{bio,medical} informatics
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Santa Cruz Sentinal
Unlikely Superman
"Jim Kent's office looks like any other: a solitary computer, a tiny window, stacks of books on listing shelves.
But this little room, in his garage, functions as a pilgrimage site for leaders in genetics. It's the site where Kent, sometimes called the "genome's unlikely superman," worked day and night under the watchful eye of colleagues to sew together the scattered pieces of the human genome."
redux [02.05.03]
"Ben Franklin is remembered for his many great ideas, inventions, and accomplishments. In presenting this year's Ben Franklin Award on behalf of Bioinformatics.Org, J.W. Bizarro reminded us that Franklin also refused to profit from many of his ideas and instead made them freely available. Bizarro pointed out that Jim Kent, this year's recipient of the award, embodies those characteristics in his work, which includes creating a browser for the human genome that is used by many thousands of biomedical researchers every day.
"You've got to admire a man who will flirt with lightning," Kent begins."
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The Scientist
It's True: Scientists Are Smart
[requires 'free' registration]
"A rowdy crowd of white-coated scientists, many recruited from the ranks of readers of The Scientist, upheld the community's braniac reputation by coming out on top in a televised national IQ test. "Test the Nation," a Fox television special, aired on June 9 in the United States. The show pitted scientists against groups of teachers, celebrities, students, hard-hatted construction workers, muscle-shirt-wearing body builders, and blonde women. The scientist group scored highest with an average IQ of 125, followed by teachers and celebrities. The construction workers tied with students at a score of 115. Bringing up the rear, true to politically incorrect expectations, were the blondes and bodybuilders, with a respectable 111."
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Bio-IT World
Marketing hijacks everything, grid developers told
""The language really matters, and confusion on language can be really damaging," Gage said. Citing Sun's experience with Java as an example, he warned developers about the dangers of hype and cautioned them that grid computing risks becoming a catch-all phrase that promises more than it ever can deliver."
"The term has been used to describe a myriad of computing scenarios, from harnessing the processing power in networked PCs build a vast, distributed "supercomputer," to an alternative architecture for the Internet that will provide the underpinnings for Web services and other distributed applications."
redux [05.21.03]
" The American Diabetes Association is using Gateway Inc.'s grid program to run a compute-intensive application designed to accelerate diabetes-related research.
The association, based in Alexandria, Va., is running the Archimedes software application, which Richard Kahn, chief scientific and medical officer for the ADA, called "the Sims City of health care." Using the program, the association can create an environment with any number of variables--such as doctors, hospitals, rooms, costs, patients and treatments--and run numerous what-if scenarios as a way of researching multiple aspects of diabetes care and running clinical studies."
redux [01.09.03]
"Clearly, grid computing means different things to different people, often at different times. To its most visionary pundits, grids symbolize the penultimate step in the evolution of computing architecture into a universal source of pervasive, utility-like computing power that companies can purchase as needed, much as they purchase electricity today. Most stalwart advocates believe that grids not only represent the IT environment of the future but also will ultimately eclipse in significance what the Internet is today."
"All hype aside, it is unlikely that grids will fundamentally change the way that scientific and technical computing is done in the near term, particularly in the private sector."
redux [09.13.02]
"A final obstacle that Stuart pointed out is of the self-inflicted variety: Grid, distributed, peer-to-peer, and other similar incarnations have become victims of their own hype. Increasing media coverage of these technologies has led to confusion in the marketplace, Stuart posited, "and when a prospect becomes confused, the easiest thing is not to do anything.""
"However, he added, there is a bright side to the publicity deluge. Citing the Gartner Group's annual "Hype Cycle of Emerging Technologies" report, which tracks new methods from the initial "tech trigger" period through the "peak of inflated expectations," the "trough of disillusionment," the "slope of enlightenment," and onto the final "plateau of productivity," Stuart noted that desktop grid computing might be working its way from the trough to the slope phase right now, largely because users are discovering which applications work best with the architecture."
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BioMedNet
Correcting ascertainment bias is no mere entertainment
[requires 'free' registration]
"However, Rasmus Nielsen of the Department of Biometrics at Cornell University, notes that, although SNP data offer crucial means to study variability within a population, current methods of SNP discovery introduce an 'ascertainment bias' that pre-empts accurate analysis. Such a bias bears significantly on the estimation of the recombination rate, among other things, which is a measure of the interdependence between different positions of the genome.
