{bio,medical} informatics
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GEN
IBM Discovery Could Shed New Light on Workings of the Human Genome
"IBM today announced its researchers have discovered numerous DNA patterns shared by areas of the human genome that were thought to have little or no influence on its function and those areas that do.
As reported today in the Proceedings of the National Academy of Sciences (PNAS), regions of the human genome that were assumed to largely contain evolutionary leftovers (called "junk DNA") may actually hold significant clues that can add to scientists' understanding of cellular processes. IBM researchers have discovered that these regions contain numerous, short DNA "motifs," or repeating sequence fragments, which also are present in the parts of the genome that give rise to proteins.
If verified experimentally, the discovery suggests a potential connection between these coding and non-coding parts of the human genome that could have a profound impact on genomic research and provide important insights on the workings of cells."
redux [03.27.06]
"Researchers at the McKusick-Nathans Institute of Genetic Medicine at The Johns Hopkins Medical Institutions in Baltimore, Md., have invented a cost-effective and highly efficient way of analyzing what many have termed "junk" DNA and identified regions critical for controlling gene function.
And they have found that these control regions from different species don't have to look alike to work alike."
redux [01.14.06]
[requires 'free' registration]
"More broadly, however, the team's findings suggest a new approach to teasing out the genetic basis of innate disorders that cannot be traced to simple protein-coding defects.
"There are about 30,000 genes in the human genome, but there are at least 150,000 different genetic disorders," Dr. Thakker said. "You can't just look at the genes that code for proteins, you've got to look at the surrounding regulatory regions, as well — the 'junk.' ""
redux [06.03.04]
"In a region of DNA long considered a genetic wasteland, Harvard Medical School researchers have discovered a new class of gene. Most genes carry out their tasks by making a product-a protein or enzyme. This is true of those that provide the body's raw materials, the structural genes, and those that control other genes' activities, the regulatory genes. The new one, found in yeast, does not produce a protein. It performs its function, in this case to regulate a nearby gene, simply by being turned on."
"Like many researchers, Winston and his colleagues may have known in the back of their minds that someday they would have to contend with junk DNA, but it was not their intention to map a new gene in those wild and relatively uncharted regions of the chromosome."
redux [05.07.04]
"If you thought we had explored all the important parts of our genome, think again."
"The segments, dubbed 'ultraconserved elements', lie in the large parts of the genome that do not code for any protein. Their presence adds to growing evidence that the importance of these areas, often dismissed as junk DNA, could be much more fundamental than anyone suspected."
redux [02.21.04]
"Genetic Technologies (GTG), the Australian biotech company at the heart of a controversy surrounding its patents on the genetic mapping applications of noncoding (junk) DNA, has added another large company to its tally of licensees -- Laboratory Corporation of America Holdings (LabCorp)."
"Last year, GTG granted licenses to Sequenom, Perlegen Sciences, Myriad Genetics, and Pyrosequencing, among others."
redux [11.18.03]
"Investors piled into Genetic Technologies yesterday after the biotech company announced that two US groups it was suing for patent infringement had settled out of court."
"The Melbourne-based Genetic Technologies has consistently warned it would sue any company, research institution or university that infringed its patent over the so-called junk DNA."
redux [08.18.03]
"An Australian biotech company, Genetic Technologies Ltd. (GTG), is stirring up controversy over its decision to enforce a series of patents, granted in the 1990s by the US Patent and Trademark Office, over the genetic diagnostic and mapping applications of non-coding, or junk, DNA."
"Scientists, including NHGRI chief Francis Collins and Sir John Sulston, are also upset over GTG's recent decision to ask academic institutions to sign research licenses."
redux [05.19.03]
[requires 'free' registration]
The dark side of the moon is a misnomer. Light reaches la luna's entire surface, but one half is unviewable from Earth. The human genome, the now essentially decoded map of life, likewise has a light side--the genes encoding mRNA and protein--and a dark side, which is coming into view for the first time. The dark side encompasses more than its opposite: The majority of the genome comprises intronic regions, stretches of repeat sequence, and other assorted gibberish that has attained the ignoble dubbing, "junk."
The first exploratory missions to the human genome's faceted surface are turning up traces regarding the extent of the junk."
redux [11.21.02]
"In a provisional patent application filed July 31, Pellionisz claims to have unlocked a key to the hidden role junk DNA plays in growth -- and in life itself.
