{bio,medical} informatics
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Forbes
The Drug Research War
"Mention the term "outsourcing," and drug development probably doesn't leap to mind. But this market, which is the heart of pharmaceutical and biotech companies, is growing at a yearly clip of 15% to 20%. Right now the lion's share of the work has gone to U.S. companies that focus on drug research for giants like Pfizer. But now, India and China are angling to get a piece.
Last year, pharmaceutical companies worldwide spent nearly $2 billion doling out parts of the drug research process, mainly to U.S. specialists. By 2007, spending should reach $6 billion, according to a report by research firm Kalorama Information."
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Newsfactor
Microsoft Moves Toward Supercomputing
"The Cornell Theory Center currently operates a cluster consisting of more than 900 processors based on Intel chips housed in Dell computers operating on Microsoft's Windows software. It represents the first steps in the development of Windows for a wide range of supercomputing applications.
Microsoft Research says its workshop brings together about 75 scientists to discuss data-intensive scientific computing as it pertains to Windows and .NET . The participants represent such fields as astronomy, material sciences, physics, archeology, oceanography, and bio-informatics and computational biology."
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Nature: Science Update
Chimp chromosome creates puzzles
"What is the difference between a chimp and a human? There could be a lot more to the answer than scientists thought, according to the first accurate DNA sequence of a chimp chromosome."
"Because chimps and humans appear broadly similar, some have assumed that most of the differences would occur in the large regions of DNA that do not appear to have any obvious function. But that was not the case."
redux [04.05.04]
"A comparison of the chimp and human genomes casts new light on why the two species are so different despite having very similar genetic code."
"One of the leading scientists on the project says the answer lies in the process that orchestrates the genes as the chimpanzee is developing."
"The latest experimental results have solidified evidence of a roughly 10% difference in gene expression from several regions of the brain."
"The researchers have confirmed their findings in four regions of the cerebral cortex, and in the cerebellum and the caudate nucleus. On the other hand, evidence relating to the linear accumulation of differences over time means "we are coming to believe that these are not all functionally relevant," Paabo added."
redux [12.12.03]
[requires 'free' registration]
"In a preliminary screen, Dr. Clark and his colleagues have found that a large number of genes shows signs of accelerated evolution in the human lineage. Those are genes that, by a statistical test applied to changes in their DNA, appear to be under strong recent pressure of natural selection and so are likely to be those that make humans differ from chimpanzees.
A prominent set of accelerated human genes are those involved in hearing, particularly the gene that makes a protein called alpha-tectorin, a component of the tectorial membrane of the inner ear."
"Another group of selected genes is involved in brain development."
redux [12.10.03]
"Researchers today released a draft version of the genetic sequence of our closest relative, the chimpanzee Pan troglodytes .
The differences between the chimp's genetic code and ours should reveal what makes us human, scientists hope. The disparities might, for example, lie in genes that control the development of the brain and language, or of human-specific diseases such as Alzheimer's, AIDS and malaria."
redux [05.20.03]
"Scientists from the Wayne State University, School of Medicine, Detroit, US, examined key genes in humans and several ape species and found our "life code" to be 99.4% the same as chimps.
They propose moving common chimps and another very closely related ape, bonobos, into the genus, Homo, the taxonomic grouping researchers use to classify people in the animal kingdom."
redux [04.29.03]
"By studying chimpanzees, scientists are honing their genetic view of humanity, researchers told this week's meeting of the Human Genome Organisation in Cancun, Mexico."
"The data call for some revision of the estimated genetic similarity between us and our closest relatives. Previously, human and chimp genetic sequences were quoted as being nearly 99% identical, with a difference of only a few DNA's letters. In fact, the similarity may be as low as 94-95%, says Todd Taylor of the RIKEN Genomic Sciences Center in Yokohama, Japan.
redux [03.04.03]
"Chimpanzees seem almost human, and scientists have maintained for decades that chimps are, in fact, 98.5 percent genetically identical to humans.
