{bio,medical} informatics
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Colorado Daily
Double majors taxing, but profitable
""Twenty years ago, no one would have put biology and computers together. Now there are things called bioinformatics and computational biology," said David Strauss, a principal with Art and Science Group, a Baltimore firm that does market research for colleges.
"Fields of study are melding with each other to answer questions that can't be answered by any single field," he said."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
The New York Times
With Gene Map Nearly Complete, Researchers Must Learn to Use It
[requires 'free' registration]
"At a conference this month at the Airlie Center in Warrenton, Va., biologists tried to explore how the study of genomes might develop over the next 20 years and what tools might be needed. Central to their vision of the future is a thorough computerization of biology, made necessary by the vast computing power of the genome itself.
The task seems likely to change the nature of biological research, requiring teams of engineers, mathematicians, nanotechnologists and computer programmers, and farms of computers if not a national computer grid."
redux [10.26.01]
[requires 'free' registration]
"Only a few brave biologists showed up today for a meeting designed to explore their common ground with mathematicians, physicists and chemists in the field of high-performance computing. The event was planned to look for "synergies across the areas," meeting organizer Julia Goodfellow told BioMedNet News, but biologists were still in the minority."
"Bioinformaticist Mark Swindells, one of the speakers, mused about "the challenge of how to do our talks so that everyone can understand the technology.""
redux [06.15.01]
"Knowledge gained from the sequencing of the human genome promises to change our lives. Powerful computing techniques have been used to acquire the knowledge gained so far, and still more powerful techniques will be required to fulfill the promises of genetically based drug design, medical diagnosis and treatment, and agricultural applications, among others. This issue of the IBM Systems Journal - and the companion issue of the IBM Journal of Research and Development - is devoted to papers on deep computing for life sciences. Included in this issue are papers that address associated biological, computational, and informational challenges."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Linux Magazine
What's Next for Linux and Open Source?
"At a summit of open source leaders convened at the O'Reilly Open Source Convention in July, I asked everyone what they thought was the most significant work of open source development in the past year. None of them came up with the answer I was looking for, yet all of them agreed once I proposed it: The work of James Kent, who wrote the gene assembler that allowed the Human Genome Project to finish its work three days before the private effort by Celera Genomics -- thus ensuring the gene sequence remains in the public domain."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Wired News
Chromosome Veers Off Genome Map
"The third of 23 human chromosomes has been sequenced, and scientists have found major discrepancies between the new sequence and the highly publicized human genome map published in February.
Researchers say the differences are a reality check that points to the need to continue to refine the human genome map and correct inaccuracies."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
BioMedNet
Proteomics? Great label! (But what is it?)
[requires 'free' registration]
""Just because you use a protein doesn't make you a proteomics researcher," Joshua LaBaer, director of the Institute of Proteomics at Harvard Medical School, told BioMedNet News.
After the success of genomics, "everyone wants to think of proteomics as the next great science," but calling themselves proteomics researchers "is not really fair," LaBaer said. "A lot of people who claim to do genomics aren't genomic researchers either," he added. "They are just studying gene sequences.""
redux [12.12.01]
[ summary can be viewed for free once registered ]
"Proteomics aims to chart the ebb and flow of tens of thousands of proteins at once to produce snapshots of life inside cells. The technology to pull it off doesn't exist yet, however, and the competition is stiff for those proteins that can be nabbed using current methods. But this young field is growing up fast. This special News Focus looks at the promise and roadblocks of biology's latest wellspring. The package includes profiles of GeneProt, the biggest proteomics test-bed to date, and Stephen Burley , a crystallographer who is leaving academia to direct research at a small start-up company. Other stories discuss the potential of protein chips for new diagnostics and research tools and the problems faced by companies attempting to patent proteins."
redux [08.15.01]
"A new study of the proteomics market forecast that the proteomics market would grow nearly six-fold to $5.6 billion by 2006 from $963 million in 2000.
