{bio,medical} informatics
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The Economist
Crick's last stand
"IT IS traditional to begin an article about Francis Crick by quoting his collaborator, James Watson, who wrote, “I have never seen Francis Crick in a modest mood.” The immodesty that carried Crick to the discovery of the structure of DNA in 1953 clearly never left him. His latest paper (and his last, for he died in 2004) proposes to explain, of all things, the neurological basis of human consciousness.
Mechanistic explanations of consciousness are hard to come by because consciousness is so poorly understood. Indeed, it is one of the few unexplained phenomena that are genuinely mysterious rather than merely problematical. But Crick, together with his long-time collaborator Christof Koch, of the California Institute of Technology in Pasadena, focused on a part of the mystery that seems tractable. This is the integrated nature of conscious sensation."
"What scientists actually do is generally assumed to be above the understanding of the common person. There is, however, the phenomenon of popular science wherein authoritative figures, often eminent scientists, present a version of their science that is accessible to the non-specialist. Such works may achieve best-seller status and are considerable money spinners for those involved. There is, then, the question of how accurately they account for the science represented and, even with the best will in the world, it is easily possible to see how readers of such works may end up being deceived as to the real achievements of the science in question and as to the actual nature of science in general."
"It is not that science is wrong, nor that explanations about mental phenomena are essentially muddled or have to be woolly. It is that there are no easy answers. There are no clear boundaries between what's the right and what's the wrong way to go about finding answer to the question of the proper relationship between minds, genes and consciousness. What is required from scientists, philosophers, and others alike is not just debate but the right sort of debate, and not just claims but modesty in claims and interim conclusions."
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Newsweek
The Shape of Things To Come
"The human genome project may be near completion, but the "real" human-genome project is just getting underway. Scientists now know the sequences of most of our genes. But they don't necessarily know how those genes work or, considering that most of the genome is "junk" DNA that doesn't contribute to the body's normal functioning, whether they work at all. In other words, we've got all the pieces, but we still need to put the puzzle together. Many of the geneticists who worked on the original HGP are now pursuing follow-up projects on their "genes of interest." Here are four who will help give us the complete picture."
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UB Reporter
Supercomputers named for rock legends
""U2" has been selected by the Center for Computational Research (CCR) as the name of its newest and most powerful supercomputer, a 1,668-processor Dell high-performance cluster that will be used to support university research ranging from genomics to groundwater modeling to the monitoring of human-rights abuses."
"According to Miller, computer labs often use quirky themes to keep straight the identities, functions and locations of their machines. Comic book heroes, planets and stars, and science fiction characters typically are represented."
"In response to the soaring demand for computational power by the hundreds of researchers who depend on it, UB has expanded the computing capacity of the Center for Computational Research in its New York State Center of Excellence in Bioinformatics and Life Sciences with the installation of a new Dell high-performance computing cluster.
The cluster, with 1,668 processors, nearly doubles the Center of Excellence's computing capacity. If this cluster was listed on the current top 500 list of the world's fastest supercomputers, (http://www.top500.org), it would be among the 40 fastest individual machines."
redux [04.15.04]
"Two years ago, Jeffrey Skolnick arrived as the leader of the University at Buffalo's new bioinformatics center and the next great hope for the region's struggling economy.
Last week, UB issued a three-page news release announcing a restructuring and expansion of the bioinformatics center that includes a new executive director.
Skolnick's name did not appear anywhere in that document."
redux [03.29.04]
"Bioinformatics star Jeffrey Skolnick has created a stir at the University at Buffalo by criticizing his Dell supercomputer -- announced with fanfare in 2002 -- and switching his allegiance to rival IBM Corp.
The highly public flap has prompted UB administrators to come to the defense of Dell, a deep-pocketed research partner."
redux [03.25.04]
"The University at Buffalo Center of Excellence in Bioinformatics has installed an IBM Corp. supercomputer built on blades and also will work with IBM researchers who will provide algorithms to aid protein pattern and correlation discovery, the company and the center announced Thursday."
"The new supercomputer that will handle the intensive computational work will have a peak performance of more than 1.32T flops and will consist of a cluster of 266 IBM eServer BladeCenter HS20 systems running Red Hat Advance Server 2.1 Linux."
redux [12.08.03]
""Unfortunately, I think there's unreal expectations," said Skolnick, the Buffalo center director. Still, he said, the center "can play a role, and perhaps a significant role" in an economic turnaround.
Even so, not everybody is on board. At Ulrich's Tavern, which calls itself Buffalo's oldest and is sandwiched between the center and an old windshield-wiper factory, an elderly man nursed a midafternoon beer and said he'd never even heard of bioinformatics.
