{bio,medical} informatics
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InfoWorld
Gates fields questions from future competitors at MIT
"Software is the engine that makes the IT industry run, and developers will need to adapt as the world of computer science changes over the next several years, said Bill Gates, chief software architect at Microsoft Corp., in a speech to students at the Massachusetts Institute of Technology (MIT) Thursday."
"A student asked Gates what fields he would consider if he were a computer science student today. After drawing laughs for alluding to his decision to drop out of neighboring Harvard University to found Microsoft with Paul Allen, Gates cited artificial intelligence and computational biology as two areas that he would like to study if he were a student again."
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The New York Review of Books
The Dawn of
McScience
"In Science in the Private Interest , a strongly argued polemic against the commercial conditions in which scientific research currently operates, he shows how universities have become little more than instruments of wealth. This shift in the mission of academia, Krimsky claims, works against the public interest. Universities have sacrificed their larger social responsibilities to accommodate a new purpose--the privatization of knowledge--by engaging in multimillion-dollar contracts with industries that demand the rights to negotiate licenses from any subsequent discovery (as Novartis did, Krimsky reports, in a $25 million deal with the University of California at Berkeley). Science has long been ripe for industrial colonization. The traditional norms of disinterested inquiry and free expression of opinion have been given up in order to harvest new and much-needed revenues."
redux [01.16.02]
"A debate is heating up in the academic community over whether software that is generated by publicly funded research must be released with an open source license. The Internet is one example of how releasing research code benefited the public, but the trend seems to be changing now, and universities are more likely to consider the profit opportunity. The Bayh-Dole Act paved the way for the privatization of publicly funded resources, but not everyone is happy with the results.
Against the tide of privatization comes a group of bioinformatics researchers and programmers with an online petition to require that all software created by publicly funded research projects be licensed as open source. They have founded a group and a Web site, OpenInformatics.org, to further this cause.
Here we present two opposing viewpoints on this issue."
redux [02.27.01]
"ONCE upon a time, pure and applied science were the same. Sir Humphry Davy discovered seven chemical elements, and invented the miner's safety lamp. Louis Pasteur investigated the properties of molecules, and worked out how to stop milk spoiling. Everybody thought that was admirable. Somehow, things have changed. Today the feeling is widespread that science and commerce should not - must not - mix. There is a queasy suspicion that the process of discovery is in some way corrupted if it is driven by profit."
"Far from compromising science, profit in both these cases - the development of new medicines and the elucidation of the genome - has animated it, and directed it towards meeting pressing human needs. It is a happy marriage. Davy and Pasteur would surely have approved."
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Information Week
Xerox Unveils New Document-Management Technology
"Scientists at Xerox's Research Centre Europe in Grenoble, France, said Thursday that they've come up with new classification software clever enough to "read" an electronic document, decide how it should be classified, then automatically route it to the right person's E-mail address or an online document-management system."
"In the pilot program that Xerox ran with the Swiss Institute of Bioinformatics, an academic nonprofit foundation, "their traditional search engines for medical articles often presented the most pertinent documents at the end of the list," said Gaussier. "Using our software, they were much more successful at finding what they were looking for, and typically had to browse less than half of the list to find the information.""
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Bioinformatics.Org:
Lincoln D. Stein to be presented the 2004 Benjamin Franklin Award in Bioinformatics
"Bioinformatics.Org is proud to present the 2004 Benjamin Franklin Award in Bioinformatics to Lincoln D. Stein of Cold Spring Harbor Laboratory, New York. As expressed by his nominators, Stein is being presented this award for his creation of a great number of open-source bioinformatics programs and for championing open-source principals in many venues, including published reviews, lectures, seminars, funding-review panels, and advisory board meetings. His current work includes the GMOD project to produce open-source software components for model organism bioinformatics; the Generic Genome Browser, a web-based genome visualization system; Genome Knowledgebase, for the ontology of core biological pathways; Gramene, a comparative genome browser for grasses; and the Bioperl software library, of which he is a core developer."
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Telegraph:
Biologist quits research laboratory to earn more money fitting
gas boilers
"A molecular biologist whose research could help arthritis and cancer sufferers is to abandon his academic career for a better paid job as a gas fitter."
"The scientist, who is married with a son, spent six years studying human biology and molecular microbiology only to realise he could earn more money and have more job security fitting boilers."
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Hindustan Times
Farming pharma
"Indian pharmas are also waking up to the fact that 'ripping off' patented drugs is becoming more difficult with 'legit piracy' no longer a real option. It's in this changed scene that India plans to make a splash.
A well-developed base industry such as pharma gives India a distinct advantage over others in the biotech boom. It already has a good network of research labs and scores of bioinformatic units have been set up by IT companies across the country. Add to these a rich biodiversity and access to diverse disease populations, and India is ready to ride the wave. At the forefront of this 'petri-dish revolution' will be drug companies -- especially those that manage to add bioinformatics to the already existing arsenal of molecule'n'mortar process."
redux [02.11.04]
"Software major Sun Microsystems would set up a Centre of Excellence (CoE) for medical bio-informatics at Centre for DNA Fingerprinting Analysis and Development (CDFD) here. The CoE would help in analysis, storage of biological research in areas like genomics, structural biology and molecular evolutionary genetics."
"The proposed CoE is the ninth major medical bio-informatics centre established by Sun in the world and first in India."
redux [10.20.03]
"Tata Consultancy Services (TCS) is on track to launch it's biotech software package 'Bio-Suite' by April '04. The software, which will be used in analysing and accelerating drug discovery processes, is being developed in partnership with the Council for Scientific and Industrial Research (CSIR)."
"The software consists of eight 'blocks' covering all aspects of computational biology ranging from genomics to structure-based drug design. In all, Bio-Suite encompasses more than 200 individual algorithms, and is designed to be highly modular so that new algorithms can be added as scientific advances take place."
redux [08.07.03]
"Sun Microsystems has made a proposal to the department of biotechnology to invest in bioinformatics projects in India and to collaborate with various R&D institutions under the department in this burgeoning area. DBT's Task Force on bioinformatics has asked to multinational to specify the quantum of investment and the specific areas of bioinformatics wherein alliances could be forged with Indian institutes."
Official sources said that the Centre for DNA Fingerprinting & Diagnostics, Hyderabad which has an alliance with software services major Tata Consultancy Services, would possibly be a nodal centre for the joint venture project with Sun."
redux [07.14.03]
"The report estimates that currently up to 10 per cent of investment in R&D is IT-related, and hence there is huge potential for Indian biotech and IT companies to enter into collaborative bioinformatics research with global pharma majors in the near term.
The report, however, indicated that despite India's IT capabilities, it may be difficuly to replicate this success in biotechnology as biotechnology differs from IT in many ways. Avendus suggests that Indian players will have to leverage upon the lower costs of infrastructure and human resources. The cost of setting up and running a bioinformatics company in India is a fraction of the cost in the US."
redux [03.18.03]
"Despite several strengths inherent, India's biotechnology industry is not able to take a quantum jump mainly due to lack of capital and low R&D spending, absence of industry-academic partnership and the mismatch between strategic research, product planning and effective collaboration.
The Associated Chambers of Commerce and Industry of India (Assocham) paper on Business of Biotechnology has pointed out that India has several options with the main focus on informatics. Bioinformatics is crucial for the advancement of the biotech industry by cutting the timeframe and costs in developing a product tremendously."