In its report, consultancy firm Frost & Sullivan said the increase would be driven by a shift towards the analysis of proteomes following the discovery that the human genome contains fewer genes than originally predicted.
"Proteomics adds value to drug discovery by charting the distribution of proteins, identifying and characterizing proteins of interest, and elucidating the participation of proteins in biochemical pathways boosting the number of potential targets around which lead compounds can be designed and screened," Eric Gay, a Frost & Sullivan analyst, said in a statement."
redux [07.11.01]
"Their bold proclamation has raised a few eyebrows in the scientific community. "It's easy to say that you'll complete a comprehensive proteome map," notes Marc Vidal of the Dana-Farber Cancer Institute in Boston. "But none of us knows what that means." There may be only one genome, but when it comes to the proteome, different proteins can be more or less active in different cells at different times during development, under different physiological conditions or in different disease states. The proteome's nature "makes it hard to define what we're doing--not just Myriad, but all of us," remarks Joshua LaBaer, director of the Institute of Proteomics at Harvard Medical School. "There's no such thing as a human proteome," adds Keith L. Williams, CEO of Proteome Systems, headquartered in Sydney, Australia. Look at the liver, for example, he says: "After a glass of red wine, you'll have a different proteome."
redux [06.20.01]
"Scientists thought about trying to catalogue all the proteins in the body a decade ago.
But it seemed impossible, and was therefore impossible to fund. Researchers moved on to the much simpler job of sequencing the human genome.
They were right to do so. Cataloguing proteins turns out to be downright confusing. Lately, more and more biotech companies are entering a field they call "proteomics," an ugly word searching for a focus group."
redux [03.13.01]
[requires 'free' registration]
"A commonly expressed opinion is that a single Human Proteome Project can never match HGP's success. Eric S. Lander , director of the Whitehead Center for Genome Research in Cambridge, Mass., notes that biologists simply don't know how to characterize the proteome "from end to end, nailing every protein. The tools are not ready. And it's not clear that [such a project] makes sense." He contrasts proteomics to HGP where "there is a certain fixed number of base pairs--about three billion--and we were going to get them all. And so it had a beginning and an end to it."
redux [01.31.01]
"Can sequencing do for the proteome what it did for the genome?
On Wednesday, a number of world-renowned researchers in the field of proteomics issued a resounding " no."
"When a company has phenomenal success with strategy A, you want to do strategy A on the next subject," said John Richards, a professor of organic and biochemistry at California Institute of Technology, referring to current corporate attempts to map the proteome.
"This doesn't work," he said."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Scientific Computing World
Drawing Power From the People
"Today, bioinformaticists are presented with a diversity of computing resources, ranging from traditional multi-processor servers to clusters of commodity (PC-class) computers to special purpose hardware-based accelerators. Where in this bestiary does P2P computing fit? Or, to put the question another way, what type of computation can make good use of a P2P platform?"
redux [11.28.01]
"IBM will supply the University of Pennsylvania and four hospitals with computers that will link into a computing "grid" to check for breast cancer, the company will announce Wednesday.
The grid will be used to detect breast cancer in patients, store mammograms in digital form and identify populations that are particularly susceptible, the company said in a statement. The system can be used, for example, to compare a new mammogram to a previous year's image to detect changes.
IBM, along with rivals such as Sun Microsystems and Compaq Computer, have been backing grid computing, which joins computers and storage systems into a large pool of computing power.
redux [11.21.01]
"The US National Science Foundation has announced a $12 million programme - called the NSF Middleware Initiative (NMI) - to develop middleware: software that allows scientists to share applications, scientific instruments and data, and collaborate with their colleagues across high-performance networks.
The effort will build on the success of the Globus project in developing middleware tools for grid computing, and will integrate Globus and other emerging middleware components into a well-tested, comprehensive, commercial-quality, middleware distribution package that runs on multiple platforms. These middleware distributions will be disseminated to research labs and universities worldwide."
redux [11.12.01]
"Platform Computing, a company that tries to harness the collective computing power on computer networks, has signed a deal to commercialize an open-source supercomputing project.