Rather than being useless evolutionary debris, he says, the mysteriously repetitive but not identical strands of genetic material are in reality building instructions organized in a special type of pattern known as a fractal. It's this pattern of fractal instructions, he says, that tells genes what they must do in order to form living tissue, everything from the wings of a fly to the entire body of a full-grown human."
redux [08.28.02]
"In a new study in the August 29 issue of Nature, researchers at The Wistar Institute identify a cohesin-containing protein complex that reshapes chromatin to allow cohesins to bind to DNA. In doing so, they also identified the locations on the human genome where the cohesins bind. Somewhat to their surprise, the binding sites were found to be a repetitive DNA sequence found throughout the human genome for which no previous role had ever been identified. These bits of DNA, known as Alu sequences, are liberally represented along those vast stretches of the human genome not known to directly control genetic activity, sometimes referred to as junk DNA."
redux [08.09.02]
"Results of a new University of Michigan study suggest that junk DNA - dismissed by many scientists as mere strings of meaningless genetic code - could have a darker side.
In a paper published in the Aug. 9 issue of Cell, scientists from the U-M Medical School report that, in cultured human cancer cells, segments of junk DNA called LINE-1 elements can delete DNA when they jump to a new location - possibly knocking out genes or creating devastating mutations in the process."
"Scientists in the past decade have discovered that remnants of ancient germ line infections called human endogenous retroviruses make up a substantial part of the human genome. Once thought to be merely "junk" DNA and inactive, many of these elements, in fact, perform functions in human cells.
Now, a new study by John McDonald of the University of Georgia and King Jordan at the National Center for Biotechnology Information at the National Institutes of Health, suggests for the first time that a burst of transpositional activity occurred at the same time humans and chimps are believed to have diverged from a common ancestor - 6 million years ago."
redux [01.20.01]
[requires 'free' registration]
"Speaking at a National Institutes of Health conference on ethical and social issues in genetics, Dr. Francis Collins said that a "spate of papers in public journals'' due out within a month will signify the incredibly rapid pace of scientific discovery seen since the announcement of the nearly complete sequencing of the human genome last summer.
The first, Collins said, will be a paper that puts the total count of human genes at between 30,000 and 35,000. "That's less than half the number most people have been predicting.'' The second is a study ascribing previously unknown biological missions to genes scientists thought were inactive, or so-called "junk genes."
"There is now clear evidence that (the junk genes) have been performing a number of functions for tens or hundreds of thousands of years,'' he said."
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Seattle Times
Microsoft taking a measured approach
"Microsoft this month launched a cross-industry group to address data-management problems posed by personalized medicine and other computational biology tasks. The BioIT Alliance is an effort to establish the company's products at the foundation of a field that could see explosive growth in the next decade.
Today, however, the place where biology and computing intersect — alternately called computational biology, bioinformatics or digital bio — is inhabited by a small group of specialized scientists.
Don Rule, a Microsoft platform-strategy adviser organizing the BioIT effort, estimated 50,000 work in bioinformatics. It's the kind of niche Microsoft might be expected to ignore, but Rule said the company sees big potential."
redux [04.04.06]
"Microsoft on April 4 announced the formation of the BioIT Alliance, a cross-industry group created to enhance the ability to use and share biomedical data, at the Life Sciences Conference and Expo in Boston.
The working group will take on a series of "proof-of-concept" projects to understand how Microsoft's platforms can enhance the integration of the life sciences and IT."
redux [02.16.06]
"Microsoft is funding a Microsoft Institute for High-Performance Computing at Cornell with annual funding of $400,000, renewable each year for an indefinite period. The new institute will greatly expand the ability of researchers to work with huge databases of DNA sequences and protein composition and shapes, and explore new software and applications for the analysis of biological information."
"Ron Elber, professor of computer science and director of CBSU, also will be director of the new institute, and it will be managed by CTC senior research associate Jaroslaw Pillardy, who manages CBSU. "The support of Microsoft is very much appreciated," Elber said. "They have supported us before, but this increased support makes it possible for the CBSU to expand and to do more interesting things and larger things based on new software technology from Microsoft.""
redux [10.29.05]
"In all, bioinformatics is a field of research that has undergone a rapid explosion in terms of the numbers of tools and techniques that it has produced. While much of this progress can be attributed to the adaptability and flexibility of open source technologies such as Linux and Perl, it is important for bioinformatics professionals to consider that disseminating their bioinformatics tools to users can be as critical to scientific progress as developing new tools. A key way to facilitate the widespread dissemination of bioinformatics applications to biologists will likely be the development of an open sourced .NET class library to serve as framework for Windows-based bioinformatics applications."
redux [05.27.04]
"The Cornell Theory Center currently operates a cluster consisting of more than 900 processors based on Intel chips housed in Dell computers operating on Microsoft's Windows software. It represents the first steps in the development of Windows for a wide range of supercomputing applications.
