Friday, January 30, 2004

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Buffalo News UB builds digital warehouse

"With 75 trillion bytes of capacity, about equal to 100,000 CDs, the "storage area network" will allow scientists at UB - and at partner research centers in Buffalo's medical campus - to tackle more data-heavy projects."

"The data warehouse at UB is capable of housing four times the information in the Library of Congress, according to HP. As a corporate backer of the bioinformatics center, the company has supplied elements of UBs supercomputer and has pledged $10 million in investment capital for area biotech start-ups."

redux [12.08.03]
Times Union A vision has yet to spark rebirth

""Unfortunately, I think there's unreal expectations," said Skolnick, the Buffalo center director. Still, he said, the center "can play a role, and perhaps a significant role" in an economic turnaround.

Even so, not everybody is on board. At Ulrich's Tavern, which calls itself Buffalo's oldest and is sandwiched between the center and an old windshield-wiper factory, an elderly man nursed a midafternoon beer and said he'd never even heard of bioinformatics.

The bar's proprietor, Jim Daley Jr., was plenty aware of it.

"I think it's the most underrated thing in Buffalo," he said. "Most people talk about the casino.""

redux [07.14.03]
UB Reporter Attendance at conference dispels any doubts about bioinformatics center

"If any doubts lingered among scientists, politicians or business executives about the future prospects for the University at Buffalo Center of Excellence in Bioinformatics, they were erased last Friday as nearly 200 scientists representing the U.S., Canada, India, the Netherlands, the United Kingdom, Italy and Japan gathered in the Adams Mark Hotel in Buffalo for the first annual "Frontiers in Bioinformatics" symposium."

"The day's events amounted to a grand show of support for the center of excellence, which was founded in 2001 by Gov. George E. Pataki"

redux [06.06.03]
Bio-IT World Senator Clinton supports bioinformatics initiative

"Despite the media barrage surrounding her new book, Senator Hillary Rodham Clinton made a brief appearance in Buffalo on Friday, June 6, to praise the University of Buffalo (UB)'s ambitious Bioinformatics Center of Excellence initiative."

""It has taken a lot of work to make the case to fund bioinformatics," Clinton said. "When we started, the response was, 'What's that?' " Despite this, Clinton and Reynolds have helped to earmark more than $9 million in federal funding for the project."

Newsday.Com Bioinformatics center seeks place on world scientific map

"Scientists on the cutting edge of drug development were comparing notes in Buffalo Friday during a symposium aimed at introducing the city's developing bioinformatics center to the scientific world."

"In Buffalo, bioinformatics is viewed as perhaps the best hope to generate jobs lost with the demise of its steel and grain-milling industries. But with several other cities around the country also investing heavily in life sciences, the center's directors are well aware of the competition for staff and resources."

redux [03.02.03]
The Buffalo News JEFFREY SKOLNICK SUPERSTAR

"Jeff Skolnick didn't sign up for all this hype.

He did not apply to the following posting:

Savior wanted: A wunderkind in cutting-edge technology who can help build a new economy and carry the hopes of a Rust Belt region of 1.2 million people.

He just took a job heading a new academic program, the University at Buffalo's Center of Excellence in Bioinformatics."

redux [07.26.02]
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."

Thursday, January 29, 2004

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Mondaq Ethics for the Life Science Company: Old Traditions Meet the Brave New World

"Companies in the life sciences face the same corporate ethics concerns as other businesses. In addition, though, the very nature of the life sciences industry entails an additional level of ethical reflection. Life sciences companies concern themselves with technologies derived from and relating to life itself, whether on the nano-level or the macro-level. These companies hence have to reckon with matters of bioethics as well as business ethics."

"Take, as an example, a bioinformatics company intending to commercialize data based on a population's genetic information. How might such a company envision itself ethically?"

