Wednesday, July 31, 2002

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Genomeweb NHGRI Says It Won't Publish Final Human-Genome Draft

"Come next April, there will be a lot of high-visibility celebrations heralding the completion of the final draft of the human-genome sequence. Just don't expect to see a journal article like the one that made public the first draft in February 2001.

Instead, the genomic community can expect a public announcement trumpeting the completion of the final draft, which will quietly be deposited into GenBank, said National Human Genome Research Institute spokesman Geoff Spencer."

Tuesday, July 30, 2002

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The New York Times Race Is Seen as Real Guide to Track Roots of Disease
[requires 'free' registration]

"Challenging the widely held view that race is a "biologically meaningless" concept, a leading population geneticist says that race is helpful for understanding ethnic differences in disease and response to drugs.

The geneticist, Dr. Neil Risch of Stanford University, says that genetic differences have arisen among people living on different continents and that race, referring to geographically based ancestry, is a valid way of categorizing these differences."

redux [02.16.02]
The Scientist Race and the Clinic: Good Science?
[requires 'free' registration]

"Categorizing people by skin color is probably recent; hunter-gatherers didn't wander far enough to encounter peoples of different colors. "The whole idea of race appeared after the age of exploration by ships," says Leda Cosmides, professor of psychology, Center for Evolutionary Psychology, University of California, Santa Barbara. "People at very different geographical points looked different enough that it made it seem like humans came in different morphs, or complexes of traits.""

"With researchers demonstrating that the human brain can easily classify people in varied ways, and human genome data revealing the gene combinations that control response to drugs, the concept of race, particularly as it relates to clinical decision-making, is at the very least headed for reconsideration. Says McLeod, "There are already a lot of SNP data to allow this to happen. The rate-limiting step is the data showing that a particular marker or set of markers is informative enough to individualize medical decisions.""

redux [10.30.01]
Nature: Science Update Race is a poor prescription

"Race should not influence drug prescriptions, warn geneticists. Genetic differences between individuals give a better indication of who will respond well to a medicine, a new study shows."

Geneticists have known this for a while. "It's no surprise that skin pigment is a lousy predictor of physiology," says Howard McLeod of Washington University School of Medicine in St Louis, Missouri. This study is the first to prove it."

redux [07.20.01]
The New York Times Genome Mappers Navigate the Tricky Terrain of Race
[requires 'free' registration]

"Scientists planning the next phase of the human genome project are being forced to confront a treacherous issue: the genetic differences between human races."

"With the decoding of the human genome largely complete, government scientists are beginning to construct a special kind of genetic map that would provide a shortcut to locating the variant human genes that predispose people to common diseases."

"The question the scientists face is whether that map should chart possible differences that may emerge among the principal population groups, those of Africans, Asians and Europeans."

redux [03.18.01]
The Atlantic Online The Genetic Archaeology of Race

"Genetics research is demonstrating that the differences in appearance among groups are profoundly incidental, but these differences do have a genetic basis. And although it's true that all people have inherited the same genetic legacy, the genetic differences among groups have important implications for our understanding of history and for biomedical research. These complications in an otherwise reassuring story have thoroughly spooked the leaders of the public and private genome efforts. The NIH has been collecting information about genetic variants from different ethnic groups in the United States, but it has refused to link specific variants with ethnicity. Celera has been sequencing DNA from an Asian, a Hispanic, a Caucasian, and an African-American, but it, too, declines to say which DNA is which.

This strategy of avoiding the issue is almost sure to backfire. It seems to imply that geneticists have something to hide. But the message emerging from laboratories around the world should be hailed, not muzzled. It is one of great hope and promise for our species."

redux [08.23.00]
The New York Times Do Races Differ? Not Really, DNA Shows
[requires 'free' registration]

"Through transglobal sampling of neutral genetic markers -- stretches of genetic material that do not help create the body's functioning proteins but instead are composed of so-called junk DNA -- researchers have found that, on average, 88 percent to 90 percent of the differences between people occur within their local populations, while only about 10 percent to 12 percent of the differences distinguish one population, or race, from another.

