. Most genes carry out their tasks by making a product-a protein or enzyme. This is true of those that provide the body's raw materials, the structural genes, and those that control other genes' activities, the regulatory genes. The new one, found in yeast, does not produce a protein. It performs its function, in this case to regulate a nearby gene, simply by being turned on."
"Like many researchers, Winston and his colleagues may have known in the back of their minds that someday they would have to contend with junk DNA, but it was not their intention to map a new gene in those wild and relatively uncharted regions of the chromosome."
redux [05.07.04]
"If you thought we had explored all the important parts of our genome, think again."
"The segments, dubbed 'ultraconserved elements', lie in the large parts of the genome that do not code for any protein. Their presence adds to growing evidence that the importance of these areas, often dismissed as junk DNA, could be much more fundamental than anyone suspected."
redux [02.21.04]
"Genetic Technologies (GTG), the Australian biotech company at the heart of a controversy surrounding its patents on the genetic mapping applications of noncoding (junk) DNA, has added another large company to its tally of licensees -- Laboratory Corporation of America Holdings (LabCorp)."
"Last year, GTG granted licenses to Sequenom, Perlegen Sciences, Myriad Genetics, and Pyrosequencing, among others."
redux [11.18.03]
"Investors piled into Genetic Technologies yesterday after the biotech company announced that two US groups it was suing for patent infringement had settled out of court."
"The Melbourne-based Genetic Technologies has consistently warned it would sue any company, research institution or university that infringed its patent over the so-called junk DNA."
redux [08.18.03]
"An Australian biotech company, Genetic Technologies Ltd. (GTG), is stirring up controversy over its decision to enforce a series of patents, granted in the 1990s by the US Patent and Trademark Office, over the genetic diagnostic and mapping applications of non-coding, or junk, DNA."
"Scientists, including NHGRI chief Francis Collins and Sir John Sulston, are also upset over GTG's recent decision to ask academic institutions to sign research licenses."
redux [05.19.03]
[requires 'free' registration]
The dark side of the moon is a misnomer. Light reaches la luna's entire surface, but one half is unviewable from Earth. The human genome, the now essentially decoded map of life, likewise has a light side--the genes encoding mRNA and protein--and a dark side, which is coming into view for the first time. The dark side encompasses more than its opposite: The majority of the genome comprises intronic regions, stretches of repeat sequence, and other assorted gibberish that has attained the ignoble dubbing, "junk."
The first exploratory missions to the human genome's faceted surface are turning up traces regarding the extent of the junk."
redux [11.21.02]
"In a provisional patent application filed July 31, Pellionisz claims to have unlocked a key to the hidden role junk DNA plays in growth -- and in life itself.
Rather than being useless evolutionary debris, he says, the mysteriously repetitive but not identical strands of genetic material are in reality building instructions organized in a special type of pattern known as a fractal. It's this pattern of fractal instructions, he says, that tells genes what they must do in order to form living tissue, everything from the wings of a fly to the entire body of a full-grown human."
redux [08.28.02]
"In a new study in the August 29 issue of Nature, researchers at The Wistar Institute identify a cohesin-containing protein complex that reshapes chromatin to allow cohesins to bind to DNA. In doing so, they also identified the locations on the human genome where the cohesins bind. Somewhat to their surprise, the binding sites were found to be a repetitive DNA sequence found throughout the human genome for which no previous role had ever been identified. These bits of DNA, known as Alu sequences, are liberally represented along those vast stretches of the human genome not known to directly control genetic activity, sometimes referred to as junk DNA."
redux [08.09.02]
"Results of a new University of Michigan study suggest that junk DNA - dismissed by many scientists as mere strings of meaningless genetic code - could have a darker side.
In a paper published in the Aug. 9 issue of Cell, scientists from the U-M Medical School report that, in cultured human cancer cells, segments of junk DNA called LINE-1 elements can delete DNA when they jump to a new location - possibly knocking out genes or creating devastating mutations in the process."
"Scientists in the past decade have discovered that remnants of ancient germ line infections called human endogenous retroviruses make up a substantial part of the human genome. Once thought to be merely "junk" DNA and inactive, many of these elements, in fact, perform functions in human cells.
