{bio,medical} informatics
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Genomeweb
San Diego Supercomputer Center Using Entropia Grid to Build
Protein-Structure Databases
"A research team at the San Diego Supercomputer Center is using a grid-based computer system from Entropia to build a set of protein structure databases."
"With the help of 250 desktop computers with processing power ranging from 180 MHz to 2.2 GHz, the platform has so far completed calculations on almost 1,000 proteins, said Elbert."
""What they've done in principle they could have done on one of their supercomputers, but those machines are heavily used for other projects," he said. "This is a way of expanding capacity. And it's a whole lot cheaper.""
redux [11.28.01]
"IBM will supply the University of Pennsylvania and four hospitals with computers that will link into a computing "grid" to check for breast cancer, the company will announce Wednesday.
The grid will be used to detect breast cancer in patients, store mammograms in digital form and identify populations that are particularly susceptible, the company said in a statement. The system can be used, for example, to compare a new mammogram to a previous year's image to detect changes.
IBM, along with rivals such as Sun Microsystems and Compaq Computer, have been backing grid computing, which joins computers and storage systems into a large pool of computing power.
redux [11.21.01]
"The US National Science Foundation has announced a $12 million programme - called the NSF Middleware Initiative (NMI) - to develop middleware: software that allows scientists to share applications, scientific instruments and data, and collaborate with their colleagues across high-performance networks.
The effort will build on the success of the Globus project in developing middleware tools for grid computing, and will integrate Globus and other emerging middleware components into a well-tested, comprehensive, commercial-quality, middleware distribution package that runs on multiple platforms. These middleware distributions will be disseminated to research labs and universities worldwide."
redux [11.12.01]
"Platform Computing, a company that tries to harness the collective computing power on computer networks, has signed a deal to commercialize an open-source supercomputing project.
Platform is working with the Globus Project to commercialize the Globus Toolkit for governing the use of computers and storage systems joined into a large computing "grid," Platform said Wednesday."
"Grid computing, though, often uses higher-powered computers than mere desktop PCs, and has attracted the interest of IBM, which thinks corporate customers as well as academics will use grid methods. IBM is working with Globus to boost this expansion.
Grid computing has long held potential for some types of computing tasks--typically those that don't require as much communication between one computing task and another. For this reason, they don't replace single mammoth supercomputers such as those from Cray. However, grid computing is popular among pharmaceutical companies and others."
"Computational Grids are emerging as a popular paradigm for solving large-scale compute and data intensive problems in science, engineering, and commerce. However, application composition, resource management and scheduling in these environments is a complex undertaking. In this paper, we illustrate the creation of a virtual laboratory environment by leveraging existing Grid technologies to enable molecular modeling for drug design on distributed resources. It involves screening millions of molecules of chemical compounds against a protein target, chemical database (CDB) to identify those with potential use for drug design. We have grid-enabled the molecular docking process by composing it as a parameter sweep application using the Nimrod-G tools. We then developed new tools for remote access to molecules in CDB small molecule database. The Nimrod-G resource broker along with molecule CDB data broker is used for scheduling and on-demand processing of jobs on distributed grid resources. The results demonstrate the ease of use and suitability of the Nimrod-G and virtual laboratory tools."
redux [04.04.01]
[requires 'free' registration]
"Intel is providing equipment and software downloads for a project in which volunteers are donating spare home computer cycles to a Stanford University project studying the protein-folding process. The project, Folding@Home, was the first to model successfully a complete protein fold - a task not even achieved by supercomputers."
""We want to increase the value of the PC," said Scott Griffin, Intel's program manager. "The PC is there when people aren't at it, like when they are in meetings. A great thing about this is you get every day users involved in research that they care about. Not only do they get to help out, but they get to help cure these terrible diseases.""
redux [09.23.01]
"IBM is spending $100 million building the world's fastest supercomputer to do cutting-edge medical research, but a distributed computing effort running on ordinary PCs may have beaten Big Blue to the punch.
IBM's proposed Blue Gene , a massively parallel supercomputer, in hopes to help diagnose and treat disease by simulating the ultra-complex process of protein folding.
