{bio,medical} informatics
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
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.""
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
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."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
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."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
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.""
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
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?""
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
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."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
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."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
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."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
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..."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
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."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
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."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
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."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Reuters Health
Scientists add some dimension to genome map
"While the human genome--the genetic road map of human development and function--has been almost completely decoded, the process of making sense of this genetic information has just begun. In a new study, a team led by Dr. David Altshuler of the Whitehead Institute for Biomedical Research at Massachusetts Institute of Technology in Cambridge has conducted a genome-wide study that has produced a sort of topographical map of the landscape of the human genome.
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Genomeweb
New University Degree Programs Fuel Surge in Bioinformatics
Grads in '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." "
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
BBC News
Finding agriculture's 'genetic signature'
"Modern Europeans can trace a great deal of their ancestry to Middle or Near Eastern farmers who moved into the continent 10,000 years ago.
The assessment comes from a new computer and genetics study which has sought to understand how the new agrarian technologies were introduced to the region."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Wired News
Scientists Map Mouse Genome
"An international team has completed the most comprehensive map ever of the genetic code of the mouse, an accomplishment that will make the laboratory animal more useful to scientists studying human health and disease.
The map covers an estimated 98 percent of the order of the nearly 3 billion letters that make up the mouse code, or genome. Two efforts have nearly completed the deciphering of those letters, and the map will serve as an atlas of the genome and allow scientists to zero in on regions of interest. It will also permit scientists to fill in gaps that remain in the deciphering efforts, which remain in draft form."
"Centuries ago, maps were views of the world around us. Today, newly drawn maps are not of the exterior world, but of the world encapsulated by our genes, and the genes of other organisms that share our heritage going back millions, or even billions, of years.
That is why researchers will be poring over the publication this morning of a complete map of the genome of the mouse, the first mammal aside from man to have had all of its DNA sequenced."
"Genomic resources for the mouse are increasing at an astounding pace. The ability to manipulate the mouse genome coupled with the availability of genome sequence make the mouse a unique research tool. This page is a gateway to mouse resources in and beyond NCBI."
redux [10.06.00]
[requires 'free' registration]
"With the work on the human genome essentially complete, the National Institutes of Health and others said today that they would spend $58 million to decode the genome of the mouse by February.
While this may seem a large sum to drop on a mouse, experts regard the mouse genome as an invaluable guide for interpreting the human genome sequence that is now in hand.
The initiative represents a continuation of the tussle between the public consortium that decoded the human genome and its competitor, the Celera Corporation."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
Science Daily
Investigators Use Guilt-By-Association Strategy To Track
Potential Cancer Causing Genes
"A detective has a slim chance of catching a crook who escapes without a trace. But an investigator who can track a culprit's friends and associates might learn much about a criminal's next target.
A "guilt-by-association" strategy turns out be just as effective in cancer biology as it is in law enforcement, since cancer-causing proteins that rob cells of their ability to divide normally also depend on co-conspirators. Such molecular partners in crime, once identified, may yield a wealth of information about how a cancer develops and how it best can be treated."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
BioMedNet
Uncle Sam needs your data-mining expertise
[requires 'free' registration]
"Scientists working in bioinformatics are welcoming a partnership announced this week between the US intelligence community and the US National Science Foundation (NSF), which promises to boost research into data mining. The Intelligence Technology Innovation Center (ITIC), which falls administratively under the Central Intelligence Agency, will provide the NSF with as much as $8 million for research into methods of extracting patterns buried in enormous sets of data such as e-mail, television broadcasts and Web pages."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
EyeForPharma
Study demonstrates crucial role IT will play in enhancing
Pharma R&D
"The analysis, conducted earlier this year, shows that pharma companies with optimally implemented informatics solutions could save as much as $264 million in R&D costs, and as much as one year in development time for each new ethical drug. According to analysts, R&D informatics promises to generate the greatest portion of the potential savings - up to $149 million of the $264 million - by integrating data and information across disciplines, pharmaceutical departments, processes and drugs."
redux [10.17.01]
""We're an information-based industry, but we've been a bit behind in the extent to which we've been using computer-based tools," Dinerstein says. "They've had better computer models for oil drilling than we've had for drug discovery."
