{bio,medical} informatics
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The New York Times
To Study Disease, Britain Plans a Genetic Census
[requires 'free' registration]
"In 2003, Britain plans to undertake the world's most ambitious study of the origins of disease.
Looking forward to the day when people will know their genetic makeups and request a precise picture of their risks of developing various diseases, the study organizers plan to assemble a database of medical information about 500,000 Britons, including their DNA."
redux [11.08.00]
"For the past decade, Stanford Medical Informatics has combined clinical informatics and bioinformatics research and training in an explicit way. The interest in applying informatics techniques to both clinical problems and problems in basic science can be traced to the Dendral project in the 1960s. Having bioinformatics and clinical informatics in the same academic unit is still somewhat unusual and can lead to clashes of clinical and basic science cultures. Nevertheless, the benefits of this organization have recently become clear, as the landscape of academic medicine in the next decades has begun to emerge. The author provides examples of technology transfer between clinical informatics and bioinformatics that illustrate how they complement each other."
"In his article "The promises of health care" J.H. Bemmel writes that "some 25 years ago, there was no shortage of optimism about expert systems in health care...it becomes clear that perhaps the early researchers were overenthusiastic, many challenges lie ahead, much fundamental research still has to be done."
Is therefore only wise not to look too far ahead, not to be too overenthusiastic again. 10 years ahead seems to be a good pick. A white paper by the American College of Informatics published recently made predictions for the year 2008, a year "not so far in the future as to be ungrounded in current realities""
"The future brings not only new innovations and applications: It will also affect Medical Informatics as a discipline:
- Its imminent merger with bioinformatics
- the emergence of sub-disciplines in medical informatics."
redux [06.07.00]
"Basic biological science has always had an impact on clinical medicine (and clinical medical information systems), and is creating a new generation of epidemiologic, diagnostic, prognostic, and treatment modalities. Bioinformatics efforts that appear to be wholly geared towards basic science are likely to become relevant to clinical informatics in the coming decade. For example, DNA sequence information and sequence annotations will appear in the medical chart with increasing frequency. The algorithms developed for research in bioinformatics will soon become part of clinical information systems. In this paper, I briefly review the intellectual roots of bioinformatics and how the field has evolved in the last few years. Fortunately, a core set of scientific paradigms have provided a focus to the field. Even in this short period, however, there has been a change in the nature of the questions being asked and the types of experiments being attempted. These changes are consistently leading bioinformatics towards problems of clinical relevance. Some molecular biology information systems already have important clinical implications. I will discuss the differences in the culture and approach to science of clinical informatics and bioinformatics, but will argue that the two disciplines share important intellectual challenges which make them very closely allied fields (despite the cultural differences). Finally, I will identify a few areas common to both disciplines where developments in one field may help catalyze faster progress in the other. For example, useful database integration technologies have (arguably) matured more rapidly within bioinformatics than in clinical informatics. At the same time, clinical informatics embraced the idea of controlled terminologies relatively early, and offers lessons to those in bioinformatics attempting similar tasks."
redux [05.15.00]
[requires 'free' registration]
""I just wanted to do something good," Mr. Fuchs said. "But once money came into the picture, why not have it be shared with me?"
These days more and more patients are asking the same question. Laboratories offer tests for more than 700 human genes, with more being discovered almost daily. And, for almost every gene, some medical institution or some company owns a patent on its use.
"The value of patients' tissues has potentially gone up enormously," said Dr. Barry Eisenstein, the vice president for science and technology at the Beth Israel Deaconess Medical Center in Boston. But, Dr. Eisenstein said, patients whose cells provided the genes that have been patented are almost never compensated."
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NHGRI
50 Years of DNA: From Double Helix to Health
"April 2003 will witness the historic culmination of one of the most important scientific projects in history: the sequencing of the human genome. In addition, April 2003 will mark the 50th anniversary of another momentous achievement in biology: James Watson and Francis Crick's Nobel Prize winning description of the DNA double helix.
Furthermore, the April 2003 publication of a landmark scientific report will describe the future of the field of genomics, and the role that the National Human Genome Research Institute (NHGRI) and the National Institutes of Health (NIH) will play in enabling that future."
[ via bioinformatics.org ]
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The Guardian Unlimited
Cult scientists claim first human cloning
"A cult which believes that humans were first created by aliens claimed yesterday that it had won the clandestine and increasingly bizarre race to produce a human clone. It said a baby girl was born on Thursday from an egg fertilised by a skin cell from her mother.
Brigitte Boisselier, who calls herself a bishop of the Raelian sect, offered no proof to back her claim at a press conference in Florida, but said an independent panel of scientists would be allowed to verify it with DNA tests in the next eight or nine days."
"A former ABC News science editor, Michael Guillen, said during the news conference that he was arranging "independent, world-class experts” to run DNA tests needed to verify successful cloning. Guillen said he was not being paid by Clonaid."
