Wednesday, October 31, 2001

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"To employ the method described in this article, it is important to ensure that all the firms being compared are similar in their developmental architecture. Typically, investors would use a set of comparable firms in valuing a firm but for illustration purposes, consider only one example. Exilixis - a company pioneering the use of genetically manipulatable model systems for biomedical research - should be compared to a company like Millenium, which has a highly integral development architecture, using a variety of technologies to develop biopharmaceuticals. The analysis shows that Exilixis is undervalued relative to Millennium.

A quick glance at equity reports shows Celera Genomics is compared to a variety of companies including Millennium. A company such as Celera, at this point in its development, has more in common with a "modular" company such as Incyte ? and analysis shows it is overvalued in relation to Incyte. Of course, to be fair to Celera, it is attempting to forward integrate into a structure similar to Millennium. The market suggests that it is midway in the continuum between modular and integral development structures."

redux [03.18.01]
GenomeWeb Three Celera Executives Leave Company, COO Moves to Applera

"According to Kowalski, the three confirmed changes were made to help the company through its "transition into the next phase" and to find staff "best fit for [those] roles."

"It's just part of the natural evolution of the company," she said in an interview. "The company is evolving on a lot of levels as we become a full-fledged therapeutic discovery company.""

redux [05.14.01]
Motley Fool Celera at a Crossroads

""Companies choose to adopt a product that is perceived to give some advantage over their immediate competitors and would like to see that protected in some way by the platform vendor (Celera) not running around selling it to everyone else, if they can avoid it. This is perceived to diminish the window of opportunity of the platform adopter to gain a lead over their immediate competitor. It is an element of sustainable advantage.'"

"Celera is certainly at a point of transition. It must either decide whether or not it wants to get into this collaborative, more vertical model of integrating itself with certain customers in big pharma or try to make its data and knowledge of it so valuable that big pharma of all walks of life simply has to have access to Celera data. I don't think the company has the time and money to do both. I don't think, for competitive reasons that I've explained earlier, big pharma is going to align itself, in large numbers, with a company that is selling the same applications to its immediate competitors."

Tuesday, October 30, 2001

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"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]
The New York Times Genome Mappers Navigate the Tricky Terrain of Race
[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]
The Atlantic Online The Genetic Archaeology of Race

"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]
The New York Times Do Races Differ? Not Really, DNA Shows
[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.""

"Through transglobal sampling of neutral genetic markers -- stretches of genetic material that do not help create the body's functioning proteins but instead are composed of so-called junk DNA -- researchers have found that, on average, 88 percent to 90 percent of the differences between people occur within their local populations, while only about 10 percent to 12 percent of the differences distinguish one population, or race, from another.

To put it another way, the citizens of any given village in the world, whether in Scotland or Tanzania, hold 90 percent of the genetic variability that humanity has to offer."

""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."

redux [08.01.00]
GeneLetter Inequalities and individualized medicine

"Over the next few years a number of competing groups - my own company, Sequenom, among them -- will sort through the diverse genetic material of the human species to find those variations called single nucleotide polymorphisms (SNPs, pronounced SNIPS) that predispose individuals to major clinical disorders."

"At present the overwhelming bulk of the effort to identify these natural variations is in the private sector. This is inevitable because SNPs that associate with major diseases are patentable, by traditional standards."

"Whatever ensues, it is clear that the rate of discovery of medically important SNPs and their conversion into clinically useful tools will not progress equally fast or uniformly for all segments of mankind."

"It will be easier to discover medically important SNPs in geographically isolated and inbred populations in which good familial records and where migration has not introduced confounding genetic variation. Iceland and Finland are strong early candidates."

redux [03.12.01]
GeneLetter Drawing DNA lines of ethnicity

"The idea of using genetics to determine ethnic heritage has been growing in popularity over recent years. When Rick Kittles, a geneticist at Howard University, offered to trace tribal roots via a $350 DNA test, African Americans flooded his telephone line with requests.

"Even if an identifying marker shows up, the result isn't necessarily definitive. While certain markers may be more common to one ethnic group, most also can be found in other populations as well.

"Because of the tremendous genetic variation within populations, it would be biologically impossible to settle on a limited number of genetic markers that could define "Native Americans," says Morris Foster, an anthropologist at the University of Oklahoma who has wrestled with the risks faced by Indian tribes interested in genetic research.

Furthermore, Foster added in an e-mail interview with GeneLetter, "it is absurd to try to define what is essentially a social identity by using biological characteristics. This, though, is how racism has historically worked."

Monday, October 29, 2001

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"The article appears in the Policy Forum section of Science, published by the American Association for the Advancement of Science. "Europe's Database Experiment" focuses on a 1996 EC decision to extend protection to ordinary facts such as telephone numbers, web addresses and weather data.European leaders have threatened to restrict the flow of information from Europe unless similar measures are passed in the U.S. Last March, U.S. congressional leaders pledged to pass a database protection bill in 2001.