While executives in this closely guarded industry won't say how much they're investing in research and development informatics, they are definitely hopping on board. Merck & Co. in Whitehouse Station, N.J., recently paid $620 million to acquire Rosetta Inpharmatics, a genomics and technology company based in Kirkland, Wash. And New York City-based Pfizer says it recently spent more than $100 million to create an "integrated system of high-speed discovery technologies." Pradip Banderjee, a senior partner with Accenture Consulting, conservatively estimates that drugmakers as a whole spend more than $4 billion a year on that kind of technology, not including the cost of hardware."
redux [08.19.01]
"In a recent forecast analysis, Gartner predicts U.S. pharmaceutical companies' IT spending will increase at a CAGR (calculated annual growth rate) of 12.8 percent - from $3 billion in 2000 to more than $5.5 billion by 2005. The group forecasts spending on software and external services will outpace spending for hardware, network equipment and internal services."
redux [05.26.00]
"Leaders in the genomics field, as in any other industry, will be companies that offer a value-added service. Large pharmaceutical companies agree on what that service should be: integration of all the genomics information available. With more information readily accessible, companies can easily decide on whether to continue investigating potential targets.
So the future of genomics companies may rest in their IT and software capabilities, a view held by Celera Genomics, a newcomer to genomics. "We are entering an era of 'cyberpharmaceutical' drug development," says Samual Broder, executive VP and chief medical officer. "Pharmaceutical corporations will use genomic databases, and other relational databases involving gene expression, proteomics etc. as the foundation of their drug discovery pipelines. One of the immediate goals... is to produce appropriate databases and software to link biologic and genomic information.""
redux [11.29.01]
[requires 'free' registration]
"Glenn Giovanetti at Ernst & Young Life Sciences Industry Services, comments "You could really compare [today's situation] to a large degree with the first biotech boom in the late eighties and early nineties where the thought was, 'Hey, this is going to lead to better drugs faster,' and clearly that hasn't been the case." Having the genome in hand has brought about more drug targets, but, explains Ma, "People are getting more concerned that novel targets are going to have a higher rate of failures because there is less information on them." And when working in 10-year drug-development cycles, failures are costly.
Ma points to a trend of growth in clinical informatics that would effectively garner more information from expensive clinical trials instead of simply treating them as regulatory hurdles. "People are beginning to think through to how ... to take greater advantage of that information," he adds. But increasingly, the suppliers of genomic information have been looking to do the same thing.
[ rhetoric ]
“Bioinformatics will be at the core of biology in the 21st century. In fields ranging from structural biology to genomics to biomedical imaging, ready access to data and analytical tools are fundamentally changing the way investigators in the life sciences conduct research and approach problems. Complex, computationally intensive biological problems are now being addressed and promise to significantly advance our understanding of biology and medicine. No biological discipline will be unaffected by these technological breakthroughs.”
BIOINFORMATICS IN THE 21st CENTURY[ search ]
[ outbound ]
biospace
/
genomeweb
/
bio-it world
/
scitechdaily
/
biomedcentral
/
the panda's thumb
/
bioinformatics.org
/
nodalpoint
/
flags and lollipops
/
on genetics
/
a bioinformatics blog
/
andrew dalke
/
the struggling grad student
/
in the pipeline
/
gene expression
/
free association
/
pharyngula
/
the personal genome
/
genetics and public health blog
/
the medical informatics weblog
/
linuxmednews
/
nanodot
/
complexity digest
/
eyeforpharma
/
nsu
/
nyt science
/
bbc scitech
/
newshub
/
biology news net
/
informatics review
/
stanford
/
bmj info in practice
/
bmj info in practice
/
[ schwag ]
look snazzy and support the site at the same time by buying some snowdeal schwag !
[ et cetera ]
valid xhtml 1.0?
This site designed by
Eric C. Snowdeal III
.
© 2000-2005