{bio,medical} informatics
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Washtech.Com
A New Outlet for Venter's Energy
"Tapping a $100 million research endowment he is creating from his stock holdings, Venter plans to scour the world's deep ocean trenches for bacteria that might be able to convert carbon dioxide, the gas released when cars and power plants burn fuel, back into solid form without needing a lot of sunlight or other energy."
"Venter emphasized that from now on, his ventures will be set up as not-for-profit corporations. "I'm not in business anymore," he said."
"Venter, who turned 55 in October, said he will use the cash and clout collected during his terms at The Institute for Genomic Research, Human Genome Sciences, and Celera as seed money for the foundations, which he will run."
"Through his foundations, though, Venter has also stuck a finger in the eyes of detractors who said he was too obsessed about financial reward to worry about good science, let alone ethics. Industry insiders may now be asking where their foundations are."
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BBC
A New Outlet for Venter's Energy
"The genetic details of 500,000 people are to be collected and stored in a central UK pool, following the approval of £45m in funding.
It is hoped the pioneering "biobank" scheme will provide valuable information to help fight illness and disease."
redux [09.02.00]
"Robert talks with Barry Eisenstein M.D., Vice President of Science and Technology for Beth Israel Deaconess Medical Center, and Professor of Medicine at Harvard Medical School, about his hospital's participation in creating an international tissue bank. They will be asking patients for permission to sell tissue left over from surgery. The tissue will be used by scientists worldwide for genetic research."
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."
redux [10.02.00]
"Several academic hospitals in the United States are forming partnerships with biotechnology companies to provide them with human tissue for research, treatment, and drug development purposes, in a series of arrangements which raise wide legal and ethical issues."
"Clearly, a bank of human tissues is needed to enable further research, diagnosis, and therapeutic development. The ability to relate the molecular findings of the human genome project to clinically relevant material and data is dependent on ventures such as those of Ardais and academic centres.
The bioethical questions and repercussions of these partnerships, however, continue to be problematic."
redux [05.11.01]
[requires 'free' registration]
"Guidelines on patient confidentiality could undermine medical research, with lethal consequences, said one of the world's leading epidemiologists today. "By making [patient] records anonymous, so even bona fide medical researchers cannot access them, [the guidelines] will cause many deaths," insisted Richard Peto, co-director of the Clinical Trial Service Unit and Epidemiological Studies Unit at the University of Oxford. "It's not beneficial to anyone.""
"Peto was highlighting concern about the threat to the UK's patient registries, which monitor disease, from heart conditions to cancer. The registries link identifiable data from numerous sources, and feed the information to researchers."
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The New York Times
Scientist Reveals Genome Secret: It's Him
[requires 'free' registration]
"When scientists at Celera Genomics announced two years ago that they had decoded the human genome, they said the genetic data came from anonymous donors and presented it as a universal human map. But the scientist who led the effort, Dr. J. Craig Venter, now says that the genome decoded was largely his own."
""That doesn't surprise me; sounds like Craig," said Dr. James D. Watson, the co-discoverer of the structure of DNA."
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The Seattle Times
Creating a 'hothouse' for bioscience research
"When Dr. Leroy Hood sits down to talk about his latest ambition, he takes all of 10 seconds to warm up.
"I think we'll lead the way toward revolutionizing new ways of understanding biology," he said."
"But Hood's enthusiasm these days has been limited by finances. More than two years after an unceremonious exit from the University of Washington, he has been scrounging for money. And his newest vision — using high-speed computers to turn the DNA jumble into something useful for predicting and preventing disease — requires lots of money."
redux [01.19.02]
"The integration of bioinformatics with these systems approaches is an integral, essential feature. One of the things that we stress is that in the future it's going to be increasingly important for people in bioinformatics to be intimately associated with data producers, because no matter how smart you are you can't model biological complexity--it's just too complex. The only way we're going to understand it is through the integration of these global experimental observations, together with powerful computational tools for analysis, and ultimately, for modeling.
