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{bio,medical} informatics

Monday, April 14, 2003

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find related articles. powered by google. UC Santa Cruz Currents UCSC Genome Browser provides portal to finished human genome sequence

"As leaders of the Human Genome Project announced the project's successful completion at a press conference today in Bethesda, Md., UCSC bioinformatics researchers made the completed reference sequence of the human genome publicly available on the web-based UCSC Genome Browser."

""We have now built the browser on top of the finished genome sequence. That sequence will serve as a new foundation for medicine and human biology, and our browser will form the most popular portal to explore our shared genetic heritage," said Haussler, who directs UCSC's Center for Biomolecular Science and Engineering (CBSE)."

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 [03.07.02]
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."

[ 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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