But the results of a new study call that figure into question, with a finding that there are actually large chunks of the human and chimp genomes that are vastly different."
"It involves sampling data from select regions of many different related species, and then comparing them within the context of their phylogenetic relationships. In the research described in the Science paper, Rubin and colleagues sampled 17 primate species closely related to human and spanning 40 million years of evolution -- insufficient time for significant genetic divergence to have taken place.
According to Rubin, phylogenetic shadowing compensates for the failure of traditional comparative genomics techniques, which "invariably miss recent changes in DNA sequence that account for primate-specific biological traits." The approach overcomes the primary challenge of comparing genomes of closely related species: the difficulty in distinguishing functional from nonfunctional sequences."
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Bio-ITWorld
Opinion: Grid Not Ready for Prime Time
"Grid computing is no empty buzz phrase. In fact, it's a very substantial approach for scaling and optimizing distributed hardware resources. Grids aggregate idle processor cycles, storage capacity and other resources throughout networks, thereby serving client applications with supercomputer-grade performance. Depending on how broadly they're implemented, grids can extend dynamic resource brokering, parallel processing and load balancing to all computers on an intranet, extranet and even a portion of the Internet."
"So grid is starting to mature, as a market and an approach for distributed processing. But the road to maturity is long, and grid computing won't be ready for enterprise prime time for at least another three to five years."
redux [04.26.04]
"Last year we did a study on the market and asked some 50-plus multibillion-dollar corporations, the CIOs and others, about the issues or barriers to grid computing. One of the biggest barriers that we discovered was that there is a group of what we call non-technical issues related to grid computing, and effectively that turned out to be organizational issues or what we described as "the politics" of grid. The issue there is really that people are unwilling to share their resources."
In the case of politics, then, what happens is most people feel -- and this came out in our study last year and again this year -- is that the politics are a significant issue."
redux [03.19.04]
"The humble personal computer used to send e-mail or surf the Internet could quietly be finding a way to stop cancer, treat smallpox or counter a bio-terror attack with anthrax spores."
Novartis is among the growing number of drug makers using in-house grids to search for new drugs. It has 2,700 PCs linked up now and aims to boost that to between 20,000 and 25,000 within two years, said Manuel Peitsch, the head of informatics and knowledge management at its drug research labs."
redux [11.29.03]
[requires 'free' registration]
"Various software packages are designed to build and manage internal grids using an enterprise's own computing resources, the market leader being Grid MP(TM) from United Devices of Austin, Texas.
Such solutions may be robust and help mop up otherwise wasted computing resources, but they still require considerable expertise to run efficiently and ensure that jobs are scheduled correctly and meet agreed priorities. The major cost of a grid lies in managing the resources rather than in the hardware itself, says Atkinson. Therefore, the cost saved by utilizing spare computing resources may be more than outweighed by the cost of additional IT staff. For this reason alone, Atkinson expects many laboratories will make use of external grids."
redux [10.01.03]
"Using the computing power of 2.5 million PCs donated by volunteers from around the world, researchers have narrowed the search for a new treatment for smallpox, now seen as a possible terrorist weapon, to 44 drug molecules that may render the smallpox protein inactive.
The volunteered computing power, set up in a grid through grid.org, contributed more than 250,000 years of computing time in the eight-month Smallpox Research Grid Project, project leaders said. "
""When this project was first explained to me, I thought it was rather Jules Verne-ish," said Army Brig. Gen. Patricia L. Nilo, acting deputy assistant for chemical and biological defense."
Collectively, the 2.5 million PCs running the grid screensaver constituted the world's largest supercomputer, said Todd S. Ramsey, IBM Corp.'s general manager for global government industry."
redux [07.17.03]
"The U.S. is falling behind Japan in the area of supercomputing, as federal research agencies have shifted their focus toward grid computing in the past decade, according to witnesses at a congressional hearing Wednesday.