Wednesday, January 28, 2004

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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 [07.07.02]
The Scientist EU Database Directive Draws Fire
[requires 'free' registration]

"The blessings of an increasingly advanced digital world are many: faster data processing, massive data storage. But with these newfound capabilities come new questions about ownership. Who owns the mountains of data contained in databases--whether stock prices, real estate values, or countless genome sequences? What intellectual property rights do database creators have? And how much protection is too much? In recent years, a European Union (EU) database directive has brought a sense of urgency to such issues--and some scientists fear that the law has gone too far."

redux [04.12.02]
GenomeWeb On the European Bioinformatics Battlefield, the New 'Database Right' Wields Considerable Strength

"In the United States, innovators have traditionally relied on copyright and confidential-information rights to protect their databases. In Europe, however, database owners have a novel weapon in their IP armamentarium: the database right.

But there's a catch: Database innovators must have sufficient nexus with Europe--actually, the European Economic Area, or EEA--in order for their databases to qualify for protection. Perhaps it's time for US database makers to consider how they might create sufficient ties with Europe to benefit from this powerful new IP right."

redux [02.27.02]
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."

Wired News An 'Atlas' to Count the Genes

"Analysts tend to value drug companies more favorably than those that sell information, and their response to Confirmant's announcement has been lukewarm.

Other biotech company officials with experience in selling database information said that large, general databases such as the protein atlas might have a challenge in finding a market.

"What we have found out is that people ... want technologies that apply to their specific research," said Lior Ma'ayan, executive vice president of corporate development at Compugen, a biotech company based in Tel Aviv."

redux [03.10.01]
eCompany Future Boy: We've Mapped the Human Genome. Now What?

"With information on the genome now rapidly becoming available, the business models for companies that sell information about the genome, such as Celera and Incyte, may soon be outmoded. Biotech companies will then have to earn their stripes the old-fashioned way: by developing blockbuster drugs. Of course, proteomics companies could arise to sell information about proteins to other drug companies, but Strosberg thinks this is a flawed approach. Given his history, he should know. "Incyte's business model," he recalls, "was originally to be an information provider. That period is over. People will not pay as much for information as they used to because so much of it is now publicly available. Information is becoming a commodity." Instead of selling information about proteins, he is focusing Hybrigenics on using its proteomics information to develop drugs, either alone or in partnership with larger pharmaceutical companies."

redux [03.20.02]
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 [05.09.01]
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.""

Tuesday, January 27, 2004

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Innovations Report European Virtual Institute for Genome Annotation receives 12 million Euro

"The Commission of the European Union has awarded 12,000,000 Euro to 24 bioinformatics groups based in 14 countries throughout Europe to create a pan-European BioSapiens Network of Excellence in Bioinformatics. The network aims to address the current fragmentation of European bioinformatics by creating a virtual research institute and by organizing a European school for training in bioinformatics."

""Europe has excellent bioinformatics environments in many countries, but in order to maximize the overall impact it needs to strengthen and reinforce that excellence by restructuring and coordinating existing research capacities and the way research is carried out," explains Janet Thornton, Director of the European Bioinformatics Institute (EBI) and coordinator of the BioSapiens project."

Monday, January 26, 2004

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BioMedNet Knowledge Domains, the movie
[requires 'free' registration]

"Want to find out what's hot and what's not in any given research area without actually having to read all the papers? Read on.

Chaomei Chen, associate professor at the College of Information Science and Technology at Drexel University in Philadelphia, USA, has devised a method that allows people to visualize how research in any particular 'knowledge domain' grows and evolves over time."

Sunday, January 25, 2004

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The Economist Malignant maths

"PRACTITIONERS of so-called hard sciences--those backed up by the mathematical rigour of formulae and equations--have traditionally looked down on the squishy end of research. That disdain has evaporated a bit over recent years, as government money has migrated from physics to biology and medicine. But it is disappearing as biologists show that they can be just as quantitative as their hard-edged colleagues.

And one example is in the field of cancer research."

Friday, January 23, 2004

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ScienceDaily Researchers Develop Computer Application To 'Read' Medical Literature, Find Data Relationships

"Until recently, researchers and their assistants spent countless hours poring over seemingly endless volumes of journals and scientific literature for information pertinent to their studies in fields such as cancer, AIDS, pediatrics and cardiology.

But thanks to new software developed by bioinformatics researchers at UT Southwestern Medical Center at Dallas, scientists can now easily identify obscure commonalities in research data and directly relate them to their studies, saving money and speeding the process of discovery."

redux [12.05.03]
eWeek Analytics Tools Mine Text

"With predictive analytics at the core of many marketing initiatives, software developers are adding predictive capabilities to text mining so that enterprises can act on information in unstructured as well as structured data."