"An environment in the scientific community of open access and free exploration is critical for advancing knowledge," says Onsrud, who chairs the U.S. national committee of CODATA, a group interested in the sharing of scientific and technical information worldwide among scientists. "We openly publish our research results. We seek peer review, invite others to critique our work, extract data from our work, retest hypotheses and challenge each other so that knowledge progresses. If you now need permission to take data from an electronic journal article before you can use it in a critique or extend from it, that has substantial potential for impeding the advancement of science.""

Friday, October 26, 2001

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"Only a few brave biologists showed up today for a meeting designed to explore their common ground with mathematicians, physicists and chemists in the field of high-performance computing. The event was planned to look for "synergies across the areas," meeting organizer Julia Goodfellow told BioMedNet News, but biologists were still in the minority."

"Bioinformaticist Mark Swindells, one of the speakers, mused about "the challenge of how to do our talks so that everyone can understand the technology.""

redux [08.08.01]
Scientific Computing World Putting a Rocket Under Computing for Life Sciences

"Rocket science, drug discovery, and bioinformatics might seem like strange bedfellows at first glance, but there is more to the story than meets the eye. Over the past year, a number of firms that specialised in aerospace and defence have announced major new initiatives: applying their computational technologies to pharmaceutical and bioinformatics problems."

"Finding solutions to datamining and information extraction problems in defence and aerospace has been a commonplace activity at the company over the years. The work, involving massive non-linear multidimensional data sets, requires integration and fusion of data from a wide variety of disparate sources as well as techniques to handle the inevitable non-linear characteristics of the phenomena of interest. Many of the problems and bottlenecks currently encountered in bioinformatics and computational biology exhibit analogous multidimensional and non-linear traits."

redux [07.21.01]
The Scientist New NIH Bioinformatics Center
[requires 'free' registration]

"Recognizing the growing importance of computational and information sciences to biology, the National Institutes of Health is establishing a new Center for Bioinformatics and Computational Biology (CBCB). The new center is designed to support research and training in areas that merge biology with computer sciences, engineering, mathematics, and physics.

"The future of the biological sciences will be driven by advances in bioinformatics and computational biology," says Marvin Cassman, director of the National Institute of General Medical Sciences (NIGMS)."

redux [06.15.01]
IBM Systems Journal Deep computing for the life sciences

"Knowledge gained from the sequencing of the human genome promises to change our lives. Powerful computing techniques have been used to acquire the knowledge gained so far, and still more powerful techniques will be required to fulfill the promises of genetically based drug design, medical diagnosis and treatment, and agricultural applications, among others. This issue of the IBM Systems Journal - and the companion issue of the IBM Journal of Research and Development - is devoted to papers on deep computing for life sciences. Included in this issue are papers that address associated biological, computational, and informational challenges."

Thursday, October 25, 2001

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"Ardais Corp. is building the world's best human tissue bank.

Starting with what would normally have been discarded tissue from major hospitals, this small private company has developed a powerful set of tools to distinguish its collection from all others: procedures to ensure the quality of the frozen tissue, protocols to protect the confidentiality of donors, and computer programs to make accessing the tissues a breeze for researchers."

"But when the phrase ''tissue bank'' was uttered during a recent interview, Ardais president and chief executive Eric B. Gordon blanched."

redux [09.02.00]
NPR : All Things Considered Tissue Banks

"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]
The New York Times Who Owns Your Genes?
[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 [05.11.01]
BioMedNet "Failure of integrity" over data protection threatens disease monitoring
[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."

Wednesday, October 24, 2001

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"More fundamentally, we are starting in the big bioinformatics set-ups to really push the limits of hardware and algorithms. A consultant came around and looked at our system and was shocked at the level we push our machines--when everything is up and running we cream through a year's worth of CPU cycles each day, and over that time track about 2 million unique processes. The consultant was gobsmacked. Each time we take it to the next level we discover something--the hardware, the network, the OS, the algorithm--scaling not quite right."

Tuesday, October 23, 2001

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"Celera Genomics has turned its gaze heavenward in its quest for more powerful bioinformatics.

The genomic pioneer has inked a deal with the Association of Universities for Research in Astronomy to license its Operational Pipeline Unified Systems software package, a system originally designed to process data collected by the Hubble telescope, AURA said on Tuesday."

Monday, October 22, 2001

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"The already teetering economy, hit hard by the Sept. 11 terrorist attacks, has pushed some struggling industries to the brink and beyond. High-tech or low -- from the telecom to the travel industry -- many companies are laying off employees or imposing hiring freezes.