Platform is working with the Globus Project to commercialize the Globus Toolkit for governing the use of computers and storage systems joined into a large computing "grid," Platform said Wednesday."
"Grid computing, though, often uses higher-powered computers than mere desktop PCs, and has attracted the interest of IBM, which thinks corporate customers as well as academics will use grid methods. IBM is working with Globus to boost this expansion.
Grid computing has long held potential for some types of computing tasks--typically those that don't require as much communication between one computing task and another. For this reason, they don't replace single mammoth supercomputers such as those from Cray. However, grid computing is popular among pharmaceutical companies and others."
"Computational Grids are emerging as a popular paradigm for solving large-scale compute and data intensive problems in science, engineering, and commerce. However, application composition, resource management and scheduling in these environments is a complex undertaking. In this paper, we illustrate the creation of a virtual laboratory environment by leveraging existing Grid technologies to enable molecular modeling for drug design on distributed resources. It involves screening millions of molecules of chemical compounds against a protein target, chemical database (CDB) to identify those with potential use for drug design. We have grid-enabled the molecular docking process by composing it as a parameter sweep application using the Nimrod-G tools. We then developed new tools for remote access to molecules in CDB small molecule database. The Nimrod-G resource broker along with molecule CDB data broker is used for scheduling and on-demand processing of jobs on distributed grid resources. The results demonstrate the ease of use and suitability of the Nimrod-G and virtual laboratory tools."
redux [11.06.01]
"Celera is utilizing a novel approach to bioinformatics to speed up its proteomics research.
The Rockville-based company is using Frontier, a proprietary technology, to harness computer power while the computers are shut down, in sleep mode, or being used for other applications."
" Through Frontier, Celera can tie together its employees' computers so that they all work on large-scale, proteomic sequencing. Frontier detects when a computer has idle capacity, and therefore room, to work on a research application. Such capacity could be available even when a person is using his or her computer during everyday tasks."
redux [04.04.01]
[requires 'free' registration]
"Intel is providing equipment and software downloads for a project in which volunteers are donating spare home computer cycles to a Stanford University project studying the protein-folding process. The project, Folding@Home, was the first to model successfully a complete protein fold - a task not even achieved by supercomputers."
""We want to increase the value of the PC," said Scott Griffin, Intel's program manager. "The PC is there when people aren't at it, like when they are in meetings. A great thing about this is you get every day users involved in research that they care about. Not only do they get to help out, but they get to help cure these terrible diseases.""
redux [09.23.01]
"IBM is spending $100 million building the world's fastest supercomputer to do cutting-edge medical research, but a distributed computing effort running on ordinary PCs may have beaten Big Blue to the punch.
IBM's proposed Blue Gene , a massively parallel supercomputer, in hopes to help diagnose and treat disease by simulating the ultra-complex process of protein folding.
"But Folding@Home , a modest distributed computing project run by Dr. Vijay Pande and a group of graduate students at Stanford University, has already managed to simulate how proteins self-assemble, something that computers, until now, have not been able to do."
redux [08.29.01]
"According to The Hitchhiker's Guide to the Galaxy, hyper-intelligent pan-dimensional beings (disguised as mice) are using us to compute The Ultimate Question of Life, The Universe, And Everything. Now earthling scientists have roped unsuspecting web servers into a similar - albeit slightly less ambitious - exercise in parasitic computing.
Using the Internet itself as a computer, Jay Brockman and colleagues at the University of Notre Dame, Indiana, have solved a mathematical problem with the unwitting assistance of machines in North America, Europe and Asia."