The bar's proprietor, Jim Daley Jr., was plenty aware of it.
"I think it's the most underrated thing in Buffalo," he said. "Most people talk about the casino.""
redux [07.14.03]
"If any doubts lingered among scientists, politicians or business executives about the future prospects for the University at Buffalo Center of Excellence in Bioinformatics, they were erased last Friday as nearly 200 scientists representing the U.S., Canada, India, the Netherlands, the United Kingdom, Italy and Japan gathered in the Adams Mark Hotel in Buffalo for the first annual "Frontiers in Bioinformatics" symposium."
"The day's events amounted to a grand show of support for the center of excellence, which was founded in 2001 by Gov. George E. Pataki"
redux [06.06.03]
"Despite the media barrage surrounding her new book, Senator Hillary Rodham Clinton made a brief appearance in Buffalo on Friday, June 6, to praise the University of Buffalo (UB)'s ambitious Bioinformatics Center of Excellence initiative."
""It has taken a lot of work to make the case to fund bioinformatics," Clinton said. "When we started, the response was, 'What's that?' " Despite this, Clinton and Reynolds have helped to earmark more than $9 million in federal funding for the project."
"Scientists on the cutting edge of drug development were comparing notes in Buffalo Friday during a symposium aimed at introducing the city's developing bioinformatics center to the scientific world."
"In Buffalo, bioinformatics is viewed as perhaps the best hope to generate jobs lost with the demise of its steel and grain-milling industries. But with several other cities around the country also investing heavily in life sciences, the center's directors are well aware of the competition for staff and resources."
redux [03.02.03]
"Jeff Skolnick didn't sign up for all this hype.
He did not apply to the following posting:
Savior wanted: A wunderkind in cutting-edge technology who can help build a new economy and carry the hopes of a Rust Belt region of 1.2 million people.
He just took a job heading a new academic program, the University at Buffalo's Center of Excellence in Bioinformatics."
redux [07.26.02]
"New York's U.S. Senators Charles Schumer and Hillary Rodham Clinton jointly announced that the Senate Appropriations Committee has approved $1 million in funding for Buffalo's planned Center of Excellence in Bioinformatics.
The $1 million was included as part of a an appropriations measure for the Departments of Veterans Affairs and Housing and Urban Development."
redux [05.01.02]
"An optimistic Pataki declared the center "will transform western New York into a 21st Century economy."
The lofty predictions come as upstate's largest city struggles to reinvent itself from a past-its-peak industrial center losing not only jobs but people: U.S. Census figures show the population has dropped to under 300,000, down from a 1950s peak of 580,000."
redux [12.07.01]
"Buffalo will be the site of a Center of Excellence for Bioinformatics thanks to a $200 million collaboration between the public and private sectors.
Gov. George Pataki announced during a swing through Buffalo on Dec. 6 that the state will contribute $50 million to help establish the 150,000 square-foot facility to be located adjacent to the emerging Buffalo Niagara Medical Campus. It is part of Pataki's $1 billion high-tech and biotech Centers of Excellence planned for across the state."
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Financial Express
Report projects bright future for bioinformatics
"The Indian bioinformatics market has the potential to increase its current share of 2.5% to 5% of the global market, according to a report prepared by the Confederation of Indian Industry (CII) and the Department of Information Technology (DIT)."
"Painting a rosy picture, the report states that 42% of the sample companies are planning to increase the scale of businesses because they are investing more in R&D and product development. It also adds that for expanding operations, there will be a huge surge in the demand for bioinformaticians."
redux [03.22.04]
"It was touted as one of the biggest markets Indian software companies could address. But somewhere along the way, the market scenario has changed and today only a few focused companies are still looking at bioinformatics as the next big opportunity, says Srikanth R P."
"While the market potential for bioinformatics is huge few Indian companies have the skill sets or the ability to capture a significant share of the market."
redux [02.23.04]
"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."
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 [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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The Boston Globe
Personalized medicine
"So, what's in it for me? That question probably crossed many minds five years ago following the news that scientists had successfully assembled the first draft of the human genome -- the genetic blueprint of a human being. The answer for most of us was ''not much."
What a difference five years can make. Today, we are witnessing a revolution in the understanding of health and disease, spurred on by the sequencing of the human genome and the subsequent creation of a map of human genetic variation. And, like most historic movements, this revolution has been given a name: personalized medicine."