Yet the local and national market for skilled biotech workers remains strong, and in select areas -- such as chemistry and bioinformatics -- there are more jobs than people to fill them, say industry experts."

Friday, October 19, 2001

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"Intel is providing equipment and software downloads for a project in which volunteers are donating spare home computer cycles to a Stanford University project studying the protein-folding process. The project, Folding@Home, was the first to model successfully a complete protein fold - a task not even achieved by supercomputers."

""We want to increase the value of the PC," said Scott Griffin, Intel's program manager. "The PC is there when people aren't at it, like when they are in meetings. A great thing about this is you get every day users involved in research that they care about. Not only do they get to help out, but they get to help cure these terrible diseases.""

redux [09.23.01]
Wired News The Little Screensaver That Could

"IBM is spending $100 million building the world's fastest supercomputer to do cutting-edge medical research, but a distributed computing effort running on ordinary PCs may have beaten Big Blue to the punch.

IBM's proposed Blue Gene , a massively parallel supercomputer, in hopes to help diagnose and treat disease by simulating the ultra-complex process of protein folding.

"But Folding@Home , a modest distributed computing project run by Dr. Vijay Pande and a group of graduate students at Stanford University, has already managed to simulate how proteins self-assemble, something that computers, until now, have not been able to do."

redux [08.29.01]
Nature: Science Update Parasite corrals computer power

"According to The Hitchhiker's Guide to the Galaxy, hyper-intelligent pan-dimensional beings (disguised as mice) are using us to compute The Ultimate Question of Life, The Universe, And Everything. Now earthling scientists have roped unsuspecting web servers into a similar - albeit slightly less ambitious - exercise in parasitic computing.

Using the Internet itself as a computer, Jay Brockman and colleagues at the University of Notre Dame, Indiana, have solved a mathematical problem with the unwitting assistance of machines in North America, Europe and Asia."

EyeForPharma Novartis evaluates Entropia's distributed computing technology for accelerating drug discovery

""The vast quantities of data involved in the genomic era of drug discovery are quickly outpacing advances in computing technology," said Robert North, Entropia CEO. "Distributed computing allows companies to cost-effectively access the massive computing power they'll need by using their existing PC networks. It's quite exciting that companies like Novartis are deploying our platform to demonstrate the potential of distributed computing as a valuable tool in drug discovery efforts.""

redux [07.22.00]
The Standard Distributed Computing Goes Commercial

"The distributed-computing model could be one of those rare cases where capitalism and pure scientific research mesh. Not every lab can afford to pay $200,000 for an eight-processor Origin 2000 SGI supercomputer, much less $1 million for a 40-processor machine, says David Fenstermacher, director of scientific computing for the medical school at the University of North Carolina at Chapel Hill. (Fenstermacher is also acting director of the campus' Center for Bioinformatics and a United Devices adviser.) And even the most powerful supercomputers need time to process data.

A project that would take several months on a supercomputer - creating a 3D model of a protein's linear be accomplished in much less time using thousands of distributed computers"

redux [10.09.00]
ACM CrossRoads The SETI@Home Problem

"The SETI@Home problem can be thought of as a special case of the distributed computation verification problem: "given a large amount of computation divided among many computers, how can malicious participating computers be prevented from doing damage?" This is not a new problem. Distributed computation is a venerable research topic, and the idea of "selling spare CPU cycles" has been a science fiction fixture for years."

"The Internet makes it possible for computation to be distributed to many more machines. However, distributing computing around the internet requires developers to consider the possibility of malicious clients."

"The general study of secure multiparty computation has produced much interesting work over the last two decades. Less well studied, unfortunately, are the tools and techniques required to move the theoretical results to the real world. The old dream of massively distributed computations is finally coming true, and yet our tools for building and analysing real systems still seem primitive. The challenge of the next few years will be to bridge this gap."

redux [04.05.00]
egroups : Decentralization Description

""*Is decentralization ever a good idea? If so, when? Is there non-anecdotal evidence on costs and benefits?

*What protocol issues are there? Can we begin assembling a good protocol for decentralized messaging? To what degree do the protocols for Freenet, Gnutella or WorldOS meet the need? Do we need an application protocol or something lower level? Can HTTP do the job? Can we implement peer routing as an add-on to existing protocols? Is there a call to develop an IETF working group?

* Given that authoring and versioning are critical but hard in a decentralized environment, how can we approach the job? Is it possible to integrate WebDAV with peer networking?

* What are the business issues? Who are the players? Who else stands to win or lose, and why?

At present many people and groups are working on the issues in isolation, some for competitive reasons and some for lack of an alternative. My belief is that a communal approach will be more productive."

Thursday, October 18, 2001

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"InforMax today announced major changes in its leadership, including CEO Alexander Titomirov leaving his post and president and COO James Bernstein retiring.

Both executives are company founders."