"Everyone in the room, from Sen. Hillary Rodham Clinton to Buffalo Mayor Anthony Masiello, was beaming at last week's announcement.
The news was that Asia's largest computer consultant has become a deep-pocket partner of the University at Buffalo. Under an agreement signed Monday, Tata Consultancy Services of India will partner with local researchers and help transform their discoveries into money-making products."
"But some in the tech community voiced concern that the state's $100 million-plus bioinformatics investment will wind up boosting the economy in Bombay instead of Buffalo."
redux [12.13.02]
[requires 'free' registration]
"India is set to reap substantial rewards in the field of functional genomics, thanks to an invaluable genetic resource and highly advanced IT expertise, predicts Samir Brahmachari, director of the country's Institute of Genomics and Integrative Biology in Delhi."
"Brahmachari sees India's genetic resource - not the biological samples themselves, but the associated information - as a tradable commodity. Data can be processed using India's unparalleled IT expertise, he says: The country's IT industry generated about $10 billion in revenues this year, and has continued to grow by 50% each year over the past decade. The information, once processed, represents an "intellectual-property protectable" commodity, he says."
redux [06.23.02]
"Also, India's success in information technology provides excellent opportunities in the field of bioinformatics.
"Traditional IT companies are translating their strong capabilities in data mining and warehousing to business models based on biological data," says the report, citing examples of IBM's India Research Lab and Satyam's five-year agreement with the Center for Cellular and Molecular Biology, Hyderabad."
redux [02.13.02]
"India's biotech boom could even dwarf software in coming years if you trust the most optimistic projections. Much of our $2.5-billion biotech market relies on low-end products like vaccines, but experts predict that as more start-ups come up, that could change dramatically."
"The need to dive into this ocean of genetic data for hidden treasures has created a whole new discipline--bio-informatics, the science of using information technology (IT) to decipher the genomic jumble. Thanks to a flourishing IT industry, bioinformatics is today the darling of venture capitalists, drug firms, and, of course, IT majors. So, Satyam Computers has signed a five-year alliance with CCMB to create, store, and annotate genetic databases, and it is angling for contracts from global bigpharma to sequence genes and build protein catalogs. Strand Genomics, a Bangalore-based bio-informatics start-up, is designing tools to accelerate drug discovery."
redux [09.17.01]
"India has the potential to garner 8-10 per cent of the global software market in the next few years from the current levels of just 1.5 per cent, but the country?s planners need to focus on improving computer penetration and use of Indian made software in the industry.
This was the view of FC Kohli, chairman, Tata Consultancy Services, while speaking at Connect 2001, an international conference and exhibition on information technology, communication technologies and bioinformatics, which opened on Thursday. Currently, India's IT exports are about $8.7 billion."
redux [08.27.01]
"THE mood is one of caution as far as bioinformatics is concerned. The beginning of the year saw hype building up around the fledgling industry as the next big gold rush for India.
But six months after the first bioinformatics seminar in the country, with the IT industry's lesson on hype fresh in mind, things are moving at a more sedate pace."
"In India, bioinformatics training institutes have already begun to mushroom. Bangalore and Hyderabad have around five private training institutes between them. However, the industry is sceptical about the quality of manpower these centres can supply because most of them have short-term courses offering basic skills, says Dr. Sabharwal. In all fairness to them she adds, "We need to wait for a few months to see the outcome of it all.""
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BioIT World
LabCorp Licenses Junk DNA Patent
"Genetic Technologies (GTG), the Australian biotech company at the heart of a controversy surrounding its patents on the genetic mapping applications of noncoding (junk) DNA, has added another large company to its tally of licensees -- Laboratory Corporation of America Holdings (LabCorp)."
"Last year, GTG granted licenses to Sequenom, Perlegen Sciences, Myriad Genetics, and Pyrosequencing, among others."
redux [11.18.03]
"Investors piled into Genetic Technologies yesterday after the biotech company announced that two US groups it was suing for patent infringement had settled out of court."
"The Melbourne-based Genetic Technologies has consistently warned it would sue any company, research institution or university that infringed its patent over the so-called junk DNA."
redux [08.18.03]
"An Australian biotech company, Genetic Technologies Ltd. (GTG), is stirring up controversy over its decision to enforce a series of patents, granted in the 1990s by the US Patent and Trademark Office, over the genetic diagnostic and mapping applications of non-coding, or junk, DNA."
"Scientists, including NHGRI chief Francis Collins and Sir John Sulston, are also upset over GTG's recent decision to ask academic institutions to sign research licenses."
redux [05.19.03]
[requires 'free' registration]
The dark side of the moon is a misnomer. Light reaches la luna's entire surface, but one half is unviewable from Earth. The human genome, the now essentially decoded map of life, likewise has a light side--the genes encoding mRNA and protein--and a dark side, which is coming into view for the first time. The dark side encompasses more than its opposite: The majority of the genome comprises intronic regions, stretches of repeat sequence, and other assorted gibberish that has attained the ignoble dubbing, "junk."
The first exploratory missions to the human genome's faceted surface are turning up traces regarding the extent of the junk."
redux [11.21.02]
"In a provisional patent application filed July 31, Pellionisz claims to have unlocked a key to the hidden role junk DNA plays in growth -- and in life itself.
Rather than being useless evolutionary debris, he says, the mysteriously repetitive but not identical strands of genetic material are in reality building instructions organized in a special type of pattern known as a fractal. It's this pattern of fractal instructions, he says, that tells genes what they must do in order to form living tissue, everything from the wings of a fly to the entire body of a full-grown human."
redux [08.28.02]
"In a new study in the August 29 issue of Nature, researchers at The Wistar Institute identify a cohesin-containing protein complex that reshapes chromatin to allow cohesins to bind to DNA. In doing so, they also identified the locations on the human genome where the cohesins bind. Somewhat to their surprise, the binding sites were found to be a repetitive DNA sequence found throughout the human genome for which no previous role had ever been identified. These bits of DNA, known as Alu sequences, are liberally represented along those vast stretches of the human genome not known to directly control genetic activity, sometimes referred to as junk DNA."
redux [08.09.02]
"Results of a new University of Michigan study suggest that junk DNA - dismissed by many scientists as mere strings of meaningless genetic code - could have a darker side.
In a paper published in the Aug. 9 issue of Cell, scientists from the U-M Medical School report that, in cultured human cancer cells, segments of junk DNA called LINE-1 elements can delete DNA when they jump to a new location - possibly knocking out genes or creating devastating mutations in the process."
"Scientists in the past decade have discovered that remnants of ancient germ line infections called human endogenous retroviruses make up a substantial part of the human genome. Once thought to be merely "junk" DNA and inactive, many of these elements, in fact, perform functions in human cells.
Now, a new study by John McDonald of the University of Georgia and King Jordan at the National Center for Biotechnology Information at the National Institutes of Health, suggests for the first time that a burst of transpositional activity occurred at the same time humans and chimps are believed to have diverged from a common ancestor - 6 million years ago."
redux [01.20.01]
[requires 'free' registration]
"Speaking at a National Institutes of Health conference on ethical and social issues in genetics, Dr. Francis Collins said that a "spate of papers in public journals'' due out within a month will signify the incredibly rapid pace of scientific discovery seen since the announcement of the nearly complete sequencing of the human genome last summer.
The first, Collins said, will be a paper that puts the total count of human genes at between 30,000 and 35,000. "That's less than half the number most people have been predicting.'' The second is a study ascribing previously unknown biological missions to genes scientists thought were inactive, or so-called "junk genes."