"We have moved rapidly beyond the mere sequencing of the genome, towards a study of variability through the study of SNPs," says Nielsen. "We have large data sets of several hundred thousand SNPs but they can not be used in standard analyses because of the protocols used in their discovery.""
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SmallTimes
BIOINFORMATICS GROWS TO KEEP PACE WITH PETABYTES OF SMALL TECH
DATA
"Today, analyzing how multiple genes function together can produce terabytes of data. But as nanotech enables greater sensing and collecting of data, the info flow could become measured in petabytes, or a quadrillion bytes of information. Muscling such large and complex raw results into useful knowledge is the goal of bioinformatics.
Front Line Strategic Consulting predicted last year that the bioinformatics business will reach $1.7 billion by 2006. The market research firm said bioinformatics would grow at a 20 percent annual rate while helping shave 33 percent of the cost, and two years of time, off the drug discovery process."
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Taipei Times
Getting to the core of the human genome using
`bioinformatics'
"Unlocking the secrets of the human genome would be impossible without the computerized manipulation of massive amounts of data, including the majority of the three billion chemical units that comprise our own species' genetic blueprint. But what this "bioinformatics" revolution has provided, above all, is stark confirmation of the evolutionary basis of all life on Earth."
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Bio-IT World
BIO2003: Systems biology leading to advances in IT,
medicine
"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 [01.10.03]
"At last count, 103 of the 341 faculty in MIT's engineering school-and we're talking aeronautic, astronautic, chemical, civil, electrical, environmental, materials science, mechanical, and nuclear engineering--were using the term "bio" to describe the nature of their research.
At a luncheon for 175 invited guests in the MIT faculty club here today, Vest gave a plug for the institute's nascent Computational and Systems Biology Initiative, an interdisciplinary program that will facilitate cross-fertilization among all of MIT's bio-interested faculty and students, whether they be engineers or in the departments of biology, chemistry, computer science, or physics."
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 [02.05.02]
"The project has been a pet of Gov. Gray Davis, who helped seed QB3 with $75 million in state funding. Intel co-founder Gordon Moore has quietly pledged an additional $10 million to launch this novel high-tech/biotech collaboration."
"Kelly said the future will involve figuring out how millions upon millions of interactions between inanimate genes and proteins somehow give rise to life at the cellular level -- a field called systems biology."
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 [03.17.01]
"When Lee Hood started the Institute for Systems Biology, a project to build an integrated research supercenter for the biological sciences, few doubted the validity of the concept, but many wondered whether the technology existed to make it work.
Now, in a sign that others are also willing to gamble on the idea, systems biology is attracting commercial attention. Beyond Genomics (BG), a startup based in Cambridge, Mass., is attempting to glean medically-relevant information from multiple systems simultaneously, from genes to metabolites, by using software that identifies patterns in these systems caused by disease."
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
Teranode Awarded $1.8M NIH Grant for Life Science Computing
Language
"Life science computing startup Teranode said today that it has been awarded $1.8 million from the National Institutes of Health to develop languages and tools for large-scale biological research.
Teranode's technology is based on a visual modeling language for sharing biological research that the company's founders, Larry Arnstein and Neil Fanger, originally developed under the University of Washington Cell Systems Initiative."
"Obvious users for software like this, drug companies. "Languages like this can help refine the design of experiments that can discover drug targets with very high volume experiments, that you can try many more possibilities much more quickly than in the past when things were done manually," says Duncan.
The software, called TeraLab, replaces handwritten notes, and provides a visual, formalized experiment that can be shared as an email attachment. The "person at the other location opens up the attachment and can see exactly what my plan was, and then run it, and they could, in theory, run it at their locations and ship me the results via email."
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The Third Culture
THE GENOME CHANGES EVERYTHING: A Talk with Matt Ridley
"The substance of what I'm interested in is that it's the genes that are related to behavior, and how they work. The big insight is that genes are the agents of nurture as well as nature. Experience is a huge part of a developing human brain, the human mind, and a human organism. We need to develop in a social world and get things in from the outside. It's enormously important to the development of human nature. You can't describe human nature without it. But that process is itself genetic, in the sense that there are genes in there designed to get the experience out of the world and into the organism. In the human case you're going to have genes that set up systems for learning that are not going to be present in other animals, language being the classic example. Language is something that in every sense is a genetic instinct. There's no question that human beings, unless they're unlucky and have a genetic mutation, inherit a capacity for learning language. That capacity is simply not inherited in anything like the same degree by a chimpanzee or a dolphin or any other creature. But you don't inherit the language; you inherit the capacity for learning the language from the environment."
