{bio,medical} informatics
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
BioMedNet
All aboard for sampling software
[requires 'free' registration]
"Tracking, collecting and tabulating data from marine samples, satellite images and shipboard information is cumbersome, but with a new software interface the task becomes more manageable and improves the data's value, say marine biologists."
"Putting all of those pieces together took time and involved referring to numerous data sources, recalls Chris Scholin, the lead biologist on the project. Now the newly designed software interface makes it an "all-in-one stop" where information about the ship's movement can be plotted onto a map and displayed in a geographical information system (GIS) program, which can be overlaid with the latest satellite data regarding water temperature or clarity, for example. Additionally, biologists can enter any new molecular data right away, and compare it with previous samples in real time."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Nature: Science Update
Dog
genome unveiled
"The dog is the latest animal to have its genome sequenced. Shadow belongs to Craig Venter, the researcher whose privately funded project sequenced the human genome using his own DNA."
"The new sequence reveals that 18,473 dog genes have human equivalents. This already surpasses the 18,311 known from the mouse sequence. The team also found genes related to a dog's life: they have many more that are linked to smell than we do."
"The researchers assembled 6.22 million sequences of canine DNA for 1.5X coverage, or 78 percent, of the genome."
""In little more than a decade genomics has advanced greatly and we now have approximately 150 completed genomes, including the human, mouse and fruit fly, in the public domain," Craig Venter, president of TCAG and the J. Craig Venter Science Foundation, which paid for the dog genome research, said in the statement. "Our new method is an efficient and effective way of sequencing that will allow more organisms to be analyzed while still providing significant information.""
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
News.Com
Start-up
Netezza taps into biotech
"The Framingham, Mass.-based company announced Monday that it has developed a specialized version of its hardware server targeted at the bioinformatics field."
"The company said it has signed up customers in the telecommunications field. Cellular providers are using the Netezza server to store six months or more of calling information--which could amount to several hundred gigabytes of data--to spot customer usage trends, according to Netezza CEO Jit Saxena."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
BBC
Will
Biobank pay off?
""I think it's a fantastic idea but people are sceptical that science by committee that is trying to appease so many different groups simultaneously rather than have a more focused approach.""
"There's concern that volunteers will be asked to donate their DNA without really knowing how it's to be used or who's going to use it ."
redux [04.29.02]
"The genetic details of 500,000 people are to be collected and stored in a central UK pool, following the approval of £45m in funding.
It is hoped the pioneering "biobank" scheme will provide valuable information to help fight illness and disease."
redux [09.02.00]
"Robert talks with Barry Eisenstein M.D., Vice President of Science and Technology for Beth Israel Deaconess Medical Center, and Professor of Medicine at Harvard Medical School, about his hospital's participation in creating an international tissue bank. They will be asking patients for permission to sell tissue left over from surgery. The tissue will be used by scientists worldwide for genetic research."
redux [05.15.00]
[requires 'free' registration]
""I just wanted to do something good," Mr. Fuchs said. "But once money came into the picture, why not have it be shared with me?"
These days more and more patients are asking the same question. Laboratories offer tests for more than 700 human genes, with more being discovered almost daily. And, for almost every gene, some medical institution or some company owns a patent on its use.
"The value of patients' tissues has potentially gone up enormously," said Dr. Barry Eisenstein, the vice president for science and technology at the Beth Israel Deaconess Medical Center in Boston. But, Dr. Eisenstein said, patients whose cells provided the genes that have been patented are almost never compensated."
redux [10.02.00]
"Several academic hospitals in the United States are forming partnerships with biotechnology companies to provide them with human tissue for research, treatment, and drug development purposes, in a series of arrangements which raise wide legal and ethical issues."
"Clearly, a bank of human tissues is needed to enable further research, diagnosis, and therapeutic development. The ability to relate the molecular findings of the human genome project to clinically relevant material and data is dependent on ventures such as those of Ardais and academic centres.
The bioethical questions and repercussions of these partnerships, however, continue to be problematic."
redux [05.11.01]
[requires 'free' registration]
"Guidelines on patient confidentiality could undermine medical research, with lethal consequences, said one of the world's leading epidemiologists today. "By making [patient] records anonymous, so even bona fide medical researchers cannot access them, [the guidelines] will cause many deaths," insisted Richard Peto, co-director of the Clinical Trial Service Unit and Epidemiological Studies Unit at the University of Oxford. "It's not beneficial to anyone.""