To put it another way, the citizens of any given village in the world, whether in Scotland or Tanzania, hold 90 percent of the genetic variability that humanity has to offer."

""Ethnicity is a broad concept that encompasses both genetics and culture," Dr. Anand said. "Thinking about ethnicity is a way to bring together questions of a person's biology, lifestyle, diet, rather than just focusing on race. Ethnicity is about phenotype and genotype, and, if you define the terms of your study, it allows you to look at differences between groups in a valid way."

redux [03.12.01]
GeneLetter Drawing DNA lines of ethnicity

"The idea of using genetics to determine ethnic heritage has been growing in popularity over recent years. When Rick Kittles, a geneticist at Howard University, offered to trace tribal roots via a $350 DNA test, African Americans flooded his telephone line with requests.

"Even if an identifying marker shows up, the result isn't necessarily definitive. While certain markers may be more common to one ethnic group, most also can be found in other populations as well.

"Because of the tremendous genetic variation within populations, it would be biologically impossible to settle on a limited number of genetic markers that could define "Native Americans," says Morris Foster, an anthropologist at the University of Oklahoma who has wrestled with the risks faced by Indian tribes interested in genetic research.

Furthermore, Foster added in an e-mail interview with GeneLetter, "it is absurd to try to define what is essentially a social identity by using biological characteristics. This, though, is how racism has historically worked."

Monday, July 29, 2002

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Wired News An Rx for the Pharmaceuticals

"Colin Hill, president and CEO of GNS, said the adoption of modeling will be slow, but even the largest and most stubborn pharmas will soon realize they have to adopt it if they want to compete.

He has seen more success selling pharmas the baby steps toward modeling: tools, such as its Diagrammatic Cell Language, software and database information, rather than actual models."

redux [11.27.00]
BusinessWeek A Software Model That Fathoms the Human Heart?

"What do a Boeing 777 and the human body have in common? Both are complex systems, dependent on millions of complex parts, whether they be a jet-propelled engine or a pumping organ such as the heart. The big difference: Engineers can design and build highly accurate computer models of the way a Boeing 777 will behave in flight. The human heart? Its complexity has long stymied efforts by researchers intent on turning drug development into a predictive science, much like building airplanes.

But that's changing. A handful of companies are developing software that can model single cells, whole organs, cellular metabolism and toxicology, diseases throughout a patient's body, and even an entire clinical trial."

redux [02.16.01]
MIT Technology Review Upstream: Biology in Silico

"Computers capable of mimicking life have long been the stuff of sci-fi nightmares - think The Terminator or 2001's HAL 9000. But for researchers struggling to make sense of vast amounts of new biological data, and for drug companies anxious to cut costs and speed development, having accurate computer simulations of living systems is still a dream. To make that dream come true, they are turning to "in silico biology," building computer models of the intricate processes that take place inside cells, organs, and even people. The ultimate goal: an entire organism modeled in silicon, allowing researchers to test new therapies much as engineers "fly" new airplane designs on supercomputers."

redux [05.15.01]
BioMedNet Cells in cyberspace promise biology real understanding
[requires 'free' registration]

""We in physics are used to studying complex systems, but the level of complexity inherent in biological systems ... is way beyond what we have experience dealing with," said Rajagopal, assistant director of research at the Cavendish Laboratory in the University of Cambridge. "Biological systems are much harder to model as they are in highly non-equilibrium states and you not only have to take into account the flow of matter and energy, but also the flow of information!"

He added: "In biology, the whole is greater than the sum of its parts. We have to move on from the "reductionist" towards an "integrationist" approach."

redux [05.15.01]
HMS Beagle Virtual Cures
[requires 'free' registration]

"For a brief period, supplying the data was enough. More genes meant more potential drug targets. But now the victims of the data flood are crying for help. Companies like Entelos, Inc. (Menlo Park, California) are coming to the rescue by building models that integrate all those data into a single, homeostatic, interconnected whole. The models allow researchers to run virtual drug trials to determine the best drug targets, treatment regimens, and patient populations."