"Guillen, who said he would find experts to perform DNA testing, is not wholly trusted by scientists. In a recent book on "Voodoo Science,” physicist Robert Park -- an outspoken critic of pseudo-science and fakery who is a professor of physics at the University of Maryland and director of the Washington office of the American Physical Society -- said of Guillen: "Although uniquely positioned to help millions of scientifically unsophisticated viewers understand how the natural world behaves, Guillen chose instead to portray the darkest superstitions that beset our species as open scientific questions.”"
"Less than six years after the cloning of a sheep named Dolly, a group claims to have engineered the first cloning of a human being."
"Here are key facts about the chronology of cloning."
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Businessweek
From Proteins to Profits
" Proteomics is the study of human proteins, the building blocks of life -- and the culprits behind diseases. Oxford was arguably the first to tackle proteomics on a large scale."
" Now, the former chief of one of the world's largest pharmaceutical companies is trying to resurrect Oxford. Some six months ago, the board hired a new CEO, Dr. David Ebsworth, who used to run the worldwide pharmaceuticals operations of Bayer (BAY ), the German drug and chemical giant. Ebsworth has wasted no time in implementing changes. He has hired new management and broadened Oxford's focus to proteomics, cancer research, and a niche drug market known as "glyco-lipid storage disorders." The goal: profitability within three years."
redux [12.06.02]
"In the twilight of 2002, the proteomics flame is a mere glimmer. The term has devolved from buzzword to dirty word, and VCs have grown skeptical of p-word business models."
"Proteome players are also fighting a backlash. "There's a lot of singed hair and burnt fingers from some of the genomic endeavors, and big pharma is being more careful," says Affinium CEO John Mendlein."
redux [11.22.02]
[requires 'free' registration]
"The Human Proteome Organization (HUPO), which will tomorrow launch its first world congress, faces the unique challenge of bringing together the public and private sectors in a coordinated global research effort aimed at mining the human proteome, says HUPO president Sam Hanash.
Contributing to that effort are researchers in Europe, Asia-Oceania, and North America. "We are witnessing a tremendous interest in proteomics on the part of countries that a decade ago were not active in genomics and that may well become leaders in proteomics in a short time," said Hanash, an oncologist at the University of Michigan in Ann Arbor."
redux [10.10.02]
"The Institute for Systems Biology, a Seattle nonprofit research center led by gene-sequencing pioneer Dr. Leroy Hood, said yesterday it has landed a $19.8 million contract from the National Institutes of Health to advance understanding of proteomics, the study of how proteins interact in the body."
In the wake of recent breakthroughs unraveling the human genetic code, proteomics is increasingly being viewed by scientists as the next step. Scientists say genes provide the instructions for making proteins, and proteins carry out the real action inside the cell."
redux [12.20.01]
[requires 'free' registration]
""Just because you use a protein doesn't make you a proteomics researcher," Joshua LaBaer, director of the Institute of Proteomics at Harvard Medical School, told BioMedNet News.
After the success of genomics, "everyone wants to think of proteomics as the next great science," but calling themselves proteomics researchers "is not really fair," LaBaer said. "A lot of people who claim to do genomics aren't genomic researchers either," he added. "They are just studying gene sequences.""
redux [12.12.01]
[ summary can be viewed for free once registered ]
"Proteomics aims to chart the ebb and flow of tens of thousands of proteins at once to produce snapshots of life inside cells. The technology to pull it off doesn't exist yet, however, and the competition is stiff for those proteins that can be nabbed using current methods. But this young field is growing up fast. This special News Focus looks at the promise and roadblocks of biology's latest wellspring. The package includes profiles of GeneProt, the biggest proteomics test-bed to date, and Stephen Burley , a crystallographer who is leaving academia to direct research at a small start-up company. Other stories discuss the potential of protein chips for new diagnostics and research tools and the problems faced by companies attempting to patent proteins."
redux [08.15.01]
"A new study of the proteomics market forecast that the proteomics market would grow nearly six-fold to $5.6 billion by 2006 from $963 million in 2000.
In its report, consultancy firm Frost & Sullivan said the increase would be driven by a shift towards the analysis of proteomes following the discovery that the human genome contains fewer genes than originally predicted.