Now, a new study by John McDonald of the University of Georgia and King Jordan at the National Center for Biotechnology Information at the National Institutes of Health, suggests for the first time that a burst of transpositional activity occurred at the same time humans and chimps are believed to have diverged from a common ancestor - 6 million years ago."
redux [01.20.01]
[requires 'free' registration]
"Speaking at a National Institutes of Health conference on ethical and social issues in genetics, Dr. Francis Collins said that a "spate of papers in public journals'' due out within a month will signify the incredibly rapid pace of scientific discovery seen since the announcement of the nearly complete sequencing of the human genome last summer.
The first, Collins said, will be a paper that puts the total count of human genes at between 30,000 and 35,000. "That's less than half the number most people have been predicting.'' The second is a study ascribing previously unknown biological missions to genes scientists thought were inactive, or so-called "junk genes."
"There is now clear evidence that (the junk genes) have been performing a number of functions for tens or hundreds of thousands of years,'' he said."
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Duke University
Marriage of Math and Genetics Forges New Scientific Landscape
"“Bioinformatics and computational biology offer particularly good examples of how universities must embrace new approaches to interdisciplinary research even as they strengthen their departments,” he says."
"“We’re trying to train a whole new kind of person that didn’t exist ten years ago in the vast majority of computer science or biology departments,” says Terrence Oas, the program’s director of graduate studies and an associate professor of biochemistry and chemistry. By enlisting faculty from both the biological and computational sciences, the program is “trying to create new scientists that are hybrids of current scientists,” Oas says."
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."
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Nature
2020 – Future of Computing
"In the last two decades advances in computing technology, from processing speed to network capacity and the internet, have revolutionized the way scientists work. From sequencing genomes to monitoring the Earth's climate, many recent scientific advances would not have been possible without a parallel increase in computing power - and with revolutionary technologies such as the quantum computer edging towards reality, what will the relationship between computing and science bring us over the next 15 years?
This Nature web focus combines commentaries from leading scientists and news features analysis from journalists assessing how computing science concepts and techniques may transform mainstream science by 2020."
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The New York Times
This Essay Breaks the Law
[requires 'free' registration]
"Nevertheless 20 percent of the genome is now privately owned. The gene for diabetes is owned, and its owner has something to say about any research you do, and what it will cost you. The entire genome of the hepatitis C virus is owned by a biotech company. Royalty costs now influence the direction of research in basic diseases, and often even the testing for diseases. Such barriers to medical testing and research are not in the public interest. Do you want to be told by your doctor, "Oh, nobody studies your disease any more because the owner of the gene/enzyme/correlation has made it too expensive to do research?"
The question of whether basic truths of nature can be owned ought not to be confused with concerns about how we pay for biotech development, whether we will have drugs in the future, and so on. If you invent a new test, you may patent it and sell it for as much as you can, if that's your goal. Companies can certainly own a test they have invented. But they should not own the disease itself, or the gene that causes the disease, or essential underlying facts about the disease. The distinction is not difficult, even though patent lawyers attempt to blur it."
redux [10.14.05]
"A new study shows that 20 percent of human genes have been patented in the United States, primarily by private firms and universities."
"The top patent assignee is Incyte, a Palo Alto, California-based drug company whose patents cover 2,000 human genes."
"[Critics] caution that patents that are very broad can obstruct future innovations by preventing researchers from looking for alternative uses for a patented gene."
[via the personal genome ]
redux [05.19.04]
"A controversial patent on a breast cancer gene has been revoked by the European Patent Office, paving the way for cheaper screening across the continent. The verdict reflects the transatlantic disparities that make gene patents much tougher to uphold in Europe than in the US."
"The EPO has yet to spell out its precise reasons for revoking the BRCA1 patent, but New Scientist understands that the primary justification was that the application was not deemed "inventive"."
redux [08.18.03]
"An Australian biotech company, Genetic Technologies Ltd. (GTG), is stirring up controversy over its decision to enforce a series of patents, granted in the 1990s by the US Patent and Trademark Office, over the genetic diagnostic and mapping applications of non-coding, or junk, DNA."
"Scientists, including NHGRI chief Francis Collins and Sir John Sulston, are also upset over GTG's recent decision to ask academic institutions to sign research licenses."
redux [05.07.03]
"Scientists and commercial firms are scrambling to patent the genetic code of the virus thought to be responsible for Sars.
The group which produced the first entire genetic sequence of the coronavirus confirmed this week that it is seeking a patent to ensure that everyone has free access to the code.