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Genomeweb
MIT, Harvard, Whitehead Join Forces to Create Über-Genomics Institute
"The Massachusetts Institute of Technology, Harvard University, Whitehead Institute have partnered to create a new institute that aims at turning information from the human genome project into real-world medical benefits.
The Eli and Edythe L. Broad Institute, which expects to open its doors later this year in the Kendall Square area of Cambridge, plans to raise up to $200 million in federal grants private support for its research programs over the next 10 years."
"The vision of The Broad Institute was encapsulated in a talk Lander gave two months ago in Washington, D.C. “This [scientific] revolution, catalyzed by the Human Genome Project, is transforming biology into an information-based science,” said Lander, “able to take a comprehensive global view of biological systems. By combining detailed knowledge about the individual components with global understanding of the system as a whole, this revolution promises to yield new insights into the mechanisms of human disease.”"
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BBC
Masculinity guardian revealed
"Scientists in the US have published the results of their detailed scrutiny of the genetic sequence of the human Y chromosome.
This DNA bundle - one of 24 distinct chromosomes found in human cells - holds the crucial information to make the male of our species."
"Reports of the demise of the Y chromosome and an impending extinction of men may have been exaggerated. The Y's full genome sequence reveals that we have underestimated its powers of self-preservation.
Instead of doubling up to protect its genetic cargo like other chromosomes, the lone Y safeguards its genes by having sex with itself, an international consortium has found."
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Slashdot
Convergence of Biology and Computers?
"Pankaj Arora asks: "This summer I am working on both Bioinformatics and Molecular Biology research projects at the Mayo Clinic Rochester. Being an MIS major with a heavy CS background, I've been learning about biochemistry performing polymerase chain reactions (PCRs) and RNA retranslation among other things. I've learned biology works a lot like computers; binary has 1s and 0s, DNA has nucleotides: A, T, C, and G. Binary has 8 bits to a byte, DNA has 3 nucleotides to a codon. Computers and biology seem to have a natural fit; information is encoded and represented 'digitally' in a sense. I was wondering what people thought about the future of biology-based and genetics-based computing due to the immense efficiencies that lie in nature."
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BusinessWeek
A Digital Oasis in the Desert
"Bioinformatics, genomics, proteomics. If you have been wondering what these words mean and what the big fuss is all about, you should check out Ed Regis' wide-ranging The Info Mesa: Science, Business, and New Age Alchemy on the Santa Fe Plateau. Many other books have delved into "complexity" theories -- the rigorous effort to understand natural phenomena based on a mingling of biology, mathematics, physics, and chemistry. But Regis' stands apart for two reasons: He weaves an interesting tale around the people who pioneered this intellectual revolution and brought it to critical mass in the Santa Fe (N.M.) area. And while the book has some organizational problems, Regis explains the major facets of complexity with minimum mumbo-jumbo, so readers can appreciate why complexity stands the traditional approach to science on its end."
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UB Reporter
Attendance at conference dispels any doubts about
bioinformatics center
"If any doubts lingered among scientists, politicians or business executives about the future prospects for the University at Buffalo Center of Excellence in Bioinformatics, they were erased last Friday as nearly 200 scientists representing the U.S., Canada, India, the Netherlands, the United Kingdom, Italy and Japan gathered in the Adams Mark Hotel in Buffalo for the first annual "Frontiers in Bioinformatics" symposium."
"The day's events amounted to a grand show of support for the center of excellence, which was founded in 2001 by Gov. George E. Pataki"
redux [06.06.03]
"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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Stanford Medical Informatics Preprint Archive
Contextualizing Heterogeneous Data for Integration
"Systems that attempt to integrate and analyze data from multiple data sources are greatly aided by the addition of specific semantic and metadata "context" that explicitly describes what a data value means. In this paper, we describe a systematic approach to constructing models of data and their context. Our approach provides a generic "template" for constructing such models. For each data source, a developer creates a customized model by filling in the template with predefined attributes and value. This approach facilitates model construction and provides consistent syntax and semantics among models created with the template. Systems that can process the template structure and attribute values can reason about any model so described. We used the template to create a detailed knowledge base for syndromic surveillance data integration and analysis. The knowledge base provided support for data integration, translation, and analysis methods."
