{bio,medical} informatics
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The O'Reilly Network
Lincoln Stein's Keynote: Building a Bioinformatics Nation
"Lincoln then summarized efforts to unify the bioinformatics data services. These efforts started 12 years ago with the Meetings of the Molecular Biology Databases (MMBD), which essentially ended in argument. Every member thought his or her way of doing things was the best way. Next came the federated models like Gaea and Kleisli , and then the data warehouses of Ensembl, UCSC, and others. This brings us to the ad hoc Web services that are currently in place. These allow programmatic access to data, as in the GenBank/EMBL example. To truly unify the services of bioinformatics data providers we need to move beyond this to a more formal Web services model.
In this Web services model, the data providers would register their services in a formalized service registry, and researchers' scripts would no longer need to be concerned with the interface details of the different databases. This model represents the unification that Lincoln, and judging by the response, apparently everyone in the audience, hopes to see in bioinformatics."
redux [09.27.01]
"As you might be aware of, flat-files have severe limitations, and we have been asked various times if we are going to distribute the EMBL data in different formats as well, XML being the one most prominently mentioned. In short, the XEMBL project will bring to the user several alternative formats of EMBL data."
"We have XEMBL running as a web service using SOAP (Simple Object Access Protocol) and WSDL (Web Service Definition Language)."
"Web Services can't create a framework in which any two arbitrary applications can interact because XML doesn't provide shared languages, merely shared alphabets. The Web Services stack pushes this shared semantics problem into higher and higher layers without solving it. Humans often cannot create perfectly transparent descriptions even when they are trying to, and they simply won't try when there's an economic incentive to stretch the truth."
redux [11.06.00]
"The semantics of services -- what they do and what data elements they manipulate mean -- is the key issue. Business value results from B2B collaborations that do the right thing. If they do something else, the damage may be dramatic. How, then, do we trust that a service does the right thing before it is used? And how do we make that determination at Internet speeds?
In small-scale OO systems, interface compatibility usually implies semantic compatibility. That is, an object that implements the right set of messages with the right types of arguments probably does "the right thing." This is true, in part, because small-scale systems tend to be built by a small team of programmers with shared understanding of how the system operates and, in part, because small systems offer little opportunity for ambiguity. However, in large-scale OO systems, the semantics provided by a given class cannot be reliably deduced from the message interface alone. Clearly, in an Internet populated with many thousands of services offered by thousands of different companies with very different agendas, compliance with some specified message set will not be sufficient to deduce the semantics of the service."
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The Motley Fool
New Tune at Celera: Should it stay or should it go now?
[requires 'free' registration]
"Possible reasons for Venter's departure range from the company's transition from bioinformatics to drug discovery and development, to personality conflicts between Venter and White, to Venter's preference for research to running a business. But the bottom line is clear: Whatever role Venter will play, his visionary leadership will no longer be at the top. Does that mean an end to Celera's business momentum, or does realizing value for shareholders require replacing the founding science brainiacs with MBAs?
We asked Motley Fool community members on the Celera, Biotechnology, Rule Breaker Strategies, and Rule Breaker Companies discussion boards to share their views about Venter's departure and Celera's business, especially in light of the Rule Breaker criteria."
redux [10.31.01]
"To employ the method described in this article, it is important to ensure that all the firms being compared are similar in their developmental architecture. Typically, investors would use a set of comparable firms in valuing a firm but for illustration purposes, consider only one example. Exilixis - a company pioneering the use of genetically manipulatable model systems for biomedical research - should be compared to a company like Millenium, which has a highly integral development architecture, using a variety of technologies to develop biopharmaceuticals. The analysis shows that Exilixis is undervalued relative to Millennium.
A quick glance at equity reports shows Celera Genomics is compared to a variety of companies including Millennium. A company such as Celera, at this point in its development, has more in common with a "modular" company such as Incyte - and analysis shows it is overvalued in relation to Incyte. Of course, to be fair to Celera, it is attempting to forward integrate into a structure similar to Millennium. The market suggests that it is midway in the continuum between modular and integral development structures."