"Earlier in the week, InforMax slashed its third-quarter revenue forecast and indicated that its losses for the period would be greater than expected as a result of purchasing delays triggered by a downturn in the overall economy."

Wednesday, October 17, 2001

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""We're an information-based industry, but we've been a bit behind in the extent to which we've been using computer-based tools," Dinerstein says. "They've had better computer models for oil drilling than we've had for drug discovery."

While executives in this closely guarded industry won't say how much they're investing in research and development informatics, they are definitely hopping on board. Merck & Co. in Whitehouse Station, N.J., recently paid $620 million to acquire Rosetta Inpharmatics, a genomics and technology company based in Kirkland, Wash. And New York City-based Pfizer says it recently spent more than $100 million to create an "integrated system of high-speed discovery technologies." Pradip Banderjee, a senior partner with Accenture Consulting, conservatively estimates that drugmakers as a whole spend more than $4 billion a year on that kind of technology, not including the cost of hardware."

redux [08.09.01]
EyeForPharma Gartner predicts Pharma's IT spending on the rise

"In a recent forecast analysis, Gartner predicts U.S. pharmaceutical companies' IT spending will increase at a CAGR (calculated annual growth rate) of 12.8 percent - from $3 billion in 2000 to more than $5.5 billion by 2005. The group forecasts spending on software and external services will outpace spending for hardware, network equipment and internal services."

"The report stresses as advances in genomics and proteomics facilitate a move toward more personalized medicine, the drivers to IT spending will become even stronger as companies attempt to:

• Rationalize therapeutic areas and compounds, as well as the sub-populations they address,
• Store and integrate clinical data with research data,
• Educate physicians about expanding product lines,
• Solicit patients to participate in targeted clinical trials, and
• Manage an increasing number of trials.

In order to address these challenges, Gartner believes IT vendors that compete in this space must develop a business process focus, rather than marketing their products on the basis of functionality. "To win those large contracts, a vendor must align its marketing message with the key corporate business issues and target an executive who will likely sponsor the project and win additional funding for the project outside those monies allocated to the general IT budget.""

redux [07.16.01]
New Jersey Online Despite hoopla, genetic information firms far from profitability

"A year after the deciphering of the human genome boggled the world, investors are realizing that manipulating genes to fight disease is still in its infancy -- and far from profitable."

Nowhere is that more clear than in the industry for genetic information, or bioinformatics."

redux [05.14.01]
Motley Fool Celera at a Crossroads

""Companies choose to adopt a product that is perceived to give some advantage over their immediate competitors and would like to see that protected in some way by the platform vendor (Celera) not running around selling it to everyone else, if they can avoid it. This is perceived to diminish the window of opportunity of the platform adopter to gain a lead over their immediate competitor. It is an element of sustainable advantage.'"

"Celera is certainly at a point of transition. It must either decide whether or not it wants to get into this collaborative, more vertical model of integrating itself with certain customers in big pharma or try to make its data and knowledge of it so valuable that big pharma of all walks of life simply has to have access to Celera data. I don't think the company has the time and money to do both. I don't think, for competitive reasons that I've explained earlier, big pharma is going to align itself, in large numbers, with a company that is selling the same applications to its immediate competitors."

redux [06.01.01]
GenomeWeb Software Vendors Hungry for a Piece of the Burgeoning Bioinformatics Consulting Market

"Justin Saeks, an analyst with Frost & Sullivan, sees plenty of room for new players in the consulting market. "I think there is definitely a demand for this," said Saeks, "Maybe equal to or more than the software sales, depending on whether you include hardware with IT consulting."

A Frost & Sullivan study conducted for IBM predicted that life sciences companies would spend nearly $6.5 billion on IT services by 2004.

One reason for the surge of interest in the field is the maturation of data-generating technology, which has left biotech and pharma clients "struggling with the rate of change and the degree of integration on their shoulders," said Bob White, vice president of Accelrys' worldwide sales and consulting division."

Tuesday, October 16, 2001

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"The Open Bioinformatics Foundation has incorporated as a not-for-profit company in Delaware in a move to sustain its growing administrative role, according to Chris Dagdigian of Blackstone Computing, who serves as the group's treasurer.

The foundation began several years ago with a core group of volunteers from various open-source bioinformatics projects, such as BioPerl, BioJava, BioPython, and BioCorba. As the projects grew, Dagdigian said, it became clear to the core group that a more formal structure would soon be necessary to support the increased responsibilities of the effort."

redux [09.11.01]
Yahoo! News Sun Microsystems Awards Grant to Support the Open Bioinformatics Foundation's Open-Source Research Tools

"Sun Microsystems, Inc. today announced that it will grant hardware, including servers and a secure storage system, to the Open Bioinformatics Foundation, which distributes, develops and supports standards-based open source tools for life science research and data integration. The foundation will use the hardware to update its infrastructure, enabling more reliable and secure distribution of its tools and collaborative services over the Web."

