Friday, June 29, 2001

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"The merits of linking two fields seemingly as disparate as geographic information systems (GIS) and bioinformatics might not seem obvious, but Virginia Tech?s recent symposium linking the twoæand its roster of renowned participants from both fieldsæhas raised expectations "Applications of GIS to Bioinformatics" was the first major public forum to cross-pollinate the disciplines, helping to fortify a relatively new, yet highly promising investigative area."

""As a result of new dialog between the fields, as we?ve had at this conference, we are gaining an important mechanistic link between individual-level processes tracked by genomics and proteomics and population-level outcomes tracked by GIS and epidemiology. This will allow us to do a far better job of monitoring, quantifying, and predicting human-health consequences associated with the environment. The potential payoff in related fields such as those looking at climate change, emerging and resurgent infectious diseases, and environmental health is enormous.""

Applications of GIS to Bioinformatics Symposium Proceedings

"The meeting brings together researchers in two of the most dynamic analytical technologies-GIS and bioinformatics. The value of GIS analytical systems and data structures to bioinformatics are only now being recognized. Similarly, the methodologies used in bioinformatics can inform GIS scholars of new approaches to pattern recognition and analysis. The purpose of the symposium is to explore the potentials for using GIS as an analytical methodology in bioinformatics and to understand the opportunities bioinformatics presents to the GIS research community. The symposium, the first to focus on the interface between these two research areas, will afford scholars the opportunity to establish new research directions in both fields of investigation."

Thursday, June 28, 2001

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"Biologists at the University of California, San Diego have identified genes in the common fruit fly, Drosophila melanogaster, that appear to be counterparts of genes responsible for more than 700 different genetic diseases in humans."

""Scientists have long known that humans share many similar genes with fruit flies," says Ethan Bier, a professor of biology at UCSD who headed the research. "The surprise is how deep these similarities really are. Basically, every category of human genetic disease is well represented with a counterpart in the fly.""

redux [05.02.00]
The Scientist Confessions of an Ex-Fly Pusher
[requires 'free' registration ]

"Perhaps the biggest puzzle of the fly genome is evident by considering the other two eukaryotes to have had their genomes laid bare--the yeast Saccharomyces cerevisiae and the nematode worm Caenorhabditis elegans.8 The million-celled fruit fly has 13,601 protein-encoding genes, compared to 18,425 for the 1,000-celled tiny worm and 6,000 or so for the unicellular yeast. "It's fascinating to think that there are only 13,601 genes, less than C. elegans and just a couple of times that of yeast. Thirteen thousand genes doesn't even sound like much to build a worm with, let alone a fly!" exclaims Michael Young, head of the laboratory of genetics at Rockefeller University, who studies clock genes.

Also surprising is that the fly seems to get along on very little. "Once we got the gene count, we realized that not many proteins are involved in this complicated little beast. The animal has a basic toolbox, and [it] can put bits and pieces of that box together to create a complex biological system that can execute a fantastic ability such as behavior," Young adds. The insect apparently employs nested genes and alternate splicing patterns that peel off different-size mRNAs from the same gene. The overall effect is to wring more than one meaning from a DNA sequence."

"And although a fly with a human head isn't a likely scenario, the human genome sequence will probably confirm and extend the homologies between us and them. More generally, the similar sizes and unexpected streamlined nature of the eukaryotic genomes sequenced to date is stimulating a great rethinking of how DNA orchestrates life. Concludes Smith, "There may only be a couple of thousand proteins in the living universe. But duplication and modification over and over has led to a plethora of genes that make up all the things that walk around our planet."

redux [10.26.00]
BioMedNet Advanced genomics promise fruit fly exposure
[requires 'free' registration ]

"According to Gos Micklam, a bioinformatics expert who joined the group from industry last year, "Drosophila is a terrific model organism to work on." Despite its complexity, he notes, the fly has only twice as many genes as yeast. It is also backed by huge research interest worldwide that goes back a century or more, which has produced detailed phenotypic data.