It fears that a commercial patent could slow down research into vaccines and treatments."
redux [09.28.02]
"The Bay Area biotech firm that started the heretical campaign to ban gene patents hopes to stir more debate on the topic by sponsoring a scholarly smackdown in Washington, D.C., on Tuesday.
Santa Clara's Affymetrix broke ranks with the biotech industry in March by arguing that the United States should quit issuing gene patents because genes were invented by nature, not science."
redux [07.23.02]
"Patents on DNA sequences "inhibit innovation and development" and should be the exception rather than the norm, says a panel of leading UK bioethicists. In the past, biotech companies have said that without such patent protection they would not have the economic incentive to invest in expensive research towards new drugs.
A discussion paper, produced by the Nuffield Council on Bioethics (NCB), says that too many patents are of doubtful validity because they are being issued for genetic discoveries that are not adequately inventive. It recommends a number of significant changes to the way patents in the field are granted in the future and to limit possible adverse effects of those already issued."
redux [03.18.02]
"It's one of the toughest questions in biotechnology: Should businesses obtain patents on genetic information about plants, animals or humans? Michael Capellas, CEO of Compaq Computer Corp., surprised an audience of biotechnology specialists yesterday when he suggested that the answer should be "no.""
"In a comment that stunned the audience into several seconds of silence, Capellas responded to a question on the issue by flatly saying that companies shouldn't be able to patent genes. But he quickly backed away from the comment, pleading ignorance of all the ramifications of the issue. "If you're asking me what should be patentable," Capellas said, "I don't know.""
redux [02.07.02]
"Patents may make some genetic tests so expensive that ordinary labs cannot afford to offer them, says a team of researchers who interviewed staff at 119 US facilities.
Patents are meant to provide an incentive for companies to put their discoveries into the public domain. But some researchers wonder if prohibitive costs could in fact have the opposite effect, by keeping standard genetic tests out of the reach of all but a few laboratories. That would have far-reaching consequences not only for health care, but for clinical research and quality control, the researchers say."
redux [08.20.01]
""Like the Terrys, a rising number of patients, doctors and ethicists are questioning how the patent system handles genetic claims. Many say it awards too many patents, overly rewards their holders, and gives too little back to patients. Yet many industry voices complain the process is moving too slowly to keep up with galloping research and to yield medical care awaited by suffering patients."
"The gold rush days are about to begin,'' says Arthur Caplan, a bioethicist at the University of Pennsylvania. "There are so many targets that look so lucrative that they're falling all over one another to pursue opportunity after opportunity.""
redux [02.27.01]
"ONCE upon a time, pure and applied science were the same. Sir Humphry Davy discovered seven chemical elements, and invented the miner's safety lamp. Louis Pasteur investigated the properties of molecules, and worked out how to stop milk spoiling. Everybody thought that was admirable. Somehow, things have changed. Today the feeling is widespread that science and commerce should not - must not - mix. There is a queasy suspicion that the process of discovery is in some way corrupted if it is driven by profit."
"Far from compromising science, profit in both these cases - the development of new medicines and the elucidation of the genome - has animated it, and directed it towards meeting pressing human needs. It is a happy marriage. Davy and Pasteur would surely have approved."
redux [08.26.00]
"Nowhere are patents more central to the creative process than in genetic drug development, where human genes and their expressed proteins themselves are developed as therapies. The biotechnology industry in the United States has brought a handful of these crucial new products (recombinant human insulin, to name one of the most familiar) to market and is on the threshold of a bonanza of genetic drugs and vastly greater relief for ill and aging populations around the world.
Patent protection is the sine qua non of that bonanza."
redux [04.26.00]
""The analogy that I would use is that of a minefield," said Bob Levy, senior VP of science and technology for American Home Products. "We are spending an incredible amount of time now, when we find exciting targets and begin to validate them, in trying to define who has rights to what. And we're finding, in almost every product that we look at, that someone has patented the protein, the gene, a fragment, a diagnostic test." Levy noted that untangling patent rights, and determining which patents are dominant, are increasingly time-consuming and expensive tasks. And patent-holders must be paid. "The royalties that will be involved soon in some of the products that we are bringing to market, they're already up into the ten, fourteen, fifteen percent [range]," said Levy. "And that may increase with time.""
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The OpenScience Project
How to make money from Open Source scientific software
"So, I’m left with a dilemma. I want this company to do well, to hire more of my students in the future, and to continue to produce high quality code. I also want the codes that we use in my field to be available for skeptical review. So today, I’m starting a set of posts in which I’ll try to hash out the following question: How can people make money from open source scientific software?