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eWeek
Stanford Cluster to Bridge Sciences
"Stanford University is using supercomputer clusters as a way to bridge the once-isolated disciplines of physics, biology and engineering."
"Bioinformatics will be among the first applications to leverage the cluster, according to Pande, in Stanford, Calif. Specifically, researchers will use the cluster technology to study and model protein structures and dynamics (also known as "protein folding")."
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Bio-IT World
Fournier test-drives Pharsight modeling software
"Drug development modeling software supplier Pharsight Corp., Mountain View, Calif., is in the final stages of a trial project at Montreal-based Fournier Pharma Inc. that has already resulted in the maker of treatments for metabolic diseases deciding to cancel a clinical trial, saving perhaps millions of dollars.
Still, Pharsight officials say, Fournier Pharma has not committed to licensing Pharsight's modeling software and services and expanding their use to other projects."
redux [11.24.02]
"This Insight presented us with a difficult problem, not in its content -- a collection of reviews showing how sophisticated mathematical concepts have illuminated and continue to illuminate the principles underlying biology at a genetic, molecular, cellular and even organismal level. The problem was what to call it.
In the end we concluded that the unifying strand that runs through all the work described in this Insight was computation, whether it be the production of sophisticated models against which reality is compared, or the subtle analyses that derive patterns and trends from vast and noisy data sets. There are other themes running through the reviews in this Insight, more than you might expect from the titles alone, but 'Computational Biology' it has become."
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 [12.17.01]
""We used to look at several data points for each experiment," says Louis Renzetti, senior director of discovery pharmacology. "Now there are dozens and dozens." Simply dump all of that data on a scientist's desk, and one of two tragicomic things will happen: Either the scientist will want to pursue every promising lead and will end up like a frazzled amusement-park visitor, or the scientists will refuse to touch the report at all, for fear that she will never be able to make sense of it.
It has taken a while to find the right approach, says James Rosinski, one of Roche's experts in the new field of bioinformatics, which covers the management of genomic data. The key, he says, is for biologists and statisticians to start talking early about how to use data from a GeneChip experiment. "It's iterative," he explains. "We can't just take a one-shot approach and tell the biologists what they ought to be interested in. We have to interact.""
redux [04.05.00]
[requires 'free' registration]
"I suspect that although the new enthusiasm for computers in biology is genuine, it overlooks some basic problems in implementation. The basic difficulty, as I see it, is that although biologists use computers, they do not trust everything that comes out of them. It is one thing to use them to print up nice-looking graphs, but it is an entirely different matter to use them to think better."
"Francis Crick was once quoted as saying that no biologist had ever made a discovery using a mathematical model. I would reply that no biologist has ever made a discovery by running an electrophoretic gel. They make discoveries by using their brains. Computers, like all scientific tools, are only as good as the person who uses them. If biologists don't understand how computer models are constructed, they won't know their strengths and limitations. Without some foundation of trust, biologists will be unlikely to utilize or accept this powerful method of data analysis."
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Bio-IT World
Senator Clinton supports bioinformatics initiative
"Despite the media barrage surrounding her new book, Senator Hillary Rodham Clinton made a brief appearance in Buffalo on Friday, June 6, to praise the University of Buffalo (UB)'s ambitious Bioinformatics Center of Excellence initiative."
""It has taken a lot of work to make the case to fund bioinformatics," Clinton said. "When we started, the response was, 'What's that?' " Despite this, Clinton and Reynolds have helped to earmark more than $9 million in federal funding for the project."
"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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Star, Malaysia
HP and Intel see potential in the life sciences market
"HEWLETT Packard Sales (M) Sdn Bhd and Intel Electronics (M) Sdn Bhd are looking at the US$2.6bil revenue potential of the Asia Pacific life sciences industry to drive their business growth in the region."
" International Data Corp (IDC) estimates the Asia Pacific life sciences market to grow at a compounded 46%, with funding injection of US$50bil from both public and private sources."
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The Scientist
NIH
names computational boss
[requires 'free' registration]
"After a 2-year process, the National Institute of General Medical Sciences (NIGMS) has named University of Illinois at Urbana-Champaign Professor Eric Jakobsson the first director of its Center for Bioinformatics and Computational Biology (CBCB)."
" "The most appealing part of the job is that it's undefined," Jakobsson told The Scientist. "I'm envisioning this job as putting together a nationally distributed software engineering project. Now, a program for molecular dynamics and another that simulates complex system such as a pathway in a cell aren't linked. We want to seamlessly connect them.""