In particular however, he draws a distinction between "deterministic" and "algorithmic" developmental mechanisms. For instance, he says, those mechanisms that create the nematode, Caenorhabditis elegans, are deterministic in that the fate of every cell is more or less pre-determined and specified from the start. But Drosophila's mechanisms are algorithmic, he notes; the cells do not have a fixed lineage, and their developmental fate is partly the result of communication between cells.

The task of integrating the huge amounts of data to produce a comprehensive profile of gene expression, which Micklam describes as "the real challenge of genomics," will take many years, he says."

Wednesday, June 27, 2001

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"Suppose that in order to use the appliances in your kitchen, an electrical engineer needs to tear down the wall and splice in wiring for the appropriate voltage converter."

Then suppose you're running a restaurant out of that kitchen.

That, according to those in the know, is what it's like to work with life-science information today, where the absence of a common programming language makes coordination between researchers a dicey prospect."

Enter IBM, which is spearheading an effort to write that common language using XML.

GenomeWeb Informatics Infrastructure Consortium Unveils Demo Protocol

"The Interoperable Informatics Infrastructure Consortium (I3C) unveiled its first demonstration of a working protocol Tuesday at the BIO 2001 Conference."

The XML-driven format allowed the exchange and analysis of sequence data across 10 different organizations? products. I3C views the demonstration as a bridge to the next step to defining components needed for a more general open architecture."

redux [05.23.01]
The Washington Post Biotech Industry Developing Worldwide Standard for Data

"The new coalition, led by the Biotechnology Industry Organization (BIO), a Washington trade group, plans to spend the next year or so creating a detailed specification for biological data. This specification would be available without fee to any company or scientist that wanted to use it to help organize and mine information."

The project has been dubbed the Interoperable Informatics Infrastructure Consortium, or I3C."

redux [02.21.01]
GenomeWeb Sun Forms Industry-Wide Collaboration to Develop Open Platform for Life Sciences

"Sun Microsystems said Wednesday it would partner with the Biotechnology Industry Organization, the National Cancer Institute, and several commercial bioinformatics vendors to support a collaborative effort to develop an open platform for the life sciences based on Java and XML.

The proposed initiative, temporarily referred to as Life Force or LI4 (Lifescience Informatics Interoperability Infrastructure Initiative) aims to develop an open platform to support data integration and interoperability and to focus the growing number of standards efforts"

"Sun intends to contribute the underlying infrastructure for the open platform, which the company hopes will form the eventual hub for a broad variety of life science computing needs, including bioinformatics, cheminformatics, genomics, proteomics, pharmacogenomics, metabolomics, and clinical informatics."

redux [03.15.01]
MIT Technology Review Gene Babel

"Small DNA-laden wafers have transformed biology. Using these DNA chips, geneticists can see which genes are turned on, or expressed, in a cell at a particular time. Such gene expression experiments allow bioscientists to diagnose different diseases, quickly screen thousands of drug candidates for efficacy and safety and even learn the functions of newly discovered genes.

"Small DNA-laden wafers have transformed biology. Using these DNA chips, geneticists can see which genes are turned on, or expressed, in a cell at a particular time. Such gene expression experiments allow bioscientists to diagnose different diseases, quickly screen thousands of drug candidates for efficacy and safety and even learn the functions of newly discovered genes.

Sharing this information over the Web could lead to an explosion in biological knowledge. But each experiment generates gigabytes of data written in one of several formats, depending on the type of chip used. And with dozens of chips on the market and hundreds of ways to analyze the data, the Web is in danger of becoming a genetic Tower of Babel."