The result is that U.S. companies have less access to supercomputing resources because demand from the U.S. government has traditionally driven the supercomputing industry in the U.S., critics of the government's efforts in high-performance computing told the U.S. House Science Committee."
redux [06.28.03]
""The language really matters, and confusion on language can be really damaging," Gage said. Citing Sun's experience with Java as an example, he warned developers about the dangers of hype and cautioned them that grid computing risks becoming a catch-all phrase that promises more than it ever can deliver."
"The term has been used to describe a myriad of computing scenarios, from harnessing the processing power in networked PCs build a vast, distributed "supercomputer," to an alternative architecture for the Internet that will provide the underpinnings for Web services and other distributed applications."
redux [05.21.03]
" The American Diabetes Association is using Gateway Inc.'s grid program to run a compute-intensive application designed to accelerate diabetes-related research.
The association, based in Alexandria, Va., is running the Archimedes software application, which Richard Kahn, chief scientific and medical officer for the ADA, called "the Sims City of health care." Using the program, the association can create an environment with any number of variables--such as doctors, hospitals, rooms, costs, patients and treatments--and run numerous what-if scenarios as a way of researching multiple aspects of diabetes care and running clinical studies."
redux [01.09.03]
"Clearly, grid computing means different things to different people, often at different times. To its most visionary pundits, grids symbolize the penultimate step in the evolution of computing architecture into a universal source of pervasive, utility-like computing power that companies can purchase as needed, much as they purchase electricity today. Most stalwart advocates believe that grids not only represent the IT environment of the future but also will ultimately eclipse in significance what the Internet is today."
"All hype aside, it is unlikely that grids will fundamentally change the way that scientific and technical computing is done in the near term, particularly in the private sector."
redux [09.13.02]
"A final obstacle that Stuart pointed out is of the self-inflicted variety: Grid, distributed, peer-to-peer, and other similar incarnations have become victims of their own hype. Increasing media coverage of these technologies has led to confusion in the marketplace, Stuart posited, "and when a prospect becomes confused, the easiest thing is not to do anything.""
"However, he added, there is a bright side to the publicity deluge. Citing the Gartner Group's annual "Hype Cycle of Emerging Technologies" report, which tracks new methods from the initial "tech trigger" period through the "peak of inflated expectations," the "trough of disillusionment," the "slope of enlightenment," and onto the final "plateau of productivity," Stuart noted that desktop grid computing might be working its way from the trough to the slope phase right now, largely because users are discovering which applications work best with the architecture."
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IBM developerWorks
Web services for bioinformatics, Part 1
"This series describes the process of building, deploying, and using high-throughput Web services for bioinformatics applications. This is meant to serve as a guide for development of software based on the Open-Bioinformatics Foundations software toolkits with packages such as BioPerl, BioJava, and BioPython. This article provides directions for how to deploy a service and present a new implementation of document-style Web services extensions to the BioPerl module that will allow a wide range of existing applications to consume such services."
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The New York Times
Collie or Pug? Study Finds the Genetic Code
[requires 'free' registration]
"In a study that alters conventional wisdom and paves the way for a better understanding of canine behavior and evolution, scientists say they have found genetic variations that allow them to distinguish among 85 dog breeds and to identify an individual dog's breed with 99 percent accuracy.
Traditionally, appearance and a written pedigree have been used to define a dog's breed. But scientists had not been able to identify breed from DNA alone in more than a few cases until now."
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The Scientist
Don't Let Science Become Another Victim of 9-11
[requires 'free' registration]
"Science and technology have been enlisted in the fight against terrorism. The US Department of Homeland Security is investing over $1 billion per year in R&D. The National Institutes of Health is devoting even more, nearly 6% of its $28 billion R&D budget. US universities, national laboratories, and industrial R&D establishments all have become involved. While the nation is calling on the scientific community to serve these vital missions, it is also implementing policies that could cause serious, long-term damage to the science and technology enterprise.