""The vast quantities of data involved in the genomic era of drug discovery are quickly outpacing advances in computing technology," said Robert North, Entropia CEO. "Distributed computing allows companies to cost-effectively access the massive computing power they'll need by using their existing PC networks. It's quite exciting that companies like Novartis are deploying our platform to demonstrate the potential of distributed computing as a valuable tool in drug discovery efforts.""
redux [10.09.00]
"The SETI@Home problem can be thought of as a special case of the distributed computation verification problem: "given a large amount of computation divided among many computers, how can malicious participating computers be prevented from doing damage?" This is not a new problem. Distributed computation is a venerable research topic, and the idea of "selling spare CPU cycles" has been a science fiction fixture for years."
"The Internet makes it possible for computation to be distributed to many more machines. However, distributing computing around the internet requires developers to consider the possibility of malicious clients."
"The general study of secure multiparty computation has produced much interesting work over the last two decades. Less well studied, unfortunately, are the tools and techniques required to move the theoretical results to the real world. The old dream of massively distributed computations is finally coming true, and yet our tools for building and analysing real systems still seem primitive. The challenge of the next few years will be to bridge this gap."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
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 [12.03.01]
"Today's battle against disease is being fought inside supercomputers as much as in laboratories.
The convergence of biotechnology and computing at the cutting edge of biology has already bred dozens of new alliances and could pave the way for mergers between previously distinct industries.
The ideal company of the future may be a combination of big pharma, a computing giant and a consumer goods player bringing marketing muscle, according to Dirk Heyman, Head of Life Sciences at Sun Microsystems.
redux [11.27.01]
The bioinformatics industry - broadly defined as using computers in drug discovery - generated revenue of $1.38 billion in 2000, analysts at Frost & Sullivan figure. That number will reach at least $6.9 billion by 2007, analysts predict.
Although computers have been used by biotechnology and drug companies for at least a decade, the bioinformatics segment has taken off only in the last three years. And most believe it isn't anywhere near its potential.
``It's an exciting area, but it's an area that will come into its own in the next three to five years,'' said Brad Peters, Frost & Sullivan senior industry analyst.
redux [11.20.01]
"A new Frost & Sullivan report augurs an explosion in the U.S. bioinformatics market from $1.38 billion in 2000 to $6.9 billion in 2007. The industry is full of players, and there's almost certain to be consolidation. The friendly capital markets of 1999 and 2000 allowed many to raise enough cash to hold out for the best bid."
redux [07.16.01]
"A year after the deciphering of the human genome boggled the world, investors are realizing that manipulating genes to fight disease is still in its infancy -- and far from profitable."
Nowhere is that more clear than in the industry for genetic information, or bioinformatics."
redux [05.14.01]
""Companies choose to adopt a product that is perceived to give some advantage over their immediate competitors and would like to see that protected in some way by the platform vendor (Celera) not running around selling it to everyone else, if they can avoid it. This is perceived to diminish the window of opportunity of the platform adopter to gain a lead over their immediate competitor. It is an element of sustainable advantage.'"
"Celera is certainly at a point of transition. It must either decide whether or not it wants to get into this collaborative, more vertical model of integrating itself with certain customers in big pharma or try to make its data and knowledge of it so valuable that big pharma of all walks of life simply has to have access to Celera data. I don't think the company has the time and money to do both. I don't think, for competitive reasons that I've explained earlier, big pharma is going to align itself, in large numbers, with a company that is selling the same applications to its immediate competitors."
redux [03.14.01]
"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 resumé 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..."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Fast Company
Roche's New Scientific Method
""We used to look at several data points for each experiment," says Louis Renzetti, senior director of discovery pharmacology. "Now there are dozens and dozens." Simply dump all of that data on a scientist's desk, and one of two tragicomic things will happen: Either the scientist will want to pursue every promising lead and will end up like a frazzled amusement-park visitor, or the scientists will refuse to touch the report at all, for fear that she will never be able to make sense of it.
