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{bio,medical} informatics

Thursday, March 16, 2006

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find related articles. powered by google. 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]
find related articles. powered by google. Nature Let data speak to data

"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, they can stipulate both rights and credits for the reuse of data, while allowing its uninterrupted access by machines."

redux [01.28.04]
find related articles. powered by google. GenomeWeb Among Databases, Open Access Is Growing Rare

"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]
find related articles. powered by google. The New Scientist Celera abandons gene sequencing

"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]
find related articles. powered by google. The O'Reilly Network Keeping Genome Data Open

"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]
find related articles. powered by google. The Scientist The Rise of Biological Databases
[requires 'free' registration]

"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]
find related articles. powered by google. The Boston Globe Scientists say sharing of key data has slowed

"''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]
find related articles. powered by google. BioMedNet Geneticists reluctant to share data
[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]
find related articles. powered by google. Salon Genome liberation

"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."

find related articles. powered by google. Tim O'Reilly In response to Paul Allen's question at Davos about data hoarding in science

"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]
find related articles. powered by google. GenomeWeb Survey Finds Only Half of Genome Database Users Aware of Free Resources

"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.""

[ rhetoric ]

Bioinformatics will be at the core of biology in the 21st century. In fields ranging from structural biology to genomics to biomedical imaging, ready access to data and analytical tools are fundamentally changing the way investigators in the life sciences conduct research and approach problems. Complex, computationally intensive biological problems are now being addressed and promise to significantly advance our understanding of biology and medicine. No biological discipline will be unaffected by these technological breakthroughs.


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