Microsoft Research says its workshop brings together about 75 scientists to discuss data-intensive scientific computing as it pertains to Windows and .NET . The participants represent such fields as astronomy, material sciences, physics, archeology, oceanography, and bio-informatics and computational biology."
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HHMI
HHMI's Experiment in Changing Scientific Culture
"Today's academic and industrial research models have become far too conservative, according to Gerald M. Rubin, director of the Howard Hughes Medical Institute's Janelia Farm Research Campus."
"Traditional academic environments are suitable for a large proportion of research projects, but Rubin believes they can be too restrictive, stifling the kinds of creative, long-term projects that can lead to true breakthroughs. This is true, in part, he said, because the reliance on external funding sources forces scientists to define their research programs in advance when they apply for grants. By setting the course of the research plan up front, scientists are restricted in their ability to pursue questions and opportunities that arise during their studies. “The bulk of the scientific community is limited to projects that can be funded by peer-review committees, which tend to be very conservative,” Rubin said. “These grants have to be reviewed every three to five years. It makes it very difficult for people to take on high-risk, high-reward projects.”"
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N J Wildberger
Set Theory: Should You Believe?
"Modern mathematics doesn't make complete sense. The unfortunate consequences include difficulty in deciding what to teach and how to teach it, many papers that are logically flawed, the challenge of recruiting young people to the subject, and an unfortunate teetering on the brink of irrelevance.
If mathematics made complete sense it would be a lot easier to teach, and a lot easier to learn. Using flawed and ambiguous concepts, hiding confusions and circular reasoning, pulling theorems out of thin air to be justified `later' (i.e. never) and relying on appeals to authority don't help young people, they make things more difficult for them." [ via scitechdaily ]
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Genomics and Proteomics
Collaboration Can Advance Pharmacogenomics
"The problem thus far has been the lack of any systematic involvement from the major pharmaceutical companies. "The major initiatives for the development of new drugs come typically from the pharmaceutical industry," Weinshilboum says. "Up until recently, the pharmaceutical industry had very little in the way of incentives to include [pharmacogenomics] in what they did. That's not to say that there isn't an understanding in the industry of individual variations in the response, which range from lack of efficacy to adverse drug responses. But the only thing this offered the pharmaceutical industry in the past was market segmentation. That's not a very good incentive from a financial point of view."
Without investment and follow-up from pharmaceutical manufacturers, current pharmacogenomics research seems like a baseball pitcher throwing warm-up tosses to the catcher in perpetuity, with no batter in sight."
""The vigorous involvement of the FDA has gotten the attention of the pharma industry in a way that academic centers are not in a position to do," says Weinshilboum. "But whether or not it will be enough to incentivize the pharmaceutical industry is still an open question.""
redux [09.23.05]
"The promise of personalised medicines — tailored to a person's genes — have been "overhyped", particularly for developing countries, according to the UK's national science academy.
Healthcare based on 'pharmacogenetics' is likely to be decades away, especially in developing countries, due to gaps in scientific knowledge and a shortage of researchers equipped to study the link between genes and disease, says a report published by the Royal Society yesterday."
redux [08.04.05]
"Wolfgang Sadee, director of the pharmacogenomics programme at Ohio State University in Columbus, adds that it will be five years until drug companies fully embrace the field. "If we train people now," he says, "in five years they will be in the right position to help out."
The earlier approach of pharmacogenetics, which targets a single gene, has already scored some successes. Herceptin (trastuzumab), for example, treats breast cancer by targeting a single receptor on tumour cells that is overabundant in women who inherit a specific gene mutation. And the analysis of individual genes that affect drug metabolism has helped to improve efficacy.
With its emphasis on multiple genes and their expression patterns, pharmacogenomics extends the reach of its predecessor."
redux [02.12.03]
[requires 'free' registration]
""The need to incorporate the teaching of pharmacogenomics into the medical curriculum is quite urgent," said Gurwitz, who this academic year has launched such a course at Tel-Aviv University, which he hopes will stimulate other medical schools to follow. "Pharmacogenomics must be incorporated within a few years ... into the general MD curriculum," he said.
The consequence of not doing so, he says, could be that any therapeutic benefits of the Human Genome Project will be severely delayed. The next generation of doctors will not have an adequate understanding of the interplay between genetics and drug metabolism, he warns."
redux [01.07.03]
"Much like the giant Homer Simpson Pez dispenser in his office, John Quackenbush, PhD, dispenses tasty tidbits when he opens his mouth."