"Companies and academics have begun creating uniform formats for representing gene expression data, designed to work on any computer."

redux [10.21.00]
Science The Babel of Bioinformatics
[summary - can be viewed for free once registered]

"As more and more genomes are sequenced, it is becoming clear that deciphering the clues latent in these sequences is anything but trivial. In this Techview, Attwood analyzes the current state of the art in sequence-structure-function bioinformatics. She highlights the need for precise terminology, and argues that a holistic view of complex biological systems will be an essential next step for bioinformatics."

redux [07.25.00]
The Scientist The Language of Bioinformatics
[requires 'free' registration ]

"Once the world had a single language and not too many words, but then clarity deteriorated into clamor. Today in the small but prolific world of bioinformatics, another Tower of Babel is rising up, with the miscommunication due as much to the rapid expansion of information as to basic changes in how it is processed. "Horrible problems" crop up as more information is computed on instead of read by a human researcher, according to Ewan Birney, a group leader in the Ensembl genome annotation project at the European Bioinformatics Institute (EBI) in Cambridge, England.

In the early days of bioinformatics, human-readable data exchange formats such as ASN.1, the format adopted for GenBank by the National Center for Biotechnology Information (NCBI) 10 years ago, were the norm. Easily editable with a text utility, ASN.1's syntactic looseness makes it congenial to the human user, but not to the machine, which likes its inputs defined with dictatorial rigidity."

redux [05.10.00]
The XML Cover Pages XML and Semantic Transparency

"We may rehearse this fundamental axiom of descriptive markup in terms of a classical SGML polemic: the doubly-delimited information objects in an SGML/XML document are described by markup in a meaningful, self-documenting way through the use of names which are carefully selected by domain experts for element type names, attribute names, and attribute values. This is true of XML in 1998, was true of SGML in 1986, and was true of Brian Reid's Scribe system in 1976. However, of itself, descriptive markup proves to be of limited relevance as a mechanism to enable information interchange at the level of the machine.

As enchanting as it is to contemplate the apparent 'semantic' clarity, flexibility, and extensibility of XML vis-à-vis HTML (e.g., how wonderfully perspicuous XML <bookTitle> seems when compared to HTML <i>), we must reckon with the cold fact that XML does not of itself enable blind interchange or information reuse. XML may help humans predict what information might lie "between the tags" in the case of <trunk> </trunk>, but XML can only help. For an XML processor, <trunk> and <i> and <booktitle> are all equally (and totally) meaningless. Yes, meaningless.

Just like its parent metalanguage (SGML), XML has no formal mechanism to support the declaration of semantic integrity constraints, and XML processors have no means of validating object semantics even if these are declared informally in an XML DTD. XML processors will have no inherent understanding of document object semantics because XML (meta-)markup languages have no predefined application-level processing semantics. XML thus formally governs syntax only - not semantics."

redux [05.10.00]
The Rand Corporation : Scaffolding the New Web: Standards and Standards Policy for the Digital Economy The Emerging Challenge of Common Semantics

"With XML has come a proliferation of consortia from every industry imagineable to populate structured material with standard terms (see Appendix B). By one estimate, a new industry consortium is founded every week, perhaps one in four of which can collect serious membership dues. Rising in concert are intermediary groups to provide a consistent dictionary in cyberspace, in which each consortium's words are registered and catalogued.

Having come so far with a syntactic standard, XML, will E-commerce and knowledge organization stall out in semantic confusion?"

"How are semantic standards to come about?"

SemanticWeb.Org Tutorial on Knowledge Markup Techniques

"There is an increasing demand for formalized knowledge on the Web. Several communities (e.g. in bioinformatics and educational media) are getting ready to offer semiformal or formal Web content. XML-based markup languages provide a 'universal' storage and interchange format for such Web-distributed knowledge representation. This tutorial introduces techniques for knowledge markup: we show how to map AI representations (e.g., logics and frames) to XML (incl. RDF and RDF Schema), discuss how to specify XML DTDs and RDF (Schema) descriptions for various representations, survey existing XML extensions for knowledge bases/ontologies, deal with the acquisition and processing of such representations, and detail selected applications. After the tutorial, participants will have absorbed the theoretical foundation and practical use of knowledge markup and will be able to assess XML applications and extensions for AI. Besides bringing to bear existing AI techniques for a Web-based knowledge markup scenario, the tutorial will identify new AI research directions for further developing this scenario."