""The grant from Sun puts us at a milestone in our project's history. With Sun hardware at the heart of our third-generation infrastructure, our users will benefit from superior performance, data integrity and security," said Chris Dagdigian, systems manager and project administrator for the Open Bioinformatics Foundation. "This will allow us to meet the growing demand for open-source bioinformatics tools, and continue to build international support for the open standards approach to life sciences research."

The Open Bioinformatics Foundation About

"The Open Bioinformatics Foundation is an umbrella group for the various bio*.org projects that grew out of the original BioPerl project. The goal of the foundation is to provide financial, administrative and technical assistance for our various open source life science projects."

Monday, October 15, 2001

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"This article will examine why a biologist would want to learn to program. There are two main reasons: scientific, and economic. I hope that the discussion will also be of some use to programmers thinking of entering the bioinformatics field. But first, I'll take a short tour of some history, define some terms, and make some general comments about how programming fits into biology research."

redux [04.05.00]
HMS Beagle Are Computers Evolving in Biology?
[requires 'free' registration]

"I suspect that although the new enthusiasm for computers in biology is genuine, it overlooks some basic problems in implementation. The basic difficulty, as I see it, is that although biologists use computers, they do not trust everything that comes out of them. It is one thing to use them to print up nice-looking graphs, but it is an entirely different matter to use them to think better."

"Francis Crick was once quoted as saying that no biologist had ever made a discovery using a mathematical model. I would reply that no biologist has ever made a discovery by running an electrophoretic gel. They make discoveries by using their brains. Computers, like all scientific tools, are only as good as the person who uses them. If biologists don't understand how computer models are constructed, they won't know their strengths and limitations. Without some foundation of trust, biologists will be unlikely to utilize or accept this powerful method of data analysis."

Friday, October 12, 2001

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"Life scientists in the US fare better on the whole than other workers, the largest and most comprehensive salary survey of life scientists has found: Compared to the salary of the average US worker ($25,508), life scientists in academia earned a median salary of $80,000. But women and postdoctoral fellows do not appear quite as successful."

Thursday, October 11, 2001

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"Counting human genes ought to be straightforward. Tracking telltale signs--motifs for promoters, translation start sites, splice sites, CpG islands--gene counters must by now be mopping up, finalizing chromosomal locations of every human gene already known, and predicting whereabouts of all the rest. Insert one human genome sequence, turn the bioinformatics crank, and genes gush out like a slot machine jackpot, right?

"No, no, no," says Bo Yuan, of Ohio State University, having a laugh over the idea that computation is all you need to tally genes. To the contrary, states the director of the bioinformatics group in the division of Human Cancer Genetics at Ohio State, trawling for genes is so labor-intensive that several years may pass before researchers possess a highly accurate count."

redux [09.04.01]
SiliconValley.Com Widely varying counts of human genes spur debate by scientists

"The central challenge is that human genes are not visible to the eye, even under a microscope. They don't blink in bright colors. Nor do they have a discernible beginning and end."

""The count is on a computer -- it's not a biological one,'' said Mike Cherry, assistant professor of genetics, research, at Stanford University Medical Center.

"These programs try to use general rules to figure out a prediction,'' he said of the computers. ""And predictions are made by studying what we know, which is only a fraction of what exists.''"

""There is no single technology that tell us: "This is a gene, this is not,'' said M.R.C. Greenwood, chancellor of the University of California-Santa Cruz. "We'll need a combination of computational technologies to get the entire genome set.''"

redux [08.24.01]
The New York Times Human Genome Now Appears More Complicated After All
[requires 'free' registration]

"After a humiliating deflation this February, human dignity is on the recovery path, at least as measured by the number of genes in the human genome.

Two new estimates put the likely number of human genes at around 40,000, up by a third from the estimate of about 30,000 in February by the two teams of scientists who decoded the human genome. The low estimate still has its defenders."

NPR: All Things Considered DNA Recount

"Recent estimates that the human genome consists of only about 30,000 genes may be way off the mark, according to a study published today in the journal Cell. NPR's Richard Harris has the story. (3:45)"

redux [01.18.01]
ScienceDaily With First Comparative Look At Human And Mouse DNA, Joint Genome Institute Team Confirms Gene Estimate

"Earlier this year, researchers mapping the human genome estimated that human DNA contains about 30,000 genes. Now, based on the first-ever look at comparable sections of human and mouse DNA, a team of Walnut Creek-based Joint Genome Institute (JGI) scientists has confirmed that estimate as roughly accurate."