It has taken a while to find the right approach, says James Rosinski, one of Roche's experts in the new field of bioinformatics, which covers the management of genomic data. The key, he says, is for biologists and statisticians to start talking early about how to use data from a GeneChip experiment. "It's iterative," he explains. "We can't just take a one-shot approach and tell the biologists what they ought to be interested in. We have to interact.""
redux [04.05.00]
[requires 'free' registration]
"I suspect that although the new enthusiasm for computers in biology is genuine, it overlooks some basic problems in implementation. The basic difficulty, as I see it, is that although biologists use computers, they do not trust everything that comes out of them. It is one thing to use them to print up nice-looking graphs, but it is an entirely different matter to use them to think better."
"Francis Crick was once quoted as saying that no biologist had ever made a discovery using a mathematical model. I would reply that no biologist has ever made a discovery by running an electrophoretic gel. They make discoveries by using their brains. Computers, like all scientific tools, are only as good as the person who uses them. If biologists don't understand how computer models are constructed, they won't know their strengths and limitations. Without some foundation of trust, biologists will be unlikely to utilize or accept this powerful method of data analysis."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
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.""
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
GenomeWeb
Big Pharma, On the Ropes, Says it Knows What it Wants from Genomics. But Will That Spur a Turnaround?
"And although the drug industry remains the most profitable worldwide—it generated profits as a percentage of revenues four times the median rate for all Fortune 500 firms during the end of the last decade, according to a Kaiser Family Foundation report released that day—an editorial in this month’s Nature Biotechnology by David Horrobin, CEO of Laxdale Research, in Stirling, Scotland, had this to say: “With rare exceptions, most of the top 20 multinational pharmaceutical companies are not generating in-house the new products needed to sustain the rates of growth they have enjoyed in the past.
“No serious industry onlooker could dispute this depressing picture,” the commentary continues. “Although a few pharmaceutical companies may survive in their present form, most cannot…. A few brave companies are recognizing the obvious: large companies excel at sales and marketing but are hopeless at innovative research.”"
redux [05.26.00]
"Leaders in the genomics field, as in any other industry, will be companies that offer a value-added service. Large pharmaceutical companies agree on what that service should be: integration of all the genomics information available. With more information readily accessible, companies can easily decide on whether to continue investigating potential targets.
So the future of genomics companies may rest in their IT and software capabilities, a view held by Celera Genomics, a newcomer to genomics. “We are entering an era of ‘cyberpharmaceutical’ drug development,” says Samual Broder, executive VP and chief medical officer. “Pharmaceutical corporations will use genomic databases, and other relational databases involving gene expression, proteomics etc. as the foundation of their drug discovery pipelines. One of the immediate goals... is to produce appropriate databases and software to link biologic and genomic information.”"
""The data suggest that the biotechnology industry used to be more productive than Big Pharma, but not any longer," said Rebecca Henderson, a professor at MIT's Sloan School of Management whose been studying the question for six years. "The public biotechs have declining productivity… and look as if they are running into the same problems as Big Pharma."
On every metric that Henderson has studied---number of scientific papers and patents per R&D dollar, cost per new drug--she found that biotech and Pharma productivity were quickly converging, and both were getting worse. After spending six years of studying the question, Henderson says she has found "no systematic evidence that small firms are more productive.""
redux [11.29.01]
[requires 'free' registration]
"Glenn Giovanetti at Ernst & Young Life Sciences Industry Services, comments "You could really compare [today's situation] to a large degree with the first biotech boom in the late eighties and early nineties where the thought was, 'Hey, this is going to lead to better drugs faster,' and clearly that hasn't been the case." Having the genome in hand has brought about more drug targets, but, explains Ma, "People are getting more concerned that novel targets are going to have a higher rate of failures because there is less information on them." And when working in 10-year drug-development cycles, failures are costly.
Ma points to a trend of growth in clinical informatics that would effectively garner more information from expensive clinical trials instead of simply treating them as regulatory hurdles. "People are beginning to think through to how ... to take greater advantage of that information," he adds. But increasingly, the suppliers of genomic information have been looking to do the same thing.