These policies have affected the ability and willingness of foreign students and visitors to come to the United States to study or work. They've affected how we handle biological agents in our laboratories, how we regard scientific publications, and how we treat sensitive information. They've affected the conditions that federal agencies attach to contracts and sometimes to grants. And they've affected the atmosphere in university labs and government installations."
redux [12.19.03]
[requires 'free' registration]
"Although many scientific journals are now aware of their responsibility regarding publication of such research, what about when they receive manuscripts on work that is not intentionally related to dangerous pathogens, but which could nevertheless be misused?"
"Even though publishers are now becoming more aware of their responsibilities, the Internet presents a threat that has so far received little attention. An audience member noted, however, that in many cases, "the cat is out of the bag" with work that is posted onto the Internet which has not been submitted for peer review in a scientific journal."
redux [09.20.03]
[requires 'free' registration]
"As exemplified by the well-publicized cases of Thomas Butler, David Kelly, and Steven J. Hatfill, the fallout from the War on Terror has been particularly hazardous for scientists. Donald A. Henderson, who was inaugural director of the US Office of Public Health Preparedness, which coordinates the national response to public health emergencies, has accused the FBI of losing "all perspective" and of being "out of control" in the Butler and Hatfill investigations.
The dangers are summed up by the case of Butler, chief of the division of infectious diseases at Texas Tech University."
redux [09.13.03]
"In one telling situation, 32 scientists and editors connected to some of the most respected scientific journals have agreed to self-censor any advances they think might compromise national security.
"That's a chilling example of knowing whatever you do might not get published because an editor might decide that it will look bad for John Ashcroft," said Barry Bloom, dean of Harvard's School of Public Health."
redux [05.09.03]
"THE rapid progress of genomics means that the publication of yet another gene sequence for one of the Earth's many millions of species is not guaranteed to raise much interest. But this is no ordinary species. Bacillus anthracis is the bug that causes anthrax. The publication, in Nature, comes two months after a group of editors of the world's leading scientific journals announced they were worried about publishing information that could be used by terrorists to evil ends. New procedures had therefore been put into place to tackle this threat. The question is, do they work?"
redux [02.15.03]
"A group of leading scientific journals has announced measures aimed at restricting the publication of research which could be used by bioterrorists.
In a joint statement, the journals' editors say it is crucial that concerns over terrorism do not affect the release of valuable medical research.
But they say they recognise there may be occasions when new research data should be withheld from publication because it could be abused.
redux [01.14.03]
"Despite fears that bioterrorists will use DNA sequence data to create 21st century superpathogens, genomic science should remain public, The Institute for Genomic Research head Claire Fraser said at a special National Academies meeting on national security and the life sciences last week.
Her explanation: genomics just isn't good enough yet to provide the kind of tools terrorists need."
redux [12.01.02]
[requires 'free' registration]
"Scientific information that the US government wants to keep mum, but which can't officially be labeled "classified," has been designated "sensitive but unclassified." One example is the National Academy of Science's recent report on agricultural bioterrorism. Its chapter on bioterror case studies is available only on a need-to-know basis. Other professional groups may find themselves in the same boat, but the rules governing the category are anything but clear.
Reference: Enserink, M. 2002. Entering the twilight zone of what material to censor. Science 298(5598):1548."
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New Scientist
Europe revokes controversial gene patent
"A controversial patent on a breast cancer gene has been revoked by the European Patent Office, paving the way for cheaper screening across the continent. The verdict reflects the transatlantic disparities that make gene patents much tougher to uphold in Europe than in the US."
"The EPO has yet to spell out its precise reasons for revoking the BRCA1 patent, but New Scientist understands that the primary justification was that the application was not deemed "inventive"."
redux [08.18.03]
"An Australian biotech company, Genetic Technologies Ltd. (GTG), is stirring up controversy over its decision to enforce a series of patents, granted in the 1990s by the US Patent and Trademark Office, over the genetic diagnostic and mapping applications of non-coding, or junk, DNA."