"Proteomics adds value to drug discovery by charting the distribution of proteins, identifying and characterizing proteins of interest, and elucidating the participation of proteins in biochemical pathways boosting the number of potential targets around which lead compounds can be designed and screened," Eric Gay, a Frost & Sullivan analyst, said in a statement."
redux [07.11.01]
"Their bold proclamation has raised a few eyebrows in the scientific community. "It's easy to say that you'll complete a comprehensive proteome map," notes Marc Vidal of the Dana-Farber Cancer Institute in Boston. "But none of us knows what that means." There may be only one genome, but when it comes to the proteome, different proteins can be more or less active in different cells at different times during development, under different physiological conditions or in different disease states. The proteome's nature "makes it hard to define what we're doing--not just Myriad, but all of us," remarks Joshua LaBaer, director of the Institute of Proteomics at Harvard Medical School. "There's no such thing as a human proteome," adds Keith L. Williams, CEO of Proteome Systems, headquartered in Sydney, Australia. Look at the liver, for example, he says: "After a glass of red wine, you'll have a different proteome."
redux [06.20.01]
"Scientists thought about trying to catalogue all the proteins in the body a decade ago.
But it seemed impossible, and was therefore impossible to fund. Researchers moved on to the much simpler job of sequencing the human genome.
They were right to do so. Cataloguing proteins turns out to be downright confusing. Lately, more and more biotech companies are entering a field they call "proteomics," an ugly word searching for a focus group."
redux [03.13.01]
[requires 'free' registration]
"A commonly expressed opinion is that a single Human Proteome Project can never match HGP's success. Eric S. Lander , director of the Whitehead Center for Genome Research in Cambridge, Mass., notes that biologists simply don't know how to characterize the proteome "from end to end, nailing every protein. The tools are not ready. And it's not clear that [such a project] makes sense." He contrasts proteomics to HGP where "there is a certain fixed number of base pairs--about three billion--and we were going to get them all. And so it had a beginning and an end to it."
redux [01.31.01]
"Can sequencing do for the proteome what it did for the genome?
On Wednesday, a number of world-renowned researchers in the field of proteomics issued a resounding " no."
"When a company has phenomenal success with strategy A, you want to do strategy A on the next subject," said John Richards, a professor of organic and biochemistry at California Institute of Technology, referring to current corporate attempts to map the proteome.
"This doesn't work," he said."
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Wired News
Gene Science: Matter of Mice, Men
"Anyone who's feeling particularly evolved this holiday season might take this into consideration: The genome of a mouse is 99 percent similar to a human being's.
Even more disturbing to those who consider themselves a higher form of life than, say, a sprig of mustard, is the fact that the human genome is only 15 percent larger than the mustard plant's.
But for scientists, these facts are thrilling."
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Nature: Science Update
Humans more similar than different
"Inuit or Basque, Laotian or Pashtun: we're much more similar than we are different, says the most detailed analysis of human genetic variation to date.
When it comes to sensitivity to drugs or diseases, the analysis also suggests that a person's account of their ethnic origin is almost as reliable an indicator as intrusive genetic tests.""
redux [11.01.02]
"In response to early concerns about racial profiling, scientists at the Human Genome Project went out of their way to downplay ethnic variations. Humans are 99.9 per cent alike, the sequencing showed, a figure that was leveraged into a call for global harmony. "The concept of race has no genetic or scientific basis," said Francis Collins, head of the Human Genome Project, at the White House ceremony to celebrate the genome completion.
Yet a great deal of controversy is now brewing over that 0.1 per cent. A growing number of scientists want to use such information as a way to find cures for devastating diseases. If we know more about the genes that cause susceptibility to cystic fibrosis in whites, or sickle cell anaemia in blacks, they argue, we will move closer to a solution for these illnesses. "Ancestry is imperative to biomedical research," says Mark Shriver, an anthropologist at Pennsylvania State University."
redux [10.30.01]
"Race should not influence drug prescriptions, warn geneticists. Genetic differences between individuals give a better indication of who will respond well to a medicine, a new study shows."
Geneticists have known this for a while. "It's no surprise that skin pigment is a lousy predictor of physiology," says Howard McLeod of Washington University School of Medicine in St Louis, Missouri. This study is the first to prove it."
redux [07.20.01]
[requires 'free' registration]
"Scientists planning the next phase of the human genome project are being forced to confront a treacherous issue: the genetic differences between human races."
"With the decoding of the human genome largely complete, government scientists are beginning to construct a special kind of genetic map that would provide a shortcut to locating the variant human genes that predispose people to common diseases."
"The question the scientists face is whether that map should chart possible differences that may emerge among the principal population groups, those of Africans, Asians and Europeans."
redux [03.18.01]
"Genetics research is demonstrating that the differences in appearance among groups are profoundly incidental, but these differences do have a genetic basis. And although it's true that all people have inherited the same genetic legacy, the genetic differences among groups have important implications for our understanding of history and for biomedical research. These complications in an otherwise reassuring story have thoroughly spooked the leaders of the public and private genome efforts. The NIH has been collecting information about genetic variants from different ethnic groups in the United States, but it has refused to link specific variants with ethnicity. Celera has been sequencing DNA from an Asian, a Hispanic, a Caucasian, and an African-American, but it, too, declines to say which DNA is which.