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News.Com
Computers replace petri dishes in biological labs
""There's been an explosion of data," says Roehr, who nowadays sits in his New Jersey branch office behind an advanced computer system that automatically pulls together all relevant project data onto a single screen. "We're looking to the information technology industry to play catch-up.""
"Biosciences organizations will spend an estimated $30 billion on technology-related purchases in 2006, up from $12 billion in 2001, according to research firm International Data Corp."
redux [11.15.02]
"The Santa Clara, Calif.-based chipmaker said this week that it is working with universities, software developers and server manufacturers to come up with supercomputer-class systems, built around Intel technology, for pharmaceutical engineering, genetic research and other biotech projects, said Rick Herrmann, Intel's manager for worldwide high-performance computing.
"There seems to be a rush toward building out the infrastructure around life sciences," Hermann said. "Every country in the world is looking for bioinformatics to be the next technology pillar: Singapore...Taiwan...the U.S. Even Ireland is looking at it.""
redux [09.04.02]
"Billionaire Michael Dell is in the Buffalo area today to help the University at Buffalo unveil a powerful new computer cluster provided by the company that he founded and continues to run."
""We've installed hundreds of these clusters. (But UB's) would be one of the larger ones, not only for us but in the world," Dell said. "And the amazing thing is we got this up and running in 60 days.""
redux [12.05.01]
"The world's largest computer makers, faced with sagging consumer demand, are betting that the huge data crunching needs of nascent biotechnology firms will grow into a multi-billion dollar market for their equipment and consulting services over the next decade."
""The average individual can't comprehend what has happened in the last half dozen years, where the two greatest medical discoveries, the genome and the microchip, have converged," said Cal Stiller, chief executive of the $250 million Canadian Medical Discoveries Fund."
"We need companies that are on the informatics side that say 'holy cow', we have just stumbled onto the mother lode! We know nothing about mining that area, but we can build the best drilling equipment out there," added Stiller."
redux [06.26.01]
"In 1998, biotech upstart Celera Genomics needed a supercomputer to help it map the human genome. It didn't turn to IBM , which built 204 of the 500 fastest supercomputers. Both Celera and its academic competition, the Human Genome Project, used machines built by Compaq Computer. Two years later, Compaq is the leading seller of supercomputers to biological researchers.
But IBM noticed that biologists now need microprocessors as much as microscopes. A year ago, it used $100 million to start a division that sells computers, software and services to biotechnology and drug companies. This life sciences division has had some success; pulling into second place behind Compaq, it must do better."
redux [08.14.01]
"For years, technologists have dreamed that information technology and biotechnology would someday converge into one seamless superscience that could crack the molecular code of disease and yield a gold mine of new treatments and cures. It always seemed so logical, even if it never quite seemed to happen. Some very big names in tech -- Bill Gates ( MSFT ), Paul Allen, and Jim Clark, among others -- for years have been placing bets on so-called convergence companies that promised to exploit the merging of computing and biotech. Allen alone has investments in more than 50 of them, mostly obscure companies that use words like "genomics," "bioinformatics," and "proteomics" to describe what they do. This industry is so new it hasn't settled on a single name yet."
"Now, like a middle-age actor who has just been discovered, convergence has hit the big time. Corporate giants such as IBM ( IBM ) and Compaq ( CPQ ) are pouring $100 million dollops of cash into "life science" projects that mesh computers and biotech."
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Genomeweb
Birney Announces Winners of Wager on Number of Human Genes
"GeneSweep, a friendly wager in which participants bet on the number of genes on the human genome, is officially over, and there are three winners -- although genome scientists have not definitively agreed on a number of genes in the human genome."
"Birney said that there were 24,500 genes in the latest Ensembl build, human build 33. But he stopped short of saying that this number represents any final tally on the number of human genes. "We are confident we have about 21,000 genes in the human genome," he said. "We are just not that confident about whether there are other genes.""
redux [02.18.03]
"A sweepstakes winner will be declared at the May meeting for guessing the number of genes in the human genome. A lively debate spawned the GeneSweep contest. The number had been so disputed that Ewan Birney of the European Bioinformatics Institute created an official betting pool in 2000 during CSHL's annual genome conference.
Birney leaned over the bar at the campus pub and took official bets in a lab notebook while sc