Modelers feel that their time has come. "Leaders in the genomics field are all coming to this realization that model building is becoming the rate-limiting step," says Palsson. "There's a major shift taking place in the biological sciences." Math is back, he says, and "biology is going to become quantitative."

Saturday, July 27, 2002

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O'Reilly Network I Hack the Body Electric

"Birney's willingness to dangle jobs in front of the OSCON audience was itself a sign of bioinformatics researchers' extreme regard for open source technologies. Birney described his ENSEMBL project, a joint effort to develop a software program to sort through and annote eukaryotic genome data, as "open source to the core" and described himself as a "Perl addict." Beyond that, Birney said, the chief advantage of open source software in the bioinformatics sphere is the ethical overlap between peer-reviewed software and peer-reviewed research.

"For us, it's straight scientific principles," Birney said. "If you want to be a scientist, open up your data and open up the code that helps you work with that data.""

ITWorld Human genome is open source, too

""You can't do science without having reproducible results," Kent said, explaining that scientists employ a system under which they conduct peer reviews on scientific discoveries before accepting them as sound. "People can't do that unless they can see your source."

Some open source developers argue that the same standards that are used for testing scientific experiments should also be used for testing software. Having access to code gives programmers the ability to dissect a software program and identify bugs, many attendees here say."

redux [05.09.01]
IEEE Spectrum Open-Source Biology And Its Impact on Industry

"The toolbox of biochemistry, the parts list--"the kernel," to stretch the software analogy--is shared by all organisms on the planet. In general, organisms differ from one another because of their order of gene expression or because of relatively subtle perturbations to protein structures common to all forms of terrestrial life. That is, innovation in the natural world in some sense has always followed the idea of a service and flow economy. If the environment is static, only when an organism figures out how to use the old toolbox to provide itself, or another organism, with a new service is advantage conferred.

The analogy to future industrial applications of biology is clear: When molecular biologists figure out the kernel of biology, innovation by humans will consist of tweaking the parts to provide new services. Because of the sheer amount of information, it is unlikely that a single corporate entity could maintain a monopoly on the kernel. Eventually, as design tasks increase in number and sophistication, corporations will have to share techniques and this information will inevitably spread widely, reaching all levels of technical ability--the currency of the day will be innovation and design. As with every other technology developed by humans, biological technology will be broadly disseminated."

Technology based on intentional, open-source biology is on its way, whether we like it or not, and the opportunity it represents will just begin to emerge in the next 50 years."

Friday, July 26, 2002

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Buffalo Business First Senate committee approves $1 million for bioinformatics center

"New York's U.S. Senators Charles Schumer and Hillary Rodham Clinton jointly announced that the Senate Appropriations Committee has approved $1 million in funding for Buffalo's planned Center of Excellence in Bioinformatics.

The $1 million was included as part of a an appropriations measure for the Departments of Veterans Affairs and Housing and Urban Development."

redux [05.01.02]
digitalMass Bioinformatics center takes shape as Buffalo seeks to redefine self

"An optimistic Pataki declared the center "will transform western New York into a 21st Century economy."

The lofty predictions come as upstate's largest city struggles to reinvent itself from a past-its-peak industrial center losing not only jobs but people: U.S. Census figures show the population has dropped to under 300,000, down from a 1950s peak of 580,000."

redux [12.07.01]
Buffalo Business First Pataki announces $200 million Bioinformatics center for Buffalo

"Buffalo will be the site of a Center of Excellence for Bioinformatics thanks to a $200 million collaboration between the public and private sectors.

Gov. George Pataki announced during a swing through Buffalo on Dec. 6 that the state will contribute $50 million to help establish the 150,000 square-foot facility to be located adjacent to the emerging Buffalo Niagara Medical Campus. It is part of Pataki's $1 billion high-tech and biotech Centers of Excellence planned for across the state."