A mistake that a lot of people in bioinformatics have tended to make is thinking that you can set up a bioinformatics center and it can work in isolation from the biology, and it can study all these great databases and learn lots and lots about biology. In vitro biology and in silico biology are all popular terms, but it isn't true, and it isn't going to be true in the future."
redux [04.18.01]
[requires 'free' registration]
"Systems biology is a loosely defined term, but the main idea is that biology is an information science, with genes a sort of digital code. Moreover, while much of molecular biology has involved studying a single gene or protein in depth, systems biology looks at the bigger picture, how all the genes and proteins interact. Ultimately the goal is to develop computer models that can predict the behavior of cells or organisms, much as Boeing can simulate how a plane will fly before it is built.
But such a task requires biologists to team up with computer scientists, engineers, physicists and mathematicians. The structure of universities makes that difficult, Dr. Hood said."
redux [03.17.01]
"When Lee Hood started the Institute for Systems Biology, a project to build an integrated research supercenter for the biological sciences, few doubted the validity of the concept, but many wondered whether the technology existed to make it work.
Now, in a sign that others are also willing to gamble on the idea, systems biology is attracting commercial attention. Beyond Genomics (BG), a startup based in Cambridge, Mass., is attempting to glean medically-relevant information from multiple systems simultaneously, from genes to metabolites, by using software that identifies patterns in these systems caused by disease."
redux [02.26.02]
"Over the last few years, there’s been an explosion of information in biology. The mapping of the human genome gave biologists unprecedented detail about some 30,000 to 40,000 genes. Efforts are also under way to identify the thousands—and potentially millions—of proteins encoded by those genes. Researchers are now pursuing the next logical step in integrating all this data: systems biology.
The goal is to understand not just the functions of individual genes, proteins and smaller molecules like hormones, but to learn how all of these molecules interact within, say, a cell. Biologists hope to then use this information to generate more accurate computer models that will help unravel the complexities of human physiology and the underlying mechanisms of disease. The biggest payoff: faster development of more-effective drugs."
redux [05.15.01]
"Our Mission is to develop an integrated, easy-to-use environment, the workbench , which will enable biologists to create, manipulate, display and analyze biological models at molecular, cellular and multicellular levels. We are focusing on biochemical networks including mass action kinetics, metabolic pathways, stochastic simulation, gene expression and regulation."
"One of the key aspects of out project is to facilitate collaboration among existing developers and users of system biology software. We aim to do this by providing an open-source software infrastructure which will enable collaborators to freely use and share each other's computational resources."
redux [07.11.00]
"For most of us, formal biology education begins with complex systems--the traditional dissection of a frog in high school biology class is virtually a rite of passage in the U.S.
But the way many people learn about and invest in biotechnology is at the smallest end of the spectrum--the genome, now often described as the "periodic table" of biology. Genomics and all its related buzzwords have been responsible for much of the media attention, government grants, and investment capital heaped on the biotech industry over the past decade.
But just as there is a whole lot of chemistry that happens in between the periodic table and a birthday cake, there is a lot of biology in between the genome and a living organism. With the completion of biology's periodic table within sight, academics and industry players alike are pondering the best way to apply our hard won knowledge.
The only problem is, the path from genome to system seems to get harder the more we learn."
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BBC
Computing power brought online
"The British arm of an ambitious plan to harness the computer processing power of the country's universities has being officially opened."
"The centre will co-ordinate national and international work to get computers connected to the net to work together on scientific problems.
"We have only begun to investigate how the Grid can help tackle some of the big challenges facing the scientific community," said Professor Malcolm Atkinson, director of the Centre."
""Internal Grids are an enormous untapped resource," said Scott Kahn of Accelrys. "It's already in-house, it's already running, and it's already being maintained. It's rare that in a day, you can change your processing power by a thousand times."
