{bio,medical} informatics
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Wired News
Mac Supercomputer Just Got Faster
"The latest semi-official numbers concerning the speed of Virginia Tech's "Big Mac" supercomputer rank it as the third-fastest machine on the planet.
The system's architect, Srinidhi Varadarajan, said Tuesday evening that the newly completed supercomputer operates at 9.55 trillion operations a second, or 9.55 teraflops."
"It's a shame that Apple no longer runs the "Switch" campaign on television. Dr. Srinidhi Varadarajan would make an excellent spokesperson for moving to the Mac."
" His ad might go something like this. "I was in the market for a new machine. I was hoping to get ten teraflops by the end of the year. I'd never used a Mac and had been looking at Dells and IBMs. Then Apple released the G5 on June 23. A week later I bought 1,100 duals online at the Apple Store. I'm Srinidhi Varadarajan and I build Supercomputers at Virginia Tech.""
redux [10.25.03]
"Tribble, one of the designers of the original Macintosh user interface, said that with the advent of the Power Mac G5 and the OS X operating system, the Macintosh now has the Unix backbone, 64-bit processing power, Windows interoperability, and open source credibility to be a viable computing platform in the life sciences space.
"Really, for the first time in this industry, you have a computer that can do all the scientific applications, and you can run Microsoft Office," he said. "It's been kind of a Holy Grail that started with Mac OS X.""
redux [10.15.03]
"Early benchmarks of Virginia Tech's brand new supercomputer -- which is strung together from 1,100 dual-processor Power Mac G5s -- may vault the machine into second place in the rankings of the worlds' fastest supercomputers, second only to Japan's monstrously big and expensive Earth Simulator."
""They're getting about 80 percent of the theoretical peak," Dongarra said. "If it holds, and it's unclear if it will, it has the potential to be the world's second most powerful machine.""
redux [09.12.03]
" 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.""
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Channel NewsAsia
Biopolis to be new focal point of biomedical research and
talent
"Singapore's premier biomedical research hub, the Biopolis, was launched on Wednesday evening by Deputy Prime MInister Tony Tan.
The $500-million complex is the first in the world to see public and private researchers working alongside each other."
"So far, the Genome Institute and Bioinformatics Institute are the two first Government research laboratories to move in."
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Bio-IT World
IT Services Prepped for Life Science Companies
"Underscoring the rising importance of life science companies as users of IT, Computer Sciences Corp. and CGI Group Inc. announced on Tuesday separate enhancements to their IT services offerings for this industry.
CSC, in El Segundo, California, announced the availability of a software and services bundle designed to provide life sciences companies, such as pharmaceuticals, medical device vendors and biotechnology firms, with content management, workflow and collaboration functions to give them control over internal procedures and documents."
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Nature: Science Update
Pharmacy data reveals impact of smoking ban
"Prompted by the US anthrax attacks of October 2001, most of the new surveillance systems are designed to pick up early warning signs of a bioterror attack, such as a hike in fevers or rashes. They use sophisticated algorithms to filter computerized health data for unusual peaks.
But the systems are untested as yet by bioterror agents - so researchers are teasing other information from them. "These data have all sorts of uses," says Julie Paulin, an expert in preventive medicine at the Walter Reed Army Institute of Research in Silver Spring, Maryland."
redux [04.17.03]
"Public health surveillance is changing in response to concerns about bioterrorism, which have increased the pressure for early detection of epidemics. Rapid detection necessitates following multiple non-specific indicators, accounting for spatial structure, and quickly characterizing aberrancies. A single analytic method cannot meet these requirements, but there is no existing framework for the interoperation of surveillance methods. In this paper, we present such a framework and report on a preliminary implementation. Our framework consists of a decomposition of the surveillance analysis task into sub-tasks, and an ontology of surveillance analysis methods, which automate the sub-tasks. As an initial implementation, we use methods developed according to this framework to analyze 911 dispatch data from San Francisco."
redux [01.22.03]
[requires 'free' registration]
"To help protect against the threat of bioterrorism, the Bush administration on Wednesday will start deploying a national system of environmental monitors that is intended to tell within 24 hours whether anthrax, smallpox and other deadly germs have been released into the air, senior administration officials said today.