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Slashdot.Org
Beginning Perl for Bioinformatics
"As the banner above the title of James Tisdall's Beginning Perl for Bioinformatics indicates, this book is 'an introduction to Perl for biologists.' What the banner doesn't mention is that it's also an introduction to biology and bioinformatics for Perl programmers, and it's also an introduction to both Perl *and* biology for people that have never really been exposed to either field. The author has clearly thought a lot about making one book to please these different audiences, and he has pulled it off nicely, in a way that manages to explain basic topics to people learning about each field for the first time while not coming off as condescending or slow-paced to those that might already have some exposure to it."
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The Washington Post
Celera Changed, Venter Couldn't
"As all that was happening, people who know him say, White, Venter's boss, was getting grumpy. He well knew that Celera, under its original business plan, could not deliver long-range earnings growth that would justify what the market was paying for Celera shares. One top genetic scientist said White snapped to him in the midst of the publicity barrage, "'This is all nice, but we need a business plan.'"
They quickly came to the same conclusion as many minds before them: In biology and medicine, the only business plan that offers the potential of extraordinary profits is drug development. All the biotechnology superstars have been companies with hit drugs."
redux [01.22.01]
"Dr Craig Venter, the US scientist who led the private effort to decode the human genome, has quit as boss of his company Celera Genomics."
""We are now at a critical juncture where my best contributions can be made in a scientific advisory role, allowing the rest of the organisation to continue Celera's progress toward becoming a successful pharmaceutical business.""
"More and more of what Celera did reflected its ongoing metamorphosis, and in a candid assessment of his best-known business, White conceded that "information will never be a multibillion dollar industry."
"The goal was always to become a user of our [own] data. Celera is in the transformation stage," he proclaimed, and not for the first time. "We have to get busy to retool to become a credible drug-discovery company." After all, that, they say, is where the real money is."
redux [06.09.00]
"Great discoveries do not necessarily make great businesses. Businesses have to sell something. Celera Genomics doesn't sell or make anything tangible. It hawks service and information. It sells access to lists of genes and computers that can sort through those messy lists. Samuel Broder, the company's executive vice president and chief medical officer, makes Celera sound like some kind of consulting company, or perhaps a library."
"Venter's quest could be a fable, with all sorts of morals about the power of capitalism and the importance of a single, brilliant, willful individual who used the market to shake the ivory towers of science. But those morals only hold if Celera succeeds, if business and science blend to propel the company into the future with breathtaking speed without rocketing it into the realities of the marketplace. Celera could become one of the great business success stories. It could also be a financial train wreck."
Right now, that makes it a very volatile stock."
redux [07.17.00]
"Craig Venter, head of Celera Genomics which last month completed the map of the human genome, has outlined his next goal.
Speaking at a conference he said his new task was to map the proteins which drive all chemical reactions in the body."
""A big part of the business is the straightforward providing of information, but I'm not complacent just to do that," Venter said."
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Bio.Com
Virginia Tech, Johns Hopkins Invest in Bioinformatics
"Virginia Bioinformatics Institute (VBI) at Virginia Tech and the Johns Hopkins University (JHU) Bloomberg School of Public Health have announced a $10 million bioinformatics research collaboration to target human infectious diseases. Each university will invest a minimum of $1 million per year for five years to better understand tuberculosis, AIDS, malaria, measles, and other deadly illnesses."
"The bioinformatics capabilities at VBI will allow comparisons of multiple human responses to different pathogens as opposed to traditional models that looked at only a single response for one disease. Experiments that were traditionally conducted on a single pathogen in a petri dish will now be performed on supercomputers housed in VBI’s core computing facility."
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PharmaBiz.Com
Bioinformatics: The next generation of market opportunities
"The prospectus for Bioinformatics are inseparable from the prospects and market structure of biotech, so a large amount of the equity investment in biotech during 2000, totaling $31 billion annual drug discovery budget on IT. That's $500 million per year. Suppliers such as MDL, Molecular Simulation, Tripose, and Oxford Molecular have grown and generate revenues between $20 million and $70 million. Oxford Molecular predicts a total market for its services totaling $1.3 billion by 2002 with 75% accessible from their own products. Other sources suggest and even larger market, moving to $10 billion in five years.