"Will access to genomic technologies be equitable? Will knowledge of human genetic variation reduce prejudice or increase it? What boundaries will need to be placed on this technology, particularly when applied to enhancement of traits rather than prevention or treatment of disease? Will we succumb to genetic determinism, neglecting the role of the environment and undervaluing the power of the human spirit?"
redux [07.12.03]
[requires 'free' registration]
"Genetics increasingly shows that racial and ethnic distinctions are real -- but often fuzzy and greatly exaggerated. Genetics will increasingly show that most humans are mongrels, and it will make a mockery of racism.
"There are meaningful distinctions among groups that may have implications for disease susceptibility," said Harry Ostrer, a genetics expert at the New York University School of Medicine. "The right-wing version of this is `The Bell Curve,' and that's pseudoscience -- that's not real. But there can be a middle ground between left-wing political correctness and right-wing meanness.""
redux [05.28.03]
"Howard University officials yesterday announced plans to create the first large-scale collection of genetic profiles of African Americans, an endeavor they described as a bid for a "place at the table in genetic research" and a pathway to improved medical care for blacks."
"However, other genetics experts question the premise that the program can help as much as Howard officials say."
redux [05.13.03]
"The use--and often misuse--of genetics to explain racial and ethnic differences is, of course, nothing new. But the HapMap, together with a series of powerful genomic tools developed over the last several years, will make it possible to spell out in great detail the genetic differences between peoples from different parts of the world. Sociologists, bioethicists, and anthropologists worry that the genetic data could be manipulated to give an air of biological credence to ethnic stereotypes, to revive discredited racial classifications, and even to fuel bogus claims of fundamental genetic differences between groups."
redux [01.25.03]
"Race doesn't exist, the mantra went. The DNA inside people with different complexions and hair textures is 99.9 percent alike, so the notion of race had no meaning in science. At a National Human Genome Research Institute (NHGRI) meeting five years ago, geneticists were all nodding in agreement. Then sociologist Troy Duster pulled a forensics paper out of his briefcase. It claimed that criminologists could find out whether a suspect was Caucasian, Afro-Caribbean or Asian Indian merely by analyzing three sections of DNA.
"It was chilling," recalls Francis S. Collins, director of the institute. He had not been aware of DNA sequences that could identify race, and it shocked him that the information can be used to investigate crimes. "It stopped the conversation in its tracks.""
redux [12.20.02]
"Inuit or Basque, Laotian or Pashtun: we're much more similar than we are different, says the most detailed analysis of human genetic variation to date.
When it comes to sensitivity to drugs or diseases, the analysis also suggests that a person's account of their ethnic origin is almost as reliable an indicator as intrusive genetic tests.""
redux [11.01.02]
"In response to early concerns about racial profiling, scientists at the Human Genome Project went out of their way to downplay ethnic variations. Humans are 99.9 per cent alike, the sequencing showed, a figure that was leveraged into a call for global harmony. "The concept of race has no genetic or scientific basis," said Francis Collins, head of the Human Genome Project, at the White House ceremony to celebrate the genome completion.
Yet a great deal of controversy is now brewing over that 0.1 per cent. A growing number of scientists want to use such information as a way to find cures for devastating diseases. If we know more about the genes that cause susceptibility to cystic fibrosis in whites, or sickle cell anaemia in blacks, they argue, we will move closer to a solution for these illnesses. "Ancestry is imperative to biomedical research," says Mark Shriver, an anthropologist at Pennsylvania State University."
redux [10.30.01]
"Race should not influence drug prescriptions, warn geneticists. Genetic differences between individuals give a better indication of who will respond well to a medicine, a new study shows."
Geneticists have known this for a while. "It's no surprise that skin pigment is a lousy predictor of physiology," says Howard McLeod of Washington University School of Medicine in St Louis, Missouri. This study is the first to prove it."
redux [07.20.01]
[requires 'free' registration]
"Scientists planning the next phase of the human genome project are being forced to confront a treacherous issue: the genetic differences between human races."
"With the decoding of the human genome largely complete, government scientists are beginning to construct a special kind of genetic map that would provide a shortcut to locating the variant human genes that predispose people to common diseases."
"The question the scientists face is whether that map should chart possible differences that may emerge among the principal population groups, those of Africans, Asians and Europeans."
redux [03.18.01]
"Genetics research is demonstrating that the differences in appearance among groups are profoundly incidental, but these differences do have a genetic basis. And although it's true that all people have inherited the same genetic legacy, the genetic differences among groups have important implications for our understanding of history and for biomedical research. These complications in an otherwise reassuring story have thoroughly spooked the leaders of the public and private genome efforts. The NIH has been collecting information about genetic variants from different ethnic groups in the United States, but it has refused to link specific variants with ethnicity. Celera has been sequencing DNA from an Asian, a Hispanic, a Caucasian, and an African-American, but it, too, declines to say which DNA is which.