"The University of Pennsylvania's Abramson Cancer Center is using Clementine and LexiQuest in combination to better analyze years' worth of textual data to gain new insights into cancer diagnosis and treatment. "We took 10 years of [medical] journal articles and mined them for terms and syntax," said Michael Liebman, the center's director of computational biology and biomedical informatics, in Philadelphia. That analysis helps the center find patterns in the data showing relationships among diseases, symptoms, treatment and other factors, Liebman said, patterns that would otherwise have to be subjectively discerned by researchers poring over the data."

redux [10.27.03]
Bio-ITWorld Digging Into Digital Quarries

"SO YOU THINK you've found a cure for psoriasis. But first you need to check 12 million journal article abstracts on the National Library of Medicine's PubMed database, piling up at the rate of 40,000 new citations a month from 4,600 journals. You missed the latest issue of the Journal of Investigative Dermatology? PubMed's Medical Subject Headings (MeSH) vocabulary might help -- a little. It has 300,000 synonyms for 19,000 basic medical terms. But if you type in "epidermopoiesis," a key concept in the MeSH entry for psoriasis, you will find ... nothing.

Can software put an end to tortured searching? Researchers and vendors say text mining in the life sciences is on the verge of a long-sought dream: distilling oceans of inchoate data into insights and hypotheses."

redux [10.17.03]
The New York Times Digging for Nuggets of Wisdom
[requires 'free' registration]

"MICHAEL N. LIEBMAN knows his limitations. Even with a Ph.D. and a long career in medical research, he cannot keep up with all the developments in his area of interest, breast cancer. Medline, the database that already houses more than 10 million abstracts for journal articles, is adding 7,000 to 8,000 abstracts per week. Only a fraction of these are about cancer, but the volume of information is daunting nonetheless."

"Yet Dr. Liebman is convinced that new cures could someday emerge for breast cancer if only someone could read all the literature and synthesize it. So he has found a solution: enlisting a computer program to read the articles for him."

redux [11.09.02]
Stanford Medical Informatics Preprint Archive Using Text Analysis to Identify Functionally Coherent Gene Groups

"The analysis of large-scale genomic information (such as sequence data or expression patterns) frequently involves grouping genes on the basis of common experimental features. Often, as with gene expression clustering, there are too many groups to easily identify the functionally relevant ones. One valuable source of information about gene function is the published literature. We present a method, neighbor divergence, for assessing whether the genes within a group share a common biological function based on their associated scientific literature. The method uses statistical natural language processing techniques to interpret biological text. It requires only a corpus of documents relevant to the genes being studied (e.g., all genes in an organism) and an index connecting the documents to appropriate genes. Given a group of genes, neighbor divergence assigns a numerical score indicating how "functionally coherent" the gene group is from the perspective of the published literature. We evaluate our method by testing its ability to distinguish 19 known functional gene groups from 1900 randomly assembled groups. Neighbor divergence achieves 79% sensitivity at 100% specificity, comparing favorably to other tested methods. We also apply neighbor divergence to previously published gene expression clusters to assess its ability to recognize gene groups that had been manually identified as representative of a common function."

redux [10.08.01]
BioNLP.Org Natural language processing of biology text

"The literature of the field of biology is the largest of all the sciences. The volume of biology literature each year, measured in bytes, is about fifty times the size of the entire human genome, junk and all. But locked in this literature is an enormous amount of information that can tell us much about the structure and function of genes, proteins, cells and organisms -- how they work as well as how they can fail.

The newly emergent interest in natural language processing for biology has been christened "Information Extraction". But work in this area has been going on for many decades under different names and this site includes a good deal of information about past and current work in NLP and in information extraction for biology in particular."

redux [04.30.01]
New Scientist Biologists in Norway use a computer program to "read" the scientific literature and successfully predict gene interactions

"Biologists in Norway have used a computer program to "read" the scientific literature and successfully predict gene interactions.

This data-mining of the "biobibliome" provides a way of dealing with the ever-increasing torrent of biological data - millions of papers a year. But even more impressively, the completely automated process can make new genetic discoveries - essentially free research."