"But Folding@Home , a modest distributed computing project run by Dr. Vijay Pande and a group of graduate students at Stanford University, has already managed to simulate how proteins self-assemble, something that computers, until now, have not been able to do."
redux [10.09.00]
"The SETI@Home problem can be thought of as a special case of the distributed computation verification problem: "given a large amount of computation divided among many computers, how can malicious participating computers be prevented from doing damage?" This is not a new problem. Distributed computation is a venerable research topic, and the idea of "selling spare CPU cycles" has been a science fiction fixture for years."
"The Internet makes it possible for computation to be distributed to many more machines. However, distributing computing around the internet requires developers to consider the possibility of malicious clients."
"The general study of secure multiparty computation has produced much interesting work over the last two decades. Less well studied, unfortunately, are the tools and techniques required to move the theoretical results to the real world. The old dream of massively distributed computations is finally coming true, and yet our tools for building and analysing real systems still seem primitive. The challenge of the next few years will be to bridge this gap."
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MIT Technology Review
Big Patents on Campus
"Originally a boon to medical schools and engineering programs, Bayh-Dole increasingly benefits new fields of research, says Judith Scholz, who directs the University of Manitoba's industry liaison office, and is president of the Association of University Technology Managers. "There's much more going on in information technology and software, and for many institutions that's relatively new," she says. But tech transfer offices must be nimble, she says; where a medical device often takes a decade to reach the market, software innovations may be obsolete before the ink on their licensing agreement is dry. Interdisciplinary fields such as bioinformatics pose additional problems, she adds, to technology managers who are unsure how--or what--to patent."
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EurekAlert
Essential cell division 'zipper' anchors to so-called junk
DNA
"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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Stanford Medical Informatics Preprint Archive
Emerging Scientific Applications in Data Mining
"Recent progress in scientific and engineering applications has accumulated huge volumes of high-dimensional data, stream data, unstructured and semi-structured data, and spatial and temporal data. Highly scalable and sophisticated data mining tools for such applications represent one of the most active research frontiers in data mining. Here, we outline the related challenges in several emerging domains."
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Genomeweb
School of Informatics moving into its envisioned role at IU
"Three years after Indiana University launched its School of Informatics, the school is growing into the role that officials envisioned."
"Perhaps most significantly, the number of IU informatics majors topped 1,100 this year, almost triple what it was a year earlier."
"The Bloomington campus had its first informatics classes in 2000 and offers master's degrees in bioinformatics, chemical informatics and human-computer interaction. Undergraduate majors study informatics along with a "cognate area" such as computer science, economics and telecommunications."
redux [08.06.02]
"The number of card-carrying bioinformaticists entering the job market more than tripled in 2002, according to a recent survey of US university degree programs."
"This new wave of graduates -- not to mention their prospective employers -- are the first beneficiaries of the remarkable growth seen over the last few years in the number of degree programs: While only six dedicated bioinformatics-degree programs existed before 1997, 13 universities added new programs in 2001, and seven schools are adding bioinformatics-related degrees in 2002."
redux [10.05.01]
"Almost all companies say they're having trouble finding people with expertise in bioinformatics, the use of computers to solve complex biological problems. The human genome's mapping has ushered in a new era of genetic medicine, but to capitalize on this knowledge, researchers need to know how to use powerful computers to translate raw biological data into information useful for developing new therapies.
"There's a struggle to have people that are well educated in both computer science as well as biology," said David Pot , InforMax's director of application sciences. "We recognize we need super scientists, but those super scientists don't have the training to write super software.""
redux [03.05.01]
"Move over Information Age. Make room for the age of bioinformation.
Experts have already dubbed bioinformatics - a hybrid profession pairing biology and computer science - the career choice of the decade.
"There is a crying need for experts in bioinformatics and this is not something that will just fade away," said Dr. Leena Peltonen, chairwoman of the Department of Human Genetics at UCLA."
redux [05.10.00]
" "The results of our current survey make it clear that the majority of these jobs are not being filled by graduates of formal programs - who by our count represent about 15 percent of the positions advertised in 1997. And, we believe the 15 percent figure to be an overestimate given that ads have been growing over time and our most recent ad count is for 1997, a year earlier than our hiring data. This leads us to infer that most of the advertised positions are being filled by individuals trained in informal programs and by individuals who change jobs. The distinct possibility exists that a number of these jobs remain vacant for a period of time, an issue not studied here. Furthermore, our pipeline estimates (see Table 2) lead us to conclude that the number of individuals currently enrolled in formal programs falls far short of the number of positions that have recently been advertised." "
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Bio-IT World
Beyond Bioinformatics
""Is there a future for bioinformatics companies?" Leroy Hood, director of the Institute for Systems Biology, asked rhetorically in his keynote address at the Sixth International Biotech & Infotech Summit*, held recently in San Francisco.