The question has been asked (and answered) many times before in non-scientific fields, and some of the answers that might work for a piece of commodity software (like a database) might not work so well for highly-specialized software. Over the next few days, I’ll lay out a set of common strategies from non-scientific fields to figure out if any of these strategies might work in the sciences."
redux [06.10.04]
"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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Canada.Com
Publicly funded labs shouldn't be allowed to hoard flu data: U.S. researcher
"A leading scientist in the field of genetic sequencing is calling on publicly funded U.S. researchers and research organizations to throw open their collections of H5N1 avian flu viruses to allow others to work toward lessening the pandemic threat the virus poses."
"These labs register their findings in a secure database so that they and the WHO can track changes in H5N1 viruses. But those virus sequences are slow to trickle out to the rest of the research world. (Typically, scientists only post data publicly when they publish findings in a journal, a process that can take months or more.)"
redux [12.02.05]
"Web tools now allow data sharing and informal debate to take place alongside published papers. But to take full advantage, scientists must embrace a culture of sharing and rethink their vision of databases."
"Scientists may be justified in retaining privileged access to data that they have invested heavily in collecting, pending publication — but there are also huge amounts of data that do not need to be kept behind walls. And few organizations seem to be aware that by making their data available under a Creative Commons licence (see http://creativecommons.org/license), they can stipulate both rights and credits for the reuse of data, while allowing its uninterrupted access by machines."
redux [01.28.04]
"Many academic scientists see nothing wrong with making their commercial brethren pay for access. After all, they reason, industry has lots of money. Why not make them pay?"
"When you choose the "soak industry" option, you are implicitly expressing the following beliefs: (1) Your database is so useful for drug development that companies will pay handsomely for it. And (2) you're willing to delay the drug developers until the company comes up with the scratch. To hell with the patients who might benefit from the drug in question! Do you really believe this?"
redux [06.13.02]
"But Celera's rival published its version free of charge on the internet, a move which damaged Celera's commercial prospects. "That has had an impact," says Bennett. "Any stand-alone information business will be challenged because the value of information degrades," he adds.
But he denies that the venture has been a failure. "We have 250 subscribers, both commercial and non-commercial," says Bennett. The business even makes a profit, but the company will not discuss the impact of the free genome data on profits."
redux [04.08.02]
"Jim Kent was a graduate student in biology at the University of California, Santa Cruz (UCSC), when he wrote the program that allowed the public human genome team to assemble its fragments just before Celera's private, commercial effort. His program ensured that the human genome data would remain in the public domain. Kent wrote the 10,000-line program in a month, because he didn't want to see the genome data locked up by commercial patents."
"Kent's work illustrates the need to think about more than just open source code; in the scientific community there is a growing awareness of the importance of open data."
redux [03.20.02]
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"The genomics revolution and the Internet have changed science in ways impossible to imagine 20 years ago. Among other advances, these forces have allowed the latest research to be routinely gathered, organized, and disseminated, typically at little or cost, through online biological information databases.
Arduous to use and filled with mostly unanalyzed data early on, these computer databases are now packed with valuable, up-to-date information made easily accessible with improved search engines. They have become so ubiquitous and integral to science today that almost every molecular biologist consults one when initiating research projects. "It would be impossible to do molecular biology properly these days without access to them."
redux [03.07.02]
"''I humbly have to admit that between only 15 to 20 percent of my requests are fulfilled. I cannot afford to do anything else,'' said Tak Mak, a leading genetics researcher at the University of Toronto.
"In fact, according to a recent study published in the Journal of the American Medical Association and led by doctors at Massachusetts General Hospital, nearly 50 percent of surveyed geneticists at major US academic institutions said that another faculty member had denied them at least one request for information in the past three years. The study also found that geneticists are vastly more likely to believe that sharing has decreased in their field over the past decade than that it has increased - a startling figure given how much easier the Internet has made the transfer of information."
redux [01.23.02]
[requires 'free' registration]
"Nearly half the academic geneticists who asked for additional information, data, or materials related to a published research report were denied their requests, a new survey reports today. Are geneticists being unfairly pilloried?"