Tuesday, June 26, 2001

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"In 1998, biotech upstart Celera Genomics needed a supercomputer to help it map the human genome. It didn't turn to IBM , which built 204 of the 500 fastest supercomputers. Both Celera and its academic competition, the Human Genome Project, used machines built by Compaq Computer. Two years later, Compaq is the leading seller of supercomputers to biological researchers.

But IBM noticed that biologists now need microprocessors as much as microscopes. A year ago, it used $100 million to start a division that sells computers, software and services to biotechnology and drug companies. This life sciences division has had some success; pulling into second place behind Compaq, it must do better."

redux [05.21.01]
Business 2.0 Tech Giants Court The Genome Crowd

"According to scientists, decoding the human genome is the most complicated civilian computational problem ever tackled, and the data generated by genomics has been doubling every six months. Proteomics eventually will generate 100 times more data than genomics and require 1,000-times more computing power.

"We don't need an evolution in computing, we need a revolution . The normal increase in CPU power is just not enough," says Marshall Peterson, vice president of infrastructure development for Celera. "This is what we call Venter's law-it states that biology will outpace Moore's law. Fast makes the difference in the very beginning of a market, but we won't be at this stage for long.""

redux [04.20.01]
USNews.Com Bytes and bits meet biotech

"Life science is the fastest-growing sector in the market for high-performance supercomputers already, and the real boom is yet to come. "DNA is digital information," says James Pierce, a professor at Philadelphia's University of the Sciences. "Life is an expression of information; that's why it's so beautifully adaptable to computers." The computer industry is adaptable, too. IBM is rushing to sell life-sciences companies everything from supercomputers to E-commerce tools, while the burgeoning market for biochips, tiny silicon wafers embedded with genetic material, has attracted high-tech powerhouses such as Motorola, Corning, and Agilent. In the new merger of infotech and biotech, biologists and drug companies will spur advances in computing power while computer geeks will play a pivotal role in the drive to treat disease."

redux [04.01.01]
BusinessWeek Bioinformatics

"The reason for this sudden feeding frenzy? Sales growth. Although analysts estimate that bioinformatics will grow into a $2 billion dollar industry in the next five years, most IT companies believe the payoffs will be much higher. An internal study commissioned by IBM, for instance, predicts that when the markets for high-performance computing, storage, and e-commerce combine with that of data management, the worldwide market for IT products and services in the life-sciences sector will swell to $43 billion by 2004. Looking at these kinds of numbers, "now is not the time to think small,'' says Caroline A. Kovac, vice-president of IBM's Global Life Sciences Business Unit."

Monday, June 25, 2001

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"The effective transfer of information across long distances is necessary for research groups that want to collaborate - and the Internet is making it possible. Researchers who share information and coordinate their investigations are forming "collaboratories" or virtual labs linked by computer networks. The trend is likely to progress with the development of better hardware, software, and legal agreements spelling out the ownership of data.

Reference: Teasley, S. and Wolinsky, S. 2001. Scientific collaborations at a distance. Science 292(5525):2254-2255."

redux [08.04.00]
Software Carpentry Internet Groupware for Scientific Collaboration

"The Web was invented so that scientists could use computer networks to collaborate -- that is, exchange documents, discuss them, coordinate work, create and publish collective knowledge. It was, in other words, supposed to be a groupware application.

Despite the popularity of the Web -- or, perhaps, because of that popularity -- it has yet to fulfill that original mission. Today's Web is more like a shotgun marriage of electronic publishing and broadcast television than it is like an engineered solution for group collaboration. True, the Internet empowers today's working scientist in ways only dreamed of even a decade ago. Yet our use of it often remains rooted in pre-Web idioms and habits -- partly because we don't fully exploit today's Internet communication tools, but mainly because we're still missing key tools and infrastructure."