"There is now clear evidence that (the junk genes) have been performing a number of functions for tens or hundreds of thousands of years,'' he said."
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News.Com
IBM plans second Blue Gene supercomputer
"IBM will install a second Blue Gene/L supercomputer as part of a radio telescope project in the Netherlands, the company plans to announce Monday.
The supercomputer will be used for a new radio telescope project called Lofar, short for low frequency array, run by a Dutch organization called Astron. The system, which is expected to be complete in 2005, will run the Linux operating system, use about 12,000 processors and perform more than 30 trillion calculations per second, sources familiar with the plan said."
redux [11.15.03]
"IBM on Friday talked up its Blue Gene/L supercomputer, the first module of which is a relatively small, dishwasher-size machine that can perform 1.4 trillion calculations per second.
The performance is enough to make the machine the world's 73rd fastest supercomputer, according to a ranking of the top 500 to be released Sunday. By the time IBM has upgraded the box's 512 chips, each with two processors, and linked it with another 127 identical systems in 2005, Big Blue hopes to take the top spot."
redux [09.19.03]
"WHATEVER happened to Blue Gene, IBM's ambitious attempt to build the world's fastest computer? The project, launched in 1999, called for the construction of a "massively parallel" computer with over 36,000 processing chips, each containing 32 processing cores roughly equivalent in power to a desktop PC. Harnessing all that computing horsepower--more than one petaflop, or 1,000 trillion floating-point calculations per second--would, it was hoped, allow scientists to simulate the folding of a protein, an extraordinarily demanding task which might help to streamline the discovery of new drugs. The idea was to achieve all of this within five years--something that even enthusiasts thought ambitious.
Four years on, the chips that will power the first Blue Gene computer are now being manufactured and tested. But the plans have changed somewhat."
redux [05.08.03]
""Blue Gene is a completely oddball, you've-never-seen-anything-like-this-before design," said Illuminata analyst Jonathan Eunice. "It is not custom everything, (but) it is still very exotic compared to anything you can buy.""
"IBM already has spent more than the original $100 million budgeted for the project and won't meet its 2004 goal for the ultimate machine, but the company has made progress bringing its ideas to fruition."
redux [02.11.03]
"THE first version of IBM's revolutionary Blue Gene chip will roll off the production line this quarter, Ajay Royyuru, head of IBM's Computational Biology Centre, has revealed."
""We plan to build a 512-node prototype Blue Gene machine in our Watson Research Centre, in New York, where I am located, hopefully before the end of the year.
Then we will build a 64,000- node Blue Gene machine and deliver it to the Lawrence Livermore laboratory by late 2004, or early 2005."
redux [10.24.02]
"Linux will be the main operating system for IBM's upcoming family of "Blue Gene" supercomputers--a major endorsement for the OS and the open-source computing model it represents."
""We had two choices of operating systems for the Blue Gene family, either use a special purpose system or Linux," Bill Pulleyblank, director of Exploratory Server Systems at IBM Research, said in a statement. "We chose Linux because it's open and because we believed it could be extended to run a computer the size of Blue Gene. We saw considerable advantage in using an operating system supported by the open-source community so that we can get their input and feedback.""
redux [07.13.01]
""Ambuj Goyal, IBM Research's general manager for software, solutions, and strategy, was more ambitious than that. Why not build a machine to model molecular dynamics using general-purpose chips rather than specialized ones? That way you'd produce a prototype for a whole new family of supercomputers. Not only would it be great technology development, it would be great marketing, too. Whereas the Department of Energy has the greatest interest in top-end supercomputing - with its need to understand how nuclear weapons work - focusing on the life sciences rather than the death sciences could make supercomputing more widely appealing. What's more, a biology program would be a way of telling one of the newest markets for big iron - the post-genome biotech world - that IBM took its interests seriously. "We believe that the life sciences are going to be a rapidly growing area," says Blue Gene project manager Bill Pulleyblank, "a huge growth area for IBM.""
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Biomedcentral
Celera
defends human sequence
""We hope it puts to rest, once and for all, all this whining that's been going on that the genome could not be assembled without the public data," J. Craig Venter, founder of Celera Genomics and coauthor of the paper, told The Scientist ."
"Bob Waterston, professor and head of the Department of Genetics at the Genome Sequencing Center, University of Washington School of Medicine, one of the leading critics of the Celera data, was not impressed."
redux [02.10.04]
"In a paper published in the Proceedings of the National Academy of Sciences, Celera Genomics has vowed to deposit the draft human genome sequence it published in 2001, as well as two more recent human genome assemblies, in GenBank.
The company also pledged to release the source code for its Celera Assembler genome assembly algorithm."
"Their report, to be published online in the Proceedings of the National Academy of Sciences, compares the accuracy of the draft sequences against the "finished" human genome sequence now available at GenBank.
According to the report, both versions "covered about the same amount of the genome, but they did so in different ways." The Celera sequence provided "more order and orientation" while the HGP sequence provided "better coverage of exact and nearly exact repeats.""
redux [06.13.02]
"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 [01.28.02]
"As all that was happening, people who know him say, White, Venter's boss, was getting grumpy. He well knew that Celera, under its original business plan, could not deliver long-range earnings growth that would justify what the market was paying for Celera shares. One top genetic scientist said White snapped to him in the midst of the publicity barrage, "'This is all nice, but we need a business plan.'"
They quickly came to the same conclusion as many minds before them: In biology and medicine, the only business plan that offers the potential of extraordinary profits is drug development. All the biotechnology superstars have been companies with hit drugs."
redux [01.22.01]
"Dr Craig Venter, the US scientist who led the private effort to decode the human genome, has quit as boss of his company Celera Genomics."
""We are now at a critical juncture where my best contributions can be made in a scientific advisory role, allowing the rest of the organisation to continue Celera's progress toward becoming a successful pharmaceutical business.""
redux [06.09.00]
"Great discoveries do not necessarily make great businesses. Businesses have to sell something. Celera Genomics doesn't sell or make anything tangible. It hawks service and information. It sells access to lists of genes and computers that can sort through those messy lists. Samuel Broder, the company's executive vice president and chief medical officer, makes Celera sound like some kind of consulting company, or perhaps a library."
"Venter's quest could be a fable, with all sorts of morals about the power of capitalism and the importance of a single, brilliant, willful individual who used the market to shake the ivory towers of science. But those morals only hold if Celera succeeds, if business and science blend to propel the company into the future with breathtaking speed without rocketing it into the realities of the marketplace. Celera could become one of the great business success stories. It could also be a financial train wreck."
Right now, that makes it a very volatile stock."
redux [07.17.00]
"Craig Venter, head of Celera Genomics which last month completed the map of the human genome, has outlined his next goal.
Speaking at a conference he said his new task was to map the proteins which drive all chemical reactions in the body."
""A big part of the business is the straightforward providing of information, but I'm not complacent just to do that," Venter said."
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Stanford News Service
New technology aids cell analysis
"Equipped with cutting-edge techniques to track the activity of tens of thousands of genes in a single experiment, biologists now face a new challenge -- determining how to analyze this tidal wave of data. Stanford Associate Professor of Computer Science Daphne Koller and her colleagues have come to the rescue with a strategic approach that reduces the trial-and-error aspect of genetic sequence analysis.
"What we're developing is a suite of computational tools that take reams of data and automatically extract a picture of what's happening in the cell," says Koller. "It tells you where to look for good biology.""