This strategy of avoiding the issue is almost sure to backfire. It seems to imply that geneticists have something to hide. But the message emerging from laboratories around the world should be hailed, not muzzled. It is one of great hope and promise for our species."
redux [06.11.01]
[requires 'free' registration]
"Scientists have long suspected that the racial categories recognized by society are not reflected on the genetic level.
But the more closely that researchers examine the human genome -- the complement of genetic material encased in the heart of almost every cell of the body -- the more most of them are convinced that the standard labels used to distinguish people by "race" have little or no biological meaning.""
""Ethnicity is a broad concept that encompasses both genetics and culture," Dr. Anand said. "Thinking about ethnicity is a way to bring together questions of a person's biology, lifestyle, diet, rather than just focusing on race. Ethnicity is about phenotype and genotype, and, if you define the terms of your study, it allows you to look at differences between groups in a valid way."
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The Guardian Unlimited
The arrogant adventurer
"During the dash to sequence the human genome, Craig Venter's adversaries called him "Hitler", "an asshole", and "an opportunistic maniac and leech". Collins sometimes ended presentations with a slide of a double helix made entirely of money, preaching against those who would sell the human genome as a commodity. The publicly funded scientists often vilified Venter when talking to reporters, which had its intended effect in the media as newspapers and magazines ran stories about Venter cashing in on human DNA. It was Time magazine that dubbed him the "bad boy of science", leading Venter to tell his wife: "I don't mind being bad boy. I just don't want to be evil boy.""
redux [05.30.03]
"Craig Venter is trapped - in a comfy white armchair overlooking the spring leaves and water of Cold Spring Harbor Laboratory in New York.
Artist Lewis Miller is sketching his portrait and the human genome pioneer has to sit still for half an hour. It's not something Venter is used to."
redux [01.31.03]
"J. Craig Venter's company, Celera Genomics, decoded the human genome faster and more cheaply than a large federally-funded effort. Join host Iraq Flatow and Venter for a discussion about his philosophy and vision for genomics. Who should own the human genome?"
redux [11.26.02]
[requires 'free' registration]
"Craig Venter's "minimal genome" project announced Wednesday is not about creating a new life form and probably doesn't pose much of a biowarfare threat, researchers say. The high-profile project was just funded by the US Department of Energy (DOE) with $3 million going to the Institute for Biological Energy Alternatives (IBEA), one of the non-profit research institutes Venter founded after leaving the newly profit-minded Celera Genomics early this year.
According to some scientists, the new project won't even define the minimal genomethe basic gene set required for lifebecause there can be no single minimal genome."
redux [10.15.02]
"But we're asking the philanthropic community to say, 'How about funding 100 genomes for patients with these diseases? Diseases that you care about or ethnogeographic groups to make sure there's sufficient diversity in the population or in some cases you yourself or your family as part of a legacy,' and everybody would have their data be part of a database that would be used for genome analysis in comparing clinical records, genotype/phenotype correlations, obviously in an anonymous fashion."
"It was misrepresented the first time in the press that this was the millionaires' genome project. Hopefully, it would not just be millionaires' genomes, although I think that would be an interesting study. I think we would find them to be remarkably similar to all the other genomes, but I think what we'd expect to happen is that there would be groups that support diseases that they really care about getting solved that they know are not going to get solved with the current paradigm..."
redux [10.03.02]
"Mapping and reading J. Craig Venter's genome took 15 years, $5 billion and some of the world's most sophisticated computers.
Wouldn't you, too, like your genome decoded?
Venter says he plans to offer the service, with the goal of burning individual human's entire DNA sequences onto shiny compact discs."
redux [05.03.02]
"Coming from a man whose life revolves around the study of genes, this might sound surprising: People are not the sum total of their genes.
But J. Craig Venter, former president of Celera Genomics and genome mapper extraordinaire, wants the American public to know that genes are not fate and he's launched a nonprofit organization to prove it. "
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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The New York Times
U.S. Will Offer Doctors Free Electronic Records System
[requires 'free' registration]
"Now, however, Medicare, which says the lack of electronic records is one of the biggest impediments to improving health care, has decided to step in. In an unprecedented move, it said it planned to announce that it would give doctors - free of charge - software to computerize their medical practices. An office with five doctors could save more than $100,000 by choosing the Medicare software rather than buying software from a private company, officials say."