The system uses advanced data analysis that officials said had been quietly adapted since the Sept. 11 attacks and tested over the past nine months. It will adapt many of the Environmental Protection Agency's 3,000 air quality monitoring stations throughout the country to register unusual quantities of a wide range of pathogens that cause diseases that incapacitate and kill."
redux [11.25.02]
"The Albuquerque physician-turned-researcher just returned from a trip to the NATO Summit in Prague, where he hoped to persuade President Bush and the other 19 member nations that a global health surveillance network is the best way to protect people from manufactured disease."
""The current system is exquisitely designed to fail," Zelicoff said."
redux [10.31.02]
"An epidemic resulting from an act of bioterrorism could be catastrophic. However, if an epidemic can be detected and characterized early on, prompt public health intervention may mitigate its impact. Current surveillance approaches do not perform well in terms of rapid epidemic detection or epidemic monitoring. One reason for this shortcoming is their failure to bring existing knowledge and data to bear on the problem in a coherent manner. Knowledge-based methods can integrate surveillance data and knowledge, and allow for careful evaluation of problem-solving methods. This paper presents an argument for knowledge-based surveillance, describes a prototype of BioSTORM, a system for real-time epidemic surveillance, and shows an initial evaluation of this system applied to a simulated epidemic from a bioterrorism attack."
redux [02.18.02]
"President George W. Bush, the National Homeland Defense Secretary, Tom Ridge, and Health and Human Services Secretary, Tommy Thompson visited the University of Pittsburgh (UP) yesterday to review one of the advanced developments in medical informatics - a collaboration of the University's Center for Biomedical Informatics and Carnegie Mellon University. The project, known as the Real-Time Outbreak and Disease Surveillance system (RODS), is an early warning system for outbreaks of disease designed to obtain and analyze existing sources of data in real time."
"The Real-time Outbreak and Disease Surveillance (RODS) system is a prototype public health surveillance system. RODS collects and analyzes relevant data automatically and in real-time, including emergency room registration data, microbiology culture results, reports of radiographs, and laboratory orders. RODS provides tools that (1) help detect the presence of a disease outbreak, and (2) support the characterization of that outbreak by a public health official. These tools include case definitions, automatic detection algorithms that can be attached to specific data streams, and data analytic tools that support temporal and spatial data analysis and visualization."
redux [06.29.01]
"The merits of linking two fields seemingly as disparate as geographic information systems (GIS) and bioinformatics might not seem obvious, but Virginia Tech's recent symposium linking the twoaeand its roster of renowned participants from both fieldsaehas raised expectations "Applications of GIS to Bioinformatics" was the first major public forum to cross-pollinate the disciplines, helping to fortify a relatively new, yet highly promising investigative area."
""As a result of new dialog between the fields, as we've had at this conference, we are gaining an important mechanistic link between individual-level processes tracked by genomics and proteomics and population-level outcomes tracked by GIS and epidemiology. This will allow us to do a far better job of monitoring, quantifying, and predicting human-health consequences associated with the environment. The potential payoff in related fields such as those looking at climate change, emerging and resurgent infectious diseases, and environmental health is enormous.""
"The meeting brings together researchers in two of the most dynamic analytical technologies-GIS and bioinformatics. The value of GIS analytical systems and data structures to bioinformatics are only now being recognized. Similarly, the methodologies used in bioinformatics can inform GIS scholars of new approaches to pattern recognition and analysis. The purpose of the symposium is to explore the potentials for using GIS as an analytical methodology in bioinformatics and to understand the opportunities bioinformatics presents to the GIS research community. The symposium, the first to focus on the interface between these two research areas, will afford scholars the opportunity to establish new research directions in both fields of investigation."
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Bio-ITWorld
Digging Into Digital Quarries
"SO YOU THINK you've found a cure for psoriasis. But first you need to check 12 million journal article abstracts on the National Library of Medicine's PubMed database, piling up at the rate of 40,000 new citations a month from 4,600 journals. You missed the latest issue of the Journal of Investigative Dermatology? PubMed's Medical Subject Headings (MeSH) vocabulary might help -- a little. It has 300,000 synonyms for 19,000 basic medical terms. But if you type in "epidermopoiesis," a key concept in the MeSH entry for psoriasis, you will find ... nothing.
Can software put an end to tortured searching? Researchers and vendors say text mining in the life sciences is on the verge of a long-sought dream: distilling oceans of inchoate data into insights and hypotheses."
redux [10.17.03]
[requires 'free' registration]
"MICHAEL N. LIEBMAN knows his limitations. Even with a Ph.D. and a long career in medical research, he cannot keep up with all the developments in his area of interest, breast cancer. Medline, the database that already houses more than 10 million abstracts for journal articles, is adding 7,000 to 8,000 abstracts per week. Only a fraction of these are about cancer, but the volume of information is daunting nonetheless."