"There isn't. The computational tools are changing so rapidly that anytime a company freezes the tools, it is left behind. One company is never going to be able to keep up with what's going on. It is going to be hard to be a straight bioinformatics play.""The graveyard of bioinformatics companies is almost as extensive as the graveyard of dot-coms," noted David Kingsbury, president of DTK Consulting. He warned that it is risky to underestimate the utility of freely available academic bioinformatics applications. Open source programs, such as BLAST, are not just free -- they are often superior to commercial offerings."
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Genomeweb
How Good is Greed for Open-Source Bioinformatics?
"Want to make money from open-source bioinformatics? As long as it's not too much you might be OK.
This was the verdict of a panel of academics and business executives who had convened last week to talk broadly about open-source bioinformatics. But the discussion, which took place at the IEEE Computer Society bioinformatics conference at Stanford University, frequently veered to whether one could, or even should, make money from it.
The answer was a resounding maybe."
redux [01.16.02]
"A debate is heating up in the academic community over whether software that is generated by publicly funded research must be released with an open source license. The Internet is one example of how releasing research code benefited the public, but the trend seems to be changing now, and universities are more likely to consider the profit opportunity. The Bayh-Dole Act paved the way for the privatization of publicly funded resources, but not everyone is happy with the results.
Against the tide of privatization comes a group of bioinformatics researchers and programmers with an online petition to require that all software created by publicly funded research projects be licensed as open source. They have founded a group and a Web site, OpenInformatics.org, to further this cause.
Here we present two opposing viewpoints on this issue."
redux [01.07.01]
"The Open Source movement is infectious, it seems. It has bubbled up in the field of bioinformatics - gene research software. Gene research is already a burgeoning area of activity, which is predicted to deliver numerous benefits to the health industry. It is also an area where software counts and where universities have managed to prosper from their activities. US universities lodge about 2000 patents each year, many in bioinformatics, and these patents contribute a good deal of revenue - an amount estimated at about $5 billion per annum, or ten percent of their total budgets. Thus Open Source activities in this area are not universally welcomed."
"Over the past several years, open-source software development has won high-profile adherents in the business world -- including the likes of IBM and Sun Microsystems. But it has always had its strongest fans in the academic world, where open-source software is seen as a natural extension of the idea that the fruits of academic research should be shared with everyone.
But now some academic programmers on the cutting edge have found that the licensing office is proving a more formidable obstacle to progress than the limits of their imagination and skill."
redux [11.26.01]
"Before computer whiz Steven E. Brenner accepted his tenure-track research post at the University of California-Berkeley last year, he demanded that the school's intellectual property police leave him alone.
Brenner prevailed. He's now one of the few experts in the emerging field of bioinformatics with the freedom to distribute his work, software used in gene research.
``It's vital to what we do,'' says Brenner, who supports a movement to force universities to allow ``open source'' publishing of gene research software code."
redux [08.18.01]
"Steve Brenner, assistant professor and leader of a computational genomics research group at the University of California, Berkeley, said he fears that many academic bioinformaticists are unaware of a legal risk they face on a daily basis: contributing to open source software projects without explicit permission from their institutions.
While many employers have clauses in their employment contracts that restrict the creation and use of open source software, bioinformatics programmers at universities are often not as attuned to copyright issues as their industry counterparts. This fact, Brenner said, raises the possibility that a good portion of biological open source software is currently being produced illegally."
"The issue seems to be coming to a head in the academic world now, as more universities are exploiting the revenue stream made possible by their copyright and patent holdings. ?If you?re a software developer, the university holds rights to your software, but if you?re an English professor or Law professor and publish a book, they?re not the least bit interested in copyright,? said Thomas Field, an attorney at the Franklin Pierce Law Center affiliated with the Association of University Technology Managers."
redux [11.05.01]
"Computers are supposed to help biotechnology, right? Isn't bioinformatics all the rage right now? Well, it is, but with popularity comes legal questions that many companies don't address until it's too late."