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New Scientist Artificial intelligence tackles breast cancer

"Techniques borrowed from artificial intelligence could help doctors assess just how serious a particular case of breast cancer is and, therefore, how to treat it."

"When tested on 100 women, the new technique proved to be nearly 90 per cent accurate at predicting the extent of this spread and whether they would survive for five years. The approach, developed by a team led by Raouf Naguib at the University of Coventry and Gajanan Sherbet at the University of Newcastle upon Tyne, builds on an existing analytical method called image cytometry. "

redux [06.26.02]
Science Daily Gene Expression Profiles Predict Survival Of Lymphoma Patients After Chemotherpy

"Patterns of genes that are active in tumor cells can predict whether patients with diffuse large B-cell lymphoma (DLBCL) are likely to be cured by chemotherapy, scientists reported today in the New England Journal of Medicine. Researchers analyzed thousands of genes in lymphoma biopsy samples from patients with DLBCL and determined that the activity of as few as 17 genes could be used to predict patients' response to treatment. "We're able to reliably predict the survival of these patients using data from a small number of genes, indicating that this technique should be entirely manageable for routine use," said National Cancer Institute (NCI) investigator Louis M. Staudt, M.D, Ph.D., the senior author on the study."

redux [05.31.01]
Wired News Fingering Cancer Genes

"Genes have fingerprints just like fingers, which got one cancer researcher thinking.

Since the FBI uses neural networks -- a type of artificial intelligence built to imitate neuron function in the brain -- to sift through masses of computerized fingerprint data to solve crimes, why not do the same for genetic fingerprint data?"

""We trained (the neural networks) to recognize this is one cancer and this is another and this is not a cancer," Kahn said. "Eventually it learned to recognize particular features that were particular for cancer.""

Family Physicians' Electronic Network Diagnostic Algorithms: results at last!

"We seem to forget, sometimes, that the first researchers in AI that chosen medicine as a problem domain did so, not because of an interest in medicine, but because of an interest in diagnosis as an example of intelligent behavior. Medical diagnosis was one example (perhaps a poor one given that there are much simpler and easier models in other physical systems). Automated diagnosis has rarely interested the medical community, not because of a fear of removing the human element (we've already done that with our reimbursement system) or of replacing humans with machines but, more simply, because diagnosis (as most people view it), is not really the problem. Most clinicians manage some form of diagnosis and most patients are treated appropriately. What is needed is better information on the utility of information and the means to obtain it which least stresses the system."

Thursday, July 25, 2002

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Bio-IT World Source of Debate

"For an industry in which 15 years can elapse between startup and first revenue, the allure of "free" software isn't hard to fathom. Biotech companies, like those in many other industries, have embraced the use of software distributed under free or open source licenses.

Now, the emergence of biotech as an industry and its growing dependence on IT-based tools has stirred debate over the use of open source software." [ via bioinformatics.org ]

Tuesday, July 23, 2002

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New Scientist Gene patents "inhibit innovation"

"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]
digitalMASS Compaq chief's comment stuns biotech crowd

"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]
NewScientist Scientists hindered by gene patent

"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]
SiliconValley.Com As disease-causing genes are discovered, the rush to the patent office grows

""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]
The Economist Science and profit

"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]
MIT Technology Review The Case for Gene Patents

"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]
Signals Homestead 2000: The Genome

""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.""

Monday, July 22, 2002

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Forbes Biotech's Cut-Rate Supercomputer

"For years, small biotech companies have used Linux to manage a lot of data on the cheap. Now that looks like a big business opportunity."

""Linux is an interesting dynamic," says Jeffrey Augen, director of life sciences strategy at IBM. "Most of the small biotech companies in the world today are standardizing on Linux platforms and Linux clusters. Small companies, even startup, round-A companies, are coming to us seeking a level of computer horsepower that traditionally you would see in larger companies.""

redux [06.25.02]
Genomeweb Linux Heavyweight Comes to Pacific Northwest National Lab

"The final version, which could be useful in protein-interaction studies, will include 1,400 next-generation Intel Itanium processors with an expected peak performance of 9.1 teraflops. It will cost $24.5 million and exceed by more than 30 times the speed of PNNL's old supercomputer, which was state of the art when it was installed in 1997."