Bioinformatics is the core enabling the platform technologies that support the biotech revolution. One can therefore expect the growth and development of the market to mirror that of biotech and to feed the increasing number of biotech companies."
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BioMedNet
Geneticists reluctant to share data
[requires 'free' registration]
"Nearly half the academic geneticists who asked for additional information, data, or materials related to a published research report were denied their requests, a new survey reports today. Are geneticists being unfairly pilloried?"
"Because they were denied access to data, 28% of geneticists reported that they had been unable to confirm published research. Other reported consequences were delays in publications, abandonment of a promising line of research, and the collapse of collaborations."
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BBC News
Genome pioneer steps down
"Dr Craig Venter, the US scientist who led the private effort to decode the human genome, has quit as boss of his company Celera Genomics."
""We are now at a critical juncture where my best contributions can be made in a scientific advisory role, allowing the rest of the organisation to continue Celera's progress toward becoming a successful pharmaceutical business.""
"More and more of what Celera did reflected its ongoing metamorphosis, and in a candid assessment of his best-known business, White conceded that "information will never be a multibillion dollar industry."
"The goal was always to become a user of our [own] data. Celera is in the transformation stage," he proclaimed, and not for the first time. "We have to get busy to retool to become a credible drug-discovery company." After all, that, they say, is where the real money is."
"Labeled the ``bad boy of genomics'' by Business Week for what it once described as his ``brash'' and ``self-promoting'' manner, Venter nonetheless has a loyal following both inside and outside the company. His resignation, announced before the company has found a successor, struck some as a sign of in-fighting at Celera, or as evidence that Venter has become tired of the job.
``You'd think if he were still very happy there he'd wait until they found the right person so that they'd have a smoother transition,'' said Noensie."
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GenomeWeb
Global Bioinformatics Market to Double by ’06; Proteomics and Pharmacogenomics Spending to Outpace Genomics
"Faster and cheaper technologies will help the worldwide bioinformatics market double in size over the next five years and reach $1.7 billion, according to an industry analysis released on Monday."
"Saying that "one of the biggest questions facing users of bioinformatics" is whether to develop IT tools and technology in-house or to license them from the many vendors on the market today, the report says that pharma and biotech firms "will continue to allocate 60 percent of their total bioinformatics spending to commercial vendors"-expenditures that Front Line estimates will blossom to $1.1 billion in 4 years."
redux [01.15.01]
"The deal, anticipated to close before April, gives Lion control of NetGenics' DiscoveryCenter platform, its 60 scientists and bioinformaticists, and a deal the privately held informatics firm has recently struck with Schering."
"The company, based in Cleveland, has been hurting recently: It earned $2.3 million during the first nine months of 2001 and spent $11.7 million during the same period."
" Its current cash position is "negligible," Glynias said in an interview, and Michael Clulow, who covers Lion for UBS Warburg, said that "NetGenics has an unhealthy balance sheet.""
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 [12.03.01]
"Today's battle against disease is being fought inside supercomputers as much as in laboratories.
The convergence of biotechnology and computing at the cutting edge of biology has already bred dozens of new alliances and could pave the way for mergers between previously distinct industries.
The ideal company of the future may be a combination of big pharma, a computing giant and a consumer goods player bringing marketing muscle, according to Dirk Heyman, Head of Life Sciences at Sun Microsystems.
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 resumé 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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O'Reilly Network
An Interview with Dr. Leroy Hood
"The integration of bioinformatics with these systems approaches is an integral, essential feature. One of the things that we stress is that in the future it's going to be increasingly important for people in bioinformatics to be intimately associated with data producers, because no matter how smart you are you can't model biological complexity--it's just too complex. The only way we're going to understand it is through the integration of these global experimental observations, together with powerful computational tools for analysis, and ultimately, for modeling.