"It seems that many biotech companies don't realize that a computer vendor may have the rights to the software, and ultimately, the work that the biotech companies do.
For example, if a biotech company orders a computer network to help it sequence the genome of yeast, the company may ask the vendor to customize the software it will use to do the sequencing. However, the question is, who owns the right to that customized software--the biotech company or the software programmer?"
redux [08.23.01]
"This report outlines recent activity in open source software development within the discipline of bioinformatics. I present the relevant highlights of two bioinformatics meetings held in July 2001 in Copenhagen, Denmark: the Bioinformatics Open Source Conference and the Intelligent Systems for Molecular Biology Conference. The report also describes a large number of projects and groups important to bioinformatics open source software development. The appendices include meeting programs, the currently accepted definition of open source software, and descriptions of important online biological data sources."
redux [07.27.00]
"Good software forms seamless connections; as George Orwell said of prose, the best is like a window pane: transparent. The obscurity of commercial binaries is an obstacle to good quality communication between systems. In healthcare, good communication is too important to remain proprietary. Software developers should remain confident that there will always be work for the future in discovering, providing, and adapting applications for organizations, and training people to use them. This, rather than the sharp-suited gouging of Bill Gates wannabees, should become the predominant business model for software in the British NHS. Software engineering will become a profession more like medicine and the law: in which practitioners earn a fair hourly reward for their experience at interpreting, evaluating and applying knowledge from a specialized domain to the benefit of their clients. Current models, which restrict the sharing and development of knowledge, are certainly counterproductive and arguably unethical. Open source is the future: all we have to do is built it."
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DigtalMass
Apple's Mac muscles in
"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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Wired News
Biology Seeks a Few Good Geeks
"According to Dr. Bernardo Huberman, a researcher at HP Labs, the problem is not necessarily attracting computer scientists to the field, but motivating them to do work that is of interest to biologists. He says that computer scientists are eager to try their methods and algorithms with the large data sets in biology, but they tend to enter the field with "a solution looking for a problem."
As a result, Huberman concedes that "biologists find a lot of work being done rather uninteresting," and notes that most bioinformatics articles are often read only by computer scientists."
redux [12.17.1]
""We used to look at several data points for each experiment," says Louis Renzetti, senior director of discovery pharmacology. "Now there are dozens and dozens." Simply dump all of that data on a scientist's desk, and one of two tragicomic things will happen: Either the scientist will want to pursue every promising lead and will end up like a frazzled amusement-park visitor, or the scientists will refuse to touch the report at all, for fear that she will never be able to make sense of it.
It has taken a while to find the right approach, says James Rosinski, one of Roche's experts in the new field of bioinformatics, which covers the management of genomic data. The key, he says, is for biologists and statisticians to start talking early about how to use data from a GeneChip experiment. "It's iterative," he explains. "We can't just take a one-shot approach and tell the biologists what they ought to be interested in. We have to interact.""
redux [04.05.00]
[requires 'free' registration]
"I suspect that although the new enthusiasm for computers in biology is genuine, it overlooks some basic problems in implementation. The basic difficulty, as I see it, is that although biologists use computers, they do not trust everything that comes out of them. It is one thing to use them to print up nice-looking graphs, but it is an entirely different matter to use them to think better."
"Francis Crick was once quoted as saying that no biologist had ever made a discovery using a mathematical model. I would reply that no biologist has ever made a discovery by running an electrophoretic gel. They make discoveries by using their brains. Computers, like all scientific tools, are only as good as the person who uses them. If biologists don't understand how computer models are constructed, they won't know their strengths and limitations. Without some foundation of trust, biologists will be unlikely to utilize or accept this powerful method of data analysis."
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The Scientist
Get with the Program
[requires 'free' registration]
"It is often said that necessity is the mother of invention. In the world of bioinformatics, the need to examine and manipulate large volumes of sequence data begat specialized computer software to handle these tasks."
"Since our last review,1 the software market has changed somewhat. New companies on our list include ApoCom Genomics, Bioinformatics Solutions, and Paracel. DoubleTwist, supplier of TwistTools, has closed, and despite repeated efforts, we were unable to reach Gentech, Biotechnix3d's supplier, to confirm either the status of that program, or even if the company is still in business (its Web site has been under construction for some time). What follows is a round up of each company's latest offerings."