Stuart Henderson of PwC Consulting said life sciences' evolving R&D model will be a "big driver" of Grid computing's growth. The emerging "learn and confirm" model will stand the old R&D model on its head by placing in silico research first and research on patients and in laboratories second."
redux [04.02.02]
"For example, Baird claims that one Platform customer, a bioinformatics company, planned to spend approximately $3 million on new hardware to expand its computing resources. Instead it spent around $150,000 to install a grid, and it no longer needs to buy the new hardware.
Despite the potential benefits, grid-ready applications remain a rare bird. The technology best serves problems that are computationally intensive using algorithms that developers can break down into discrete computational units, such as genetic research where scientists must mathematically analyze thousands of genes in combination to find matches."
redux [03.04.02]
"It is commonly observed that people overestimate the short-term impact of change but underestimate long-term effects.10 It will surely take longer than some expect before Grid concepts and technologies transform the practice of science, engineering, and business, but the combination of exponential technology trends and R&D advances noted in this article are real and will ultimately have dramatic impacts.
In a future in which computing, storage, and software are no longer objects that we possess, but utilities to which we subscribe, the most successful scientific communities are likely to be those that succeed in assembling and making effective use of appropriate Grid infrastructures and thus accelerating the development and adoption of new problem solving-methods within their discipline."
redux [02.19.02]
[requires 'free' registration]
"A worldwide computing project known as grid, whose long-term vision is to bring the power of supercomputing to individuals, is taking a step out of the laboratory and into the commercial mainstream."
"The grid researchers in the labs have used their technology to enable far-flung groups of scientists to collaborate on complex projects that require lots of computing firepower including climate modeling, high-energy physics, genetic research and earthquake simulations."
redux [02.06.01]
"Sixty-nine percent (69%) of respondents said they were addressing the lack of processing power by deploying GRID, clustered or distributed computing technologies. Of those, 100% are utilizing clusters. And according to the study, 69% of those are Linux clusters.
"In addition, 46% are deploying distributed computing technology and 23% are utilizing GRID computing somewhere in their organization."
redux [11.28.01]
"IBM will supply the University of Pennsylvania and four hospitals with computers that will link into a computing "grid" to check for breast cancer, the company will announce Wednesday.
The grid will be used to detect breast cancer in patients, store mammograms in digital form and identify populations that are particularly susceptible, the company said in a statement. The system can be used, for example, to compare a new mammogram to a previous year's image to detect changes.
IBM, along with rivals such as Sun Microsystems and Compaq Computer, have been backing grid computing, which joins computers and storage systems into a large pool of computing power.
redux [11.21.01]
"The US National Science Foundation has announced a $12 million programme - called the NSF Middleware Initiative (NMI) - to develop middleware: software that allows scientists to share applications, scientific instruments and data, and collaborate with their colleagues across high-performance networks.
The effort will build on the success of the Globus project in developing middleware tools for grid computing, and will integrate Globus and other emerging middleware components into a well-tested, comprehensive, commercial-quality, middleware distribution package that runs on multiple platforms. These middleware distributions will be disseminated to research labs and universities worldwide."
redux [11.12.01]
"Platform Computing, a company that tries to harness the collective computing power on computer networks, has signed a deal to commercialize an open-source supercomputing project.
Platform is working with the Globus Project to commercialize the Globus Toolkit for governing the use of computers and storage systems joined into a large computing "grid," Platform said Wednesday."
"Grid computing, though, often uses higher-powered computers than mere desktop PCs, and has attracted the interest of IBM, which thinks corporate customers as well as academics will use grid methods. IBM is working with Globus to boost this expansion.
Grid computing has long held potential for some types of computing tasks--typically those that don't require as much communication between one computing task and another. For this reason, they don't replace single mammoth supercomputers such as those from Cray. However, grid computing is popular among pharmaceutical companies and others."