"The goal of Internet groupware should be to reclaim the original vision of the Web as a medium of collaboration. It's no accident that vision arose in a scientific milieu since the enterprise of science is so deeply rooted in collaboration."

redux [03.29.00]
UIUC Collaboratory for Structural Biology

"The Theoretical Biophysics Group at the University of Illinois is proud to announce the initial public release of BioCoRE, a collaborative research environment. BioCoRE software is freely available for use at the Theoretical Biophysics Group website. BioCoRE development is supported by the NIH National Center for Research Resources.

Modern computational structural biology requires scientists to employ a wide range of tools and techniques to solve complex problems while keeping accurate and complete records of research activities. Additional complications are introduced by the need to effectively engage in interdisciplinary collaborations with geographically dispersed colleagues. The software BioCoRE, a collaborative research environment for molecular modeling and simulations, addresses these challenges."

Saturday, June 23, 2001

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"Measuring the expression of most or all of the genes in a biological system raises major analytic challenges. A wealth of recent reports uses microarray expression data to examine diverse biological phenomena -- from basic processes in model organisms to complex aspects of human disease. After an initial flurry of methods for clustering the data on the basis of similarity, the field has recognized some longer-term challenges. Firstly, there are efforts to understand the sources of noise and variation in microarray experiments in order to increase the biological signal. Secondly, there are efforts to combine expression data with other sources of information to improve the range and quality of conclusions that can be drawn. Finally, techniques are now emerging to reconstruct networks of genetic interactions in order to create integrated and systematic models of biological systems."

Friday, June 22, 2001

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"O'Reilly & Associates is pleased to announce its first Bioinformatics Technology Conference, an event that will explore the engineering and tool-building aspects of bioinformatics. The conference will be held January 28 - 31, 2002, at the La Paloma resort in Tucson, AZ."

Bioinformatics is the art and science of using computational tools to find answers to biological questions. Practitioners in each discipline--biological science and computational science--struggle to understand the mission, mindset, and issues faced by the other. This conference attempts to bridge the gap between the communities and address what is perhaps the most important issue in bioinformatics: how to get the job done."

Thursday, June 21, 2001

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"Humans did not acquire genes directly from bacteria as previously thought, American researchers said Wednesday."

Scientists working for the International Human Genome Sequencing Consortium, which sequenced the 3.1 billion letters of DNA that make up humans, found genes they thought had come directly from bacteria, although they did not understand the mechanism by which they had transferred.

But researchers at pharmaceutical giant GlaxoSmithKline's research center in Pennsylvania have debugged the theory."

Wednesday, June 20, 2001

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"An Israeli company founded by an elite group of former military engineers is transforming the way scientists look at genes and proteins.

Compugen (CGEN) on Wednesday released two new "proteomics" products: one to help researchers find proteins more accurately, and one to help them look at proteins in various disease states."

Compugen's "black box," what Ma'ayan likes to call their algorithm, translates the raw mass spec data in to a meaningful list of proteins that researchers can query against a publicly available protein database, or, for a fee, against Compugen's own protein database."

Forbes Proteins Are Back To Confuse Investors

"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 [03.31.01]
The Scientist Is a Human Proteome Project Next?
[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."

Tuesday, June 19, 2001

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"Despite the hubbub of earlier this year, the human genome is not yet complete.

This might surprise people who saw the headlines in February announcing this groundbreaking achievement, but genome scientists know very well that they're in the midst of the most difficult part of mapping the human genome: assembling it after they've torn it apart."