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Bio-IT World
IBM's Intelligent Miner traces protein communication for AxCell
Biosciences
""IBM's technology combs through," Becker says. "It tells you what you need to know." Data mining technology like Intelligent Miner uses algorithms to sift through data, analyzing and identifying trends and patterns. Intelligent Miner's algorithms include clustering algorithms that segment data with similar patterns, predictive algorithms that score data by factors such as behavioral propensity, and time-sequence algorithms that reveal similar progressions of a disease over a period of time."
""We will not be making our mining tools specifically available for [life-science] companies, but when we have a company that is interested in using them and testing them ... we're certainly going to sell to them," Nunes said in an interview.
But she stressed that IBM is not interested in setting its foot on bioinfomatics turf full-time. "Our focus is really on the architecture and the middleware," Nunes said. "We are not intending to go full-force into any area that has to do with bioinformatics tools.""
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Slashdot
Moving from Corporate IT to Science?
"EdinBear asks: "I've been working as a SysAdmin in an increasingly corporate internet services company, which has been hit hard by the fallout from the .com bust. When I started some years ago, I felt I was helping small and interesting companies get benefit from the burgeoning Internet through useful and attractive web services. However, since the Internet became 'normal', the focus has been purely commercial - and instead of helping an enterprise get exposure in an interesting way, it's all about money and finance. I now feel I want to move into Science to use my skills in a productive, 'big picture' kind of way, rather than just helping a client get more rich through financial services. I'm interested to hear if other people have found themselves in a similar position; is the transfer to Science/Research/Academia difficult? Is the grass greener on the other side? The money is less, but is the job satisfaction more?""
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Genomeweb
TIGR and Venter's Nonprofits Plan New Genome-Sequencing
Center
"The three research centers founded and funded by Craig Venter will collaborate to build a new high-throughput genome-sequencing center whose goal will be to sequence a human genome in a fraction of the time it currently takes, the three centers said today.
"Unlike the data compiled by Celera, which Venter founded and ran until he left in January, data harvested by his new nonprofit will be freely available to all researchers."
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New Scientist
Gene study gives language lesson
"Two mutations in a human language gene have been strongly selected for over the past 200,000 years, new research shows. The finding provides evidence for the idea that language spread by giving a major survival or mating advantage to those who possessed it, and that it is not merely a handy by-product of big brains."
"Pinker believes the analytical approach used is powerful: "It's not an idle just-so story to say that something is a product of selection." The work demonstrates that the two mutations were rushed through the population because they conferred a considerable advantage, he says."
redux [10.04.01]
"The discovery of the gene is fueling the ongoing debate about the relationship between genes and higher cognitive functions like language.
While few researchers would claim that language and genes are not related, there has been little evidence so far that language is directly encoded in our genes.
At stake is a popular theory, originated by Noam Chomsky, about language and the brain.
"The way to make the general assumptions less obscure is to discover the nature of the various specialized "learning mechanisms" -- the systems LT(O,D), in my terminology -- among them the "language organ" FL, the states it can in principle attain, the "neural circuits" involved, etc. That is also the way to arrive at one or another "position...in the domain-generality vs. domain-specificity debate," a very tentative position I would think, given the limits of current understanding. I concede that I don't really understand what this debate is about in the way it is usually waged (without my participation). There are very interesting questions about just what might be specific to human language (part of LT(Human, Language), the dedicated "learning mechanism" that is the "language organ"). These are the topics of inquiry in all study of language and other cognitive systems that I know of. But I do not understand the more general "debate" that seems to arouse much passion."
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Bio-IT World
Necessary Liasons:Making Standards Work
"For researchers it's really about using the absolute best applications. Our universities are turning out a tremendous number of the most important applications that people are using -- there's huge innovation that happens in government and university labs. We need to be able to integrate the applications that come from both public and private sectors.
So the idea of I3C is to make this layer open, and agree on a set of standards. There will have to be a lot of domain specifics to this middleware architecture, probably done as XML vocabulary around particular areas of chemistry and biology and expression data analysis. And the applications will have to become compliant, so it is a little bit of work for the [informatics suppliers], but ultimately there's a value proposition for everybody."
redux [05.10.00]
"We may rehearse this fundamental axiom of descriptive markup in terms of a classical SGML polemic: the doubly-delimited information objects in an SGML/XML document are described by markup in a meaningful, self-documenting way through the use of names which are carefully selected by domain experts for element type names, attribute names, and attribute values. This is true of XML in 1998, was true of SGML in 1986, and was true of Brian Reid's Scribe system in 1976. However, of itself, descriptive markup proves to be of limited relevance as a mechanism to enable information interchange at the level of the machine.