"Computational Grids are emerging as a popular paradigm for solving large-scale compute and data intensive problems in science, engineering, and commerce. However, application composition, resource management and scheduling in these environments is a complex undertaking. In this paper, we illustrate the creation of a virtual laboratory environment by leveraging existing Grid technologies to enable molecular modeling for drug design on distributed resources. It involves screening millions of molecules of chemical compounds against a protein target, chemical database (CDB) to identify those with potential use for drug design. We have grid-enabled the molecular docking process by composing it as a parameter sweep application using the Nimrod-G tools. We then developed new tools for remote access to molecules in CDB small molecule database. The Nimrod-G resource broker along with molecule CDB data broker is used for scheduling and on-demand processing of jobs on distributed grid resources. The results demonstrate the ease of use and suitability of the Nimrod-G and virtual laboratory tools."
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MIT Technology Review
Biotech Computing Opens Up
"Open-source programming created a revolution in operating systems, making Linux a popular alternative to Microsoft’s Windows. The idea—to make software source code open for modification by anyone—has caught on in large part because more eyes on the software means rapid improvements and fewer bugs; companies like Red Hat have turned the idea into profits by selling easily installed, well-supported versions of Linux. Now Cape Town, South Africa-based Electric Genetics is, for the first time, applying that business model to biomedical software.""
redux [02.01.02]
"First, Ewan argued that open source makes sense because it follows good and well-known scientific principles."
"Second, Ewan emphasized that in biological research it's not the software that's important--it's the data. Since the actual data matters much more than the tools used to process it, there's a big benefit in sharing software."
"The third reason Ewan gave for supporting open source was that molecular biology and medicine will be most advanced by the creation of a common infrastructure--and this is something best done with open source tools."
"In the face of the mounting discussion around this topic, the Open Bioinformatics Foundation - the non-profit umbrella group that supports BioPerl, BioPython, BioJava, BioDAS and other projects -- released a position statement at today's panel discussion. According to OBF board member Steven Brenner of the University of California, Berkeley, the statement was necessary to distinguish the OBF from organizations "with similar sounding names" and "because everybody was asking us where we stood on the topic."
The OBF statement takes a more moderate stance than the openinformatics.org petition. Noting that "scientific software developed with public support should be distributed under terms analogous to those applied to biological materials," it concludes, "We encourage institutions to delegate to their scientists the opportunity to select non-restrictive and open source licenses for their software.""
redux [01.16.01]
"A debate is heating up in the academic community over whether software that is generated by publicly funded research must be released with an open source license. The Internet is one example of how releasing research code benefited the public, but the trend seems to be changing now, and universities are more likely to consider the profit opportunity. The Bayh-Dole Act paved the way for the privatization of publicly funded resources, but not everyone is happy with the results.
Against the tide of privatization comes a group of bioinformatics researchers and programmers with an online petition to require that all software created by publicly funded research projects be licensed as open source. They have founded a group and a Web site, OpenInformatics.org, to further this cause.
Here we present two opposing viewpoints on this issue."
redux [01.07.01]
"The Open Source movement is infectious, it seems. It has bubbled up in the field of bioinformatics – gene research software. Gene research is already a burgeoning area of activity, which is predicted to deliver numerous benefits to the health industry. It is also an area where software counts and where universities have managed to prosper from their activities. US universities lodge about 2000 patents each year, many in bioinformatics, and these patents contribute a good deal of revenue – an amount estimated at about $5 billion per annum, or ten percent of their total budgets. Thus Open Source activities in this area are not universally welcomed."
"Over the past several years, open-source software development has won high-profile adherents in the business world -- including the likes of IBM and Sun Microsystems. But it has always had its strongest fans in the academic world, where open-source software is seen as a natural extension of the idea that the fruits of academic research should be shared with everyone.
But now some academic programmers on the cutting edge have found that the licensing office is proving a more formidable obstacle to progress than the limits of their imagination and skill."
redux [11.26.01]
"Before computer whiz Steven E. Brenner accepted his tenure-track research post at the University of California-Berkeley last year, he demanded that the school's intellectual property police leave him alone.