"Yet Dr. Liebman is convinced that new cures could someday emerge for breast cancer if only someone could read all the literature and synthesize it. So he has found a solution: enlisting a computer program to read the articles for him."
redux [11.09.02]
"The analysis of large-scale genomic information (such as sequence data or expression patterns) frequently involves grouping genes on the basis of common experimental features. Often, as with gene expression clustering, there are too many groups to easily identify the functionally relevant ones. One valuable source of information about gene function is the published literature. We present a method, neighbor divergence, for assessing whether the genes within a group share a common biological function based on their associated scientific literature. The method uses statistical natural language processing techniques to interpret biological text. It requires only a corpus of documents relevant to the genes being studied (e.g., all genes in an organism) and an index connecting the documents to appropriate genes. Given a group of genes, neighbor divergence assigns a numerical score indicating how "functionally coherent" the gene group is from the perspective of the published literature. We evaluate our method by testing its ability to distinguish 19 known functional gene groups from 1900 randomly assembled groups. Neighbor divergence achieves 79% sensitivity at 100% specificity, comparing favorably to other tested methods. We also apply neighbor divergence to previously published gene expression clusters to assess its ability to recognize gene groups that had been manually identified as representative of a common function."
redux [10.08.01]
"The literature of the field of biology is the largest of all the sciences. The volume of biology literature each year, measured in bytes, is about fifty times the size of the entire human genome, junk and all. But locked in this literature is an enormous amount of information that can tell us much about the structure and function of genes, proteins, cells and organisms -- how they work as well as how they can fail.
The newly emergent interest in natural language processing for biology has been christened "Information Extraction". But work in this area has been going on for many decades under different names and this site includes a good deal of information about past and current work in NLP and in information extraction for biology in particular."
redux [04.30.01]
"Biologists in Norway have used a computer program to "read" the scientific literature and successfully predict gene interactions.
This data-mining of the "biobibliome" provides a way of dealing with the ever-increasing torrent of biological data - millions of papers a year. But even more impressively, the completely automated process can make new genetic discoveries - essentially free research."
"Annotating the tremendous amount of sequence information being generated requires accurate automated methods for recognizing homology. Although sequence similarity is only one of many indicators of evolutionary homology, it is often the only one used. Here we find that supplementing sequence similarity with information from biomedical literature is successful in increasing the accuracy of homology search results. We modified the PSI-BLAST algorithm to use literature similarity in each iteration of its database search. The modified algorithm is evaluated and compared to standard PSI-BLAST in searching for homologous proteins. The performance of the modified algorithm achieved 32% recall with 95% precision, while the original one achieved 33% recall with 84% precision; the literature similarity requirement preserved the sensitive characteristic of the PSI-BLAST algorithm while improving the precision."
"And the future of data-mining technology? Wide open, says Fayyad - especially as researchers begin to move beyond the field's original focus on highly structured, relational databases. One very hot area is "text data mining": extracting unexpected relationships from huge collections of free-form text documents. The results are still preliminary, as various labs experiment with natural-language processing, statistical word counts and other techniques. But the University of California at Berkeley's LINDI system, to take one example, has already been used to help geneticists search the biomedical literature and produce plausible hypotheses for the function of newly discovered genes."
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Bio-IT World
Scientific Computing: Apple's Next Big Leap?
"Tribble, one of the designers of the original Macintosh user interface, said that with the advent of the Power Mac G5 and the OS X operating system, the Macintosh now has the Unix backbone, 64-bit processing power, Windows interoperability, and open source credibility to be a viable computing platform in the life sciences space.
"Really, for the first time in this industry, you have a computer that can do all the scientific applications, and you can run Microsoft Office," he said. "It's been kind of a Holy Grail that started with Mac OS X.""
redux [10.15.03]
"Early benchmarks of Virginia Tech's brand new supercomputer -- which is strung together from 1,100 dual-processor Power Mac G5s -- may vault the machine into second place in the rankings of the worlds' fastest supercomputers, second only to Japan's monstrously big and expensive Earth Simulator."
""They're getting about 80 percent of the theoretical peak," Dongarra said. "If it holds, and it's unclear if it will, it has the potential to be the world's second most powerful machine.""
redux [09.12.03]
" 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.""