"According to HP, the system, scheduled to begin delivery in the fall and go fully on-line next spring, will be the world's most powerful Linux-based system."

The New York Times At Los Alamos, Two Visions of Supercomputing
[requires 'free' registration]

"Though Q will be almost 200 times as fast, it will cost 640 times as much -- $215 million, compared with $335,000 for Green Destiny. And that does not count housing expenses -- the $93 million Metropolis center that provides the temperature-controlled, dust-free environment Q demands."

" Green Destiny belongs to a class of makeshift supercomputers called Beowulf clusters."

redux [07.13.01]
Scientific American The Do-It-Yourself Supercomputer

"Our solution was to construct a computing cluster using obsolete PCs that ORNL would have otherwise discarded. Dubbed the Stone SouperComputer because it was built essentially at no cost, our cluster of PCs was powerful enough to produce ecoregion maps of unprecedented detail. Other research groups have devised even more capable clusters that rival the performance of the world's best supercomputers at a mere fraction of their cost. This advantageous price-to-performance ratio has already attracted the attention of some corporations, which plan to use the clusters for such complex tasks as deciphering the human genome. In fact, the cluster concept promises to revolutionize the computing field by offering tremendous processing power to any research group, school or business that wants it."

"Above all, the Beowulf concept is an empowering force. It wrests high-level computing away from the privileged few and makes low-cost parallel-processing systems available to those with modest resources. Research groups, high schools, colleges or small businesses can build or buy their own Beowulf clusters, realizing the promise of a supercomputer in every basement. Should you decide to join the parallel-processing proletariat, please contact us through our Web site (http://extremelinux.esd.ornl.gov/) and tell us about your Beowulf-building experiences."

Tuesday, July 16, 2002

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Thursday, July 11, 2002

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Washington Monthly May the Source Be With You

"In 1984, Internet pioneer Stewart Brand made one of the most prescient observations of the technology era: "On the one hand, information wants to be expensive because it is so valuable. The right information in the right place just changes your life. On the other hand, information wants to be free because the cost of getting it out is getting lower and lower all the time. So you have these two fighting against each other."

Brand's insight is famous among computer programmers. But it is probably even more apt in explaining what is happening today in biology."

redux [02.01.02]
O'Reilly Network Ewan Birney's Keynote: A Case for Open Source Bioinformatics

"First, Ewan argued that open source makes sense because it follows good and well-known scientific principles."

"Second, Ewan emphasized that in biological research it's not the software that's important--it's the data. Since the actual data matters much more than the tools used to process it, there's a big benefit in sharing software."

"The third reason Ewan gave for supporting open source was that molecular biology and medicine will be most advanced by the creation of a common infrastructure--and this is something best done with open source tools."

GenomeWeb Debate Drives Bioinformatics Open Source Community to Clarify Positions on Public Funding

"In the face of the mounting discussion around this topic, the Open Bioinformatics Foundation - the non-profit umbrella group that supports BioPerl, BioPython, BioJava, BioDAS and other projects -- released a position statement at today's panel discussion. According to OBF board member Steven Brenner of the University of California, Berkeley, the statement was necessary to distinguish the OBF from organizations "with similar sounding names" and "because everybody was asking us where we stood on the topic."

The OBF statement takes a more moderate stance than the openinformatics.org petition. Noting that "scientific software developed with public support should be distributed under terms analogous to those applied to biological materials," it concludes, "We encourage institutions to delegate to their scientists the opportunity to select non-restrictive and open source licenses for their software.""

redux [01.16.01]
O'Reilly Network Does Publicly Funded Research Have to Result in Open Source Code?

"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]
IT-Analysis Open Source in Bioinformatics

"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."