This strategy of avoiding the issue is almost sure to backfire. It seems to imply that geneticists have something to hide. But the message emerging from laboratories around the world should be hailed, not muzzled. It is one of great hope and promise for our species."
redux [06.11.01]
[requires 'free' registration]
"Scientists have long suspected that the racial categories recognized by society are not reflected on the genetic level.
But the more closely that researchers examine the human genome -- the complement of genetic material encased in the heart of almost every cell of the body -- the more most of them are convinced that the standard labels used to distinguish people by "race" have little or no biological meaning.""
""Ethnicity is a broad concept that encompasses both genetics and culture," Dr. Anand said. "Thinking about ethnicity is a way to bring together questions of a person's biology, lifestyle, diet, rather than just focusing on race. Ethnicity is about phenotype and genotype, and, if you define the terms of your study, it allows you to look at differences between groups in a valid way."
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Genomeweb
International Collaboration Announces Draft Sequence of Rice Genome
Scientists today announced the completion of a draft of the rice genome Oryza sativa japonica ."
""The rice genome's sequence is crucial to our scientific understanding of the staples of life," Rita Colwell, director of the National Science Foundation, said in a statement. "With this data we open new doors at all levels of research [including] universities, private industry and government.""
redux [09.06.02]
"Unravelling the blueprint of rice may be the most important breakthrough genetic science has achieved."
"Because rice is mankind's most important food crop - the staple diet for half of humanity - the researchers say reading its genome is of more importance than decoding mankind's own genetic code."
redux [04.06.02]
[requires 'free' registration]
"Rice is "the Rosetta stone of the cereals," Dr. Wing said. Once researchers have found an important gene in rice, they can look for its counterpart in other crop plants, or insert the rice gene itself since the genes of all these crops are thought to be largely interchangeable."
"Syngenta has already developed a microchip holding an array of DNA fragments that recognizes some 24,000 rice genes and can tell which genes are switched on at each stage of the plant's development. Because of corn's genetic similarity to rice, the rice gene chip can also recognize 90 percent of the genes in corn.""
redux [03.28.02]
"One of the world's largest agricultural companies is putting finishing touches on a plan to make public huge amounts of genetic information about the rice plant, an effort to accelerate research aimed at improving one of mankind's most important crops."
"The plan Syngenta is working on is, in part, an effort to stave off an incipient controversy."
"Syngenta's decision to share some data with the International Rice Genome Sequencing Project may help to quiet a growing controversy about public access to data gathered through privately funded sequence projects. But the decision by Science to allow Syngenta to publish without making its data available in Genbank will undoubtedly spur further debate."
redux [03.19.02]
"Prominent gene researchers fear that access to the complete DNA sequence of rice, the world's most important food crop, will be restricted when it is published in a scientific journal."
"Science says the issue is complex. "We have to weigh the benefit of publishing some data so that it is in the public domain or having it all deposited as privately held trade secrets," says Science spokesperson Ginger Pinholster. "In the case of the human genome it was felt that publishing was the best option - for rice, the case is even stronger.""
"Twenty leading geneticists are protesting against a deal that will allow a multinational company to control who has access to the complete DNA sequence of the rice genome - the most important food crop in the developing world.
The scientists, who include British Nobel laureates Sir Paul Nurse and Sir Aaron Klug, are up in arms against a plan to lock away the entire rice sequence on a company database rather than having it published in the open scientific literature."
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The Mercury News
Margaret Steen: Be realistic about shifting to biotech
"If you do decide to go back to school, consider what area of biotech will make the best use of the skills you already have.
For example, bioinformatics -- the intersection of biology and computer science -- needs people with a background in computer science who also understand biology enough to help companies handle the data that their research generates. If you find an area where you can build on your previous experience, rather than trying to start from scratch, you'll have a better chance of success."
redux [08.26.02]
"Three years after Indiana University launched its School of Informatics, the school is growing into the role that officials envisioned."
"Perhaps most significantly, the number of IU informatics majors topped 1,100 this year, almost triple what it was a year earlier."
"The Bloomington campus had its first informatics classes in 2000 and offers master's degrees in bioinformatics, chemical informatics and human-computer interaction. Undergraduate majors study informatics along with a "cognate area" such as computer science, economics and telecommunications."
redux [08.06.02]
"The number of card-carrying bioinformaticists entering the job market more than tripled in 2002, according to a recent survey of US university degree programs."
"This new wave of graduates -- not to mention their prospective employers -- are the first beneficiaries of the remarkable growth seen over the last few years in the number of degree programs: While only six dedicated bioinformatics-degree programs existed before 1997, 13 universities added new programs in 2001, and seven schools are adding bioinformatics-related degrees in 2002."
redux [10.05.01]
"Almost all companies say they're having trouble finding people with expertise in bioinformatics, the use of computers to solve complex biological problems. The human genome's mapping has ushered in a new era of genetic medicine, but to capitalize on this knowledge, researchers need to know how to use powerful computers to translate raw biological data into information useful for developing new therapies.
