2.9.2001

Wired News Gene Map: Help or Hype?
"The moment genetic researchers have been waiting for is upon us: the publications of the human genome maps.

Some researchers say the complete human genome map may herald a revolution in medicine, giving physicians the material they need to predict, prevent and even treat disease.

But what significance the map truly holds is being challenged by at least one researcher who says both papers -- one published by a for-profit company and the other from an international, publicly funded consortium -- are next to useless."

The Washington Post Big Buildup to the Genome
"Behind new brick walls in Germantown, drills whir and saws whine as workers put finishing touches on a laboratory unlike any ever built. By the azure waters of San Francisco Bay rises the steel skeleton of a new university research center. Another is going up in Baltimore. A Toronto company lays plans to triple its laboratory space, backed by one of the biggest names in U.S. business.

Sensing the opportunity of a lifetime, top scientists around the world are preparing huge new laboratories, launching institutes, ordering massive computers and striking collaborations in order to tackle one of mankind's greatest challenges: understanding the human body down to the level of molecules."

posted by e3 9:00:43 AM

2.8.2001

The Washington Post Celera to Share Human Genetic Map
"Moving to quell a long-running controversy, Celera Genomics Corp. has agreed to supply academic and commercial scientists with the complete data set on which it is basing a forthcoming scientific paper describing the human genetic map.

The Rockville company yesterday released the terms of four agreements it has drawn up in collaboration with Science, the journal that is publishing the paper."

"The new agreements would permit academic scientists to download a limited amount of Celera data every week by clicking an agreement on the World Wide Web. Academic or commercial scientists who need more would be able to sign one of two standard contracts with Celera permitting them to receive disks containing the entire data set."

"It is unclear whether Celera's move will satisfy scientists who have been skeptical about the company's promises of access."

redux [12.08.00]
The New York Times Celera to Charge Other Companies to Use Its Genome Data
[requires 'free' registration]
"Company that deciphered the human genome has just submitted a paper for publication. But, in a highly unusual move, the company will not be adhering to the customary practice of simultaneously depositing its gene sequence data in a public repository freely available to all.

Instead, the company, Celera Genomics, will put the data on its Web site, making them available to researchers free and to companies for a fee."

""The bottom line," Dr. Samuel Broder, Celera's executive vice president for medical affairs, said, "is that we want to make sure that the work and considerable effort is put to the benefit of the people who took the risk to invest in Celera. Therefore, we don't want to set up a system where other database providers can repackage the data and sell it on their own."

BBC Genome data access row
"In a statement explaining its decision, Science said it would be keeping a copy of the database in escrow "to insure that there will be no changes in the ability of the public to have full access to the data".

The decision has provoked an angry reaction among some scientists.

"Science magazine seems confused about the purpose of scientific publication," Dr Eric Lander, one of the leaders of the Human Genome Project in the US, told an American newspaper."

"If authors can restrict the ways that readers can use knowledge, the pace of discovery will be slowed and the public will lose.""

GenomeWeb Celera’s Submission to Science Fuels Controversy, Journal Responds
"Celera’s Wednesday evening announcement that it had submitted its human genome sequence data to Science has already provoked controversy in the scientific community and fueled speculation about how the Human Genome Project data will be published, leading Science to issue a statement Thursday to clarify the way it is handling Celera’s submission."

BioMedNet Celera and Science agree on access to genome data
[requires 'free' registration]
"David Lipman, director of the National Center for Biotechnology Information, which manages GenBank, says the tremendous progress in genomics has been due in part to the policy of requiring sequence data be submitted to this centralized repository. "I believe that the editors of Science are about to make a major mistake that will ... seriously compromise a major field of scientific research," biologist Michael Ashburner of Cambridge University told the LA Times."

"While Science does require data to be published in a public database, the journal does not stipulate that the depository be GenBank, the AAAS says. Science plans to keep a copy of the database in escrow "to insure there will be no changes in the ability of the public to have full access to the data."

posted by e3 5:39:09 AM

2.7.2001

Yahoo! News New Website, www.biolisp.org, Promotes the Use of Lisp in Bioinformatics
"Lisp, the second oldest programming language in common use, remains the principal language of knowledge representation, knowledge-based programming, and automated reasoning. Unlike Perl, the current language of choice among many bioinformaticians, Lisp is one of the few programming languages robust and powerful enough to manage the complex systems modeling, knowledge-based annotation, and automated scientific reasoning needed to take bioinformatics to the next level.

Larry Hunter, Director of the Center for Computational Pharmacology and a member of www.biolisp.org's Steering Committee, says that although there are many competing programming environments for bioinformaticians, Lisp provides some powerful advantages."

biolisp.org Intelligent applications in BioComputing
"BioLisp.org is a public resource supporting scientists who use Lisp to develop intelligent applications in the biological sciences. We collect and disseminate Lisp biocomputing code, and gather pointers to Lisp and other Intelligent BioComputing methods. Please contribute, or make suggestions by writing the editor."

posted by e3 5:57:22 AM

2.5.2001

Scientific American Shrinking to Enormity
"With each successive generation of microarray technology, the size of the probe spots shrinks, the number of genes per chip rises, and biologists' schemes for using the devices swell in grandeur. "We can now put over 60 million probes on a single glass wafer," Fodor says excitedly. He figures the entire human genome will fit on 200 to 300 wafers. And in fact, in September, Affymetrix spun off Perlegen, a subsidiary that plans to use microarrays to sequence, from scratch, the genomes contained in both chromosomes of 50 people to detect the subtle variations both within and among them. "In these patterns we will find the signature of human evolution. The potential for scientific discovery," Fodor boasts, "is fantastic."

So is the potential for confusion and error, Young and others caution."

[via bioinformatics.org]

The Scientist Microarrays Beyond Reach
[requires 'free' registration]
"Using the subheading "Microarray tools open genomes to discoverers" in the Jan. 22 Hot Papers article1 is much like telling a group of kindergartners: "Any of you can become the president of the United States." The fact is most of them will never be the president no matter how hard they try. Microarrays are excellent tools, but their exorbitant price makes them beyond the reach of most researchers. The few papers that have been published so far using the "chips" came from either rich labs or labs that have industrial/proprietary connections.

I don't think the microarray hot papers of today will remain hot for long. They were neither conceptually novel nor hard to do; they simply represent "proof of concept" or application of a great but easy technology."

posted by e3 7:45:45 PM