"Because they were denied access to data, 28% of geneticists reported that they had been unable to confirm published research. Other reported consequences were delays in publications, abandonment of a promising line of research, and the collapse of collaborations."
redux [02.27.02]
"For the scientists working on the Human Genome Project, the data defining who we are is too important to be left to Celera -- or any other company. David Haussler, a team leader at the University of California at Santa Cruz who helped Kent and others put the genome online, expresses the credo of a data liberator succinctly: "Information about the human genome is better in public hands than secretly locked up somewhere."
"But it's not just the research data itself that is at the center of the tug of war between corporations and scientists. When working with data as complex and vast as the human genome, the software tools necessary to manipulate that data are as important as the genetic code itself."
"It's really clear that there are some real issues here, but there are people taking up the guerdon on behalf of openness as well as those who are working for secrecy and private advantage. So I'm hopeful that in the end, openness will win.
Especially in a field like bioinformatics, the natural advantages of open source really do outweigh the advantages of secrecy. No one controls all the data. Talk after talk at the conference focused on the way that matching up data from other researcher's databases is the key to making sense out of your own data."
redux [05.09.01]
"It may seem surprising, considering the amount of publicity the Human Genome Project has garnered over the past year, but a recent Wellcome Trust survey indicates that only half of biomedical researchers using genome databases are familiar with the services provided by Ensembl and other freely available options.
Although the number of hits on the Ensembl website has doubled since the publication of the Human Genome Project's findings in Nature in February, a questionnaire sent to 777 individuals funded by the Wellcome Trust found that only 82 used Ensembl regularly, 189 used it occasionally, and only 50 percent of those who used DNA databases regularly used Ensembl at all.
Even more surprising was the finding that of those who didn't use Ensembl, 50 percent had never heard of it.""
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Globe and Mail
Code 2
"The traditional idea that we are the passive carriers of our genes is being challenged by the notion that we are their custodians. Our lifestyles — what we eat, how much we exercise, whether we smoke — may play a role in a chemical switching system that activates or deactivates our genes. There are signs that our behaviour may program sections of our children's DNA, and that how we live may even affect our grandchildren's genes.
“It introduces the concept of responsibility into genetics,” said Dr. Moshe Szyf, a researcher at McGill University in Montreal and a pioneer in the field of epigenetics, the study of genetic changes that don't involve mutations in DNA."
redux [12.15.05]
"Although the human genome was sequenced more than five years ago, it can provide scientists with comparatively few clues to the origins and treatment of disease.
The bulk of that information lies buried in the "epigenome" -- from the Greek epi, meaning "in addition to." The epigenome consists of chemical "amendments" to strings of DNA that spell out the human genetic code.
Now, an international group of 40 leading cancer scientists are proposing a new effort -- the Human Epigenome Project -- to map these chemical modifications.
And it would appear some of these altered genes are passed on to future generations with a range of studies emerging to support the idea.
redux [11.30.05]
"What we eat may influence our health by changing specific genes, researchers believe.
Several studies in rodents have shown that nutrients and supplements can change the genetics of animals by switching on or off certain genes."
redux [08.18.05]
"The more we learn about the human genome, the less DNA looks like destiny.
As scientists discover more about the "epigenome," a layer of biochemical reactions that turns genes on and off, they're finding that it plays a big part in health and heredity.
By mapping the epigenome and linking it with genomic and health information, scientists believe they can develop better ways to predict, diagnose and treat disease."
redux [07.02.04]
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"In a written commentary, evolutionary biologist Massimo Pigliucci said that Ruden's experiment was "one of the most convincing pieces of evidence that epigenetic variation is far from being a curious nuisance to evolutionary biologists." Pigluicci doesn't go so far as to say that the heritable changes caused by Hsp90 alterations are Lamarckian, but Ruden does. "Epigenetics has always been Lamarckian. I really don't think there's any controversy," he says.
Not that Mendelian genetics is wrong; far from it. The increased understanding of epigenetic change and the recent evidence indicating its role in inheritance and development doesn't give epigenetics greater importance than DNA. Genetics and epigenetics go "hand in hand," says Ohlsson. In the case of disease, says Reik, "there are clearly genetic factors involved, but there are also other factors involved. My suspicion is that it will be a combination of genetic and epigenetic factors, as well as environmental factors, that determine all these diseases.""
redux [10.07.03]
"The Human Epigenome Project will look for patterns in our "life code" that are associated with gene regulation but are also implicated in causing disease."
"Researchers at Epigenomics AG in Berlin and the Sanger Institute in Cambridge will take part in the five-year study."