Salon Public money, private code

"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]
SiliconValley.Com Computer scientists push to publish code powering genetic research

"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]
GenomeWeb Legal Pitfalls of Free Bioinformatics Software May Loom Large

"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]
Boston Business Journal Legal issues surround programming bioinformatics

"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]
Stanford Medical Informatics Preprint Archive Open Source Initiatives in Bioinformatics

"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."

redux [07.27.00]
Informatics Review Open Source Software in Healthcare

"Good software forms seamless connections; as George Orwell said of prose, the best is like a window pane: transparent. The obscurity of commercial binaries is an obstacle to good quality communication between systems. In healthcare, good communication is too important to remain proprietary. Software developers should remain confident that there will always be work for the future in discovering, providing, and adapting applications for organizations, and training people to use them. This, rather than the sharp-suited gouging of Bill Gates wannabees, should become the predominant business model for software in the British NHS. Software engineering will become a profession more like medicine and the law: in which practitioners earn a fair hourly reward for their experience at interpreting, evaluating and applying knowledge from a specialized domain to the benefit of their clients. Current models, which restrict the sharing and development of knowledge, are certainly counterproductive and arguably unethical. Open source is the future: all we have to do is built it."

Wednesday, July 10, 2002

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News24 South Africa Supercomputer switched on

"The Cray SV1 supercomputer, housed at the South African National Bioinformatics Institute (Sanbi) will be used for tasks that include the search for greater understanding of HIV."

"[Sanbi director Prof Winston Hide] said the supercomputer made South Africa as competitive in the challenging field of genome analysis as research centres anywhere else in the world. "

redux [06.17.02]
Mail and Guardian Online Super-fast computer aids genetic research

"It may not be able to provide the answer to life, the universe and everything else, but the new million-dollar supercomputer about to arrive at the South African National Bioinformatics Institute (Sanbi) may help find why some Africans are immune to HIV.

The supercomputer, as yet unnamed, will be the first research-orientated machine on the continent. It is being handed over by United States-based company Cray, as part of a collaborative research effort with Sanbi, which is part of the University of the Western Cape."

Tuesday, July 09, 2002

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Washington Business Journal Venture capital scarce for bioinformatics players

"Most agree that venture money is there for companies -- but the pressure must seem insurmountable for entrepreneurs, who probably feel like they have to give the perfect business pitch to venture capitalists just to get a foot in the door.

"If people aren't rethinking their models, they're nuts; if they were waiting for Viaken to be their wake-up call, they're nuts," Nelson says."

redux [04.18.02]
GenomeWeb After the Fall, DoubleTwist's Williamson Performs Stoic Postmortem

""Bioinformatics is heterogeneous, but many bioinformatics [tools] fulfill a narrow niche," said Williamson. "There is room for someone to consolidate, but I don't know if that is needed or necessary. Plus there's always an academic coming up with the next thing. So it's a hard business to sustain."

Bioinformatics "is great for smaller companies," he went on. And there are "people who can tie the islands of analysis together, and who have the resources to pull it off, but is that a business? That's the million dollar question. And will anyone buy it if you can pull it together? Everybody wants to be the Microsoft Office of bioinformatics, but I'm not sure that's going to happen.""

redux [04.10.02]
vnunet Gene genie promises IT boom

"Bioinformatics is the gene genie that could bring back the boom years for IT."

"Bioinformatics is inherently different to the dotcoms because it is based on real rather than perceived needs," she said. "We will need cancer drugs, Aids drugs and more food, so the business projection is much more stable."

redux [03.12.02]
EyeForPharma Bio-IT sector gains momentum despite recession according to new research from IDC

"While other IT sectors are struggling to keep their heads above water, the Bio-IT sector is gaining rapid momentum, according to analysis from IDC's new research and advisory service, Bio-IT Infrastructure. In addition, the research suggests the Bio-IT market will increase at a compound annual growth rate (CAGR) of 24% to nearly $38 billion by 2006."

redux [12.05.01]
News.Com IT firms bet on biotech to lift high-end sales

"The world's largest computer makers, faced with sagging consumer demand, are betting that the huge data crunching needs of nascent biotechnology firms will grow into a multi-billion dollar market for their equipment and consulting services over the next decade."