"There's a struggle to have people that are well educated in both computer science as well as biology," said David Pot , InforMax's director of application sciences. "We recognize we need super scientists, but those super scientists don't have the training to write super software.""
redux [03.05.01]
"Move over Information Age. Make room for the age of bioinformation.
Experts have already dubbed bioinformatics - a hybrid profession pairing biology and computer science - the career choice of the decade.
"There is a crying need for experts in bioinformatics and this is not something that will just fade away," said Dr. Leena Peltonen, chairwoman of the Department of Human Genetics at UCLA."
redux [05.10.00]
" "The results of our current survey make it clear that the majority of these jobs are not being filled by graduates of formal programs - who by our count represent about 15 percent of the positions advertised in 1997. And, we believe the 15 percent figure to be an overestimate given that ads have been growing over time and our most recent ad count is for 1997, a year earlier than our hiring data. This leads us to infer that most of the advertised positions are being filled by individuals trained in informal programs and by individuals who change jobs. The distinct possibility exists that a number of these jobs remain vacant for a period of time, an issue not studied here. Furthermore, our pipeline estimates (see Table 2) lead us to conclude that the number of individuals currently enrolled in formal programs falls far short of the number of positions that have recently been advertised." "
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Forbes
Genomics Revolution Actually Happens
"Investors may have stopped watching, but drug companies are finally beginning to wrench tangible benefits from the human genome. Two years after a boom fed by hype, a revolution finally is starting to take hold not in how drugs are invented, but in how they are tested.
Merck (nyse: MRK - news - people ), the world's third-largest drug company, is using gene expression arrays, also known as DNA chips, to keep clinical duds from reaching expensive animal or human trials. Separately, Millennium Pharmaceuticals (nasdaq: MLNM - news - people ) used similar chips in its late-stage clinical studies of its cancer drug, Velcade. Millennium's work is a big step toward so-called personalized medicine, in which treatment would be tailored toward individual patients based on genetic makeup."
redux [10.07.02]
"Perlegen has spent upwards of $50 million on the chemistry, instruments, computers and brain power needed to pull off this hellish job of proofreading.
Yet there was only a muted celebration a few weeks ago, when Perlegen's scientists decided they'd found the last of the 1,717,015 SNPs that biotech firms have been seeking since the human genome was sequenced in 2000.
[requires 'free' registration]
"Pharmacogenomics holds the promise of delivering safer, better designer drugs--and profits--to pharmaceutical manufacturers. But the technology also poses a challenge to the industry's current, highly successful business model that relies on one-size-fits-all blockbuster drugs.
For small biotech companies and large drug manufacturers alike, pharmacogenomics remains only one component of genome-based research and consumes only a small part of the $30 billion (US) in annual pharmaceutical research and development funding, according to the Pharmaceutical Research and Manufacturers of America (PhRMA). "It's an area where we are seeing movement, but it's not there yet," says Gillian Woollett, associate vice president for biologics and biotechnology at PhRMA."
redux [09.10.02]
"Collins is unimpressed by the hubbub that has shaken the industry lately. "In some quarters there was a misunderstanding, or naivete, about how having the sequence was going to solve everything. And there were some business models built solely upon the notion of quick profits, particularly selling subscription databases."
He dismisses talk about a foundering industry. "I think that every pharmaceutical company is still expecting that genomics will be the platform upon which they will build the next generation of drugs," says Collins. Others echo Collins' perspective. "We will change the treatment of cancer," says Variagenics' Adams. And there is no hint of doubt in his voice."
redux [08.08.01]
"Pharmacogenomics requires the integration and analysis of genomic, molecular, cellular, and clinical data, and thus offers a remarkable set of challenges to biomedical informatics. These include infrastructural challenges such as the creation of data models and data bases for storing this data, the integration of these data with external databases, the extraction of information from natural language text, and the protection of databases with sensitive information. There are also scientific challenge in creating tools to support gene expression analysis, three-dimensional structural analysis, and comparative genomic analysis. In this review, we summarize the current uses of informatics within pharmacogenomics, and show how the technical challenges that remain for biomedical informatics are typical of those that will be confronted in the post-genomic era."
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The New York Times
New Premise in Science: Get the Word Out Quickly, Online
[requires 'free' registration]
"A group of prominent scientists is mounting an electronic challenge to the leading scientific journals, accusing them of holding back the progress of science by restricting online access to their articles so they can reap higher profits.
Supported by a $9 million grant from the Gordon and Betty Moore Foundation, the scientists say that this week they will announce the creation of two peer-reviewed online journals on biology and medicine, with the goal of cornering the best scientific papers and immediately depositing them in the public domain."
redux [11.15.02]
"Having persuaded the Energy Department to pull the plug on PubScience, a Web site that offered free access to scientific and technical articles, commercial publishers are taking aim at government-funded information services offering free legal and agricultural data.