"The announcement follows the completion of an HEP pilot project that studied methylation patterns within the Major Histocompatibility Complex in chromosome 6 to determine the methylation status of over 100,000 sites. Data from the pilot study, which was funded by the European Union, was released today on the HEP's website."
"The methylation data will be integrated with the human genome sequence using the Ensembl interface and publicly released at www.epigenome.org and at www.sanger.ac.uk/epigenome."
redux [10.06.03]
[requires 'free' registration]
"With the help of some fat yellow mice, scientists have discovered exactly how a mother's diet can permanently alter the functioning of genes in her offspring without changing the genes themselves."
"The research is a milestone in the relatively new science of epigenetics, the study of how environmental factors like diet, stress and maternal nutrition can change gene function without altering the DNA sequence in any way."
redux [09.13.01]
[requires 'free' registration]
"The term was introduced by Conrad H. Waddington in 1942.1 To paraphrase an erudite epistolary exchange in Science, he is said to contrast genetics with epigenetics , the study of the processes by which genotype gives rise to phenotype. In 1942 we had barely any clue as to what those processes are, so "epigenetic" had no connotation of the underlying chemical mechanism, whatever it was that modulated cell differentiation.
In 1994, as cited in the same issue of Science, Robin Holliday voiced a commonly apprehended drift in meaning, and redefined epigenetic as "Nuclear inheritance which is not based on differences in DNA sequence." These two memes are freely circulating and can cause muddle or mischief mainly when they recombine, namely when epigenetic-H is automatically applied to epigenetic-W."
"This neology of nucleic, epinucleic, extranucleic, has attracted few followers, I think largely because so few people had really thought through the distinctions. There is much merit in Ben Johnson's caution about unbridled proliferation of terms: "A man coins not a new word without some peril, and less fruit; for if it happen to be received, the praise is but moderate; if refus'd, the scorn is assur'd." But is a polysemy to be preferred, with thought-muddling as a further peril?"
redux [08.16.01]
[ summary can be viewed for free once registered ]
"Some of the weirdest genetic phenomena have very little to do with the genes themselves. True, as the units of DNA that define the proteins needed for life, genes have played biology's center stage for decades. But whereas the genes always seem to get star billing, work over the past few years suggests that they are little more than puppets. An assortment of proteins and, sometimes, RNAs, pull the strings, telling the genes when and where to turn on or off."
""The unit of inheritance, i.e., a gene, [now] extends beyond the sequence to epigenetic modifications of that sequence," explains Emma Whitelaw, a biochemist at the University of Sydney, Australia."
""[Epigenetic effects] give you a mechanism by which the environment can very stably change things," says Rudolph Jaenisch, a developmental biologist at the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts. Researchers are hoping to harness these effects to design drugs that correct cancer and other diseases brought on by gene misregulation."
redux [07.11.00]
"Genes are tricksters. They can be turned on or off -- and whether they're on or off decides whether the gene-owner will develop disease.
Gene researchers have embarked on a new field of research, called epigenomics, to determine whether genes are in the on or off position. This type of marker could prove an important diagnostic or therapeutic tool for all types of cancer.
"At Johns Hopkins, researchers are performing clinical trials on about 15 patients with leukemia and other cancers to find out if epigenomics might give pharmaceutical companies a lead for developing cancer drugs.
The research, like all epigenomics research, is studying a chemical found in everyone's DNA called cytosine. Cytosine is the only chemical of the four that make up human DNA (the others are adenine, thymine, and guanine) that is prone to a phenomenon called methylation. When cytosine is methylated, it tuns off its gene."
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The New York Times
The Twists and Turns of History, and of DNA
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"EAST ASIAN and European cultures have long been very different, Richard E. Nisbett argued in his recent book "The Geography of Thought." East Asians tend to be more interdependent than the individualists of the West, which he attributed to the social constraints and central control handed down as part of the rice-farming techniques Asians have practiced for thousands of years.
A separate explanation for such long-lasting character traits may be emerging from the human genome. Humans have continued to evolve throughout prehistory and perhaps to the present day, according to a new analysis of the genome reported last week by Jonathan Pritchard, a population geneticist at the University of Chicago. So human nature may have evolved as well.
If so, scientists and historians say, a fresh look at history may be in order. Evolutionary changes in the genome could help explain cultural traits that last over many generations as societies adapted to different local pressures."