" I think if you review the microarray literature, everybody in the early days was saying, oh, we're going to find out what all the pathways are. And now I think everyone is realizing that what comes out of the arrays are associations. It's the whole link, the disjunction between correlation and causality. I may discover that mass murderers drink more milk than anybody else but that doesn't mean drinking milk makes you a mass murderer."
redux [12.17.02]
"Investors may have stopped watching, but drug companies are finally beginning to wrench tangible benefits from the human genome. Two years after a boom fed by hype, a revolution finally is starting to take hold not in how drugs are invented, but in how they are tested.
Merck (nyse: MRK - news - people ), the world's third-largest drug company, is using gene expression arrays, also known as DNA chips, to keep clinical duds from reaching expensive animal or human trials. Separately, Millennium Pharmaceuticals (nasdaq: MLNM - news - people ) used similar chips in its late-stage clinical studies of its cancer drug, Velcade. Millennium's work is a big step toward so-called personalized medicine, in which treatment would be tailored toward individual patients based on genetic makeup."
redux [10.07.02]
[requires 'free' registration]
"Pharmacogenomics holds the promise of delivering safer, better designer drugs--and profits--to pharmaceutical manufacturers. But the technology also poses a challenge to the industry's current, highly successful business model that relies on one-size-fits-all blockbuster drugs.
For small biotech companies and large drug manufacturers alike, pharmacogenomics remains only one component of genome-based research and consumes only a small part of the $30 billion (US) in annual pharmaceutical research and development funding, according to the Pharmaceutical Research and Manufacturers of America (PhRMA). "It's an area where we are seeing movement, but it's not there yet," says Gillian Woollett, associate vice president for biologics and biotechnology at PhRMA."
redux [09.10.02]
"Collins is unimpressed by the hubbub that has shaken the industry lately. "In some quarters there was a misunderstanding, or naivete, about how having the sequence was going to solve everything. And there were some business models built solely upon the notion of quick profits, particularly selling subscription databases."
He dismisses talk about a foundering industry. "I think that every pharmaceutical company is still expecting that genomics will be the platform upon which they will build the next generation of drugs," says Collins. Others echo Collins' perspective. "We will change the treatment of cancer," says Variagenics' Adams. And there is no hint of doubt in his voice."
redux [08.08.01]
"Pharmacogenomics requires the integration and analysis of genomic, molecular, cellular, and clinical data, and thus offers a remarkable set of challenges to biomedical informatics. These include infrastructural challenges such as the creation of data models and data bases for storing this data, the integration of these data with external databases, the extraction of information from natural language text, and the protection of databases with sensitive information. There are also scientific challenge in creating tools to support gene expression analysis, three-dimensional structural analysis, and comparative genomic analysis. In this review, we summarize the current uses of informatics within pharmacogenomics, and show how the technical challenges that remain for biomedical informatics are typical of those that will be confronted in the post-genomic era."
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The New York Times
Taking the Least of You
[requires 'free' registration]
"Though he died 21 years ago, Slavin is worth keeping track of. Not because his cells produced extremely valuable proteins that were important for scientific research. But because Slavin's relationship to those cells was unique: they weren't just part of his body; they were his business, his property. Slavin was one of the first people in history to decide that contrary to the way things usually work in science, he would maintain complete control over any blood and tissues removed from his body. He would determine who used them for research, how and, most important to Slavin, who made money from them.
This may not sound like a particularly groundbreaking idea, unless you consider it with a little-known fact: blood samples and other excised human tissues have an afterlife. When you go to the doctor for a routine blood test or mole removal, when you have an appendectomy, tonsillectomy or any other kind of ectomy, the stuff you leave behind doesn't always get thrown out. Doctors, hospitals and laboratories keep them. Often indefinitely."
redux [09.12.05]
"RESEARCHERS in Western Australia have created a vast population database containing 17.5 million records of highly sensitive personal information about 3.6 million of the state's residents.
Next, they're planning to build a BioBank - a human genetics database containing the DNA of every consenting adult in the state. That will propel WA into the global bioinformatics research marketplace."
[Democrats Senator Natasha Stott Despoja] said there was great therapeutic potential in the analysis of DNA through databases and BioBanks, but there were also "frightening" privacy and ethical implications."
redux [10.19.03]
[requires 'free' registration]
"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]
[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."
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People's Daily Online
Chinese science journals go global
""Although much of our research and clinical data has been published domestically, most of it is inaccessible to foreign researchers," said Peng.
As a result, the significant scientific breakthrough has been greeted with indifference or suspicion by many foreign researchers, according to a recent article in the UK-based journal Nature Reviews Drug Discovery."
"Various attempts have been made to promote Chinese research, such as publishing English versions of the Chinese journals, establishing international reviewers' boards, distributing the Chinese journals internationally.