A mistake that a lot of people in bioinformatics have tended to make is thinking that you can set up a bioinformatics center and it can work in isolation from the biology, and it can study all these great databases and learn lots and lots about biology. In vitro biology and in silico biology are all popular terms, but it isn't true, and it isn't going to be true in the future."
redux [04.18.01]
[requires 'free' registration]
"Systems biology is a loosely defined term, but the main idea is that biology is an information science, with genes a sort of digital code. Moreover, while much of molecular biology has involved studying a single gene or protein in depth, systems biology looks at the bigger picture, how all the genes and proteins interact. Ultimately the goal is to develop computer models that can predict the behavior of cells or organisms, much as Boeing can simulate how a plane will fly before it is built.
But such a task requires biologists to team up with computer scientists, engineers, physicists and mathematicians. The structure of universities makes that difficult, Dr. Hood said."
redux [03.17.01]
"When Lee Hood started the Institute for Systems Biology, a project to build an integrated research supercenter for the biological sciences, few doubted the validity of the concept, but many wondered whether the technology existed to make it work.
Now, in a sign that others are also willing to gamble on the idea, systems biology is attracting commercial attention. Beyond Genomics (BG), a startup based in Cambridge, Mass., is attempting to glean medically-relevant information from multiple systems simultaneously, from genes to metabolites, by using software that identifies patterns in these systems caused by disease."
redux [07.13.00]
"A new mathematical biology is emerging. Building on experimental data from developing organisms, it uses the power of computational methods to explore the properties of real gene networks."
"Our understanding of gene networks is at an early stage. We perceive their complexity only after it has been filtered by the limitations of the techniques used to study them. Genome databases and DNA-chip technology, which enables huge numbers of genes to be screened for activity, will undoubtedly provide more, and much more complicated, data than anything produced by Drosophila genetics. If a relatively simple gene network such as the segment-polarity system is hard to understand intuitively, we can be certain that modelling will be essential to make sense of the flood of new data.
But this will not be elegant theoretical modelling: rather, it will be rooted in the arbitrary complexity of evolved organisms. The task will require a breed of biologist–mathematician as familiar with handling differential equations as with the limitations of messy experimental data. There will be plenty of vacancies, and, on present showing, not many qualified applicants."
redux [05.15.01]
"Our Mission is to develop an integrated, easy-to-use environment, the workbench , which will enable biologists to create, manipulate, display and analyze biological models at molecular, cellular and multicellular levels. We are focusing on biochemical networks including mass action kinetics, metabolic pathways, stochastic simulation, gene expression and regulation."
"One of the key aspects of out project is to facilitate collaboration among existing developers and users of system biology software. We aim to do this by providing an open-source software infrastructure which will enable collaborators to freely use and share each other's computational resources."
redux [07.11.00]
"For most of us, formal biology education begins with complex systems--the traditional dissection of a frog in high school biology class is virtually a rite of passage in the U.S.
But the way many people learn about and invest in biotechnology is at the smallest end of the spectrum--the genome, now often described as the "periodic table" of biology. Genomics and all its related buzzwords have been responsible for much of the media attention, government grants, and investment capital heaped on the biotech industry over the past decade.
But just as there is a whole lot of chemistry that happens in between the periodic table and a birthday cake, there is a lot of biology in between the genome and a living organism. With the completion of biology's periodic table within sight, academics and industry players alike are pondering the best way to apply our hard won knowledge.
The only problem is, the path from genome to system seems to get harder the more we learn."
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BioMedCentral
Computer turns detective in the hunt for novel pathogens
"The potential for rapid discovery of new, disease-causing microbes, is on the horizon with successful results from a study with a new computerized technique - computational subtraction - that uses DNA matching to isolate and identify microbial gene sequences.