Brenner prevailed. He's now one of the few experts in the emerging field of bioinformatics with the freedom to distribute his work, software used in gene research.
``It's vital to what we do,'' says Brenner, who supports a movement to force universities to allow ``open source'' publishing of gene research software code."
redux [08.18.01]
"Steve Brenner, assistant professor and leader of a computational genomics research group at the University of California, Berkeley, said he fears that many academic bioinformaticists are unaware of a legal risk they face on a daily basis: contributing to open source software projects without explicit permission from their institutions.
While many employers have clauses in their employment contracts that restrict the creation and use of open source software, bioinformatics programmers at universities are often not as attuned to copyright issues as their industry counterparts. This fact, Brenner said, raises the possibility that a good portion of biological open source software is currently being produced illegally."
"The issue seems to be coming to a head in the academic world now, as more universities are exploiting the revenue stream made possible by their copyright and patent holdings. ?If you?re a software developer, the university holds rights to your software, but if you?re an English professor or Law professor and publish a book, they?re not the least bit interested in copyright,? said Thomas Field, an attorney at the Franklin Pierce Law Center affiliated with the Association of University Technology Managers."
redux [11.05.01]
"Computers are supposed to help biotechnology, right? Isn't bioinformatics all the rage right now? Well, it is, but with popularity comes legal questions that many companies don't address until it's too late."
"It seems that many biotech companies don't realize that a computer vendor may have the rights to the software, and ultimately, the work that the biotech companies do.
For example, if a biotech company orders a computer network to help it sequence the genome of yeast, the company may ask the vendor to customize the software it will use to do the sequencing. However, the question is, who owns the right to that customized software--the biotech company or the software programmer?"
redux [08.23.01]
"This report outlines recent activity in open source software development within the discipline of bioinformatics. I present the relevant highlights of two bioinformatics meetings held in July 2001 in Copenhagen, Denmark: the Bioinformatics Open Source Conference and the Intelligent Systems for Molecular Biology Conference. The report also describes a large number of projects and groups important to bioinformatics open source software development. The appendices include meeting programs, the currently accepted definition of open source software, and descriptions of important online biological data sources."
redux [07.27.00]
"Good software forms seamless connections; as George Orwell said of prose, the best is like a window pane: transparent. The obscurity of commercial binaries is an obstacle to good quality communication between systems. In healthcare, good communication is too important to remain proprietary. Software developers should remain confident that there will always be work for the future in discovering, providing, and adapting applications for organizations, and training people to use them. This, rather than the sharp-suited gouging of Bill Gates wannabees, should become the predominant business model for software in the British NHS. Software engineering will become a profession more like medicine and the law: in which practitioners earn a fair hourly reward for their experience at interpreting, evaluating and applying knowledge from a specialized domain to the benefit of their clients. Current models, which restrict the sharing and development of knowledge, are certainly counterproductive and arguably unethical. Open source is the future: all we have to do is built it."
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The Boston Globe
Life sciences boost slumping IT firms
""We'll spend 20 to 25 percent more each year [on IT] as we expand into areas we have not been in before," says John Murphy, the CuraGen chief information officer. Many biotechs like CuraGen are moving into clinical trials and developing drugs in addition to their traditional role of supporting large pharmaceutical companies in identifying drug targets."
""We're heavily invested in bioinformatics so we need fewer people," Murphy says. "We're fully computerized and [big pharmaceutical companies] are not. They have legacy systems and would love to be able to do what we do. We can [find new drugs] faster, cheaper, and with greater probability of success.""
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The New York Times
Celera Shifts Marketing of Database
[requires 'free' registration]
"The Celera Genomics Group is moving out of the business of selling the database it developed by sequencing the human genome, people close to the company said."
"The move, expected to be announced this morning, is the next step in Celera's shift from being an information vendor — the "Bloomberg of biology," company officials have called it — to being a drug developer. It will partially divorce the company from what has been its core business since it was founded in 1998 and raced the publicly funded Human Genome Project to determine the three billion letters of the human genetic code."