"Scientists, including NHGRI chief Francis Collins and Sir John Sulston, are also upset over GTG's recent decision to ask academic institutions to sign research licenses."
redux [05.07.03]
"Scientists and commercial firms are scrambling to patent the genetic code of the virus thought to be responsible for Sars.
The group which produced the first entire genetic sequence of the coronavirus confirmed this week that it is seeking a patent to ensure that everyone has free access to the code.
It fears that a commercial patent could slow down research into vaccines and treatments."
redux [09.28.02]
"The Bay Area biotech firm that started the heretical campaign to ban gene patents hopes to stir more debate on the topic by sponsoring a scholarly smackdown in Washington, D.C., on Tuesday.
Santa Clara's Affymetrix broke ranks with the biotech industry in March by arguing that the United States should quit issuing gene patents because genes were invented by nature, not science."
redux [07.23.02]
"Patents on DNA sequences "inhibit innovation and development" and should be the exception rather than the norm, says a panel of leading UK bioethicists. In the past, biotech companies have said that without such patent protection they would not have the economic incentive to invest in expensive research towards new drugs.
A discussion paper, produced by the Nuffield Council on Bioethics (NCB), says that too many patents are of doubtful validity because they are being issued for genetic discoveries that are not adequately inventive. It recommends a number of significant changes to the way patents in the field are granted in the future and to limit possible adverse effects of those already issued."
redux [03.18.02]
"It's one of the toughest questions in biotechnology: Should businesses obtain patents on genetic information about plants, animals or humans? Michael Capellas, CEO of Compaq Computer Corp., surprised an audience of biotechnology specialists yesterday when he suggested that the answer should be "no.""
"In a comment that stunned the audience into several seconds of silence, Capellas responded to a question on the issue by flatly saying that companies shouldn't be able to patent genes. But he quickly backed away from the comment, pleading ignorance of all the ramifications of the issue. "If you're asking me what should be patentable," Capellas said, "I don't know.""
redux [02.07.02]
"Patents may make some genetic tests so expensive that ordinary labs cannot afford to offer them, says a team of researchers who interviewed staff at 119 US facilities.
Patents are meant to provide an incentive for companies to put their discoveries into the public domain. But some researchers wonder if prohibitive costs could in fact have the opposite effect, by keeping standard genetic tests out of the reach of all but a few laboratories. That would have far-reaching consequences not only for health care, but for clinical research and quality control, the researchers say."
redux [08.20.01]
""Like the Terrys, a rising number of patients, doctors and ethicists are questioning how the patent system handles genetic claims. Many say it awards too many patents, overly rewards their holders, and gives too little back to patients. Yet many industry voices complain the process is moving too slowly to keep up with galloping research and to yield medical care awaited by suffering patients."
"The gold rush days are about to begin,'' says Arthur Caplan, a bioethicist at the University of Pennsylvania. "There are so many targets that look so lucrative that they're falling all over one another to pursue opportunity after opportunity.""
redux [02.27.01]
"ONCE upon a time, pure and applied science were the same. Sir Humphry Davy discovered seven chemical elements, and invented the miner's safety lamp. Louis Pasteur investigated the properties of molecules, and worked out how to stop milk spoiling. Everybody thought that was admirable. Somehow, things have changed. Today the feeling is widespread that science and commerce should not - must not - mix. There is a queasy suspicion that the process of discovery is in some way corrupted if it is driven by profit."
"Far from compromising science, profit in both these cases - the development of new medicines and the elucidation of the genome - has animated it, and directed it towards meeting pressing human needs. It is a happy marriage. Davy and Pasteur would surely have approved."
redux [08.26.00]
"Nowhere are patents more central to the creative process than in genetic drug development, where human genes and their expressed proteins themselves are developed as therapies. The biotechnology industry in the United States has brought a handful of these crucial new products (recombinant human insulin, to name one of the most familiar) to market and is on the threshold of a bonanza of genetic drugs and vastly greater relief for ill and aging populations around the world.