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
BRW
Biotechnology: A bio-info bonding
"When IBM's new and well-funded life sciences division announced in November that one of its first global strategic alliances was with Proteome Systems, the reaction of most analysts was 'Who?'"
"The deal between the information technology giant and the biotechnology start-up is also an interesting pointer to the future of biotechnology. Information technology has a rapidly increasing role in biotechnology.
The term coined to describe the link between information technologies and life sciences is bioinformatics. Around the world, bioinformatics has become a substantial biotechnology sub-sector, although it is in its infancy in Australia."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Science
High-Speed Biologists Search for Gold in Proteins
[ summary can be viewed for free once registered ]
"Proteomics aims to chart the ebb and flow of tens of thousands of proteins at once to produce snapshots of life inside cells. The technology to pull it off doesn't exist yet, however, and the competition is stiff for those proteins that can be nabbed using current methods. But this young field is growing up fast. This special News Focus looks at the promise and roadblocks of biology's latest wellspring. The package includes profiles of GeneProt, the biggest proteomics test-bed to date, and Stephen Burley , a crystallographer who is leaving academia to direct research at a small start-up company. Other stories discuss the potential of protein chips for new diagnostics and research tools and the problems faced by companies attempting to patent proteins."
redux [08.15.01]
"A new study of the proteomics market forecast that the proteomics market would grow nearly six-fold to $5.6 billion by 2006 from $963 million in 2000.
In its report, consultancy firm Frost & Sullivan said the increase would be driven by a shift towards the analysis of proteomes following the discovery that the human genome contains fewer genes than originally predicted.
"Proteomics adds value to drug discovery by charting the distribution of proteins, identifying and characterizing proteins of interest, and elucidating the participation of proteins in biochemical pathways boosting the number of potential targets around which lead compounds can be designed and screened," Eric Gay, a Frost & Sullivan analyst, said in a statement."
redux [07.11.01]
"Their bold proclamation has raised a few eyebrows in the scientific community. "It's easy to say that you'll complete a comprehensive proteome map," notes Marc Vidal of the Dana-Farber Cancer Institute in Boston. "But none of us knows what that means." There may be only one genome, but when it comes to the proteome, different proteins can be more or less active in different cells at different times during development, under different physiological conditions or in different disease states. The proteome's nature "makes it hard to define what we're doing--not just Myriad, but all of us," remarks Joshua LaBaer, director of the Institute of Proteomics at Harvard Medical School. "There's no such thing as a human proteome," adds Keith L. Williams, CEO of Proteome Systems, headquartered in Sydney, Australia. Look at the liver, for example, he says: "After a glass of red wine, you'll have a different proteome."
redux [06.20.01]
"Scientists thought about trying to catalogue all the proteins in the body a decade ago.
But it seemed impossible, and was therefore impossible to fund. Researchers moved on to the much simpler job of sequencing the human genome.
They were right to do so. Cataloguing proteins turns out to be downright confusing. Lately, more and more biotech companies are entering a field they call "proteomics," an ugly word searching for a focus group."
redux [03.13.01]
[requires 'free' registration]
"A commonly expressed opinion is that a single Human Proteome Project can never match HGP's success. Eric S. Lander , director of the Whitehead Center for Genome Research in Cambridge, Mass., notes that biologists simply don't know how to characterize the proteome "from end to end, nailing every protein. The tools are not ready. And it's not clear that [such a project] makes sense." He contrasts proteomics to HGP where "there is a certain fixed number of base pairs--about three billion--and we were going to get them all. And so it had a beginning and an end to it."
redux [01.31.01]
"Can sequencing do for the proteome what it did for the genome?
On Wednesday, a number of world-renowned researchers in the field of proteomics issued a resounding " no."
"When a company has phenomenal success with strategy A, you want to do strategy A on the next subject," said John Richards, a professor of organic and biochemistry at California Institute of Technology, referring to current corporate attempts to map the proteome.