As enchanting as it is to contemplate the apparent 'semantic' clarity, flexibility, and extensibility of XML vis--vis HTML (e.g., how wonderfully perspicuous XML <bookTitle> seems when compared to HTML <i>), we must reckon with the cold fact that XML does not of itself enable blind interchange or information reuse. XML may help humans predict what information might lie "between the tags" in the case of <trunk> </trunk>, but XML can only help. For an XML processor, <trunk> and <i> and <booktitle> are all equally (and totally) meaningless. Yes, meaningless .
Just like its parent metalanguage (SGML), XML has no formal mechanism to support the declaration of semantic integrity constraints, and XML processors have no means of validating object semantics even if these are declared informally in an XML DTD. XML processors will have no inherent understanding of document object semantics because XML (meta-)markup languages have no predefined application-level processing semantics. XML thus formally governs syntax only - not semantics."
"With XML has come a proliferation of consortia from every industry imagineable to populate structured material with standard terms (see Appendix B). By one estimate, a new industry consortium is founded every week, perhaps one in four of which can collect serious membership dues. Rising in concert are intermediary groups to provide a consistent dictionary in cyberspace, in which each consortium's words are registered and catalogued.
Having come so far with a syntactic standard, XML, will E-commerce and knowledge organization stall out in semantic confusion?"
"How are semantic standards to come about?"
"There is an increasing demand for formalized knowledge on the Web. Several communities (e.g. in bioinformatics and educational media) are getting ready to offer semiformal or formal Web content. XML-based markup languages provide a 'universal' storage and interchange format for such Web-distributed knowledge representation. This tutorial introduces techniques for knowledge markup: we show how to map AI representations (e.g., logics and frames) to XML (incl. RDF and RDF Schema), discuss how to specify XML DTDs and RDF (Schema) descriptions for various representations, survey existing XML extensions for knowledge bases/ontologies, deal with the acquisition and processing of such representations, and detail selected applications. After the tutorial, participants will have absorbed the theoretical foundation and practical use of knowledge markup and will be able to assess XML applications and extensions for AI. Besides bringing to bear existing AI techniques for a Web-based knowledge markup scenario, the tutorial will identify new AI research directions for further developing this scenario."
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Genomeweb
InforMax's Whiteley Sniffs Out Bioinformatics' Sweet Spots
"Since leaving as head of Amersham Biosciences' bioinformatics division at the end of March, Whiteley says he has reassessed the informatics market both in drug discovery and disease research. His verdict is that the space is sick, but not terminally. InforMax, for its part, happens to be a long-term patient."
"For a while there was a sweet spot for an integrated bioinformatics solution for startup companies who just got VC funding and needed an infrastructure and they needed it tomorrow to get it going. I think our sense is that sweet spot has changed where people are really going back to saying, 'Don't necessarily reinvent my whole IT infrastructure. Give me an analysis tool that helps my bench scientists, that talks to other applications, and has a growth story behind it.'"
redux [01.03.01]
"Inside the laboratories of the world's major pharmaceutical companies and biotechnology start-ups, an emerging science is quietly transforming the drug industry. Bioinformatics -- the use of computers to analyze the inner workings of biology -- is helping researchers pinpoint the roots of diseases and design sophisticated medicines to treat them.
But even as it becomes a vital part of drug research, bioinformatics as a business is losing favor with investors. Shares of publicly traded firms that sell biological data and software tools are slumping, and venture capitalists are increasingly wary of investing in such companies.
"Don't call Protein Pathways a bioinformatics company. At least not anymore."