Patent protection is the sine qua non of that bonanza."
redux [04.26.00]
""The analogy that I would use is that of a minefield," said Bob Levy, senior VP of science and technology for American Home Products. "We are spending an incredible amount of time now, when we find exciting targets and begin to validate them, in trying to define who has rights to what. And we're finding, in almost every product that we look at, that someone has patented the protein, the gene, a fragment, a diagnostic test." Levy noted that untangling patent rights, and determining which patents are dominant, are increasingly time-consuming and expensive tasks. And patent-holders must be paid. "The royalties that will be involved soon in some of the products that we are bringing to market, they're already up into the ten, fourteen, fifteen percent [range]," said Levy. "And that may increase with time.""
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The Scientist
Protein
expression patent fight
[requires 'free' registration]
"A fundamental U.S. biotech patent expired last week (May 5), accompanied by a flurry of legal activity. The patent holder and its licensee filed a patent-infringement lawsuit the day before the patent's expiration. They also asked the US Patent and Trade Office (USPTO) to extend the life of the patent.
Massachusetts biotech firm Repligen and the Massachusetts Institute of Technology (MIT) filed suit May 4 in US District Court, Boston, in which they allege patent infringement by ImClone Systems Inc., in the development and manufacturing processes of its anti-cancer drug, Erbitux (Cetuximab)."
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Bio-IT World
EBI Launches Genome Reviews Database
"The database addresses an important problem: The hundreds of complete genome sequences in the three public DNA databases - EMBL-Bank, GenBank and DDBJ - typically remain static after they have been deposited, even though they are constantly being annotated, revised, and updated by the research community.
Updated every two weeks, Genome Reviews includes some 2.5 million cross-references to many other resources such as encoded proteins in UniProt, the GO Annotation database, or information about related proteins in InterPro. "Perhaps most importantly," says developer Paul Kersey, "we've standardized annotations that are used inconsistently in the original submissions, so it's now much easier to compare the data across several genomes."
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Genome News Network
Biologists and Computers
"Moody's well-reviewed first book was Rebel Code , a history of the open-source movement focusing on Linux and its creator, Linus Torvald. In his second book, The Digital Code of Life , Moody shifts his focus to bioinformatics, which he defines as "the marriage of molecular biology and computing.""
"Moody's determination to include as much technical information as possible leaves little room for storytelling. And without a narrative to engage readers, some may remember that reading is a gateway activity that often leads to napping."
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Bio-IT World
Expert: Open Source Development Models Fall Flat
"Typical open source project development strategies work well for free software but don't flourish in commercial settings, according to one expert."
"Specifically, [Professor Jim Herbsleb of Carnegie Mellon University's International School of Computer Science] looked at cases where many developers from all over the world would successfully collaborate and coordinate to work on one piece of software. While looking at this, he also examined why this distributed development model has not thrived in industry. In fact, Herbsleb found that it takes companies more than twice as long to develop software in disparate locations than in one location."
redux [03.31.04]
"Australia's bioinformatics industry will increasingly rely on open source software as researchers look for inexpensive point solutions that are not just a "black box", according to delegates at an Australian Technology Park Innovations bioinformatics symposium in Sydney.
Sydney University senior lecturer in bioinformatics, Dr Bret Church, said open source is undoubtedly the founding stone of bioinformatics.
"We love it," Dr Church said. "It is made for research, and there was plenty out there when bioinformatics came along. On the way to solutions, and while exploring possibilities and avenues, open source code tends to play a leading role.""
redux [12.18.03]
"3rd Millennium wants to cash in on the software it spent seven years developing for various government and commercial clients - by giving it away free.
The Waltham, Mass.-based informatics consultancy and services firm has released its Data Centric Knowledge Management System for biotech and drug R&D under a GNU general public license (GPL)."