Stanford Medical Informatics Preprint Archive Improving Biological Literature Improves Homology Search

"Annotating the tremendous amount of sequence information being generated requires accurate automated methods for recognizing homology. Although sequence similarity is only one of many indicators of evolutionary homology, it is often the only one used. Here we find that supplementing sequence similarity with information from biomedical literature is successful in increasing the accuracy of homology search results. We modified the PSI-BLAST algorithm to use literature similarity in each iteration of its database search. The modified algorithm is evaluated and compared to standard PSI-BLAST in searching for homologous proteins. The performance of the modified algorithm achieved 32% recall with 95% precision, while the original one achieved 33% recall with 84% precision; the literature similarity requirement preserved the sensitive characteristic of the PSI-BLAST algorithm while improving the precision."

MIT Technology Review Emerging Technologies That Will Change the World: Data Mining

"And the future of data-mining technology? Wide open, says Fayyad - especially as researchers begin to move beyond the field's original focus on highly structured, relational databases. One very hot area is "text data mining": extracting unexpected relationships from huge collections of free-form text documents. The results are still preliminary, as various labs experiment with natural-language processing, statistical word counts and other techniques. But the University of California at Berkeley's LINDI system, to take one example, has already been used to help geneticists search the biomedical literature and produce plausible hypotheses for the function of newly discovered genes."

Thursday, January 22, 2004

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Macworld Xserve G5 cluster unveiled

"Apple's focus on creating products that should be of use to the high-performance computing markets has spawned a new, little-known product combo - the Apple Workgroup Cluster for Bioinformatics.

This is a pre-configured bioinformatics cluster built around the new Xserve G5. The cluster includes between four and 16 servers, a rack to hold the them, cabling, and systems and application software. The bundled system includes The BioTeam's iNquiry software with 200 informatics applications including BLAST and HMMER. It costs from $27,999."

Bio-IT World Apple Update: Focus on HPC

"To address raw HPC processing power needs, Apple introduced a new version of its Xserve rack-mounted server that includes the PowerPC G5 processor. The new Xserve G5 delivers more than 30 gigaFLOPS (30 billion floating point operations per second). This is about 60 percent more raw processing than the original Xserve, which used the PowerPC G4 processor."

"Apple has always been known for its easy-to-use products. So as the company moves into the enterprise HPC market, it is trying to retain the well-liked "ease-of-use" features in more-complex computing environments."

redux [01.06.04]
MacDailyNews Apple previews Xgrid technology; uses Rendezvous to make cluster computing easy

"Apple today previewed Xgrid, a computational clustering technology from Apple's Advanced Computation Group (ACG). Xgrid helps scientists and others working in compute intensive environments to fully utilize all IT resources, including desktops and servers, by creating a grid enabled "virtual" IT environment that takes advantage of unused computing capacity to run batch and workload processing."

""The Xgrid BLAST application enables bioinformatics researchers to perform distributed BLAST searches on a cluster running the Xgrid software," said Richard H. Scheller, Ph.D., senior vice president of Research, Genentech in the press release. "We tested Xgrid BLAST by querying DNA sequence files for matches against multi- gigabyte genomic databases on a cluster of four dual-processor Xserves.""

redux [11.26.03]
Computerworld Singapore Muscling up apple power

"Dr Elia Stupka (left), Bioinformatics Programme manager, Laboratory of Computational Biology said, "The Xserve is suitable to TTL because the operating system (OS) X Unix-based open source application can be ported and run easily. And integration with specific software tools is seamless.""

"In addition, he could use the same OS on his desktops, portable computers and network cluster. Stupka sought to tap on the unused computing power of all the devices in the cluster."

redux [10.31.03]
Wired News Mac Supercomputer Just Got Faster

"The latest semi-official numbers concerning the speed of Virginia Tech's "Big Mac" supercomputer rank it as the third-fastest machine on the planet.

The system's architect, Srinidhi Varadarajan, said Tuesday evening that the newly completed supercomputer operates at 9.55 trillion operations a second, or 9.55 teraflops."