The most recent move towards promotion took place late last month. Under a package deal, China's 34 leading English science journals were collected into ScienceDirect, an online academic database operated by the Amsterdam-based publishing giant Elsevier."
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ITBusiness.ca
Unleashed Informatics goes on the offense to protect IP
"A company that started out as a life sciences IT project within a Canadian hospital has entered the commercial market by warning competitors to take their hands off its intellectual property.
Unleashed Informatics has given a deadline of June 1 to any for-profit firm that is selling a software product or service that falls under its patent, which is described as a “System for electronically managing, finding, and/or displaying biomolecular interactions.”"
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Yale Daily News
Professors develop computer technology
" Professors in the math and computer science departments have developed a new memory technology system that Pixar Animation Studios utilized during the production of their upcoming film "Cars," which is scheduled to debut on June 9. The team, led by computer science professor Steven Zucker and mathematics professor Steven Orszag, is also currently working on the creation of a new data organization structure that will, for example, make Internet searches on google.com more successful."
"This will help solve problems in I/O bound computing, like data mining," he said. "Data mining is any sort of problem where you have to extract data from large data sets, like in bioinformatics, or with large computations in other areas like fluid mechanics and materials design. But these problems also arise throughout commerce and industry, so, for example, it can affect multimedia access and even movie making. The applications involve using this newfound capability of rapidly accessing very large data sets to address scientific problems that involve very large amounts of data.""
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The Tribune
Bioinformatics a well-informed choice
" In addition, India’s human gene pools offer an exciting opportunity for genomic research. In recent years, the government has funded around 52 centres across the country to collect data relating to the Indian genotype. Given India’s expertise in IT and its tradition of academic excellence in the disciplines of basic sciences, particularly in mathematics, bioinformatics is the ideal subject for Indian science students. Jamshed Tata, a senior scientist with the Medical Research Council at the National Institute of Medical Research, London, has noted “India has a large pool of well-educated and computer literate people. Bio-informatics should be the next success story for Indian science and technology.’’"
redux [07.27.05]
"The Indian bioinformatics market has the potential to increase its current share of 2.5% to 5% of the global market, according to a report prepared by the Confederation of Indian Industry (CII) and the Department of Information Technology (DIT)."
"Painting a rosy picture, the report states that 42% of the sample companies are planning to increase the scale of businesses because they are investing more in R&D and product development. It also adds that for expanding operations, there will be a huge surge in the demand for bioinformaticians."
redux [03.22.04]
"It was touted as one of the biggest markets Indian software companies could address. But somewhere along the way, the market scenario has changed and today only a few focused companies are still looking at bioinformatics as the next big opportunity, says Srikanth R P."
"While the market potential for bioinformatics is huge few Indian companies have the skill sets or the ability to capture a significant share of the market."
redux [02.23.04]
"Indian pharmas are also waking up to the fact that 'ripping off' patented drugs is becoming more difficult with 'legit piracy' no longer a real option. It's in this changed scene that India plans to make a splash.
A well-developed base industry such as pharma gives India a distinct advantage over others in the biotech boom. It already has a good network of research labs and scores of bioinformatic units have been set up by IT companies across the country. Add to these a rich biodiversity and access to diverse disease populations, and India is ready to ride the wave. At the forefront of this 'petri-dish revolution' will be drug companies -- especially those that manage to add bioinformatics to the already existing arsenal of molecule'n'mortar process."
redux [02.11.04]
"Software major Sun Microsystems would set up a Centre of Excellence (CoE) for medical bio-informatics at Centre for DNA Fingerprinting Analysis and Development (CDFD) here. The CoE would help in analysis, storage of biological research in areas like genomics, structural biology and molecular evolutionary genetics."
"The proposed CoE is the ninth major medical bio-informatics centre established by Sun in the world and first in India."
redux [10.20.03]
"Tata Consultancy Services (TCS) is on track to launch it's biotech software package 'Bio-Suite' by April '04. The software, which will be used in analysing and accelerating drug discovery processes, is being developed in partnership with the Council for Scientific and Industrial Research (CSIR)."
"The software consists of eight 'blocks' covering all aspects of computational biology ranging from genomics to structure-based drug design. In all, Bio-Suite encompasses more than 200 individual algorithms, and is designed to be highly modular so that new algorithms can be added as scientific advances take place."
redux [08.07.03]
"Sun Microsystems has made a proposal to the department of biotechnology to invest in bioinformatics projects in India and to collaborate with various R&D institutions under the department in this burgeoning area. DBT's Task Force on bioinformatics has asked to multinational to specify the quantum of investment and the specific areas of bioinformatics wherein alliances could be forged with Indian institutes."