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SFGate
Intel fights cancer Diagnostic tools to assist Seattle research
center
"Intel Corp. is sharing technology originally developed to detect computer chip contaminants with a major Seattle cancer research center to help it detect subtle diagnostic markers for cancer and other diseases."
""The goal is to determine if this technology, previously used to detect microscopic imperfections on silicon chips, can also detect subtle traces of disease,'' said Andrew Berlin, the lead researcher in Intel's Precision biology program."
"Intel already uses a type of Raman analyzer to examine and detect defects in the transistors on its microchips, which are expected to approach 10 billionths of a meter (nanometer) in size by 2011, according to Andrew Berlin, the lead researcher with Intel's Precision Biology program.
Biological samples are much larger than this, said Berlin. Viruses, for example, tend to be in the 100 nanometer range, or about twice the size of the 50-nanometer transistors made using Intel's state-of-the-art 90 nanometer process, he said."
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BBC
Worms
hold 'eternal life' secret
"A tiny round worm can live six times longer than normal if certain genes and hormones are tweaked, according to a report in the journal Science."
"They went on to stay healthy and active for a human equivalent of 500 years, which is the longest life-span extension ever achieved by scientists."
"The researchers pointed out that the chief mechanism they tampered with - a signalling pathway involving insulin - was common in many species, including mammals.
But many people might find the price of immortality a little high. The worms with the longest lifespans also had their reproductive systems removed."
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Salon
How I decoded the human genome
"There were facts aplenty at the O'Reilly Bioinformatics Conference. Hundreds of millions of facts, as it turns out: every damn C or A or T or G for every damn critter under the sun was there; I felt like I was drowning in facts. And there were facts at the Whitehead Institute for Biomedical Research -- that part of the distributed Mecca of the Human Genome Project that's located in Cambridge, Mass. -- where I went next. And at the Hastings Center, the bioethical think tank in Garrison, N.Y."
"Facts were everywhere. But where was the genuine insight into ethical quandaries?"
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The New York Times
A New Kind of Genomics, With an Eye on Ecosystems
[requires 'free' registration]
"Determining the complete DNA sequence of a single species has become almost commonplace. It has been done for humans, mice, rice plants and a host of microbes, among others. Now some scientists are moving to a more audacious challenge, sequencing "metagenomes," the DNA of entire ecosystems."
""We think this is a window on biology that is really unprecedented in its implications," said Dr. Jo Handelsman, a professor of plant pathology at the University of Wisconsin, who coined the term metagenomics to refer to the new field. Others call it community genomics, environmental genomics, or microbial population genomics."
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indiatimes
TCS' biotech software on course for April launch
"Tata Consultancy Services (TCS) is on track to launch it's biotech software package 'Bio-Suite' by April '04. The software, which will be used in analysing and accelerating drug discovery processes, is being developed in partnership with the Council for Scientific and Industrial Research (CSIR)."
"The software consists of eight 'blocks' covering all aspects of computational biology ranging from genomics to structure-based drug design. In all, Bio-Suite encompasses more than 200 individual algorithms, and is designed to be highly modular so that new algorithms can be added as scientific advances take place."
redux [08.07.03]
"Sun Microsystems has made a proposal to the department of biotechnology to invest in bioinformatics projects in India and to collaborate with various R&D institutions under the department in this burgeoning area. DBT's Task Force on bioinformatics has asked to multinational to specify the quantum of investment and the specific areas of bioinformatics wherein alliances could be forged with Indian institutes."
Official sources said that the Centre for DNA Fingerprinting & Diagnostics, Hyderabad which has an alliance with software services major Tata Consultancy Services, would possibly be a nodal centre for the joint venture project with Sun."
redux [07.14.03]
"The report estimates that currently up to 10 per cent of investment in R&D is IT-related, and hence there is huge potential for Indian biotech and IT companies to enter into collaborative bioinformatics research with global pharma majors in the near term.
The report, however, indicated that despite India's IT capabilities, it may be difficuly to replicate this success in biotechnology as biotechnology differs from IT in many ways. Avendus suggests that Indian players will have to leverage upon the lower costs of infrastructure and human resources. The cost of setting up and running a bioinformatics company in India is a fraction of the cost in the US."
redux [03.18.03]
"Despite several strengths inherent, India's biotechnology industry is not able to take a quantum jump mainly due to lack of capital and low R&D spending, absence of industry-academic partnership and the mismatch between strategic research, product planning and effective collaboration.