"The company is betting that, of those life science organizations deploying the software, some will want to buy support and maintenance contracts."
redux [11.20.02]
"Until recently, open source has often appeared to bioscientists as some sort of novelty, or, worse, a threat to IP protection. In the last few years, though, solid achievements in clustering, genomic data management, Web publication, and scores of specific "vertical" applications have established open source as a serious technical alternative.
Big Pharma and other biosciences are just starting to realize how open source can systematically cut costs, improve security, allow their own workers to shift attention back to their "core competences" from proprietary IT expertise, and even promote better science. We're in the midst of a dramatic evangelical movement that teaches better ways for open source IT to support bioscientific goals. Perhaps the most consequential shift is that participants have begun to understand that standards-based open source can enhance biosciences' fundamental values. These are exciting times for open source bioinformatics."
redux [09.30.02]
"Brenner, for example, stressed that while open sourcing "has potential in a generic sort of way," success depends on the operational and business models of specific companies.
Even considering a move to open sourcing can meet with resistance. "All of the instrument companies were brought up in closed-source shops, so they would have to change this fundamental attitude," explained Hood."
"THE OPEN SOURCE MOVEMENT has gained significant momentum of late, particularly within the bioinformatics field. While open source licenses vary widely, distribution of open source software typically requires delivery of both the object code and the source code. Most commercial software is delivered only in object code form, which is not easily read and modified by programmers.
The decision of whether to use open source software requires a careful analysis of various factors. In the right situations, open source software can be an excellent choice. In other cases, it can be disastrous."
redux [08.21.02]
"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."
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San Diego Union Tribune
Group seeks standards for handling data
""The idea is to collect this data from medical research and clinical environments and be able to make sense of it in ways that will drive down the cost of bringing new medicines to the people that need it," said Dr. John Reed, who heads the Burnham Institute in San Diego."
"Sun Microsystem's Howard Asher, director of Global Life Sciences in San Diego, worked with UCSD's Global Connect program to move ahead with the idea for developing standards."
""This (institute) is just one piece of many that can cut drug development time and cost to get a drug to market," said Dr. Jonathan Morris, chief executive of ProSanos. "It's not a magic bullet or panacea . . . but it does address part of the problem.""
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Macworld
Apple's $200,000 research-donation
"Apple will donate a Workgroup Cluster for Bioinformatics to five of "America's most important, innovative and visionary scientific research projects."
"The purpose of program is to provide innovative scientists with computer hardware that will enhance their ability to conduct their research in unique ways," according to Apple."
redux [03.23.04]
"The Xserve G5 uses a new version of the G5 processor from IBM that uses less power and generates less heat than the version used in Apple's current Power Mac G5 models. The Xserve line itself is a major component of Apple's push into the new server-oriented markets such as rendering farms, IT server rooms, and even scientific uses, which brings us to Apple's other announcement today, a new bio sciences cluster.
The company has announced the Apple Workgroup Cluster for Bioinformatics. The Cluster is based on the Xserve G5, and, as the name implies, is configured specifically for bio sciences. The solution comes with a software package from The Bio Team."
redux [02.12.04]
""For our [Mars] landing site work, we always get the highest-end desktop Mac we can find, so we just got one of the G5s with dual 2-GB processors and 8 GB of RAM," Matt Golombek, a planetary geologist at NASA's Jet Propulsion Laboratory, told the E-Commerce Times."
""If you pull up a shot of NASA after the [first] Mars landing and look at the desktops, you'll see a couple of PC laptops there, but you'll see more PowerBooks," Jon Rubinstein, senior vice president for hardware engineering at Apple, told the E-Commerce Times."
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The Scientist
How Did Natural Selection Shape Human Genes?