"This doesn't work," he said."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Bio.OReilly.Com
An Interview with Lincoln Stein
"Today, Lincoln is a researcher at the Cold Spring Harbor Laboratory in Cold Spring Harbor, New York, as well as a prolific programmer and author. In addition to the significant contributions he has made to Perl and the Web, he writes software for biological databases, data analysis and visualization, and sharing results. He writes for Web Techniques and The Perl Journal, and he has written several books on related subjects."
"We spoke to Lincoln about his current projects, his opinion on patent issues in biology, and why Perl has become the programming language of choice in bioinformatics."
redux [04.05.00]
"A researcher working on the Human Genome Project is using Napster technology, and he's not looking for T3 connections to download Moby.
Dr. Lincoln Stein, an associate professor of bioinformatics at the Cold Spring Harbor Lab in New York, is investigating ways to use Napster-type technology to allow scientists to share their discoveries of the genome.
"I was very interested when I saw Napster," Stein said. "It has a similar architecture (to what we use now), but it allows for 'peer-to-peer' data exchange and it dawned on me that it would be marvelous for our annotation system."
"The pace of human genomic sequencing has outstripped the ability of sequencing centers to annotate and understand the sequence prior to submitting it to the archival databases. Multiple third-party groups have stepped into the breach and are currently annotating the human sequence with a combination of computational and experimental methods. Their analytic tools, data models, and visualization methods are diverse, and it is self-evident that this diversity enhances, rather than diminishes, the value of their work."
"The solution that we advocate allows sequence annotation to be decentralized among multiple third-party annotators and integrated on an as-needed basis by client-side software.
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Advogato
Academic free software
"Most academic software is released under a "free for academic use" license, which makes it impossible to use such software in a free software project. Some notable counterexamples exist. I am looking for more examples of academic software that has been successfully released under truly free licenses."
"Can anyone point to successful free software projects primarily authored by academic researchers, for which the release under a free software license has benefited the research being undertaken?"
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
HBS Working Knowledge
Healthcare Conference Looks At Ailing Industry
"The goal now is to redefine disease based on the underlying biological mechanisms, Lander said. By that token, diseases are going to surprise us. Reclassifying them means that some diseases will get split in half and other diseases will get lumped together because they have the same mechanism, although they may look different to us, he said.
What this portends commercially is up to smart companies to figure out, he said. Companies will need the ability to integrate scale and informatics; they'll need what he called a "fleetness" with technologies—not just one favored technology, but many kinds. They shouldn't worry too much about hoarding intellectual property rights nor depend on one technology platform. It is more important to understand the big picture in the first place in order to choose the right target, Lander said."
redux [08.01.01]
"Pharmacogenomics requires the integration and analysis of genomic, molecular, cellular, and clinical data, and thus offers a remarkable set of challenges to biomedical informatics. These include infrastructural challenges such as the creation of data models and data bases for storing this data, the integration of these data with external databases, the extraction of information from natural language text, and the protection of databases with sensitive information. There are also scientific challenge in creating tools to support gene expression analysis, three-dimensional structural analysis, and comparative genomic analysis. In this review, we summarize the current uses of informatics within pharmacogenomics, and show how the technical challenges that remain for biomedical informatics are typical of those that will be confronted in the post-genomic era."
redux [11.16.00]
"Neither we nor our critics defined a revolution in medicine. We mean a paradigm shift in theory or practice. Sotos and Rienhoff's plea for "precise diagnosis" epitomizes the current paradigm. In most of those who will have common disorders, the interaction of genetic, environmental, and behavioral factors makes the quest for precise diagnosis illusive."
"The revolution in medicine will come with the recognition, based in part on genetic research, that the quest for single causes for common diseases will seldom be fruitful and that a new paradigm of a causal web must be adopted. Interventions must be directed at the most vulnerable points in the web. Sometimes this will involve biomedical interventions. At other times, it will involve modifying aspects of our social structure, lifestyle, or environment that increase the risk of disease."
redux [08.06.01]
[ summary can be viewed for free once registered ]
"The human genome sequence will dramatically alter how we define, prevent, and treat disease. As more and more genetic variations among individuals are discovered, there will be a rush to label many of these variations as disease-associated. We need to define the term disease so that it incorporates our expanding genetic knowledge, taking into account the possible risks and adverse consequences associated with certain genetic variations, while acknowledging that a definition of disease cannot be based solely on one genetic abnormality."