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The Boston Globe
The big picture
"Now, quite suddenly, biology is being consumed by a fast-moving intellectual revolution that could profoundly change the course of science -- and medicine -- in the new century. Called "systems biology," it is an audacious attempt to transcend molecular biology and understand organisms as complex interacting systems that are more than the sum of their parts -- that the best way to understand ants, for instance, is to study colonies rather than just the individual insects.
In only a few years, the idea has gone from fringe concept to rallying cry as Harvard, MIT and universities around the world scramble to establish large new systems biology efforts."
redux [02.04.04]
"Big Pharma is going to be a dinosaur. I think the whole industry is going to be restructured and they'll never be able to get systems biology, so they'll be out of the discovery business. Big Pharma is the worst of silos, even worse than medical schools.
Maybe there are a few like Amgen that'll be flexible enough to really change things. But even there, Roger Perlmutter [executive VP, R&D, Amgen], he's chairman of our board and he still doesn't get systems biology - and he's a really smart guy! See, these guys are too embedded in a billion-dollar-a-year drug [philosophy]. That's exactly the wrong attitude."
redux [01.14.04]
"But is big pharma up to the task of using systems biology to transform drug discovery? In spite of efforts like the one at Novartis to create breeding grounds for systems biology, some say that traditional pharmaceutical companies lack the organizational flexibility to make it work. Industry observers say big pharma may be able to integrate data from various biological experiments, or extract patterns from genomic data, but they doubt that systems biology will flourish there. That's because the ultimate goal of systems biology - constructing models of complex biological systems that would enable researchers to predict the outcome of particular experiments - may be beyond the ken of the highly structured behemoths."
"Even with the plethora of existing biological data, Sorger contends that biology is data-poor in "systematically acquired sets of data. All the interesting data in what I work in seems to be missing," he said. "We need to be able to link unstructured data in a systematic way."
"The barrier here is going to be crossed by creativity, not more CPUs," Sorger continued. "The goal is to usher in a systems biology approach without losing the small science that has sustained" the field."
redux [11.01.03]
"Dealing with the immediate challenge requires a shift to what researchers are calling systems biology, an emerging field of math-based predictive biology."
""I'm up to my eyes in targets," said Ken Kupfer, head of scientific informatics at Bayer's office in Berkeley, Calif. "The time it takes us to develop the depth of understanding we need blows our business models.""
redux [09.22.03]
"In a further validation of Big Pharma's acceptance of systems biology, GlaxoSmithKline has licensed part of the Ingenuity Pathways Knowledge Base to facilitate genome-wide computational analysis of biological systems underlying disease."
"According to Frank Mara, Ingenuity's senior vice president of marketing, "GSK will be using the Ingenuity Knowledge Base to internally build systems biology applications. Every biotech group out there should pay attention when GSK licenses this thing.""
"But major challenges remain in the area of systems biology, Hood said. On the academic level, where centers for systems biology and integrative biology are being established, the biggest challenge, according to Hood, is integration. "How do you create a cross disciplinary faculty?," he asked. "How do you put together the high-throughput technology? How do you deal with salary scales of software engineers and engineers so you doint get funneled off to industry?"
And then, while the centers themselves have received abundant funding, there is the issue of how to fund the research. A major challenge remains in getting the funding agencies, especially at the level of study sections, to understand that systems biology is more than "a big fishing expedition.," Hood said. "But we are pushing to get that.""
redux [09.05.03]
"With sights set on provoking the next wave of bio developments, schools including Cornell, Duke, MIT, Princeton, Stanford, the University of California, and the University of Michigan have undertaken bold initiatives to foster cross-fertilization among faculty and students of diverse disciplines. With state-of-the-art labs and mod monikers such as Bio-X and QB3, the programs will push scientists to seek interdepartmental solutions to biological questions raised by, among other things, genome data. And their directors - scientists who've had illustrious careers in biology, computational genomics, engineering, genetics, and medicine - are systems biology's new vanguard."
"As David Botstein, director of Princeton's fledgling Lewis-Sigler Institute for Integrative Genomics, notes, "We're in very early days. What we have here is high concept." But if concepts become reality, the training, research, and technologies that flow from these centers will instruct the future of the field that's becoming commonly known as systems biology."
redux [08.21.03]
"Some time last year, the "gene bubble" burst when the investment community became disenchanted with the deliverables of genomics, which were not quite as spectacular as promised. Now, a local researcher has predicted that the current hot topic of bioinformatics will not exist within the next ten years. Instead, its position will eventually be usurped by disciplines such as system biology and transcriptome research, which will be the focus for pharmaceutical research in the near future."
"System biology is an emergent field that aims at system-level understanding of biological systems. While system-level understanding has been a long-standing goal of biological sciences, it was only recently that system-level analysis, grounded on discoveries at molecular-level, could be made."
redux [06.24.03]
"The study of systems biology, the field of research that creates predictive models of complex biological processes, will lead to advances in pharmaceuticals and medical treatment, but also to advances in computer science, a leading systems biologist predicted Monday.
""I think biology is going to give fundamental new insights to IT," Hood said. "Really understanding the evolution of gene regulatory networks is going to provide completely new strategies for how one deals with this horrendous computational problem of taking big programs ... and restructuring them really efficiently so that you don't restructure them simply by adding more onto them.""
redux [04.21.03]
"One of the critical priorities now is to take all the components we can detect, and reconstruct the interaction networks inside cells that underlie biological processes. This type of reconstruction is very tricky: People call it 'integration of heterogeneous databases.' Collating these data files is like stacking playing cards -- each piece of data stands upon, and influences, the reliability of other pieces.
The next priority is then to generate computer models that can be used for simulations -- in silico biology. There are three categories of models we need to build: models for metabolism, DNA regulation, and cell signaling."
redux [02.2.03]
[requires 'free' registration]
"Systems biology, a siren in a sea of dark prospects, has lured investors frustrated with low returns in biotechnology and anxious to set a new course of drug discovery. Institutions have also geared up training programs, but the excitement in the new field has failed to arrest downsizing in the biotech industry."
"Despite the interest of the pharmaceutical industry, prospective systems biologists should think carefully before investing in training in hopes of landing a job in the new field."
redux [03.08.02]
[ summary can be viewed for free once registered ]
"To understand biology at the system level, we must examine the structure and dynamics of cellular and organismal function, rather than the characteristics of isolated parts of a cell or organism. Properties of systems, such as robustness, emerge as central issues, and understanding these properties may have an impact on the future of medicine. However, many breakthroughs in experimental devices, advanced software, and analytical methods are required before the achievements of systems biology can live up to their much-touted potential."
redux [02.26.02]
"Over the last few years, there's been an explosion of information in biology. The mapping of the human genome gave biologists unprecedented detail about some 30,000 to 40,000 genes. Efforts are also under way to identify the thousands--and potentially millions--of proteins encoded by those genes. Researchers are now pursuing the next logical step in integrating all this data: systems biology.
The goal is to understand not just the functions of individual genes, proteins and smaller molecules like hormones, but to learn how all of these molecules interact within, say, a cell. Biologists hope to then use this information to generate more accurate computer models that will help unravel the complexities of human physiology and the underlying mechanisms of disease. The biggest payoff: faster development of more-effective drugs."