Official sources said that the Centre for DNA Fingerprinting & Diagnostics, Hyderabad which has an alliance with software services major Tata Consultancy Services, would possibly be a nodal centre for the joint venture project with Sun."
redux [07.14.03]
"The report estimates that currently up to 10 per cent of investment in R&D is IT-related, and hence there is huge potential for Indian biotech and IT companies to enter into collaborative bioinformatics research with global pharma majors in the near term.
The report, however, indicated that despite India's IT capabilities, it may be difficuly to replicate this success in biotechnology as biotechnology differs from IT in many ways. Avendus suggests that Indian players will have to leverage upon the lower costs of infrastructure and human resources. The cost of setting up and running a bioinformatics company in India is a fraction of the cost in the US."
redux [03.18.03]
"Despite several strengths inherent, India's biotechnology industry is not able to take a quantum jump mainly due to lack of capital and low R&D spending, absence of industry-academic partnership and the mismatch between strategic research, product planning and effective collaboration.
The Associated Chambers of Commerce and Industry of India (Assocham) paper on Business of Biotechnology has pointed out that India has several options with the main focus on informatics. Bioinformatics is crucial for the advancement of the biotech industry by cutting the timeframe and costs in developing a product tremendously."
redux [12.13.02]
[requires 'free' registration]
"India is set to reap substantial rewards in the field of functional genomics, thanks to an invaluable genetic resource and highly advanced IT expertise, predicts Samir Brahmachari, director of the country's Institute of Genomics and Integrative Biology in Delhi."
"Brahmachari sees India's genetic resource - not the biological samples themselves, but the associated information - as a tradable commodity. Data can be processed using India's unparalleled IT expertise, he says: The country's IT industry generated about $10 billion in revenues this year, and has continued to grow by 50% each year over the past decade. The information, once processed, represents an "intellectual-property protectable" commodity, he says."
redux [06.23.02]
"Also, India's success in information technology provides excellent opportunities in the field of bioinformatics.
"Traditional IT companies are translating their strong capabilities in data mining and warehousing to business models based on biological data," says the report, citing examples of IBM's India Research Lab and Satyam's five-year agreement with the Center for Cellular and Molecular Biology, Hyderabad."
redux [02.13.02]
"India's biotech boom could even dwarf software in coming years if you trust the most optimistic projections. Much of our $2.5-billion biotech market relies on low-end products like vaccines, but experts predict that as more start-ups come up, that could change dramatically."
"The need to dive into this ocean of genetic data for hidden treasures has created a whole new discipline--bio-informatics, the science of using information technology (IT) to decipher the genomic jumble. Thanks to a flourishing IT industry, bioinformatics is today the darling of venture capitalists, drug firms, and, of course, IT majors. So, Satyam Computers has signed a five-year alliance with CCMB to create, store, and annotate genetic databases, and it is angling for contracts from global bigpharma to sequence genes and build protein catalogs. Strand Genomics, a Bangalore-based bio-informatics start-up, is designing tools to accelerate drug discovery."
redux [08.27.01]
"THE mood is one of caution as far as bioinformatics is concerned. The beginning of the year saw hype building up around the fledgling industry as the next big gold rush for India.
But six months after the first bioinformatics seminar in the country, with the IT industry's lesson on hype fresh in mind, things are moving at a more sedate pace."
"In India, bioinformatics training institutes have already begun to mushroom. Bangalore and Hyderabad have around five private training institutes between them. However, the industry is sceptical about the quality of manpower these centres can supply because most of them have short-term courses offering basic skills, says Dr. Sabharwal. In all fairness to them she adds, "We need to wait for a few months to see the outcome of it all.""
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Technology Review
Gene Hunting in Canada
In the 17th century, 15,000 French immigrants bravely made their way to eastern Canada. Some headed further west, many returned to France, but a hardy few stayed in Quebec. Starting with a total of just 2,600 people between 1608 and 1760, this group would grow 800-fold over the next 10 or so generations, with little marriage outside the group. The result is the Quebec "founder" population -- a genetically homogenous group of individuals that is ideally suited to the genetic study of disease."
"Today's best-known gene-hunting company, deCODE genetics, an Icelandic gene and drug discovery company, has identified genes for diabetes, heart disease, and asthma within the small Icelandic population. Now a biotech company, Genizon BioSciences, is finding similar success with the French Canadians of Quebec. Based in Quebec, the company is taking advantage of new advances in genomics to find disease genes that have been hard to detect with other methods."
redux [01.16.06]
[requires 'free' registration]
"Scientists have discovered a variant gene that leads to a sizable extra risk of Type 2 diabetes and is carried by more than a third of the American population.