The Associated Chambers of Commerce and Industry of India (Assocham) paper on Business of Biotechnology has pointed out that India has several options with the main focus on informatics. Bioinformatics is crucial for the advancement of the biotech industry by cutting the timeframe and costs in developing a product tremendously."
"Everyone in the room, from Sen. Hillary Rodham Clinton to Buffalo Mayor Anthony Masiello, was beaming at last week's announcement.
The news was that Asia's largest computer consultant has become a deep-pocket partner of the University at Buffalo. Under an agreement signed Monday, Tata Consultancy Services of India will partner with local researchers and help transform their discoveries into money-making products."
"But some in the tech community voiced concern that the state's $100 million-plus bioinformatics investment will wind up boosting the economy in Bombay instead of Buffalo."
redux [12.13.02]
[requires 'free' registration]
"India is set to reap substantial rewards in the field of functional genomics, thanks to an invaluable genetic resource and highly advanced IT expertise, predicts Samir Brahmachari, director of the country's Institute of Genomics and Integrative Biology in Delhi."
"Brahmachari sees India's genetic resource - not the biological samples themselves, but the associated information - as a tradable commodity. Data can be processed using India's unparalleled IT expertise, he says: The country's IT industry generated about $10 billion in revenues this year, and has continued to grow by 50% each year over the past decade. The information, once processed, represents an "intellectual-property protectable" commodity, he says."
redux [06.23.02]
"Also, India's success in information technology provides excellent opportunities in the field of bioinformatics.
"Traditional IT companies are translating their strong capabilities in data mining and warehousing to business models based on biological data," says the report, citing examples of IBM's India Research Lab and Satyam's five-year agreement with the Center for Cellular and Molecular Biology, Hyderabad."
redux [02.13.02]
"India's biotech boom could even dwarf software in coming years if you trust the most optimistic projections. Much of our $2.5-billion biotech market relies on low-end products like vaccines, but experts predict that as more start-ups come up, that could change dramatically."
"The need to dive into this ocean of genetic data for hidden treasures has created a whole new discipline--bio-informatics, the science of using information technology (IT) to decipher the genomic jumble. Thanks to a flourishing IT industry, bioinformatics is today the darling of venture capitalists, drug firms, and, of course, IT majors. So, Satyam Computers has signed a five-year alliance with CCMB to create, store, and annotate genetic databases, and it is angling for contracts from global bigpharma to sequence genes and build protein catalogs. Strand Genomics, a Bangalore-based bio-informatics start-up, is designing tools to accelerate drug discovery."
redux [09.17.01]
"India has the potential to garner 8-10 per cent of the global software market in the next few years from the current levels of just 1.5 per cent, but the country?s planners need to focus on improving computer penetration and use of Indian made software in the industry.
This was the view of FC Kohli, chairman, Tata Consultancy Services, while speaking at Connect 2001, an international conference and exhibition on information technology, communication technologies and bioinformatics, which opened on Thursday. Currently, India's IT exports are about $8.7 billion."
redux [08.27.01]
"THE mood is one of caution as far as bioinformatics is concerned. The beginning of the year saw hype building up around the fledgling industry as the next big gold rush for India.
But six months after the first bioinformatics seminar in the country, with the IT industry's lesson on hype fresh in mind, things are moving at a more sedate pace."
"In India, bioinformatics training institutes have already begun to mushroom. Bangalore and Hyderabad have around five private training institutes between them. However, the industry is sceptical about the quality of manpower these centres can supply because most of them have short-term courses offering basic skills, says Dr. Sabharwal. In all fairness to them she adds, "We need to wait for a few months to see the outcome of it all.""
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The Scientist
Individuality and Medicine
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"For complex diseases, we are entering the third phase of a multiphase process. The first was the sequencing of the genome; the second, identifying population variation, such as single nucleotide polymorphisms. Phase 3 is epidemiology: connecting genetic variation to future illness. Phase 3 is the biobank era."
"For some, the very concept of Biobanks is flawed. They characterize such projects as a politically motivated wild-goose chase in which inadequate medical records will produce all sorts of spurious leads. "Garbage in, garbage out," they say. However, let's not forget that phases 1 and 2, especially phase 1, took a great deal of criticism and came up trumps. There is a fair chance that phase 3 will do likewise."
redux [09.25.03]
""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]
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""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]
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"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."