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."
redux [01.19.02]
"The integration of bioinformatics with these systems approaches is an integral, essential feature. One of the things that we stress is that in the future it's going to be increasingly important for people in bioinformatics to be intimately associated with data producers, because no matter how smart you are you can't model biological complexity--it's just too complex. The only way we're going to understand it is through the integration of these global experimental observations, together with powerful computational tools for analysis, and ultimately, for modeling.
A mistake that a lot of people in bioinformatics have tended to make is thinking that you can set up a bioinformatics center and it can work in isolation from the biology, and it can study all these great databases and learn lots and lots about biology. In vitro biology and in silico biology are all popular terms, but it isn't true, and it isn't going to be true in the future."
redux [04.18.01]
[requires 'free' registration]
"Systems biology is a loosely defined term, but the main idea is that biology is an information science, with genes a sort of digital code. Moreover, while much of molecular biology has involved studying a single gene or protein in depth, systems biology looks at the bigger picture, how all the genes and proteins interact. Ultimately the goal is to develop computer models that can predict the behavior of cells or organisms, much as Boeing can simulate how a plane will fly before it is built.
But such a task requires biologists to team up with computer scientists, engineers, physicists and mathematicians. The structure of universities makes that difficult, Dr. Hood said."
redux [07.13.00]
"A new mathematical biology is emerging. Building on experimental data from developing organisms, it uses the power of computational methods to explore the properties of real gene networks."
"Our understanding of gene networks is at an early stage. We perceive their complexity only after it has been filtered by the limitations of the techniques used to study them. Genome databases and DNA-chip technology, which enables huge numbers of genes to be screened for activity, will undoubtedly provide more, and much more complicated, data than anything produced by Drosophila genetics. If a relatively simple gene network such as the segment-polarity system is hard to understand intuitively, we can be certain that modelling will be essential to make sense of the flood of new data.
But this will not be elegant theoretical modelling: rather, it will be rooted in the arbitrary complexity of evolved organisms. The task will require a breed of biologist-mathematician as familiar with handling differential equations as with the limitations of messy experimental data. There will be plenty of vacancies, and, on present showing, not many qualified applicants."
redux [05.15.01]
"Our Mission is to develop an integrated, easy-to-use environment, the workbench , which will enable biologists to create, manipulate, display and analyze biological models at molecular, cellular and multicellular levels. We are focusing on biochemical networks including mass action kinetics, metabolic pathways, stochastic simulation, gene expression and regulation."
"One of the key aspects of out project is to facilitate collaboration among existing developers and users of system biology software. We aim to do this by providing an open-source software infrastructure which will enable collaborators to freely use and share each other's computational resources."
redux [07.11.00]
"For most of us, formal biology education begins with complex systems--the traditional dissection of a frog in high school biology class is virtually a rite of passage in the U.S.
But the way many people learn about and invest in biotechnology is at the smallest end of the spectrum--the genome, now often described as the "periodic table" of biology. Genomics and all its related buzzwords have been responsible for much of the media attention, government grants, and investment capital heaped on the biotech industry over the past decade.
But just as there is a whole lot of chemistry that happens in between the periodic table and a birthday cake, there is a lot of biology in between the genome and a living organism. With the completion of biology's periodic table within sight, academics and industry players alike are pondering the best way to apply our hard won knowledge.
The only problem is, the path from genome to system seems to get harder the more we learn."
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The Scientist
Scientists Abandon their Software
[requires 'free' registration]
"Vitacolonna isn't alone in abandoning a good project at the end of his postdoc term. It's a ritual of many a bioinformatician. If a person's postdoc project is wildly successful and published in multiple journals, he or she can continue overseeing the program in a junior professor job. If it's just ho-hum work, the creator will probably move on to more interesting projects on the next step up the career ladder.
In the field of bioinformatics, this process, which results in programs known as abandonware, has a debilitating impact."
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Genomeweb
NHGRI Releases RFAs for '$1,000 Genome'
"The National Human Genome Research Institute today released two RFAs aimed at reducing the costs of sequencing a single, full-length mammalian genome to $1,000 - down from current average costs of $10 to $50 million per genome - by the end of a 10-year time frame."
"The RFAs gave several potential applications of cost reduction efforts, including: expanding comparative genomic analysis across species, applying human genetic variation studies to individual health care, and analyzing microbial genomes for food and environment monitoring."
redux [09.23.03]
"Just before lunch today at the GSAC conference, Craig Venter stood before the crowd and announced a mouth-watering proposition: a $500,000 Genomic Technology Prize to be awarded by the J. Craig Venter Science Foundation to a person or organization that develops technology "to significantly advance" automated DNA sequencing toward making the $1,000 genome a reality.
"Look at [the number of] important medical, and environmental advances that would happen if we could sequence a genome in the same time as we are having this conversation," Venter told GenomeWeb News today after the session ended. "
redux [09.08.03]
"It's been three years since scientists completed a rough draft of the human genetic code, but nobody's rushing out yet for a personal DNA analysis. That's because the first draft took 12 years and cost billions of dollars.
Today, the cost has fallen, but only to around $50 million. The target price is orders of magnitude away: $1,000 for an individual's DNA sequence."
redux [10.15.02]
""We are proposing to give people their own sequence if they'll have it," says genomicist George Church of Harvard Medical School."
"Church and other experts think this is no longer a pipe dream. They believe that in less than a decade, people will be able to get their own genomes sequenced for about the price of a laptop or a flat-screen TV. When that happens, the thinking goes, a whole new industry of personal genomics will take off."
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Macworld
Scientists: The Latest Mac Converts
""For our [Mars] landing site work, we always get the highest-end desktop Mac we can find, so we just got one of the G5s with dual 2-GB processors and 8 GB of RAM," Matt Golombek, a planetary geologist at NASA's Jet Propulsion Laboratory, told the E-Commerce Times."
""If you pull up a shot of NASA after the [first] Mars landing and look at the desktops, you'll see a couple of PC laptops there, but you'll see more PowerBooks," Jon Rubinstein, senior vice president for hardware engineering at Apple, told the E-Commerce Times."
redux [01.22.04]
"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."
"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]
"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]
"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]
"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."
"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]
"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]
"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]
"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]
"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]
"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]
"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]
"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."
" 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]
"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.""
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The Times of India
Sun sets sight on centre for bio-informatics
"Software major Sun Microsystems would set up a Centre of Excellence (CoE) for medical bio-informatics at Centre for DNA Fingerprinting Analysis and Development (CDFD) here. The CoE would help in analysis, storage of biological research in areas like genomics, structural biology and molecular evolutionary genetics."
"The proposed CoE is the ninth major medical bio-informatics centre established by Sun in the world and first in India."
redux [10.20.03]
"Tata Consultancy Services (TCS) is on track to launch it's biotech software package 'Bio-Suite' by April '04. The software, which will be used in analysing and accelerating drug discovery processes, is being developed in partnership with the Council for Scientific and Industrial Research (CSIR)."
"The software consists of eight 'blocks' covering all aspects of computational biology ranging from genomics to structure-based drug design. In all, Bio-Suite encompasses more than 200 individual algorithms, and is designed to be highly modular so that new algorithms can be added as scientific advances take place."
redux [08.07.03]
"Sun Microsystems has made a proposal to the department of biotechnology to invest in bioinformatics projects in India and to collaborate with various R&D institutions under the department in this burgeoning area. DBT's Task Force on bioinformatics has asked to multinational to specify the quantum of investment and the specific areas of bioinformatics wherein alliances could be forged with Indian institutes."