O'Reilly Network: MacDevCenter Confessions of the World's Largest Switcher

"It's a shame that Apple no longer runs the "Switch" campaign on television. Dr. Srinidhi Varadarajan would make an excellent spokesperson for moving to the Mac."

" His ad might go something like this. "I was in the market for a new machine. I was hoping to get ten teraflops by the end of the year. I'd never used a Mac and had been looking at Dells and IBMs. Then Apple released the G5 on June 23. A week later I bought 1,100 duals online at the Apple Store. I'm Srinidhi Varadarajan and I build Supercomputers at Virginia Tech.""

redux [10.25.03]
Bio-IT World Scientific Computing: Apple's Next Big Leap?

"Tribble, one of the designers of the original Macintosh user interface, said that with the advent of the Power Mac G5 and the OS X operating system, the Macintosh now has the Unix backbone, 64-bit processing power, Windows interoperability, and open source credibility to be a viable computing platform in the life sciences space.

"Really, for the first time in this industry, you have a computer that can do all the scientific applications, and you can run Microsoft Office," he said. "It's been kind of a Holy Grail that started with Mac OS X.""

redux [03.30.03]
Bio-IT World Xserve and iPod simplify cluster setup

"iNquiry combines the technology The BioTeam developed for Texas A&M into a system that other bioscientists can use to create their own Xserve clusters in a matter of minutes instead of weeks, according to Van Etten. The secret is another Apple product -- the iPod.

Wholly self-contained in about 2GB of storage space on the iPod, iNquiry uses a Perl-based script that's controlled through a simple graphical configuration utility. The user tells the configuration utility how to configure the Xserve cluster, how many nodes it has, how the network is configured, and how to use the individual drive bays in each Xserve."

redux [11.06.02]
Wired News Beyond MP3s: iPod Holds Genome

"While it sounds neat to put the human genome on a hip-looking device people more commonly use to crank out Mos Def tunes, some researchers say using it to store the blueprint for humankind is not entirely practical."

""If you're walking back and forth (to transfer data) that's not good," said Richard Gibbs, director of the human genome sequencing center at Baylor College of Medicine. "It's often tempting to do that because of bandwidth, but the smart thing to do is make sure you have the proper infrastructure to (transfer data).""

redux [10.29.02]
Apple: Pro/Science Performing Feats of Bioinfomagic

"Dr. Will Gilbert likes to carry the human genome around on his iPod. It's the easiest way, he says, to transfer the genome -- 3 billion chemical "letters" that make up a person's genetic code, or DNA -- to the computers of other researchers at the Hubbard Center for Genome Studies at the University of New Hampshire.

Gilbert had set up a research project involving the human genome on his Power Mac, using the Apple/Genentech version of BLAST. A breakthrough implementation of the popular bioinformatics tool from the National Center for Biotechnology Information (NCBI), A/G BLAST conducts high-speed DNA searches in biomedical research and drug discovery. "But," says Gilbert, "I wanted to run the project down the hall on another Mac. Rather than copy it across the network, I'd pull out my iPod. Plug it in, drag, drop, zip, boom, bang and walk it down the hall.""

redux [08.20.02]
DigtalMass Apple's Mac muscles in

"High-powered computers are the "tech" in biotechnology. So it's no surprise that Cambridge-based biotech giant Genzyme Corp. uses lots of muscular workstation machines, most of them running the sophisticated Unix operating system.

But what is surprising is that some of these powerful Unix boxes bear the trademark of Apple Computer Inc. They're Macintoshes -- the same user-friendly computers that have earned Apple a loyal following among artists, publishers, and home computer users."

redux [07.01.02]
Genomeweb Apple Becomes First Corporate Member of Bioinformatics.org's Co-Lab Program

"Apple Computer has become the first member of a program launched by open-source advocacy-group Bioinformatics.org that aims at linking open-source developers with bioinformatics hardware and software vendors.

Apple's new Co-Lab program hopes to nurture industry involvement either by co-locating software projects at its SourceForge-based Open Lab project or by hosting and sharing those projects with developers at vendor sites via the web, according to Bioinformatics.org president and founder Jeff Bizarro."

redux [05.19.02]
Grid Computing Planet Mac OS X Gets A Grid Solution

"Platform Computing plans to make its flagship Platform LSF software available for Apple's new Xserve, extending support for Mac OS X and Apple's new server, storage and systems management offerings.