""There had been speculation that aligning the human and mouse DNA sequence might reveal many more genes," Stubbs said. "However, if chromosome 19 is indicative of other chromosomes, the estimate of 30,000 genes is fairly accurate.""

BBC Dispute over number of human genes

"Two rival teams that cracked the human genome may have underestimated the number of human genes, according to a new computer analysis."

Scientists in the United States claim humans are built from 66,000 genes, nearly twice as many as the current consensus."

"But the new analysis, published on the website of the journal Genome Biology, has been dismissed by the Sanger Centre, in Cambridgeshire, UK, which was responsible for about a third of the human genome sequencing effort."

""The experimental evidence actually points to 30-40,000 genes," Dr Hubbard told BBC News Online. "I don't believe the argument in this paper that there are a lot more genes. This is an entirely computational paper and I don't think it's very credible.""

redux [11.13.00]
BioMedNet UK geneticist offers exact count of human genes
[requires 'free' registration]

"If James Watson, co-discoverer of DNA's structure, says we don't know how many genes there are, you're inclined to believe him. So it was a great surprise to hear the legend denounced, albeit with due deference. At the last count, insisted Kay Davies, professor of anatomy at the University of Oxford, humans are reckoned to have 40,944 tiny protein factories.

She was drawing on statistics that define the proteome, the protein equivalent of the genome, as the set of all expressed proteins in humans, for which 40,944 genes are individually responsible. Not a huge figure, she noted, barely the equivalent of three flies or a couple of worms. "Apologies Jim, let's talk over tea," she added."

redux [06.08.01]
Red Herring Genomics offers an odd proposition

"Research on the human genome may well pay fat dividends in 10 or 20 years, but you can make money on it now, the old-fashioned way: by gambling. Find out how on the Web site of Project Ensembl, a European organization that develops genome-related software."

At the May 2000 Annual Meeting on Genome Sequencing and Biology at the Cold Spring Harbor Laboratory in Long Island, New York, Ewan Birney, team leader of Project Ensembl, proposed GeneSweep, a betting pool to guess the total number of human genes. All bets must be entered by hand, in person, in ink, in a book kept at the Cold Spring Harbor Laboratory. The winner of the pool, which now stands at a whopping $348, will be announced at the 2003 genome meeting."

redux [05.13.00]
Wired News Amped Geneticists Bet on Genome

"Well, they weren't all men, but mostly. The betting in the pub continued, the lowest bet being 29,800 genes placed by Pat Tome and the highest number coming from John Quackenbush at 118,259.

The pool was organized by Erwin Birney, a team leader at the European Bioinformatics Institute. He tried to convince the bartender to oversee the betting, but was told in no uncertain terms that no gambling was allowed in the Cold Spring bar.

Guesses on the number of genes in the human genome have lowered considerably since the mapping of chromosome 21, which researchers found to contain only 225 genes, far fewer than previously predicted. The researchers on the chromosome 21 study predicted their results could mean that there are as few as 40,000 genes in the entire human genome.

"Someone from Incyte will probably show up and bet 150,000," one gambler said."

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"Recent genome-sequencing efforts have confirmed that traditional "good-citizen" genes (those that encode functional RNA and protein molecules of obvious benefit to the organism) constitute only a small fraction of the genomic populace in humans and other multicellular creatures. The rest of the DNA sequence includes an astonishing collection of noncoding regions, regulatory modules, deadbeat pseudogenes, legions of repetitive elements, and hosts of oft-shifty, self-interested nomads, renegades, and immigrants. To help visualize functional operations in such intracellular genomic societies and to better encapsulate the evolutionary origins of complex genomes, new and evocative metaphors may be both entertaining and research-stimulating."

Tuesday, October 09, 2001

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"A new technique should aid the hunt for genes in the human genome sequence. The method, which tracks only switched-on genes in cells, will help researchers to distinguish between diseased and normal tissues, and could point the way to new treatments.

Andrew Simpson, of the Ludwig Institute for Cancer Research in Sao Paulo, Brazil, and colleagues have produced a whopping 700,000 DNA tags, representing the genes that are active in 24 normal and cancerous tissues."

BioMedNet Brazil homes in on genome's coding core
[requires 'free' registration]

"Geneticists in Brazil who have devised a short-cut for decoding the human genome have made a "serious" contribution to the international effort, according to one of the field's leading analysts. The work represents "a significant contribution by people outside the mainstream US/UK axis," said Ian Hubbard, head of the human genome analysis group at the Sanger Center in the UK."

Monday, October 08, 2001

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"Cyrus said the work with Virtual Genetics is the initial step of a three-phase effort to create a "complete literature package." The ultimate goal, Cyrus said, will be the creation of derivative products that summarize the most salient facts within relevant journal articles. Celera is currently in the process of integrating each of the new features within CDS."