Official sources said that the Centre for DNA Fingerprinting & Diagnostics, Hyderabad which has an alliance with software services major Tata Consultancy Services, would possibly be a nodal centre for the joint venture project with Sun."
redux [07.14.03]
"The report estimates that currently up to 10 per cent of investment in R&D is IT-related, and hence there is huge potential for Indian biotech and IT companies to enter into collaborative bioinformatics research with global pharma majors in the near term.
The report, however, indicated that despite India's IT capabilities, it may be difficuly to replicate this success in biotechnology as biotechnology differs from IT in many ways. Avendus suggests that Indian players will have to leverage upon the lower costs of infrastructure and human resources. The cost of setting up and running a bioinformatics company in India is a fraction of the cost in the US."
redux [03.18.03]
"Despite several strengths inherent, India's biotechnology industry is not able to take a quantum jump mainly due to lack of capital and low R&D spending, absence of industry-academic partnership and the mismatch between strategic research, product planning and effective collaboration.
The Associated Chambers of Commerce and Industry of India (Assocham) paper on Business of Biotechnology has pointed out that India has several options with the main focus on informatics. Bioinformatics is crucial for the advancement of the biotech industry by cutting the timeframe and costs in developing a product tremendously."
"Everyone in the room, from Sen. Hillary Rodham Clinton to Buffalo Mayor Anthony Masiello, was beaming at last week's announcement.
The news was that Asia's largest computer consultant has become a deep-pocket partner of the University at Buffalo. Under an agreement signed Monday, Tata Consultancy Services of India will partner with local researchers and help transform their discoveries into money-making products."
"But some in the tech community voiced concern that the state's $100 million-plus bioinformatics investment will wind up boosting the economy in Bombay instead of Buffalo."
redux [12.13.02]
[requires 'free' registration]
"India is set to reap substantial rewards in the field of functional genomics, thanks to an invaluable genetic resource and highly advanced IT expertise, predicts Samir Brahmachari, director of the country's Institute of Genomics and Integrative Biology in Delhi."
"Brahmachari sees India's genetic resource - not the biological samples themselves, but the associated information - as a tradable commodity. Data can be processed using India's unparalleled IT expertise, he says: The country's IT industry generated about $10 billion in revenues this year, and has continued to grow by 50% each year over the past decade. The information, once processed, represents an "intellectual-property protectable" commodity, he says."
redux [06.23.02]
"Also, India's success in information technology provides excellent opportunities in the field of bioinformatics.
"Traditional IT companies are translating their strong capabilities in data mining and warehousing to business models based on biological data," says the report, citing examples of IBM's India Research Lab and Satyam's five-year agreement with the Center for Cellular and Molecular Biology, Hyderabad."
redux [02.13.02]
"India's biotech boom could even dwarf software in coming years if you trust the most optimistic projections. Much of our $2.5-billion biotech market relies on low-end products like vaccines, but experts predict that as more start-ups come up, that could change dramatically."
"The need to dive into this ocean of genetic data for hidden treasures has created a whole new discipline--bio-informatics, the science of using information technology (IT) to decipher the genomic jumble. Thanks to a flourishing IT industry, bioinformatics is today the darling of venture capitalists, drug firms, and, of course, IT majors. So, Satyam Computers has signed a five-year alliance with CCMB to create, store, and annotate genetic databases, and it is angling for contracts from global bigpharma to sequence genes and build protein catalogs. Strand Genomics, a Bangalore-based bio-informatics start-up, is designing tools to accelerate drug discovery."
redux [09.17.01]
"India has the potential to garner 8-10 per cent of the global software market in the next few years from the current levels of just 1.5 per cent, but the country?s planners need to focus on improving computer penetration and use of Indian made software in the industry.
This was the view of FC Kohli, chairman, Tata Consultancy Services, while speaking at Connect 2001, an international conference and exhibition on information technology, communication technologies and bioinformatics, which opened on Thursday. Currently, India's IT exports are about $8.7 billion."
redux [08.27.01]
"THE mood is one of caution as far as bioinformatics is concerned. The beginning of the year saw hype building up around the fledgling industry as the next big gold rush for India.
But six months after the first bioinformatics seminar in the country, with the IT industry's lesson on hype fresh in mind, things are moving at a more sedate pace."
"In India, bioinformatics training institutes have already begun to mushroom. Bangalore and Hyderabad have around five private training institutes between them. However, the industry is sceptical about the quality of manpower these centres can supply because most of them have short-term courses offering basic skills, says Dr. Sabharwal. In all fairness to them she adds, "We need to wait for a few months to see the outcome of it all.""
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Genomeweb
Celera Pledges to Deposit Human Genome in GenBank, Release
Assembler Source Code
"In a paper published in the Proceedings of the National Academy of Sciences, Celera Genomics has vowed to deposit the draft human genome sequence it published in 2001, as well as two more recent human genome assemblies, in GenBank.
The company also pledged to release the source code for its Celera Assembler genome assembly algorithm."
"Their report, to be published online in the Proceedings of the National Academy of Sciences, compares the accuracy of the draft sequences against the "finished" human genome sequence now available at GenBank.
According to the report, both versions "covered about the same amount of the genome, but they did so in different ways." The Celera sequence provided "more order and orientation" while the HGP sequence provided "better coverage of exact and nearly exact repeats.""
redux [06.13.02]
"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 [01.28.02]
"As all that was happening, people who know him say, White, Venter's boss, was getting grumpy. He well knew that Celera, under its original business plan, could not deliver long-range earnings growth that would justify what the market was paying for Celera shares. One top genetic scientist said White snapped to him in the midst of the publicity barrage, "'This is all nice, but we need a business plan.'"
They quickly came to the same conclusion as many minds before them: In biology and medicine, the only business plan that offers the potential of extraordinary profits is drug development. All the biotechnology superstars have been companies with hit drugs."
redux [01.22.01]
"Dr Craig Venter, the US scientist who led the private effort to decode the human genome, has quit as boss of his company Celera Genomics."
""We are now at a critical juncture where my best contributions can be made in a scientific advisory role, allowing the rest of the organisation to continue Celera's progress toward becoming a successful pharmaceutical business.""
redux [06.09.00]
"Great discoveries do not necessarily make great businesses. Businesses have to sell something. Celera Genomics doesn't sell or make anything tangible. It hawks service and information. It sells access to lists of genes and computers that can sort through those messy lists. Samuel Broder, the company's executive vice president and chief medical officer, makes Celera sound like some kind of consulting company, or perhaps a library."
"Venter's quest could be a fable, with all sorts of morals about the power of capitalism and the importance of a single, brilliant, willful individual who used the market to shake the ivory towers of science. But those morals only hold if Celera succeeds, if business and science blend to propel the company into the future with breathtaking speed without rocketing it into the realities of the marketplace. Celera could become one of the great business success stories. It could also be a financial train wreck."
Right now, that makes it a very volatile stock."
redux [07.17.00]
"Craig Venter, head of Celera Genomics which last month completed the map of the human genome, has outlined his next goal.
Speaking at a conference he said his new task was to map the proteins which drive all chemical reactions in the body."
""A big part of the business is the straightforward providing of information, but I'm not complacent just to do that," Venter said."
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Sunday Tasmanian
Tassie DNA rights shock
"AN INTERSTATE biotech company owns intellectual property rights in research from DNA donated by Tasmanians.
The IP deal was behind the collapse of the original $20 million Intelligent Island Bioinformatics Centre for Excellence.