BioMedNet Peaceable genome
[requires 'free' registration]

"Researchers from the rival public and private genome sequencing projects have met to work out their differences and seek out common interests. Participants at the meeting agreed that future projects will probably employ a mix of the whole-genome shotgun sequencing advocated by Celera Genomics and the clone-by-clone method used by the publicly funded project. Sean Eddy of Washington University in St. Louis urged both projects to pay more attention to cleaning up their draft sequences. "Right now, with both the Celera and the public data sets, it is difficult to tell the difference between an interesting variant and a mistake in the data," he said.

Reference: MacIlwain, C. 2001. Meeting hints at thaw in relations between genome rivals. Nature 411(6839):726."

Fortune Bill Haseltine

"One jab that drew chuckles: "You may have read that you're not much different from a flatworm," he told the crowd, referring to the decoders' startling claim that our set of genes isn't much larger than that of worms. At Human Genome Sciences, "we don't think so."

In fact, Haseltine says his Rockville, Md., company has found more than 90,000 human genes. In contrast, both the government-funded Human Genome Project and Celera Genomics, the Rockville company that mounted a parallel effort to decipher the genome, recently estimated that we have only about 35,000 genes. The dispute has big implications. If Haseltine is wrong, his company may have wasted millions of dollars trying to patent genes that don't exist. If he's right, the genome projects may be no better than "reading smudged text through foggy glasses," as Haseltine recently put it, when it comes to identifying genes."

Monday, June 18, 2001

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"Everything from liking rollercoasters to attitudes to the death penalty is influenced by our genes, say researchers."

"Liking rollercoaster rides and sweets are just two of the things that may be determined by our genes, according to research published in the Journal of Personality and Social Psychology."

redux [07.07.00]
UniSci Book Cites Dangers Of Misunderstanding Human Genetics

"Kaplan examines the roles genetic explanations for these types of differences play in our culture -- and how science has been used inappropriately to "medicalize" problems that should be more properly addressed as complex social issues.

Kaplan explores six specific areas -- intelligence (IQ), criminality and violence, homosexuality, depression, obesity, and the centrality of genetics in defining parenthood."

"He also explains the problems involved in "finding genes" for complex human behaviors by comparing the genomes of people who have a particular trait with the genomes of those who do not. The resulting medicalization centers the problem on the individual."

"... an emphasis on the biochemical and the genetic share the property that they make the condition out to be internal to the patient. Once a genetic explanation is offered, and any plausible sounding pathway proposed, the opportunities for claiming that there are other ways of approaching the problem are radically curtailed."

The problem becomes entirely that of personal biochemistry: the danger is in adopting easy solutions without looking at other reasons for the problem -- and without questioning the framework in which certain temperaments or sexual orientations become defined as problems."

Saturday, June 16, 2001

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"COMMUNICATIONS giant Marconi and pharmaceutical group Oxford Glycosciences (OGS) have joined forces to launch an online map of the human genome."

" The groundbreaking project, which underlines the importance of computing power to the biotechnology industry, involves the two companies put £15 million each, into the establishment of a new business called Confirmant which will produce online a "protein atlas" developed by OGS, which is a map of human genome."

Friday, June 15, 2001

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"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, June 14, 2001

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"The National Center for Genome Resources will launch a full users' release of ISYS(TM), NCGR's Integrated System, at the Beyond Genome 2001 Conference from June 17-20 at the Fairmont Hotel in San Francisco. ISYS is an innovative new product that integrates independent bioinformatic software tools and databases.

This software tool enables genomic investigators to go beyond single-focus analysis tools by creating an integrated environment in which they can more easily and rapidly discover new knowledge. ISYS is capable of integrating data sources and analysis tools from an investigator's own laboratory with those developed elsewhere. Free evaluation copies of ISYS can be downloaded and installed from the ISYS Web site, www.ncgr.org/isys."

Wednesday, June 13, 2001

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"Celera Genomics will acquire Axys Pharmaceuticals in an effort to support Celera?s drug discovery capabilities, the companies said Wednesday.