Computational subtraction is an in silico approach that takes advantage of the nearly completed DNA sequence of the human genome, made available through the Human Genome Project . By subtracting out the full complement of human DNA sequences from DNA libraries derived from human tissues, researchers at the Dana-Farber Cancer Institute and Harvard Medical School found they were left with a small number of DNA sequences, presumably of nonhuman origin. They could then search these sequences for evidence of microbial genes, and establish possible links between previously unknown organisms and human disease."
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UniSci
Intelligence: Heredity-Environment Debate Resolved?
"According to neuro and cognitive scientists, different intellectual abilities are based on neural circuits that require environmental stimulation for development -- and are open to change.
However, intelligence researchers argue that there is a general factor of intelligence ("G") that is highly heritable and defines intelligence as an overall innate ability to perform well on different measures of intelligence -- which are not open to change."
redux [06.18.00]
"Everything from liking rollercoasters to attitudes to the death penalty is influenced by our genes, say researchers."
"Liking rollercoaster rides and sweets are just two of the things that may be determined by our genes, according to research published in the Journal of Personality and Social Psychology."
redux [07.07.00]
"Kaplan examines the roles genetic explanations for these types of differences play in our culture -- and how science has been used inappropriately to "medicalize" problems that should be more properly addressed as complex social issues.
Kaplan explores six specific areas -- intelligence (IQ), criminality and violence, homosexuality, depression, obesity, and the centrality of genetics in defining parenthood."
"... an emphasis on the biochemical and the genetic share the property that they make the condition out to be internal to the patient. Once a genetic explanation is offered, and any plausible sounding pathway proposed, the opportunities for claiming that there are other ways of approaching the problem are radically curtailed."
redux [08.31.00]
"The 'implication' that seems to worry people most of all is so-called 'genetic determinism'. It's the notion that, if human nature was shaped by evolution, then it's fixed and so we're simply stuck with it — there's nothing we can do about it. We can never change the world to be the way we want, we can never institute fairer societies; policy-making and politics are pointless.
Now, that's a complete misunderstanding. It doesn't distinguish between human nature — our evolved psychology — and the behavior that results from it. Certainly, human nature is fixed. It's universal and unchanging — common to every baby that's born, down through the history of our species. But human behavior — which is generated by that nature — is endlessly variable and diverse. After all, fixed rules can give rise to an inexhaustible range of outcomes. Natural selection equipped us with the fixed rules — the rules that constitute our human nature. And it designed those rules to generate behavior that's sensitive to the environment. So, the answer to 'genetic determinism' is simple. If you want to change behavior, just change the environment. And, of course, to know which changes would be appropriate and effective, you have to know those Darwinian rules. You need only to understand human nature, not to change it."
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O'Reilly Network
Does Publicly Funded Research Have to Result in Open Source Code?
"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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GenomeWeb
Lion to Gobble NetGenics for $17M; Deal Would Marry Bio and Chem Data
"The deal, anticipated to close before April, gives Lion control of NetGenics' DiscoveryCenter platform, its 60 scientists and bioinformaticists, and a deal the privately held informatics firm has recently struck with Schering."
"The company, based in Cleveland, has been hurting recently: It earned $2.3 million during the first nine months of 2001 and spent $11.7 million during the same period."
" Its current cash position is "negligible," Glynias said in an interview, and Michael Clulow, who covers Lion for UBS Warburg, said that "NetGenics has an unhealthy balance sheet.""
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 [12.03.01]
"Today's battle against disease is being fought inside supercomputers as much as in laboratories.
The convergence of biotechnology and computing at the cutting edge of biology has already bred dozens of new alliances and could pave the way for mergers between previously distinct industries.
The ideal company of the future may be a combination of big pharma, a computing giant and a consumer goods player bringing marketing muscle, according to Dirk Heyman, Head of Life Sciences at Sun Microsystems.
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 resumé 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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Time: Europe
Easier to Swallow
"The blueprint of the human genome — a first-draft map of all the genes in the human body — was outlined faster and for less money than anyone predicted, thanks to the use of high-powered computational tools. But that achievement, announced in June 2000, was merely an initial step. Like all scientific successes, the Human Genome Project raised more questions than it answered by handing scientists vast quantities of new genetic data.