"In the "bioinformatics business model [there] is not enough money to interest venture capitalists," said Matteo Pellegrini, Protein Pathways' president and co-founder. "So to grow a company beyond a niche software company you have to move to drug discovery. We don't see the database software model as viable for us. We see informatics as internal to drug discovery.""
redux [12.18.01]
"There comes a point in the life cycle of every organism when it must change or perish. For bioinformatics, the time for metamorphosis is now. Though computational biology is already an intrinsic part of the drug discovery process, the business models adopted by most bioinformatics firms have failed to produce profits. Competition -- from the IT industry and big pharma itself -- is growing and investors, both public and private, are unimpressed. While some companies are hoping persistence pays off, many are pursuing new business models that should allow them to retain a bigger share of the profits they are helping to create."
redux [11.27.01]
The bioinformatics industry - broadly defined as using computers in drug discovery - generated revenue of $1.38 billion in 2000, analysts at Frost & Sullivan figure. That number will reach at least $6.9 billion by 2007, analysts predict.
Although computers have been used by biotechnology and drug companies for at least a decade, the bioinformatics segment has taken off only in the last three years. And most believe it isn't anywhere near its potential.
``It's an exciting area, but it's an area that will come into its own in the next three to five years,'' said Brad Peters, Frost & Sullivan senior industry analyst.
redux [11.20.01]
"A new Frost & Sullivan report augurs an explosion in the U.S. bioinformatics market from $1.38 billion in 2000 to $6.9 billion in 2007. The industry is full of players, and there's almost certain to be consolidation. The friendly capital markets of 1999 and 2000 allowed many to raise enough cash to hold out for the best bid."
redux [07.16.01]
"A year after the deciphering of the human genome boggled the world, investors are realizing that manipulating genes to fight disease is still in its infancy -- and far from profitable."
Nowhere is that more clear than in the industry for genetic information, or bioinformatics."
redux [05.14.01]
""Companies choose to adopt a product that is perceived to give some advantage over their immediate competitors and would like to see that protected in some way by the platform vendor (Celera) not running around selling it to everyone else, if they can avoid it. This is perceived to diminish the window of opportunity of the platform adopter to gain a lead over their immediate competitor. It is an element of sustainable advantage.'"
"Celera is certainly at a point of transition. It must either decide whether or not it wants to get into this collaborative, more vertical model of integrating itself with certain customers in big pharma or try to make its data and knowledge of it so valuable that big pharma of all walks of life simply has to have access to Celera data. I don't think the company has the time and money to do both. I don't think, for competitive reasons that I've explained earlier, big pharma is going to align itself, in large numbers, with a company that is selling the same applications to its immediate competitors."
redux [03.14.01]
"The story proclaimed in its lead, "Move over Information Age. Make room for the age of bioinformation." You could picture bleary eyes opening all over the Bay Area. The story went on to note that a San Jose consulting firm was predicting a 10 percent annual growth in the bioinformatics market for years to come; and that the National Science Foundation estimated that 20,000 new jobs in the field would be created in the field in just the next four years.
If that wasn't enough, the rest of the section was filled with page after page of biotech firms listing job openings - in powerful juxtaposition to the endless lists of dot-com layoffs just a few pages earlier. Picture Starbucks spit-takes from Marin to Santa Cruz.
Wow! Rewrite that resume to emphasize that biology course you took in college. Roll your Aeron chair down to the nearest lab. Trade that black turtleneck for a white lab coat..."
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TheDeal.Com
Lion Bioscience licks its wounds
"Troubled German biotech pioneer Lion Bioscience AG is hoping that one divestiture can clear the mess it's made of an aggressive acquisition and venture capital program and usher in profitability."
"As part of its turnaround strategy following the plunge of its shares, Lion is in advanced talks with potential buyers of its drug discovery unit, which accounts for 50% of its costs but none of its revenue."
"Lion Bioscience today reported a decrease in first-quarter revenue on top of expanding net losses."
"Net loss for the quarter ballooned to Û19.2 million, or Û.97 per share, from Û11.2 million, or Û.60 per share, one year ago. The company attributed increased losses to costs integrating NetGenics, acquired in January, as well as a year-over-year drop in revenue."
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Science Daily
Jumping Genes Can Knock Out DNA; Alter Human Genome
"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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USA Today
Scientists hunt for disease genes
"Now a team of Ohio scientists reports it has found 169 regions of the human genome that appear genetically unstable because they're surrounded by so many DNA duplicates -- spots the researchers contend could harbor answers to the causes of various genetic diseases.
In Friday's edition of the journal Science, the researchers explain that they found these potential genetic hot spots by using a new statistics method to read draft maps of the human genome and identify true duplicates."
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