"Peto was highlighting concern about the threat to the UK's patient registries, which monitor disease, from heart conditions to cancer. The registries link identifiable data from numerous sources, and feed the information to researchers."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
ONJava.Com
Java for Bioinformatics
"Bioinformatics challenges developers to create widely distributable tools that elucidate biological relationships. The principal value of these tools is measured in the contribution they provide to research biologists. Furthermore, as the amount and nature of available data increases, bioinformaticians are forced to provide rapidly evolving tools to their user communities. Java has allowed bioinformaticians to rapidly develop user-friendly, cross-platform applications that are accessible to users at all levels of computational ability."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Genomeweb
Venter Announces $500K Prize for Significant Advances Toward
$1,000 Genome
"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."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Bio-IT World
GlaxoSmithKline Reveals Ingenuity
"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."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
The Scientist
Save the Lab from Patriotic Correctness
[requires 'free' registration]
"As exemplified by the well-publicized cases of Thomas Butler, David Kelly, and Steven J. Hatfill, the fallout from the War on Terror has been particularly hazardous for scientists. Donald A. Henderson, who was inaugural director of the US Office of Public Health Preparedness, which coordinates the national response to public health emergencies, has accused the FBI of losing "all perspective" and of being "out of control" in the Butler and Hatfill investigations.
The dangers are summed up by the case of Butler, chief of the division of infectious diseases at Texas Tech University."
redux [09.13.03]
"In one telling situation, 32 scientists and editors connected to some of the most respected scientific journals have agreed to self-censor any advances they think might compromise national security.
"That's a chilling example of knowing whatever you do might not get published because an editor might decide that it will look bad for John Ashcroft," said Barry Bloom, dean of Harvard's School of Public Health."
redux [05.09.03]
"THE rapid progress of genomics means that the publication of yet another gene sequence for one of the Earth's many millions of species is not guaranteed to raise much interest. But this is no ordinary species. Bacillus anthracis is the bug that causes anthrax. The publication, in Nature, comes two months after a group of editors of the world's leading scientific journals announced they were worried about publishing information that could be used by terrorists to evil ends. New procedures had therefore been put into place to tackle this threat. The question is, do they work?"
redux [02.15.03]
"A group of leading scientific journals has announced measures aimed at restricting the publication of research which could be used by bioterrorists.
In a joint statement, the journals' editors say it is crucial that concerns over terrorism do not affect the release of valuable medical research.
But they say they recognise there may be occasions when new research data should be withheld from publication because it could be abused.
redux [01.14.03]
"Despite fears that bioterrorists will use DNA sequence data to create 21st century superpathogens, genomic science should remain public, The Institute for Genomic Research head Claire Fraser said at a special National Academies meeting on national security and the life sciences last week.
Her explanation: genomics just isn't good enough yet to provide the kind of tools terrorists need."
redux [12.01.02]
[requires 'free' registration]
"Scientific information that the US government wants to keep mum, but which can't officially be labeled "classified," has been designated "sensitive but unclassified." One example is the National Academy of Science's recent report on agricultural bioterrorism. Its chapter on bioterror case studies is available only on a need-to-know basis. Other professional groups may find themselves in the same boat, but the rules governing the category are anything but clear.
Reference: Enserink, M. 2002. Entering the twilight zone of what material to censor. Science 298(5598):1548."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
The Economist
Soul of a newer machine
"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.""
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Biomednet
Predicting carcinogenicity early: the latest in silico
solution
[requires 'free' registration]
"Under the terms of the CRADA, MDL and the FDA will jointly develop a series of predictive software modules that represent major toxicological endpoints of interest to regulatory agencies and the pharmaceutical industry. The agreement debuted with the release of the MDL? Carcinogenicity Module in July 2003; the endpoints upon which future modules will focus include human adverse effects such as QT effects, liver toxicity, teratogenicity (the ability to cause birth defects) and mutagenicity. The software modules will enable scientists to identify and eliminate compounds with high potential for toxicity early in the drug discovery process."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Infoworld
Paul Allen invests $100M in brain research center
"Researchers will create a research tool that will be accessible to the public and will overlay the brain's structural imagery with details about locations and functions of active genes in the brain, according to a statement announcing the institute and the financial pledge.
Allen Institute co-founder Jo Allen Patton and project director Dr. Mark Boguski, a researcher in bioinformatics and genomics, will lead the Atlas project team. The institute and project Web site is at http://www.brainatlas.org/. "
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Popular Science
The Worst Jobs in Science
"Ah, science! Ennobling. Fascinating. Deeply challenging. Also, dangerous, gross and mind-bogglingly boring. We at Popular Science are sometimes brought up short by the realization that there are aspects of science--entire jobs, even--that, when you strip away the imposing titles and advanced degrees, sound at best distasteful and at worst unbearable. Having chosen last month our second annual Brilliant 10--a group of dynamic researchers making remarkable discoveries--we turned to this pressing question: For the rest out there, just how bad can a science job get? "
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Bio-IT World
Molecular Biology Software Breakthrough Seen
"A new software package developed by two research scientists could give molecular biologists a badly needed tool to speed DNA sequencing experiments by streamlining the process of creating virtual clones and choosing vectors."