"We're delighted with the decision [to shut down PubScience]," LeDuc said. "The administration has done a tremendous job of hearing our concerns and responding to what we've always considered to be our legitimate concern."
redux [09.24.02]
[requires 'free' registration]
"The UK's Office of Fair Trading says that the prices for scientific, technical, and medical (STM) journals are too high because normal competitive forces have been suspended. Libraries are paying too much. The prices of STMs are rising faster than inflation, and the disparity between for-profit and not-for-profit journals is obvious. Part of the problem is that the journals compete on quality, not price, so libraries are prone to skip the cheaper journals for the better, more expensive ones. Bundling journals also skews the market.
Goodman, S. 2002. "Unusual forces" are pushing journal market off course. Nature 419(6904):239.
redux [09.05.01]
[requires 'free' registration]
"Publishers of established scientific journals have thus far resisted demands for freer access. In its campaign to make biomedical research literature available free online, Public Library of Science is now taking a new tack: It hopes to publish peer-reviewed, electronic journals.
"If we really want to change the publication of scientific research, we must do the publishing ourselves," says an announcement posted Sept. 1 on the group's Web site. "It is time for us to work together to create the journals we have called for."
redux [04.24.01]
"When a molecular biologist or a biochemist has made a discovery - often after many months or even years of tedious experiments - they tell the rest of the world by publishing their results in a scientific journal. So far, these journals have controlled who can read them and who cannot - but maybe not for much longer.
E-mail, Internet discussion groups, electronic databases and pre- or e-print servers have already transformed the way scientists openly exchange their results. And in the life sciences, researchers are now demanding that their work be included in at least one free central electronic archive of published literature, challenging the traditional ownership of publishers. The demand has sparked widespread discussions among scientists, publishers, scientific societies and librarians about the future of scientific publishing. The outcome may be nothing short of a revolution in the scientific publishing world."
redux [09.20.00]
"How should biomedical research be communicated? How should research be assessed and validated?"
"Below are abstracts, transcripts, and biographies from the conference. Some presentations did not lend themselves to transcription. Where possible we have supplemented them with editorials from the speakers.
We have also commissioned editorial articles from several speakers and delagates at the meeting."
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BioMedNet
India's millions mint a genomics treasure
[requires 'free' registration]
"India is set to reap substantial rewards in the field of functional genomics, thanks to an invaluable genetic resource and highly advanced IT expertise, predicts Samir Brahmachari, director of the country's Institute of Genomics and Integrative Biology in Delhi."
"Brahmachari sees India's genetic resource - not the biological samples themselves, but the associated information - as a tradable commodity. Data can be processed using India's unparalleled IT expertise, he says: The country's IT industry generated about $10 billion in revenues this year, and has continued to grow by 50% each year over the past decade. The information, once processed, represents an "intellectual-property protectable" commodity, he says."
redux [06.23.02]
"Also, India's success in information technology provides excellent opportunities in the field of bioinformatics.
"Traditional IT companies are translating their strong capabilities in data mining and warehousing to business models based on biological data," says the report, citing examples of IBM's India Research Lab and Satyam's five-year agreement with the Center for Cellular and Molecular Biology, Hyderabad."
redux [02.13.02]
"India's biotech boom could even dwarf software in coming years if you trust the most optimistic projections. Much of our $2.5-billion biotech market relies on low-end products like vaccines, but experts predict that as more start-ups come up, that could change dramatically."
"The need to dive into this ocean of genetic data for hidden treasures has created a whole new discipline--bio-informatics, the science of using information technology (IT) to decipher the genomic jumble. Thanks to a flourishing IT industry, bioinformatics is today the darling of venture capitalists, drug firms, and, of course, IT majors. So, Satyam Computers has signed a five-year alliance with CCMB to create, store, and annotate genetic databases, and it is angling for contracts from global bigpharma to sequence genes and build protein catalogs. Strand Genomics, a Bangalore-based bio-informatics start-up, is designing tools to accelerate drug discovery."
redux [09.17.01]
"India has the potential to garner 8-10 per cent of the global software market in the next few years from the current levels of just 1.5 per cent, but the country?s planners need to focus on improving computer penetration and use of Indian made software in the industry.
This was the view of FC Kohli, chairman, Tata Consultancy Services, while speaking at Connect 2001, an international conference and exhibition on information technology, communication technologies and bioinformatics, which opened on Thursday. Currently, India's IT exports are about $8.7 billion."
redux [08.27.01]
"THE mood is one of caution as far as bioinformatics is concerned. The beginning of the year saw hype building up around the fledgling industry as the next big gold rush for India.
But six months after the first bioinformatics seminar in the country, with the IT industry's lesson on hype fresh in mind, things are moving at a more sedate pace."