"Terms of the intra-corporate transaction call for Celera to give ABI exclusive marketing and distribution rights to the CDS, as well as access to its content, in exchange for a royalty stream on revenues to be generated by the new knowledge business. Celera will continue to earn revenue from current CDS customers, it said.
The move was made to "free Celera's executive team to focus on therapeutic discovery and development with the same access to this genomic and biological information it has presently while maximizing the return to Celera from its CDS product," Applera said."
"The failure is representative of the difficulty that bioinformatics startups are having in selling genomic information to pharmaceutical companies. Although the market for bioinformatics tools is estimated to be more than $1 billion, most of that money is being spent on in-house efforts at "big pharma," rather than on what smaller outfits have to offer."
"Others that built businesses around selling bioinformatics tools--like Celera Genomics and Incyte Genomics--realized the limitations of only selling tools and have already begun working on drug development."
redux [01.28.02]
"As all that was happening, people who know him say, White, Venter's boss, was getting grumpy. He well knew that Celera, under its original business plan, could not deliver long-range earnings growth that would justify what the market was paying for Celera shares. One top genetic scientist said White snapped to him in the midst of the publicity barrage, "'This is all nice, but we need a business plan.'"
They quickly came to the same conclusion as many minds before them: In biology and medicine, the only business plan that offers the potential of extraordinary profits is drug development. All the biotechnology superstars have been companies with hit drugs."
redux [06.09.00]
"Great discoveries do not necessarily make great businesses. Businesses have to sell something. Celera Genomics doesn't sell or make anything tangible. It hawks service and information. It sells access to lists of genes and computers that can sort through those messy lists. Samuel Broder, the company's executive vice president and chief medical officer, makes Celera sound like some kind of consulting company, or perhaps a library."
"Venter's quest could be a fable, with all sorts of morals about the power of capitalism and the importance of a single, brilliant, willful individual who used the market to shake the ivory towers of science. But those morals only hold if Celera succeeds, if business and science blend to propel the company into the future with breathtaking speed without rocketing it into the realities of the marketplace. Celera could become one of the great business success stories. It could also be a financial train wreck."
Right now, that makes it a very volatile stock."
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The New York Times
Despite Billions for Discoveries, Pipeline of Drugs Is Far From Full
[requires 'free' registration]
"This should be the golden age for pharmaceutical scientists. The deciphering of the human genome is laying bare the blueprint of human life. Medical research has increased understanding of disease. Robots and computers are turning drug discovery from a mixing of chemicals in a test tube to an industrialized, automated process."
"Instead of narrowing the list of compounds that might be useful in drugs, automation has broadened it — greatly increasing the number of formulas tested without yet delivering commensurate growth in safe and effective drugs."
redux [12.14.01]
"And although the drug industry remains the most profitable worldwide—it generated profits as a percentage of revenues four times the median rate for all Fortune 500 firms during the end of the last decade, according to a Kaiser Family Foundation report released that day—an editorial in this month’s Nature Biotechnology by David Horrobin, CEO of Laxdale Research, in Stirling, Scotland, had this to say: “With rare exceptions, most of the top 20 multinational pharmaceutical companies are not generating in-house the new products needed to sustain the rates of growth they have enjoyed in the past.
“No serious industry onlooker could dispute this depressing picture,” the commentary continues. “Although a few pharmaceutical companies may survive in their present form, most cannot…. A few brave companies are recognizing the obvious: large companies excel at sales and marketing but are hopeless at innovative research.”"
redux [05.26.00]
"Leaders in the genomics field, as in any other industry, will be companies that offer a value-added service. Large pharmaceutical companies agree on what that service should be: integration of all the genomics information available. With more information readily accessible, companies can easily decide on whether to continue investigating potential targets.