"The combination of the Mac Xserve with Platform Computing's technology will enhance the quality and speed of work for Mac applications in life sciences, education and business," Ron Okamoto, Apple's vice president of Worldwide Developer Relations, said in a statement."

MacCentral Apple announces new rack-mount server

" Genentech -- Guy Kraines, vice president, Corporate IT. We got to use them, and we've got some observations. First, this is not a desktop box with rack-mount ears. From the physical design, the hot-swap capabilities, the remote monitoring -- this is a data center box. My guys in the data center are fully accepting of it. They did it right, right down to cable management. Second, performance. The G4 itself is a heck of a processor, especially with what we do. Velocity Engine doesn't just do Photoshop rendering well -- it does matching of genetic code really well too. The single most common application in bioinformatics is Blast. I'm not going to give you numbers today in terms of what we've done, but let's just say that this is not just a measurable improvement, but a meaningful improvement in helping us do what we need to do."

redux [12.16.01]
The O'Reilly Network Bioinformatics Meets Mac OS X

"Scientists are porting bioinformatics tools to the Macintosh platform because often they are already Macintosh users, and they want the convenience of being able to perform their research on their primary desktop computers. Traditionally scientific researchers have needed a desktop computer for all of their productivity applications, and a separate platform for the compute engine to support their research. "The tremendous benefit of Mac OS X is it gives you both," says Van Etten. "The only thing that comes close is Linux, but for most bioinformaticists, the Linux desktop user experience is a little sophisticated.""

Wednesday, January 21, 2004

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BBC Virtual lab aids drugs research

"Pharmaceutical and chemical firms stumped by tricky research problems are turning to an international, net-based community of scientists for aid.

Called Innocentive, the organisation has on its books more than 45,000 researchers that get paid if they provide a solution to a research problem that has foxed in-house teams."

Tuesday, January 20, 2004

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The New York Times Dr. Norman Heatley, 92, Pioneer in Penicillin Supply, Dies
[requires 'free' registration]

"Dr. Norman G. Heatley, an Oxford University biochemist who helped revolutionize medicine by isolating early samples of penicillin and helping to convert it into a powerful drug that gave Allied troops an advantage in World War II, died Jan. 5 at his home in Oxford, England, according to the university. He was 92.

Penicillin was first identified by Dr. Alexander Fleming in 1928, but his efforts to extract the active substance from its mold were unsuccessful. He published a paper on his discovery and moved on to other projects."

Monday, January 19, 2004

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Line56 Supercomputing for Pharma Giant

"Pharmaceutical company Bristol-Myers Squibb has found a new way to do supercomputing -- by running 64 IBM eServer 325 machines as a cluster, running on AMD Opteron processors. The supercomputer is based on Linux, which has enjoyed longer use in scientific and research environments than in the enterprise."

"Brian Henry, spokesperson for Bristol-Myers Squibb, explains the uses of the supercomputer. "We're targeting bioinformatics and quantum mechanics -- characteristics of molecules -- in our early discovery program." "

Friday, January 16, 2004

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The Register IBM's Storage Tank spotted in Ohio

"The motorcycle riding Frankensteins in IBM's storage tank lab have managed to bring their precious file system to life in an Ohio data center, as part of a major storage deal with the Ohio Supercomputer Center (OSC), IBM announced today."

"In total, OSC has boosted its storage capacity five-fold over a previous system, which is good news for researchers. They are using the storage for collecting bioinformatics data, collider experimental data, seismic data and radiological data."

Thursday, January 15, 2004

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The New York Times Kudos for Designer of Gene Experiment in Lab. Well Done, Robot!
[requires 'free' registration]

"British scientists say they have developed a robotic system that for the first time can design a genetics experiment, carry it out and interpret the results.

No difference was found between the laboratory bench results generated by the robot scientist and those gathered by graduate students doing similar work, the researchers report today in the journal Nature."

"The robot scientist uses a type of reasoning called abduction. Dr. King said it was the kind of reasoning the police used to reconcile clues when investigating a crime."