BioNLP.Org Natural language processing of biology text

"The literature of the field of biology is the largest of all the sciences. The volume of biology literature each year, measured in bytes, is about fifty times the size of the entire human genome, junk and all. But locked in this literature is an enormous amount of information that can tell us much about the structure and function of genes, proteins, cells and organisms -- how they work as well as how they can fail.

The newly emergent interest in natural language processing for biology has been christened "Information Extraction". But work in this area has been going on for many decades under different names and this site includes a good deal of information about past and current work in NLP and in information extraction for biology in particular."

redux [04.30.01]
New Scientist Biologists in Norway use a computer program to "read" the scientific literature and successfully predict gene interactions

"Biologists in Norway have used a computer program to "read" the scientific literature and successfully predict gene interactions.

This data-mining of the "biobibliome" provides a way of dealing with the ever-increasing torrent of biological data - millions of papers a year. But even more impressively, the completely automated process can make new genetic discoveries - essentially free research."

Stanford Medical Informatics Preprint Archives Improving Biological Literature Improves Homology Search

"Annotating the tremendous amount of sequence information being generated requires accurate automated methods for recognizing homology. Although sequence similarity is only one of many indicators of evolutionary homology, it is often the only one used. Here we find that supplementing sequence similarity with information from biomedical literature is successful in increasing the accuracy of homology search results. We modified the PSI-BLAST algorithm to use literature similarity in each iteration of its database search. The modified algorithm is evaluated and compared to standard PSI-BLAST in searching for homologous proteins. The performance of the modified algorithm achieved 32% recall with 95% precision, while the original one achieved 33% recall with 84% precision; the literature similarity requirement preserved the sensitive characteristic of the PSI-BLAST algorithm while improving the precision."

MIT Technology Review Emerging Technologies That Will Change the World: Data Mining

"And the future of data-mining technology? Wide open, says Fayyad - especially as researchers begin to move beyond the field's original focus on highly structured, relational databases. One very hot area is "text data mining": extracting unexpected relationships from huge collections of free-form text documents. The results are still preliminary, as various labs experiment with natural-language processing, statistical word counts and other techniques. But the University of California at Berkeley's LINDI system, to take one example, has already been used to help geneticists search the biomedical literature and produce plausible hypotheses for the function of newly discovered genes."

Friday, October 05, 2001

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"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]
SFGate Why Bioinformatics Is Hot Career

"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 [07.25.00]
Advogato Hacking your genome

"Are you a hacker? Do you yearn for something more important to work on than yet-another-gnome-applet? Are you annoyed that you can't find a problem that is fun to code and stretches your brain in new ways... bioinformatics might be the answer."

"The amount of data is growing faster than anyone expected and only a handful of people can both remain with academic ideals and coding potential. We need hackers to join any number of projects out there. And there are a host to join. If you just liking hacking perl or you prefer compiler technology, there is something to suit you. "

redux [09.19.00]
SFGate Enjoying the Best of Both Worlds Molecular biology, programming is gold Programming skills, molecular biology can pay big dividends

"If job searching were a poker game, Alan Williams would be sitting pretty with a full house.

Fresh out of graduate school, he happens to have a rare combination of skills that drives employers to offer hefty salaries, stock options and bonuses. And it's not even a dot-com job.

Williams has a combination of computer programming and molecular biology know- how. His job is to use computers to mine the vast store of data in the human genome model."

redux [09.01.00]
Science : NextWave Bioinformatics Feature
[ can be viewed for free once registered]

"Since Next Wave last covered bioinformatics, in our July 1996 Profiles of Bioinformaticians and February 1997 Bioinformatics Skills features, the prominence of the bioinformatician's role in modern biology has only increased. This month, Next Wave provides a comprehensive picture of the current state of bioinformatics, from the funding situation in Europe and the U.S. to the new bioinformatics degree programs and the immediate hiring needs of industrial and academic labs around the world."

redux [05.10.00]
Alfred P. Sloan Foundation Hiring Patterns Experienced by Students Enrolled in Bioinformatics/Computational Biology Programs

"As expected, salaries for the most part climb as the level of training rises, starting in the $40,000-$50,000 range for BAs and reaching over $100,000 for one post doc. But there are exceptions. For example, two of the three undergraduates who were placed received salaries between $50,0000 to $60,000. This is higher than that earned by seven of the masters students, although ten of the nineteen masters students for whom we have salary information earn more than $60,000. One masters student received a starting salary of over $100,000. Reported salaries for five hires at the doctorate level are over $70,000. One is between $80,000 to $90,000; another is over $100,000; yet another is between $60,000 to $70,000. Three post docs received placements with a salary between $80,000 to $90,000. One post doc was placed at a salary of over $100,000. One institution reported that one or more masters student(s) received a signing bonus."

"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."