So the future of genomics companies may rest in their IT and software capabilities, a view held by Celera Genomics, a newcomer to genomics. “We are entering an era of ‘cyberpharmaceutical’ drug development,” says Samual Broder, executive VP and chief medical officer. “Pharmaceutical corporations will use genomic databases, and other relational databases involving gene expression, proteomics etc. as the foundation of their drug discovery pipelines. One of the immediate goals... is to produce appropriate databases and software to link biologic and genomic information.”"
""The data suggest that the biotechnology industry used to be more productive than Big Pharma, but not any longer," said Rebecca Henderson, a professor at MIT's Sloan School of Management whose been studying the question for six years. "The public biotechs have declining productivity… and look as if they are running into the same problems as Big Pharma."
On every metric that Henderson has studied---number of scientific papers and patents per R&D dollar, cost per new drug--she found that biotech and Pharma productivity were quickly converging, and both were getting worse. After spending six years of studying the question, Henderson says she has found "no systematic evidence that small firms are more productive.""
redux [11.29.01]
[requires 'free' registration]
"Glenn Giovanetti at Ernst & Young Life Sciences Industry Services, comments "You could really compare [today's situation] to a large degree with the first biotech boom in the late eighties and early nineties where the thought was, 'Hey, this is going to lead to better drugs faster,' and clearly that hasn't been the case." Having the genome in hand has brought about more drug targets, but, explains Ma, "People are getting more concerned that novel targets are going to have a higher rate of failures because there is less information on them." And when working in 10-year drug-development cycles, failures are costly.
Ma points to a trend of growth in clinical informatics that would effectively garner more information from expensive clinical trials instead of simply treating them as regulatory hurdles. "People are beginning to think through to how ... to take greater advantage of that information," he adds. But increasingly, the suppliers of genomic information have been looking to do the same thing.
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GenomeWeb
After the Fall, DoubleTwist’s Williamson Performs Stoic Postmortem
""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 [04.10.02]
"Bioinformatics is the gene genie that could bring back the boom years for IT."
"Bioinformatics is inherently different to the dotcoms because it is based on real rather than perceived needs," she said. "We will need cancer drugs, Aids drugs and more food, so the business projection is much more stable."
redux [03.12.02]
"While other IT sectors are struggling to keep their heads above water, the Bio-IT sector is gaining rapid momentum, according to analysis from IDC's new research and advisory service, Bio-IT Infrastructure. In addition, the research suggests the Bio-IT market will increase at a compound annual growth rate (CAGR) of 24% to nearly $38 billion by 2006."
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 [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 resumé to emphasize that biology course you took in college. Roll your Aeron chair down to the nearest lab. Trade that black turtleneck for a white lab coat..."
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BBC
Gene knowledge gap
"Research into human genetics is being limited by a lack of knowledge in other areas of science, say delegates at the Seventh International Human Genome Meeting (HUGO) in China.
Professor Lap-Chee Tsui, HUGO's outgoing president, says that our poor understanding of even basic human anatomy means that the human genome project is not delivering cures for genetic diseases as was hoped."
redux [12.08.01]
"The goal now is to redefine disease based on the underlying biological mechanisms, Lander said. By that token, diseases are going to surprise us. Reclassifying them means that some diseases will get split in half and other diseases will get lumped together because they have the same mechanism, although they may look different to us, he said.
What this portends commercially is up to smart companies to figure out, he said. Companies will need the ability to integrate scale and informatics; they'll need what he called a "fleetness" with technologies—not just one favored technology, but many kinds. They shouldn't worry too much about hoarding intellectual property rights nor depend on one technology platform. It is more important to understand the big picture in the first place in order to choose the right target, Lander said."
redux [08.01.01]
"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."
redux [11.16.00]
"Neither we nor our critics defined a revolution in medicine. We mean a paradigm shift in theory or practice. Sotos and Rienhoff's plea for "precise diagnosis" epitomizes the current paradigm. In most of those who will have common disorders, the interaction of genetic, environmental, and behavioral factors makes the quest for precise diagnosis illusive."