"In India, bioinformatics training institutes have already begun to mushroom. Bangalore and Hyderabad have around five private training institutes between them. However, the industry is sceptical about the quality of manpower these centres can supply because most of them have short-term courses offering basic skills, says Dr. Sabharwal. In all fairness to them she adds, "We need to wait for a few months to see the outcome of it all.""
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The Economist
The race to computerise biology
"Bioinformatics: In life-sciences establishments around the world, the laboratory rat is giving way to the computer mouse—as computing joins forces with biology to create a bioinformatics market that is expected to be worth nearly $40 billion within three years."
"Welcome to the world of bioinformatics—a branch of computing concerned with the acquisition, storage and analysis of biological data. Once an obscure part of computer science, bioinformatics has become a linchpin of biotechnology's progress. In the struggle for speed and agility, bioinformatics offers unparalleled efficiency through mathematical modelling. In the quest for new drugs, it promises new ways to look at biology through data mining. And it is the only practical way of making sense of the ensuing deluge of data."
redux [11.30.02]
"Bioinformatics as a business, not to be confused with bioinformatics as a field of study, is at an interesting crossroads. As an academic branch of learning, bioinformatics remains mostly what it always was -- a cross-disciplinary endeavor between computer science and molecular biology. But bioinformatics as a money-making proposition has different criteria for success, and it has received a lot of bad press lately, some of it deserved."
"During this golden age, bioinformaticists developed software that computational biologists could use to make biological discoveries based on genomic data. But the industry swerved off course by selling expensive systems that focused on the individual pieces of a solution, without heeding downstream processes that were the actual bread-and-butter of our customers. Bioinformatics has always been about integrating data and converting it into information. When it loses that focus, it loses its value to the customer."
redux [11.05.02]
[requires 'free' registration]
"The biotechnology industry is facing one of its worst financial squeezes ever. The prices of many biotechnology stocks have plummeted, and Wall Street's vaults have snapped nearly shut, making it almost impossible for capital-hungry companies to finance themselves."
"Another sector that has suffered is bioinformatics, which uses computers to analyze masses of genetic data. Several young companies have gone out of business or been acquired for a pittance after sales did not meet expectations."
redux [07.09.02]
"Most agree that venture money is there for companies -- but the pressure must seem insurmountable for entrepreneurs, who probably feel like they have to give the perfect business pitch to venture capitalists just to get a foot in the door.
"If people aren't rethinking their models, they're nuts; if they were waiting for Viaken to be their wake-up call, they're nuts," Nelson says."
redux [04.18.02]
""Bioinformatics is heterogeneous, but many bioinformatics [tools] fulfill a narrow niche," said Williamson. "There is room for someone to consolidate, but I don't know if that is needed or necessary. Plus there's always an academic coming up with the next thing. So it's a hard business to sustain."
Bioinformatics "is great for smaller companies," he went on. And there are "people who can tie the islands of analysis together, and who have the resources to pull it off, but is that a business? That's the million dollar question. And will anyone buy it if you can pull it together? Everybody wants to be the Microsoft Office of bioinformatics, but I'm not sure that's going to happen.""
redux [03.11.02]
"The emerging field of bioinformatics, the use of computers to analyze the inner workings of biology, is transforming an industry that just a decade ago relied on the manual labor of chemists and biologists. But even as it does so, bioinformatics is floundering as a business.
Shares of public companies that sell biological data or software are trading at a fraction of what they did two years ago. Dozens of companies have crowded into the field. Some have folded; others have survived only by morphing into drug-discovery companies.
''It's a hard market to build a business around,'' said Oliver Fetzer, a vice president at Boston Consulting Group."
redux [02.11.02]
"LIKE EVERY BUBBLE, this one had to burst. Stock prices of many bioinformatics firms have fallen sharply in recent years. LION Biosciences of Germany went public at $40 a share and now trades at about $13. Iceland's DeCode is worth a fourth of its former high. Even Celera, the U.S. firm that helped decode the human genome, is off its peak.
Falling stock prices are a symptom of a greater disappointment in bioinformatics. A few years ago the laborious and quirky process of drug discovery seemed on the verge of giving way to new streamlined, data-driven methods. Some firms organized the blizzard of genetic data into databases that researchers could mine with search engines from still other firms. Software companies built computer programs that modeled what goes on in human cells and even whole organs. Many investors came to believe that bioinformatics would open a new avenue to the discovery of drugs. But this avenue simply hasn't materialized. Says biotech analyst Earling Refsum at Nomura Bank in London: "Bioinformatics has not helped Big Pharma get more drugs into the pipeline.""
redux [01.03.02]
"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.