"In thinking about how clinicians use the term disease, we think that three elements should be considered: disease is a state that places individuals at increased risk of adverse consequences . Treatment is given to those with a disease to prevent or ameliorate adverse consequences. The key element in this definition is risk: deviations from normal that are not associated with risk should not be considered synonymous with disease. Our definition has three definable elements and should serve clinicians well. Of course, its success will depend on whether it becomes clinically useful."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
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."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
GenomeWeb
Oracle Ties the Knot on Long-Term Relationship with Life Sciences
"Oracle had a coming out party of sorts on Wednesday: It announced its dedication to focus more of its resources on capturing the life sciences market.
"Life sciences is special," Oracle CEO Larry Ellison said during a luncheon and series of talks at the OpenWorld conference here, which Oracle organized. "I think it will become the next big thing. The rate of discovery in my industry has gone down. [But] it's radically different in the life sciences industry where horizons are wide open. [There's] lots of new companies and new products. For very cold-hearted reasons we've decided to focus on life sciences.""
redux [06.07.01]
"The researchers seemed to agree that the software now available for analyzing genomic data simply isn't adequate."
Despite significant pushes to cater to the life sciences from the likes of IBM, Compaq, Oracle, and Sun, scientists have yet to see the benefits.
"We've got to do something about what's current out there in the public," said Suzannah Lewis, head of informatics at the Berkeley Drosophila Genome Project.
Her comments quickly became a common theme."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
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 [03.14.01]
"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 resumé 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..."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Bio.OReilly.Com
Speedup at What Cost?
"BLAST is arguably the most valuable bioinformatics tool developed to date, but it is not the only program that can perform sequence similarity searches, nor is it the best choice for all applications. As other choices become more prevalent in the community, it is vital that we develop a shared understanding of the fundamental biological questions addressed as well as a methodology for transforming, comparing, and replicating results produced with different implementations and algorithms.
In this article, I discuss some example scenarios in which life scientists perform sequence-based homology searches, and the pitfalls they should be aware of when using any heuristic algorithm."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Yahoo! News
Biotech and IT Link Up as Technologies Converge
"Today's battle against disease is being fought inside supercomputers as much as in laboratories.
The convergence of biotechnology and computing at the cutting edge of biology has already bred dozens of new alliances and could pave the way for mergers between previously distinct industries.
The ideal company of the future may be a combination of big pharma, a computing giant and a consumer goods player bringing marketing muscle, according to Dirk Heyman, Head of Life Sciences at Sun Microsystems.
[ 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.”
BIOINFORMATICS IN THE 21st CENTURY[ search ]
[ outbound ]
biospace
/
genomeweb
/
bio-it world
/
scitechdaily
/
biomedcentral
/
the panda's thumb
/
bioinformatics.org
/
nodalpoint
/
flags and lollipops
/
on genetics
/
a bioinformatics blog
/
andrew dalke
/
the struggling grad student
/
in the pipeline
/
gene expression
/
free association
/
pharyngula
/
the personal genome
/
genetics and public health blog
/
the medical informatics weblog
/
linuxmednews
/
nanodot
/
complexity digest
/
eyeforpharma
/
nsu
/
nyt science
/
bbc scitech
/
newshub
/
biology news net
/
informatics review
/
stanford
/
bmj info in practice
/
bmj info in practice
/
[ schwag ]
look snazzy and support the site at the same time by buying some snowdeal schwag !
[ et cetera ]
valid xhtml 1.0?
This site designed by
Eric C. Snowdeal III
.
© 2000-2005