The program begins next month, and the software is a version of a well-proven electronic health record system, called Vista, that has been used for two decades by hospitals, doctors and clinics with the Department of Veterans Affairs. Medicare will also provide a list of companies that have been trained to install and maintain the system."
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Genomeweb
Harvard Researchers Discuss Systems Biology
"So if what we’re doing is going to become anything more than a kind of niche activity for a small group of computational biologists and become part of working practice then I think we have to solve a number of problems. One, of course, is we have to explain to people what they get out of this that’s different. That’s a very important thing, but let’s leave it for a second. One of the things we have to move away from is this idea that every time I want to study a particular system, I have to build from scratch a kind of monolithic model of it, and not take advantage of the fact that lots of other people will have actually bitten off various different parts of it."
redux [03.01.04]
[requires 'free' registration]
"Imagine being able to discover the latest blockbuster drug using nothing but a PC and some highly sophisticated software. It's not as far-fetched as it sounds. A growing number of labs--both industrial and academic--are going "in silico," simulating everything from cells to clinical trials. The result is a sea change in pharmaceutical research, with resources once earmarked for bench work now being shunted into central processing unit clock cycles."
redux [09.09.02]
"Consistent with his lifelong reputation as a visionary and provocateur, Brenner challenged a crowd of over 250 bioinformaticists gathered at the Wellcome Trust Genome Campus in Hinxton, UK, to "forget the genome."
"The more you annotate the genome, the more you make it opaque," he warned in a keynote speech delivered at the joint Cold Spring Harbor Laboratory/Wellcome Trust Genome Informatics conference on Saturday. "We need to focus on our cells."
Brenner questioned the ability of computational approaches to derive functional knowledge from genomic sequence alone--a "hideously difficult task," he said--because some problems are simply "not soluble or computable." The future, according to Brenner, requires going back to the bench. Old-fashioned data on the biochemistry of the cell would then be used to flesh out the cell map, which would serve as "a framework to think of genomes and their products.""
redux [07.29.02]
"Colin Hill, president and CEO of GNS, said the adoption of modeling will be slow, but even the largest and most stubborn pharmas will soon realize they have to adopt it if they want to compete.
He has seen more success selling pharmas the baby steps toward modeling: tools, such as its Diagrammatic Cell Language, software and database information, rather than actual models."
redux [11.27.00]
"What do a Boeing 777 and the human body have in common? Both are complex systems, dependent on millions of complex parts, whether they be a jet-propelled engine or a pumping organ such as the heart. The big difference: Engineers can design and build highly accurate computer models of the way a Boeing 777 will behave in flight. The human heart? Its complexity has long stymied efforts by researchers intent on turning drug development into a predictive science, much like building airplanes.
But that's changing. A handful of companies are developing software that can model single cells, whole organs, cellular metabolism and toxicology, diseases throughout a patient's body, and even an entire clinical trial."
redux [02.16.01]
"Computers capable of mimicking life have long been the stuff of sci-fi nightmares - think The Terminator or 2001's HAL 9000. But for researchers struggling to make sense of vast amounts of new biological data, and for drug companies anxious to cut costs and speed development, having accurate computer simulations of living systems is still a dream. To make that dream come true, they are turning to "in silico biology," building computer models of the intricate processes that take place inside cells, organs, and even people. The ultimate goal: an entire organism modeled in silicon, allowing researchers to test new therapies much as engineers "fly" new airplane designs on supercomputers."
redux [05.15.01]
[requires 'free' registration]
""We in physics are used to studying complex systems, but the level of complexity inherent in biological systems ... is way beyond what we have experience dealing with," said Rajagopal, assistant director of research at the Cavendish Laboratory in the University of Cambridge. "Biological systems are much harder to model as they are in highly non-equilibrium states and you not only have to take into account the flow of matter and energy, but also the flow of information!"
He added: "In biology, the whole is greater than the sum of its parts. We have to move on from the "reductionist" towards an "integrationist" approach."
redux [05.15.01]
[requires 'free' registration]
"For a brief period, supplying the data was enough. More genes meant more potential drug targets. But now the victims of the data flood are crying for help. Companies like Entelos, Inc. (Menlo Park, California) are coming to the rescue by building models that integrate all those data into a single, homeostatic, interconnected whole. The models allow researchers to run virtual drug trials to determine the best drug targets, treatment regimens, and patient populations."
Modelers feel that their time has come. "Leaders in the genomics field are all coming to this realization that model building is becoming the rate-limiting step," says Palsson. "There's a major shift taking place in the biological sciences." Math is back, he says, and "biology is going to become quantitative."
[ 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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