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 [03.14.01]
"The story proclaimed in its lead, "Move over Information Age. Make room for the age of bioinformation." You could picture bleary eyes opening all over the Bay Area. The story went on to note that a San Jose consulting firm was predicting a 10 percent annual growth in the bioinformatics market for years to come; and that the National Science Foundation estimated that 20,000 new jobs in the field would be created in the field in just the next four years.
If that wasn't enough, the rest of the section was filled with page after page of biotech firms listing job openings - in powerful juxtaposition to the endless lists of dot-com layoffs just a few pages earlier. Picture Starbucks spit-takes from Marin to Santa Cruz.
Wow! Rewrite that resume to emphasize that biology course you took in college. Roll your Aeron chair down to the nearest lab. Trade that black turtleneck for a white lab coat..."
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O'Reilly Network
An Interview with Jim Kent
"Jim Kent was a graduate student in biology at the University of California, Santa Cruz (UCSC), when he wrote the program that allowed the public human genome team to assemble its fragments just before Celera's private commercial effort. His program ensured that the human genome data would remain in the public domain. Kent wrote the 10,000-line program in a month because he didn't want to see the genome data locked up by commercial patents.
Kent will give a keynote speech at O'Reilly's upcoming Bioinformatics Technology Conference, February 3-6, in San Diego. Here we talk to Kent about the future of genomics, modeling biological processes, and open source bioinformatics."
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eWeek
Gateway Gears Up Grid Computing Push
"Gateway Inc., the PC maker best known for its consumer systems and talking cow, is linking thousands of display PCs in its nationwide chain of stores to create a grid computing environment capable of scaling to 14 teraflops of performance."
In a pilot test, Inpharmatica Ltd. reproduced the results of a bioinformatics job run on the Processing on Demand system and its own computer farm, said CIO Pat Leach. The London-based company turned to Gateway because it wants to cut the amount of time it spends managing its 2,300-processor computer farm. "We are a drug discovery company, not an IT shop," Leach said. "We would much rather employ people to do innovative analysis of the data than spend time building computers.""
redux [11.15.02]
"The Santa Clara, Calif.-based chipmaker said this week that it is working with universities, software developers and server manufacturers to come up with supercomputer-class systems, built around Intel technology, for pharmaceutical engineering, genetic research and other biotech projects, said Rick Herrmann, Intel's manager for worldwide high-performance computing.
"There seems to be a rush toward building out the infrastructure around life sciences," Hermann said. "Every country in the world is looking for bioinformatics to be the next technology pillar: Singapore...Taiwan...the U.S. Even Ireland is looking at it.""
redux [09.04.02]
"Billionaire Michael Dell is in the Buffalo area today to help the University at Buffalo unveil a powerful new computer cluster provided by the company that he founded and continues to run."
""We've installed hundreds of these clusters. (But UB's) would be one of the larger ones, not only for us but in the world," Dell said. "And the amazing thing is we got this up and running in 60 days.""
redux [12.05.01]
"The world's largest computer makers, faced with sagging consumer demand, are betting that the huge data crunching needs of nascent biotechnology firms will grow into a multi-billion dollar market for their equipment and consulting services over the next decade."
""The average individual can't comprehend what has happened in the last half dozen years, where the two greatest medical discoveries, the genome and the microchip, have converged," said Cal Stiller, chief executive of the $250 million Canadian Medical Discoveries Fund."
"We need companies that are on the informatics side that say 'holy cow', we have just stumbled onto the mother lode! We know nothing about mining that area, but we can build the best drilling equipment out there," added Stiller."
redux [06.26.01]
"In 1998, biotech upstart Celera Genomics needed a supercomputer to help it map the human genome. It didn't turn to IBM , which built 204 of the 500 fastest supercomputers. Both Celera and its academic competition, the Human Genome Project, used machines built by Compaq Computer. Two years later, Compaq is the leading seller of supercomputers to biological researchers.
But IBM noticed that biologists now need microprocessors as much as microscopes. A year ago, it used $100 million to start a division that sells computers, software and services to biotechnology and drug companies. This life sciences division has had some success; pulling into second place behind Compaq, it must do better."
redux [08.14.01]
"For years, technologists have dreamed that information technology and biotechnology would someday converge into one seamless superscience that could crack the molecular code of disease and yield a gold mine of new treatments and cures. It always seemed so logical, even if it never quite seemed to happen. Some very big names in tech -- Bill Gates ( MSFT ), Paul Allen, and Jim Clark, among others -- for years have been placing bets on so-called convergence companies that promised to exploit the merging of computing and biotech. Allen alone has investments in more than 50 of them, mostly obscure companies that use words like "genomics," "bioinformatics," and "proteomics" to describe what they do. This industry is so new it hasn't settled on a single name yet."
"Now, like a middle-age actor who has just been discovered, convergence has hit the big time. Corporate giants such as IBM ( IBM ) and Compaq ( CPQ ) are pouring $100 million dollops of cash into "life science" projects that mesh computers and biotech."