Now the same high-tech, automated methods that helped complete the project are being used to manage and analyze that wealth of information, accomplishing in days, if not hours, tasks that once took years."
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Wired News
3-D Models Give Proteins Shape
"Researchers trying to discover drugs have more data than they can sift through, so many are using computer modeling to deal with the data. But not everyone trusts computer models enough to bet their businesses on them.
Since the human genome was decoded , the amount of gene and protein information has skyrocketed. Whenever researchers are confronted with loads of data, computing power is an obvious solution. But most believe that although computers can speed research, they can't take the place of the laboratory bench."
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The Scientist
Human Genetics Society Ponders New Age
[requires 'free' registration]
"By welcoming scientists who are not card-carrying human geneticists but who work in bioinformatics, medicine, model organisms, chip development, as well as those working in industry, ASHG members can find and develop "effective bridges that connect basic science to medicine," and span the "gulf" between universities and industry. "As the ranks of those in industry who are interested in human genetics increases, we have a lot to gain by finding ways of continuing to break bread with them and a lot to lose if we don't," Willard warned. "We have entered the age of genomic reductionism, where everything, it seems, has to have an explanation embedded in our genome sequence."
As people everywhere pause to reevaluate their lives in the coming months, Willard encouraged geneticists to do the same in their work. It is often there, he advised, that the greatest mysteries unravel. "It takes great intellectual discipline to put your pipette down and just think about the data to look for doors where none appear to exist.""
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Stanford Medical Informatics Preprint Archive
Ontology Development for a Pharmacogenetics Knowledge Base
"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 [09.20.01]
"Cycorp Inc. is planning to release an open-source subset of its Cyc knowledge base, which will let programmers and developers infuse common sense into everything from search engines to CRM apps."
"Users who install the OpenCyc knowledge base will have the freedom to develop proprietary applications, which is not the case with most open-source software. They will, however, have to share any general knowledge they add to the database. De Oliveira says that, over time, Cycorp will release the bulk of the Cyc knowledge base, but it will always keep the most recent additions under wraps so it can develop some proprietary technologies of its own."
"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."
redux [05.10.00]
"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."
redux [03.22.01]
"To realize the full potential of biological databases requires more than the interactive, hypertext flavor of database interoperation that is now so popular in the bioinformatics community. Interoperation based on declarative queries to multiple network-accessible databases will support analyses and investigations that are orders of magnitude faster and more powerful than what can be accomplished through interactive navigation. I present a vision of the capabilities that a query-based interoperation infrastructure should provide, and identify assumptions behind, and requirements of, this vision. I then propose an architecture for query-based interoperation that identifies a number of novel components of an information infrastructure for molecular biology. Those components include: A knowledge base that describes relationships among the conceptualizations used in different biological databases; a module that can determine what known DBs are relevant to a particular query; a module that can translate a query, or the results of a query, from one conceptualization to another; a family of DB drivers that provide uniform physical access to different DBMSs; a family of translators that can interconvert among different database schema languages; and a database that describes the network location and access methods for biological databases. A number of the components are translators because biological databases exhibit heterogeneity at several different levels, including the conceptual level, the data model, the query language, and data formats."
redux [02.28.01]
"The integration of heterogeneous data sources and software systems is a major issue in the biomedical community and several approaches have been explored: linking databases, "on-the-fly" integration through views, and integration through warehousing. In this paper we report on our experiences with two systems that were developed at the University of Pennsylvania: an integration system called K2, which has primarily been used to provide views over multiple external data sources and software systems; and a data warehouse called GUS which downloads, cleans, integrates and annotates data from multiple external data sources. Although the view and warehouse approaches each have their advantages, there is no clear "winner". Therefore, users must consider how the data is to be used, what the performance guarantees must be, and how much programmer time and expertise is available to choose the best strategy for a particular application. Our experiences also point to some practical tips on how updates should be published by the community, and how XML can be used to facilitate the processing of updates in a warehousing environment."
redux [01.17.01]