"Creating a virtual clone using a commercial software package could take 45 steps and require 45 minutes, Bruenn said in the recent statement. The suite under development requires seven steps and less than two minutes, and keeps records of what was done for use in later experiments, eliminating the need to start from scratch."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
The New York Times
Getting More From a PC's Spare Time
[requires 'free' registration]
"This fall, distributed computing will take a step forward when its largest project, SETI@home (short for Search for Extraterrestrial Intelligence), introduces a software program named for its University of California origins: Berkeley Open Infrastructure for Network Computing, or Boinc."
"The University of Maryland's Center for Bioinformatics and Computational Biology plans to use Boinc next spring for a project analyzing DNA sequence data to investigate molecular evolution, particularly of bacteria that cause tuberculosis and leprosy. The project provides opportunities for many people to contribute to scientific research in ways other than through their taxes," said Michael P. Cummings, a visiting associate professor at the center."
redux [10.23.02]
"Scientists at Stanford University have demonstrated tangible proof that scientific experiments can be conducted using thousands of low-end PCs wrangled together into loosely linked networks.
A group of chemists, including Stanford assistant professor Vijay Pande, said they successfully predicted the folding rate of a protein using calculations worked out on a so-called distributed computing network. Their research, conducted last year, was published this week in the science journal Nature."
redux [04.04.01]
[requires 'free' registration]
"Intel is providing equipment and software downloads for a project in which volunteers are donating spare home computer cycles to a Stanford University project studying the protein-folding process. The project, Folding@Home, was the first to model successfully a complete protein fold - a task not even achieved by supercomputers."
""We want to increase the value of the PC," said Scott Griffin, Intel's program manager. "The PC is there when people aren't at it, like when they are in meetings. A great thing about this is you get every day users involved in research that they care about. Not only do they get to help out, but they get to help cure these terrible diseases.""
redux [09.23.01]
"IBM is spending $100 million building the world's fastest supercomputer to do cutting-edge medical research, but a distributed computing effort running on ordinary PCs may have beaten Big Blue to the punch.
IBM's proposed Blue Gene , a massively parallel supercomputer, in hopes to help diagnose and treat disease by simulating the ultra-complex process of protein folding.
"But Folding@Home , a modest distributed computing project run by Dr. Vijay Pande and a group of graduate students at Stanford University, has already managed to simulate how proteins self-assemble, something that computers, until now, have not been able to do."
redux [10.09.00]
"The SETI@Home problem can be thought of as a special case of the distributed computation verification problem: "given a large amount of computation divided among many computers, how can malicious participating computers be prevented from doing damage?" This is not a new problem. Distributed computation is a venerable research topic, and the idea of "selling spare CPU cycles" has been a science fiction fixture for years."
"The Internet makes it possible for computation to be distributed to many more machines. However, distributing computing around the internet requires developers to consider the possibility of malicious clients."
"The general study of secure multiparty computation has produced much interesting work over the last two decades. Less well studied, unfortunately, are the tools and techniques required to move the theoretical results to the real world. The old dream of massively distributed computations is finally coming true, and yet our tools for building and analysing real systems still seem primitive. The challenge of the next few years will be to bridge this gap."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Wired News
Science Suffers Security Complex
"In one telling situation, 32 scientists and editors connected to some of the most respected scientific journals have agreed to self-censor any advances they think might compromise national security.
"That's a chilling example of knowing whatever you do might not get published because an editor might decide that it will look bad for John Ashcroft," said Barry Bloom, dean of Harvard's School of Public Health."
redux [05.09.03]
"THE rapid progress of genomics means that the publication of yet another gene sequence for one of the Earth's many millions of species is not guaranteed to raise much interest. But this is no ordinary species. Bacillus anthracis is the bug that causes anthrax. The publication, in Nature, comes two months after a group of editors of the world's leading scientific journals announced they were worried about publishing information that could be used by terrorists to evil ends. New procedures had therefore been put into place to tackle this threat. The question is, do they work?"
redux [02.15.03]
"A group of leading scientific journals has announced measures aimed at restricting the publication of research which could be used by bioterrorists.
In a joint statement, the journals' editors say it is crucial that concerns over terrorism do not affect the release of valuable medical research.