"The revolution in medicine will come with the recognition, based in part on genetic research, that the quest for single causes for common diseases will seldom be fruitful and that a new paradigm of a causal web must be adopted. Interventions must be directed at the most vulnerable points in the web. Sometimes this will involve biomedical interventions. At other times, it will involve modifying aspects of our social structure, lifestyle, or environment that increase the risk of disease."
redux [08.06.01]
[ summary can be viewed for free once registered ]
"The human genome sequence will dramatically alter how we define, prevent, and treat disease. As more and more genetic variations among individuals are discovered, there will be a rush to label many of these variations as disease-associated. We need to define the term disease so that it incorporates our expanding genetic knowledge, taking into account the possible risks and adverse consequences associated with certain genetic variations, while acknowledging that a definition of disease cannot be based solely on one genetic abnormality."
"In thinking about how clinicians use the term disease, we think that three elements should be considered: disease is a state that places individuals at increased risk of adverse consequences . Treatment is given to those with a disease to prevent or ameliorate adverse consequences. The key element in this definition is risk: deviations from normal that are not associated with risk should not be considered synonymous with disease. Our definition has three definable elements and should serve clinicians well. Of course, its success will depend on whether it becomes clinically useful."
redux [07.11.00]
"For most of us, formal biology education begins with complex systems--the traditional dissection of a frog in high school biology class is virtually a rite of passage in the U.S.
But the way many people learn about and invest in biotechnology is at the smallest end of the spectrum--the genome, now often described as the "periodic table" of biology. Genomics and all its related buzzwords have been responsible for much of the media attention, government grants, and investment capital heaped on the biotech industry over the past decade.
But just as there is a whole lot of chemistry that happens in between the periodic table and a birthday cake, there is a lot of biology in between the genome and a living organism. With the completion of biology's periodic table within sight, academics and industry players alike are pondering the best way to apply our hard won knowledge.
The only problem is, the path from genome to system seems to get harder the more we learn."
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Wired News
Sea Squirt Savants Celebrate
"It was a gorgeous, unseasonably warm 84-degree day in San Francisco suburb of Walnut Creek on Friday, but the jamboree attendees couldn't have cared less about the weather. Packed into one room, they stared at the sea squirt genome data on their laptops. Someone announced lunch. No one looked up. A reporter snapped their photographs -- still, no one moved."
""They've worked on aspects of this animal in some cases for most of their lives," said Dan Rokhsar, associate director for computational genomics at JGI and organizer of the jamboree. "This is their first glimpse of what the genome looks like.""
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BusinessToday
DNA chips leading medical revolution
"They're called DNA chips, and an increasing number of researchers couldn't do without them in their work developing drugs and improving on disease diagnosis and prediction."
""It's been a major technological breakthrough in biology," said Potter, a pediatrics professor at Cincinnati Children's Hospital Medical Center. "I think `revolutionized' is the proper word.""
"If it lives up to its promise, increasingly powerful microarray technology could revolutionize toxicology testing and provide entirely new insights of drug mechanisms.
But when can the pharmaceutical industry start trusting the technology? When should it make the leap from investigative, experimental technique to industry standard? And should the FDA start using microarray data to make critical decisions about the safety and efficacy of new drugs?
In short, are microarrays ready for regulatory primetime?"
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The Scientist
Once Promising Proteomics Market Sags
[requires 'free' registration]
"The once white-hot investment climate for proteomics has cooled, sending companies scrambling to recast themselves. Biotech analysts and investors say interest in proteomics companies peaked about a year ago with a rash of them competing in the technology and database sectors. In Europe, proteomics companies have also experienced a downturn, with biotech stocks falling 40% from their peak in 2000. Developing a new generation of technology and digitally mapping the proteome was, relatively speaking, the easy part.
Investors now dismiss such technology and database products as low-profit commodities."
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