Thursday, October 04, 2001

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"A team of geneticists and linguists say they have found a gene that underlies speech and language, the first to be linked to this uniquely human faculty.

The discovery buttresses the idea that language is acquired and generated by specific neural circuitry in the brain, rather than by general brain faculties."

BioMedNet Cognitive science reaps its first fruits of genome project
[requires 'free' registration]

"The discovery of the first language gene heralds the "dawn of cognitive genetics," says one of the world's leading speech and language experts. "Cognitive scientists haven't looked at genes at all," said Steve Pinker, professor of cognitive science at the Massachusetts Institute of Technology."

"The findings should encourage other cognitive scientists to join forces with geneticists. "I think it will be a hot new field," he said. "It will be part of behavioral genetics (BG), [which] already exists, but the Bee Gees in the past have tended to look at very coarse traits like IQ or personality test scores, not fine-grained mental talents."

Wired News First Language Gene Found

"The discovery of the gene is fueling the ongoing debate about the relationship between genes and higher cognitive functions like language.

Some researchers argue that the KE family proves the existence of a "grammar gene."

While few researchers would claim that language and genes are not related, there has been little evidence so far that language is directly encoded in our genes.

At stake is a popular theory, originated by Noam Chomsky, about language and the brain.

The Third Culture Marc D. Hauser

"For humans, Chomsky's insights into the computational mechanisms underlying language really revolutionized the field, even though not all would agree with the approach he has taken. Nonetheless, the fact that he pointed to the universality of many linguistic features, and the poverty of the input for the child acquiring language, suggested that an innate computational mechanism must be at play. This insight revolutionized the field of linguistics, and set much of the cognitive sciences in motion. That's a verbal claim, and as Chomsky himself would quickly recognize, we really don't know how the brain generates such computation."

Brain and Language An On-Line Interview with Noam Chomsky: On the nature of pragmatics and related issues

"The way to make the general assumptions less obscure is to discover the nature of the various specialized "learning mechanisms" -- the systems LT(O,D), in my terminology -- among them the "language organ" FL, the states it can in principle attain, the "neural circuits" involved, etc. That is also the way to arrive at one or another "position...in the domain-generality vs. domain-specificity debate," a very tentative position I would think, given the limits of current understanding. I concede that I don't really understand what this debate is about in the way it is usually waged (without my participation). There are very interesting questions about just what might be specific to human language (part of LT(Human, Language), the dedicated "learning mechanism" that is the "language organ"). These are the topics of inquiry in all study of language and other cognitive systems that I know of. But I do not understand the more general "debate" that seems to arouse much passion."

Wednesday, October 03, 2001

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"Bye bye, bioinformatics. Adieu, proteomics. Hello, chemical genomics!"

"That's the message from a growing number of biotechnology venture capitalists who are quietly shifting their investment emphasis to so-called chemical genomics in the everlasting search for a quicker, more efficient drug discovery process."

redux [08.09.01]
EyeForPharma Gartner predicts Pharma's IT spending on the rise

"In a recent forecast analysis, Gartner predicts U.S. pharmaceutical companies' IT spending will increase at a CAGR (calculated annual growth rate) of 12.8 percent - from $3 billion in 2000 to more than $5.5 billion by 2005. The group forecasts spending on software and external services will outpace spending for hardware, network equipment and internal services."

"The report stresses as advances in genomics and proteomics facilitate a move toward more personalized medicine, the drivers to IT spending will become even stronger as companies attempt to:

• Rationalize therapeutic areas and compounds, as well as the sub-populations they address,
• Store and integrate clinical data with research data,
• Educate physicians about expanding product lines,
• Solicit patients to participate in targeted clinical trials, and
• Manage an increasing number of trials.

In order to address these challenges, Gartner believes IT vendors that compete in this space must develop a business process focus, rather than marketing their products on the basis of functionality. "To win those large contracts, a vendor must align its marketing message with the key corporate business issues and target an executive who will likely sponsor the project and win additional funding for the project outside those monies allocated to the general IT budget.""

redux [07.16.01]
New Jersey Online Despite hoopla, genetic information firms far from profitability

"A year after the deciphering of the human genome boggled the world, investors are realizing that manipulating genes to fight disease is still in its infancy -- and far from profitable."

Nowhere is that more clear than in the industry for genetic information, or bioinformatics."

redux [06.01.01]
GenomeWeb Software Vendors Hungry for a Piece of the Burgeoning Bioinformatics Consulting Market

"Justin Saeks, an analyst with Frost & Sullivan, sees plenty of room for new players in the consulting market. "I think there is definitely a demand for this," said Saeks, "Maybe equal to or more than the software sales, depending on whether you include hardware with IT consulting."

A Frost & Sullivan study conducted for IBM predicted that life sciences companies would spend nearly $6.5 billion on IT services by 2004.