The finding is being reported today in the journal Nature Genetics by researchers at Decode Genetics, a company in Reykjavik, Iceland, that specializes in finding the genetic roots of human diseases. Decode Genetics first found the variant gene - one of many different versions that exist in the human population - in Icelanders and has now confirmed the finding in a Danish and an American population."
redux [06.08.04]
"Researchers on a hunt for the causes of obesity are looking for clues in the genetic makeup of 3,000 inhabitants of the Micronesian island of Kosrae in the western Pacific.
Gene hunters from Rockefeller University announced Monday that they will use gene chips developed by Affymetrix in Santa Clara to look through hundreds of thousands of variations in the genetic code of the Kosrae population to discover why most of them are seriously overweight -- and why others on the island are not."
redux [02.09.04]
"AN INTERSTATE biotech company owns intellectual property rights in research from DNA donated by Tasmanians.
The IP deal was behind the collapse of the original $20 million Intelligent Island Bioinformatics Centre for Excellence.
The bioinformatics centre was going to have to pay to use the information."
redux [03.10.03]
"The newest resources "discovered" in Estonia are the genes of its 1.4 million citizens. The country's government and a Silicon Valley start-up called EGeen International are treating the Estonian gene pool as a commodity to be exploited for medical research and profit.
EGeen owns the exclusive commercial rights to data from the Estonian Gene Bank Project. In March the bank will begin a full-scale effort to collect blood samples and medical histories that will help scientists understand Estonians from the inside out."
redux [02.17.01]
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"A good gene pool, like love, is where you find it. Now genomics researchers have two new ones to swoon over: one from Estonia, a crossroads of Scandinavian cultures and the northernmost of the former Soviet Union's Baltic republics; and from Tonga, an island kingdom half a world away where a Polynesian people has lived in near-perfect isolation for close to 3,500 years. Tonga and Estonia laid final plans last November and December, respectively, for national gene pool exploration programs aimed at discovering disease-associated genes and developing therapies based on the discoveries.
They follow the trail blazed by Iceland, where for several years the gene pool of 275,000 Icelanders has been the fishing preserve of Reykjavik-based deCODE Genetics which is hunting for gene variants that affect serious, often chronic diseases by finding statistical links between Icelanders' genotypes and their inherited illnesses."
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Bio-IT World
Spearheading the Semantic Web
"Sharing their passion for the Semantic Web at the Bio-IT World Life Sciences Conference + Expo session on Tuesday were several prominent leaders of the movement.
Providing a clinical perspective was Tonya Hongsermeier of Partners Healthcare, who said the Semantic Web is necessary for knowledge management because “the market is balking at healthcare inflation.” She said eight datapoints are now kept for each patient (age, height, weight, etc.), but with new tests and personalized medicine, the number could balloon to 3000. The Semantic Web can reduce the cost and liability of knowledge management, said Hongsermeier, and is a critical component of translational medicine going forward."
redux [09.29.05]
"The research histories of both biology and ontologies originate with the philosopher Aristotle. For 2,400 years, the two subjects have taken separate paths. Now, with the rise of bioinformatics, they are reunited in the 'hot' research topic of biological ontologies. So why are biological ontologies important? As more and more biological data are stored on computers, the problem of efficient retrieval and analysis of these data becomes the most important scientific bottleneck, and the problem is particularly acute in biology because biological data are notorious for their complex form and semantics. Ontologies can help because they embody the abstract knowledge required for data integration and analysis. The utility of ontologies has been clearly demonstrated in several biological domains (e.g., Gene Ontology1). However, within biology, the enthusiasm for ontologies has been accompanied by a general lack of awareness of what exactly ontologies are and how to use them. This lack of awareness is reflected in the fact that many, perhaps all, 'bio-ontologies' fail to follow international standards for ontology design and description. This failure is important because it places a serious restriction on their applicability to knowledge sharing, reuse and inference.
In this article, we analyze the current state of application of ontologies in biology, try to reveal the reasons for the existing difficulties, recommend a possible solution to the current problems and describe prospects and future challenges for the application of ontological engineering in biological domains."
[ via nodalpoint ]redux [03.17.02]
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"The great challenge in biological research today is how to turn data into knowledge. I have met people who think data is knowledge but these people are then striving for a means of turning knowledge into understanding. Knowledge and science are related words and to know, I believe, is to understand. Before rushing to convert genomics to 'genamics' and finding that it is another dead end, we should consider evacuating the Tower of Babel. We need a theoretical framework in which to embed biological data so that the endless stream of data, filled with the flotsam and jetsam of evolution, can be sifted and abstracted.