The bioinformatics centre was going to have to pay to use the information."
redux [03.10.03]
"The newest resources "discovered" in Estonia are the genes of its 1.4 million citizens. The country's government and a Silicon Valley start-up called EGeen International are treating the Estonian gene pool as a commodity to be exploited for medical research and profit.
EGeen owns the exclusive commercial rights to data from the Estonian Gene Bank Project. In March the bank will begin a full-scale effort to collect blood samples and medical histories that will help scientists understand Estonians from the inside out."
redux [02.17.01]
[requires 'free' registration]
"A good gene pool, like love, is where you find it. Now genomics researchers have two new ones to swoon over: one from Estonia, a crossroads of Scandinavian cultures and the northernmost of the former Soviet Union's Baltic republics; and from Tonga, an island kingdom half a world away where a Polynesian people has lived in near-perfect isolation for close to 3,500 years. Tonga and Estonia laid final plans last November and December, respectively, for national gene pool exploration programs aimed at discovering disease-associated genes and developing therapies based on the discoveries.
They follow the trail blazed by Iceland, where for several years the gene pool of 275,000 Icelanders has been the fishing preserve of Reykjavik-based deCODE Genetics which is hunting for gene variants that affect serious, often chronic diseases by finding statistical links between Icelanders' genotypes and their inherited illnesses."
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Bio-IT World
Forum Examines Life Science R&D Productivity
"Life science researchers increasingly must identify, assimilate, interpret, and pull together many more new sources of information to conduct their work. This is an enormous challenge that will get more difficult as research efforts become more specialized, further compartmentalizing information into isolated silos."
"To increase R&D productivity, "technology is a key enabler, but there are also cultural and organizational barriers," says Bedi."
redux [03.19.03]
[requires 'free' registration]
"Which approach is more likely to make a biotechnology company successful: a focus on novel technologies or on development of novel compounds?
Getting into clinical compounds has been portrayed as the route out of tough times like those the biotech industry is suffering through now, according to Mark G. Edwards, founder of Recombinant Capital, a California consulting firm and purveyor of biotech financial databases. But the data show, he says, that there doesn't seem to be any sure route out; companies specializing in compounds have fallen just like those specializing in technology."
redux [04.19.02]
[requires 'free' registration]
"This should be the golden age for pharmaceutical scientists. The deciphering of the human genome is laying bare the blueprint of human life. Medical research has increased understanding of disease. Robots and computers are turning drug discovery from a mixing of chemicals in a test tube to an industrialized, automated process."
"Instead of narrowing the list of compounds that might be useful in drugs, automation has broadened it -- greatly increasing the number of formulas tested without yet delivering commensurate growth in safe and effective drugs."
redux [12.14.01]
"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]
""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.
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San Mateo County Times Online
Incyte swaps genomics for drugs
"John Keller, Incyte's chief business officer, said the vast amount of genetic information available today has made it difficult to sell subscriptions to the company's genomic data product lines."
"Many firms hoped to profit from the mapping of the human genome, which was expected to usher in a new form of personalized medicine able to target potential diseases in individuals before they struck. The field was billed as one of the breakthroughs of the new century. But the human genome field was over-hyped for the near-term, although it may yet prove promising for the future."
redux [01.28.04]
"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]
[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]
"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]
"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."
"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]
"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]
[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]
"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.""
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Bio-IT World
Catching Up with Leroy Hood on Systems Biology
"Big Pharma is going to be a dinosaur. I think the whole industry is going to be restructured and they'll never be able to get systems biology, so they'll be out of the discovery business. Big Pharma is the worst of silos, even worse than medical schools.
Maybe there are a few like Amgen that'll be flexible enough to really change things. But even there, Roger Perlmutter [executive VP, R&D, Amgen], he's chairman of our board and he still doesn't get systems biology - and he's a really smart guy! See, these guys are too embedded in a billion-dollar-a-year drug [philosophy]. That's exactly the wrong attitude."
redux [01.14.04]
"But is big pharma up to the task of using systems biology to transform drug discovery? In spite of efforts like the one at Novartis to create breeding grounds for systems biology, some say that traditional pharmaceutical companies lack the organizational flexibility to make it work. Industry observers say big pharma may be able to integrate data from various biological experiments, or extract patterns from genomic data, but they doubt that systems biology will flourish there. That's because the ultimate goal of systems biology - constructing models of complex biological systems that would enable researchers to predict the outcome of particular experiments - may be beyond the ken of the highly structured behemoths."
"Even with the plethora of existing biological data, Sorger contends that biology is data-poor in "systematically acquired sets of data. All the interesting data in what I work in seems to be missing," he said. "We need to be able to link unstructured data in a systematic way."
"The barrier here is going to be crossed by creativity, not more CPUs," Sorger continued. "The goal is to usher in a systems biology approach without losing the small science that has sustained" the field."
redux [11.01.03]
"Dealing with the immediate challenge requires a shift to what researchers are calling systems biology, an emerging field of math-based predictive biology."
""I'm up to my eyes in targets," said Ken Kupfer, head of scientific informatics at Bayer's office in Berkeley, Calif. "The time it takes us to develop the depth of understanding we need blows our business models.""
redux [09.22.03]
"In a further validation of Big Pharma's acceptance of systems biology, GlaxoSmithKline has licensed part of the Ingenuity Pathways Knowledge Base to facilitate genome-wide computational analysis of biological systems underlying disease."
"According to Frank Mara, Ingenuity's senior vice president of marketing, "GSK will be using the Ingenuity Knowledge Base to internally build systems biology applications. Every biotech group out there should pay attention when GSK licenses this thing.""
"But major challenges remain in the area of systems biology, Hood said. On the academic level, where centers for systems biology and integrative biology are being established, the biggest challenge, according to Hood, is integration. "How do you create a cross disciplinary faculty?," he asked. "How do you put together the high-throughput technology? How do you deal with salary scales of software engineers and engineers so you doint get funneled off to industry?"
And then, while the centers themselves have received abundant funding, there is the issue of how to fund the research. A major challenge remains in getting the funding agencies, especially at the level of study sections, to understand that systems biology is more than "a big fishing expedition.," Hood said. "But we are pushing to get that.""
redux [09.05.03]
"With sights set on provoking the next wave of bio developments, schools including Cornell, Duke, MIT, Princeton, Stanford, the University of California, and the University of Michigan have undertaken bold initiatives to foster cross-fertilization among faculty and students of diverse disciplines. With state-of-the-art labs and mod monikers such as Bio-X and QB3, the programs will push scientists to seek interdepartmental solutions to biological questions raised by, among other things, genome data. And their directors - scientists who've had illustrious careers in biology, computational genomics, engineering, genetics, and medicine - are systems biology's new vanguard."
"As David Botstein, director of Princeton's fledgling Lewis-Sigler Institute for Integrative Genomics, notes, "We're in very early days. What we have here is high concept." But if concepts become reality, the training, research, and technologies that flow from these centers will instruct the future of the field that's becoming commonly known as systems biology."
redux [08.21.03]
"Some time last year, the "gene bubble" burst when the investment community became disenchanted with the deliverables of genomics, which were not quite as spectacular as promised. Now, a local researcher has predicted that the current hot topic of bioinformatics will not exist within the next ten years. Instead, its position will eventually be usurped by disciplines such as system biology and transcriptome research, which will be the focus for pharmaceutical research in the near future."