But they say they recognise there may be occasions when new research data should be withheld from publication because it could be abused.
redux [01.14.03]
"Despite fears that bioterrorists will use DNA sequence data to create 21st century superpathogens, genomic science should remain public, The Institute for Genomic Research head Claire Fraser said at a special National Academies meeting on national security and the life sciences last week.
Her explanation: genomics just isn't good enough yet to provide the kind of tools terrorists need."
redux [12.01.02]
[requires 'free' registration]
"Scientific information that the US government wants to keep mum, but which can't officially be labeled "classified," has been designated "sensitive but unclassified." One example is the National Academy of Science's recent report on agricultural bioterrorism. Its chapter on bioterror case studies is available only on a need-to-know basis. Other professional groups may find themselves in the same boat, but the rules governing the category are anything but clear.
Reference: Enserink, M. 2002. Entering the twilight zone of what material to censor. Science 298(5598):1548."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Businessweek
A Mac-Style Supercomputer
" Here's a groundbreaker in computing, one that Apple can't take credit for: A group of scientists at Virginia Tech has figured out how to build the world's next supercomputer -- on the cheap no less -- using Macs. And they're in the process of doing it."
"And they would have it for chicken feed, relatively speaking. The Mac cluster will cost no more than $5.2 million, which is "quite modest," according to Tech officials. To save more money, the university is recruiting students to help set up 19.25 tons of computers, routers, and other equipment."
redux [09.03.03]
"Apple Computer is shipping about 1,100 of the company's G5 Power Macs - a dual-processor computer being billed as the world's fastest personal computer - to Tech during the next month. Tech engineers and computer scientists then hope to connect, or "cluster," the G5s to create a supercomputer capable of handling massive calculations needed in such fields as nanoscale electronics and computational chemistry.
Tech is racing to complete the project by Oct. 1, the deadline for consideration in a popular ranking of the world's top supercomputers."
"The Virginia Bioinformatics Institute, a state institute run by Tech, has two supercomputers at its location in the Virginia Tech Corporate Research Center."
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.""
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Perl.Com
A Chromosome at a Time with Perl, Part 1
" For some time now, the use of Perl in biology has been standard practice. Perl remains the most popular language among biologists for a multitude of programming tasks. The same reasons why Perl has been a success story among system administrators, as well as one of the big success stories in the early days of the Web and CGI programming, have also made it the lingua franca of programming in biology, known as bioinformatics."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Bio-IT World
Soul Searching
"Their makeshift home was a cramped, rectangular conference room. Token ventilation was provided by an oscillating fan that pushed around warm, stale air. An entire wall was festooned with an unintentional mosaic of fluorescent Post-it Notes.
Here, a team of eight software engineers would work around the clock. Several times a day, the tangle of electrical wires and cords would accidentally be kicked out of the power strip, crashing the network until one of the programmers crawled underneath the table and restored power.
This was the unlikely setting of a revolution in mass fatality identification science."
redux [08.23.03]
"To help the New York City medical examiner identify the remains of the thousands of victims of 9/11, tiny bioinformatics company Gene Codes created M-FISys--the first software capable of managing such massive amounts of genetic evidence."
"M-FISys brings together three types of DNA analysis--some standard, some not generally used for identification purposes--for repeated "all-against-all" comparisons among victim and kinship samples. The program constructs "virtual" DNA profiles where actual ones have literally gone up in smoke and permits users to add or subtract sample analyses from the composites as the evidence changes. It can link to other databases, such as those containing descriptions of, say, family relationships or what the victim wore to work the day of the disaster, or the medical examiner's postmortem findings. It can present a snapshot of not just every test done on a sample but of the progression of those tests, as well as the forensic scientists' comments. "M-FISys allows us to do quality checks on the software, on the samples, on the analysis," says Robert C. Shaler, director of the Department of Forensic Biology for New York City. "We can, at a glance, get an idea of what samples we have and what results we have on them so that we can quickly go through and ascertain what else we need to do.""
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Ecommerce Times
Oracle's Focus Shifts to Technology from Takeovers
"The new package will increase the amount of data that the application can be aware of at any one time to eight exabytes, or eight million terabytes."
"BioMed Central is a biomedical research publisher that allows free access to the bioinformatics research it publishes. The organization publishes peer-reviewed research articles that are rich in graphics, video content and text. It is using the database to make it easier for scientists to manage the publishing process."
""At BioMed Central we are using Oracle 10g manageability features, together with its XML and rich-media capabilities, to deliver Web tools that allow scientists to perform tasks such as manuscript submission, document tracking, peer review and editorial decision-making," said Matthew Cockerill, technical director at BioMed Central Limited."