Very simply, the network we should be interested is not the network of names but the network of the objects themselves. The language of these objects is not the Oxford Dictionary of Molecular Biology--the Ontology Consortium's main source--but that of molecular recognition, the language of molecular biology itself."
redux [01.08.02]
"Research directed toward discovering how genetic factors influence a patient's response to drugs requires coordination of data produced from laboratory experiments, computational methods, and clinical studies. A public respository of pharmacogenetic data to which investigators from different centers can contribute will facilitate hypothesis generation for further research. We are developing a pharmacogenetics knowledge base (PharmGKB) that will support storage and retrieval of experimental data and conceptual knowledge. We are confronted with the challenge of designing an Internet-based resource that integrates complex biological, pharmacological, and clinical data in such a way that researchers can submit their data and users can retrieve information that supports genotype phenotype correlations. Successful management of the names, meaning, and organization of concepts used within the system is crucial. We have selected a frame-based knowledge-representation system for development of an ontology of concepts and relationships that represent the domain and that will permit storage of experimental data. Preliminary experience shows that the ontology we have developed for gene-sequence data submissions is appropriate for experimental data that researchers will enter."
redux [06.27.01]"Ontologies are specifications of the concepts in a given field and the relationships among those concepts. The development of ontologies for molecular-biology information and the sharing of those ontologies within the bioinformatics community are central problems in bioinformatics. If the bioinformatics community is to share ontologies effectively, ontologies must be exchanged in a form that uses standardized syntax and semantics. This paper reports on an effort among the authors to evaluate a number of alternative ontology-exchange languages, and to recommend one or more languages for use within the larger bioinformatics community. The study selected a set of candidate languages, and defined a set of capabilities that the ideal ontology-exchange language should satisfy. The study scored the languages according to the degree to which they provided each capability. In addition, the authors performed several ontology-exchange experiments with the two languages that received the highest scores: OML and Ontolingua. The result of those experiments, and the main conclusions of this study, was that the frame-based semantic model of Ontolingua is preferable to the conceptual graph model of OML, but that the XML-based syntax of OML is preferable to the Lisp-based syntax of Ontolingua."
"Suppose that in order to use the appliances in your kitchen, an electrical engineer needs to tear down the wall and splice in wiring for the appropriate voltage converter."
Then suppose you're running a restaurant out of that kitchen.
That, according to those in the know, is what it's like to work with life-science information today, where the absence of a common programming language makes coordination between researchers a dicey prospect."
Enter IBM, which is spearheading an effort to write that common language using XML.
redux [05.23.01]"The Interoperable Informatics Infrastructure Consortium (I3C) unveiled its first demonstration of a working protocol Tuesday at the BIO 2001 Conference."
The XML-driven format allowed the exchange and analysis of sequence data across 10 different organizations? products. I3C views the demonstration as a bridge to the next step to defining components needed for a more general open architecture."
"The new coalition, led by the Biotechnology Industry Organization (BIO), a Washington trade group, plans to spend the next year or so creating a detailed specification for biological data. This specification would be available without fee to any company or scientist that wanted to use it to help organize and mine information."
The project has been dubbed the Interoperable Informatics Infrastructure Consortium, or I3C."
redux [02.21.01]
"Sun Microsystems said Wednesday it would partner with the Biotechnology Industry Organization, the National Cancer Institute, and several commercial bioinformatics vendors to support a collaborative effort to develop an open platform for the life sciences based on Java and XML.
The proposed initiative, temporarily referred to as Life Force or LI4 (Lifescience Informatics Interoperability Infrastructure Initiative) aims to develop an open platform to support data integration and interoperability and to focus the growing number of standards efforts"
"Sun intends to contribute the underlying infrastructure for the open platform, which the company hopes will form the eventual hub for a broad variety of life science computing needs, including bioinformatics, cheminformatics, genomics, proteomics, pharmacogenomics, metabolomics, and clinical informatics."
redux [03.15.01]
"Small DNA-laden wafers have transformed biology. Using these DNA chips, geneticists can see which genes are turned on, or expressed, in a cell at a particular time. Such gene expression experiments allow bioscientists to diagnose different diseases, quickly screen thousands of drug candidates for efficacy and safety and even learn the functions of newly discovered genes.
"Small DNA-laden wafers have transformed biology. Using these DNA chips, geneticists can see which genes are turned on, or expressed, in a cell at a particular time. Such gene expression experiments allow bioscientists to diagnose different diseases, quickly screen thousands of drug candidates for efficacy and safety and even learn the functions of newly discovered genes.
Sharing this information over the Web could lead to an explosion in biological knowledge. But each experiment generates gigabytes of data written in one of several formats, depending on the type of chip used. And with dozens of chips on the market and hundreds of ways to analyze the d