"System biology is an emergent field that aims at system-level understanding of biological systems. While system-level understanding has been a long-standing goal of biological sciences, it was only recently that system-level analysis, grounded on discoveries at molecular-level, could be made."
redux [06.24.03]
"The study of systems biology, the field of research that creates predictive models of complex biological processes, will lead to advances in pharmaceuticals and medical treatment, but also to advances in computer science, a leading systems biologist predicted Monday.
""I think biology is going to give fundamental new insights to IT," Hood said. "Really understanding the evolution of gene regulatory networks is going to provide completely new strategies for how one deals with this horrendous computational problem of taking big programs ... and restructuring them really efficiently so that you don't restructure them simply by adding more onto them.""
redux [04.21.03]
"One of the critical priorities now is to take all the components we can detect, and reconstruct the interaction networks inside cells that underlie biological processes. This type of reconstruction is very tricky: People call it 'integration of heterogeneous databases.' Collating these data files is like stacking playing cards -- each piece of data stands upon, and influences, the reliability of other pieces.
The next priority is then to generate computer models that can be used for simulations -- in silico biology. There are three categories of models we need to build: models for metabolism, DNA regulation, and cell signaling."
redux [02.2.03]
[requires 'free' registration]
"Systems biology, a siren in a sea of dark prospects, has lured investors frustrated with low returns in biotechnology and anxious to set a new course of drug discovery. Institutions have also geared up training programs, but the excitement in the new field has failed to arrest downsizing in the biotech industry."
"Despite the interest of the pharmaceutical industry, prospective systems biologists should think carefully before investing in training in hopes of landing a job in the new field."
redux [03.08.02]
[ summary can be viewed for free once registered ]
"To understand biology at the system level, we must examine the structure and dynamics of cellular and organismal function, rather than the characteristics of isolated parts of a cell or organism. Properties of systems, such as robustness, emerge as central issues, and understanding these properties may have an impact on the future of medicine. However, many breakthroughs in experimental devices, advanced software, and analytical methods are required before the achievements of systems biology can live up to their much-touted potential."
redux [02.26.02]
"Over the last few years, there's been an explosion of information in biology. The mapping of the human genome gave biologists unprecedented detail about some 30,000 to 40,000 genes. Efforts are also under way to identify the thousands--and potentially millions--of proteins encoded by those genes. Researchers are now pursuing the next logical step in integrating all this data: systems biology.
The goal is to understand not just the functions of individual genes, proteins and smaller molecules like hormones, but to learn how all of these molecules interact within, say, a cell. Biologists hope to then use this information to generate more accurate computer models that will help unravel the complexities of human physiology and the underlying mechanisms of disease. The biggest payoff: faster development of more-effective drugs."
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."
redux [01.19.02]
"The integration of bioinformatics with these systems approaches is an integral, essential feature. One of the things that we stress is that in the future it's going to be increasingly important for people in bioinformatics to be intimately associated with data producers, because no matter how smart you are you can't model biological complexity--it's just too complex. The only way we're going to understand it is through the integration of these global experimental observations, together with powerful computational tools for analysis, and ultimately, for modeling.
A mistake that a lot of people in bioinformatics have tended to make is thinking that you can set up a bioinformatics center and it can work in isolation from the biology, and it can study all these great databases and learn lots and lots about biology. In vitro biology and in silico biology are all popular terms, but it isn't true, and it isn't going to be true in the future."
redux [04.18.01]
[requires 'free' registration]
"Systems biology is a loosely defined term, but the main idea is that biology is an information science, with genes a sort of digital code. Moreover, while much of molecular biology has involved studying a single gene or protein in depth, systems biology looks at the bigger picture, how all the genes and proteins interact. Ultimately the goal is to develop computer models that can predict the behavior of cells or organisms, much as Boeing can simulate how a plane will fly before it is built.
But such a task requires biologists to team up with computer scientists, engineers, physicists and mathematicians. The structure of universities makes that difficult, Dr. Hood said."
redux [07.13.00]
"A new mathematical biology is emerging. Building on experimental data from developing organisms, it uses the power of computational methods to explore the properties of real gene networks."
"Our understanding of gene networks is at an early stage. We perceive their complexity only after it has been filtered by the limitations of the techniques used to study them. Genome databases and DNA-chip technology, which enables huge numbers of genes to be screened for activity, will undoubtedly provide more, and much more complicated, data than anything produced by Drosophila genetics. If a relatively simple gene network such as the segment-polarity system is hard to understand intuitively, we can be certain that modelling will be essential to make sense of the flood of new data.
But this will not be elegant theoretical modelling: rather, it will be rooted in the arbitrary complexity of evolved organisms. The task will require a breed of biologist-mathematician as familiar with handling differential equations as with the limitations of messy experimental data. There will be plenty of vacancies, and, on present showing, not many qualified applicants."
redux [05.15.01]
"Our Mission is to develop an integrated, easy-to-use environment, the workbench , which will enable biologists to create, manipulate, display and analyze biological models at molecular, cellular and multicellular levels. We are focusing on biochemical networks including mass action kinetics, metabolic pathways, stochastic simulation, gene expression and regulation."
"One of the key aspects of out project is to facilitate collaboration among existing developers and users of system biology software. We aim to do this by providing an open-source software infrastructure which will enable collaborators to freely use and share each other's computational resources."
redux [07.11.00]
"For most of us, formal biology education begins with complex systems--the traditional dissection of a frog in high school biology class is virtually a rite of passage in the U.S.
But the way many people learn about and invest in biotechnology is at the smallest end of the spectrum--the genome, now often described as the "periodic table" of biology. Genomics and all its related buzzwords have been responsible for much of the media attention, government grants, and investment capital heaped on the biotech industry over the past decade.
But just as there is a whole lot of chemistry that happens in between the periodic table and a birthday cake, there is a lot of biology in between the genome and a living organism. With the completion of biology's periodic table within sight, academics and industry players alike are pondering the best way to apply our hard won knowledge.
The only problem is, the path from genome to system seems to get harder the more we learn."
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Genomeweb
First Genetic Trust Gets Patent for Banking System
"First Genetic Trust has received a patent for an electronic genetic banking system, the company said today.
The patent, US patent No. 6,460,211 B1, covers methods, processes, and electronic systems for securely storing, analyzing, and managing genetic data.
First Genetic Trust, headquartered in Chicago, is aiming to develop and commercialize genetic banking and research management applications for biomedical research."
"The system of the present invention thus allows a patient to voluntarily bank genetic information that can be used quickly to determine genetic and medical information about that individual, particularly information that relates to whether the individual carries genetic information associated with known diseases. The system provides restrictions, however, that allow the user to retain privacy and limit unauthorized access to his/her genetic information. The system is thus unlike a system, for example, in which DNA information, like fingerprint information, is stored for identification purposes to use DNA information to identify individuals involved in specific criminal activities; in such a case, the individual who provides the sample would generally not have voluntary control to establish the ability of others to access the information, and such systems would generally not have the ability to test for a number of different medical purposes for which the DNA information can be accessed by others."
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Wired
Living Machines
"Life isn't the exception, but the rule.
The notion that the inorganic world is alive is as old as mythology; think of Poseidon, the Greek personification of the sea. However, the tools available to examine life at its most essential - DNA sequencing, bioinformatics, gene chips - are new. We're beginning to discern life processes at their fundamental level, and as we re-create these processes in silico, we're starting to see how they work in inorganic settings. It turns out that many of life's properties - emergence, self-organization, reproduction, coevolution - show up in systems generally regarded as nonliving."
[ 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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