[requires 'free' registration]
Many selective forces must have influenced human evolution, but the only one that all population geneticists seem to agree upon is malaria. Time and again, studies have identified certain DNA polymorphisms--most famously, the ß-globin variant underlying red-cell sickling--that helped people resist this mosquito- borne disease. The reproductive success of such individuals spread these polymorphisms throughout regions where malaria is endemic.
Geneticists have been much more reluctant, in contrast, to conclude that other selective forces favored or dis-favored particular polymorphisms. That attitude is changing, however, as technological advances allow the rapid sequencing and analysis of genomes."
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Nature: Science Update
'Junk'
DNA reveals vital role
"If you thought we had explored all the important parts of our genome, think again."
"The segments, dubbed 'ultraconserved elements', lie in the large parts of the genome that do not code for any protein. Their presence adds to growing evidence that the importance of these areas, often dismissed as junk DNA, could be much more fundamental than anyone suspected."
redux [02.21.04]
"Genetic Technologies (GTG), the Australian biotech company at the heart of a controversy surrounding its patents on the genetic mapping applications of noncoding (junk) DNA, has added another large company to its tally of licensees -- Laboratory Corporation of America Holdings (LabCorp)."
"Last year, GTG granted licenses to Sequenom, Perlegen Sciences, Myriad Genetics, and Pyrosequencing, among others."
redux [11.18.03]
"Investors piled into Genetic Technologies yesterday after the biotech company announced that two US groups it was suing for patent infringement had settled out of court."
"The Melbourne-based Genetic Technologies has consistently warned it would sue any company, research institution or university that infringed its patent over the so-called junk DNA."
redux [08.18.03]
"An Australian biotech company, Genetic Technologies Ltd. (GTG), is stirring up controversy over its decision to enforce a series of patents, granted in the 1990s by the US Patent and Trademark Office, over the genetic diagnostic and mapping applications of non-coding, or junk, DNA."
"Scientists, including NHGRI chief Francis Collins and Sir John Sulston, are also upset over GTG's recent decision to ask academic institutions to sign research licenses."
redux [05.19.03]
[requires 'free' registration]
The dark side of the moon is a misnomer. Light reaches la luna's entire surface, but one half is unviewable from Earth. The human genome, the now essentially decoded map of life, likewise has a light side--the genes encoding mRNA and protein--and a dark side, which is coming into view for the first time. The dark side encompasses more than its opposite: The majority of the genome comprises intronic regions, stretches of repeat sequence, and other assorted gibberish that has attained the ignoble dubbing, "junk."
The first exploratory missions to the human genome's faceted surface are turning up traces regarding the extent of the junk."
redux [11.21.02]
"In a provisional patent application filed July 31, Pellionisz claims to have unlocked a key to the hidden role junk DNA plays in growth -- and in life itself.
Rather than being useless evolutionary debris, he says, the mysteriously repetitive but not identical strands of genetic material are in reality building instructions organized in a special type of pattern known as a fractal. It's this pattern of fractal instructions, he says, that tells genes what they must do in order to form living tissue, everything from the wings of a fly to the entire body of a full-grown human."
redux [08.28.02]
"In a new study in the August 29 issue of Nature, researchers at The Wistar Institute identify a cohesin-containing protein complex that reshapes chromatin to allow cohesins to bind to DNA. In doing so, they also identified the locations on the human genome where the cohesins bind. Somewhat to their surprise, the binding sites were found to be a repetitive DNA sequence found throughout the human genome for which no previous role had ever been identified. These bits of DNA, known as Alu sequences, are liberally represented along those vast stretches of the human genome not known to directly control genetic activity, sometimes referred to as junk DNA."
redux [08.09.02]
"Results of a new University of Michigan study suggest that junk DNA - dismissed by many scientists as mere strings of meaningless genetic code - could have a darker side.
In a paper published in the Aug. 9 issue of Cell, scientists from the U-M Medical School report that, in cultured human cancer cells, segments of junk DNA called LINE-1 elements can delete DNA when they jump to a new location - possibly knocking out genes or creating devastating mutations in the process."