""The average individual can't comprehend what has happened in the last half dozen years, where the two greatest medical discoveries, the genome and the microchip, have converged," said Cal Stiller, chief executive of the $250 million Canadian Medical Discoveries Fund."

"We need companies that are on the informatics side that say 'holy cow', we have just stumbled onto the mother lode! We know nothing about mining that area, but we can build the best drilling equipment out there," added Stiller."

redux [03.11.02]
The Boston Globe No boom yet in analysis of drug data

"The emerging field of bioinformatics, the use of computers to analyze the inner workings of biology, is transforming an industry that just a decade ago relied on the manual labor of chemists and biologists. But even as it does so, bioinformatics is floundering as a business.

Shares of public companies that sell biological data or software are trading at a fraction of what they did two years ago. Dozens of companies have crowded into the field. Some have folded; others have survived only by morphing into drug-discovery companies.

''It's a hard market to build a business around,'' said Oliver Fetzer, a vice president at Boston Consulting Group."

redux [02.11.02]
MSNBC The Gene Bubble

"LIKE EVERY BUBBLE, this one had to burst. Stock prices of many bioinformatics firms have fallen sharply in recent years. LION Biosciences of Germany went public at $40 a share and now trades at about $13. Iceland's DeCode is worth a fourth of its former high. Even Celera, the U.S. firm that helped decode the human genome, is off its peak.

Falling stock prices are a symptom of a greater disappointment in bioinformatics. A few years ago the laborious and quirky process of drug discovery seemed on the verge of giving way to new streamlined, data-driven methods. Some firms organized the blizzard of genetic data into databases that researchers could mine with search engines from still other firms. Software companies built computer programs that modeled what goes on in human cells and even whole organs. Many investors came to believe that bioinformatics would open a new avenue to the discovery of drugs. But this avenue simply hasn't materialized. Says biotech analyst Earling Refsum at Nomura Bank in London: "Bioinformatics has not helped Big Pharma get more drugs into the pipeline.""

redux [01.03.02]
WashTech.Com Low Fliers Behind the Drugs

"Inside the laboratories of the world's major pharmaceutical companies and biotechnology start-ups, an emerging science is quietly transforming the drug industry. Bioinformatics -- the use of computers to analyze the inner workings of biology -- is helping researchers pinpoint the roots of diseases and design sophisticated medicines to treat them.

But even as it becomes a vital part of drug research, bioinformatics as a business is losing favor with investors. Shares of publicly traded firms that sell biological data and software tools are slumping, and venture capitalists are increasingly wary of investing in such companies.

redux [12.18.01]
Signals Magazine Bioinformatics: Time to Morph

"There comes a point in the life cycle of every organism when it must change or perish. For bioinformatics, the time for metamorphosis is now. Though computational biology is already an intrinsic part of the drug discovery process, the business models adopted by most bioinformatics firms have failed to produce profits. Competition -- from the IT industry and big pharma itself -- is growing and investors, both public and private, are unimpressed. While some companies are hoping persistence pays off, many are pursuing new business models that should allow them to retain a bigger share of the profits they are helping to create."

redux [03.14.01]
ABCNews.Com The Next Bubble: Is Bioinformatics the Next Big Boom...and Bust?

"The story proclaimed in its lead, "Move over Information Age. Make room for the age of bioinformation." You could picture bleary eyes opening all over the Bay Area. The story went on to note that a San Jose consulting firm was predicting a 10 percent annual growth in the bioinformatics market for years to come; and that the National Science Foundation estimated that 20,000 new jobs in the field would be created in the field in just the next four years.

If that wasn't enough, the rest of the section was filled with page after page of biotech firms listing job openings - in powerful juxtaposition to the endless lists of dot-com layoffs just a few pages earlier. Picture Starbucks spit-takes from Marin to Santa Cruz.

Wow! Rewrite that resume to emphasize that biology course you took in college. Roll your Aeron chair down to the nearest lab. Trade that black turtleneck for a white lab coat..."