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The New York Times
Digging for Nuggets of Wisdom
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"MICHAEL N. LIEBMAN knows his limitations. Even with a Ph.D. and a long career in medical research, he cannot keep up with all the developments in his area of interest, breast cancer. Medline, the database that already houses more than 10 million abstracts for journal articles, is adding 7,000 to 8,000 abstracts per week. Only a fraction of these are about cancer, but the volume of information is daunting nonetheless."
"Yet Dr. Liebman is convinced that new cures could someday emerge for breast cancer if only someone could read all the literature and synthesize it. So he has found a solution: enlisting a computer program to read the articles for him."
redux [11.09.02]
"The analysis of large-scale genomic information (such as sequence data or expression patterns) frequently involves grouping genes on the basis of common experimental features. Often, as with gene expression clustering, there are too many groups to easily identify the functionally relevant ones. One valuable source of information about gene function is the published literature. We present a method, neighbor divergence, for assessing whether the genes within a group share a common biological function based on their associated scientific literature. The method uses statistical natural language processing techniques to interpret biological text. It requires only a corpus of documents relevant to the genes being studied (e.g., all genes in an organism) and an index connecting the documents to appropriate genes. Given a group of genes, neighbor divergence assigns a numerical score indicating how "functionally coherent" the gene group is from the perspective of the published literature. We evaluate our method by testing its ability to distinguish 19 known functional gene groups from 1900 randomly assembled groups. Neighbor divergence achieves 79% sensitivity at 100% specificity, comparing favorably to other tested methods. We also apply neighbor divergence to previously published gene expression clusters to assess its ability to recognize gene groups that had been manually identified as representative of a common function."
redux [10.08.01]
"The literature of the field of biology is the largest of all the sciences. The volume of biology literature each year, measured in bytes, is about fifty times the size of the entire human genome, junk and all. But locked in this literature is an enormous amount of information that can tell us much about the structure and function of genes, proteins, cells and organisms -- how they work as well as how they can fail.
The newly emergent interest in natural language processing for biology has been christened "Information Extraction". But work in this area has been going on for many decades under different names and this site includes a good deal of information about past and current work in NLP and in information extraction for biology in particular."
redux [04.30.01]
"Biologists in Norway have used a computer program to "read" the scientific literature and successfully predict gene interactions.
This data-mining of the "biobibliome" provides a way of dealing with the ever-increasing torrent of biological data - millions of papers a year. But even more impressively, the completely automated process can make new genetic discoveries - essentially free research."
"Annotating the tremendous amount of sequence information being generated requires accurate automated methods for recognizing homology. Although sequence similarity is only one of many indicators of evolutionary homology, it is often the only one used. Here we find that supplementing sequence similarity with information from biomedical literature is successful in increasing the accuracy of homology search results. We modified the PSI-BLAST algorithm to use literature similarity in each iteration of its database search. The modified algorithm is evaluated and compared to standard PSI-BLAST in searching for homologous proteins. The performance of the modified algorithm achieved 32% recall with 95% precision, while the original one achieved 33% recall with 84% precision; the literature similarity requirement preserved the sensitive characteristic of the PSI-BLAST algorithm while improving the precision."
"And the future of data-mining technology? Wide open, says Fayyad - especially as researchers begin to move beyond the field's original focus on highly structured, relational databases. One very hot area is "text data mining": extracting unexpected relationships from huge collections of free-form text documents. The results are still preliminary, as various labs experiment with natural-language processing, statistical word counts and other techniques. But the University of California at Berkeley's LINDI system, to take one example, has already been used to help geneticists search the biomedical literature and produce plausible hypotheses for the function of newly discovered genes."
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Perl.Com
A Chromosome at a Time with Perl, Part 2
"In my previous article, A Chromosome at a Time with Perl, Part I, I showed you some programming "tricks" that help you avoid the trap of using up all your main memory when coding for very long strings, such as chromosomes and entire genomes."
"This article will continue that discussion. I'll show you more about how references can greatly speed up a subroutine call by avoiding making copies of very large strings. I'll show you how you can bypass the overhead of subroutine calls entirely. I'll extend the previous example of a buffer window into a large file, making it suited to any situation where you know the minimum and maximum length of a pattern for which you're searching. And I'll show you how to quantify the behavior of your code by measuring its speed and space usage."
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