Celera of Rockvile, Md., said it expects that Axys? experience in the development of small molecule therapeutics will complement its capabilities in generating and analyzing genomic data. Axys offers chemical libraries and facilities, high-throughput screening, medicinal chemistry, structural biology, and pre-clinical capabilities that will support Celera?s efforts to identify and optimize small molecule therapeutic candidates for its genomic and proteomics discoveries."

Tuesday, June 12, 2001

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"The biological and computing challenges posed by mapping the genome are daunting: What is the function of the more than 30,000 human genes decoded last summer? How many human proteins exist? (Scientists think there are at least a million.) Which proteins keep the heart beating; which ones repair damaged tissue; which ones help digest food? Just as important, how does a protein behave when a disease like Alzheimer's or colon cancer takes root? And which genes are generating those flawed proteins?

Some of these tasks, such as determining the function of different proteins, can be tackled with existing computer power - albeit lots of it. Others, such as understanding the role of proteins in promoting disease, can require a computer of a different magnitude. A bio-supercomputer is not radically different from a conventional supercomputer, but it does require certain strengths, including the ability to recognize complex chemical and biological patterns and carry out complicated data searches."

Monday, June 11, 2001

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"Making sense of genome data of entire organisms may become easier with the launch next Friday of a database that enables researchers to predict which pathways - metabolic, gene regulatory or signalling - are likely to operate in their chosen organism.

"There's no standard software system that's arisen for putting genomes on the Web and facilitating ongoing genome databases on the Web," said Peter Karp, a computer scientist at SRI International in Menlo Park, California, who led the bioinformatics team that developed the new software."

Saturday, June 09, 2001

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"The Human Genome Project's discovery1 that the human body runs on an instruction manual of a mere 35,000 or so genes--compared to the worm's 19,000, the fruit fly's 13,000, and the tiny mustard relative Arabidopsis thaliana's 25,000--placed humanity on an even playing field with these other, supposedly simpler, organisms. It was a humbling experience, but humility quickly gave way to awe with the realization that the human genome might encode 100,000 to 200,000 proteins. Scientists base this number on the analysis of DNA sequences--called expressed sequence tags, or ESTs--that are reverse-transcribed from mRNAs. The question is, where is the information for all those extra proteins?"

Friday, June 08, 2001

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"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 [02.11.01]
USA Today Human genome makes mind-boggling reading

"The first close reading of the "The Book of Life" ?the 3 billion letters that make up the human genetic code ? reveals that it's packed with more mysteries and surprises than a pulp thriller. Perhaps the biggest surprise since the code was deciphered in June is that it takes just 30,000 to 40,000 genes to make, maintain and repair a human. That's far fewer than the 140,000 genes some had predicted and not many more than an earthworm or a common weed. "If you're judging the complexity of an organism by the number of genes it has, we've just taken a big hit in the pride department," says National Genome Research Institute's director Francis Collins, who also heads the U.S. arm of the international Human Genome Project (HGP)."

BBC Human genome: Nature or nurture?

""The human genome project has revealed that our genetic make-up is far less complicated than first thought.

Researchers have worked out that as few as 30,000 genes are needed to produce a human, only twice as many as the humble fruitfly.

One of the scientists behind the project, Dr Craig Venter says this would suggest our behaviour is not determined by our genes, with environmental factors playing a large part in shaping our thoughts and actions."

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."

Thursday, June 07, 2001

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"The researchers seemed to agree that the software now available for analyzing genomic data simply isn't adequate."

Despite significant pushes to cater to the life sciences from the likes of IBM, Compaq, Oracle, and Sun, scientists have yet to see the benefits.

"We've got to do something about what's current out there in the public," said Suzannah Lewis, head of informatics at the Berkeley Drosophila Genome Project.

Her comments quickly became a common theme."

Wednesday, June 06, 2001

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"Scientists from the Human Genome Project and Celera Genomics left their long-standing rivalry behind Wednesday to participate in the Joint Genome Sequencing Workshop, a meeting designed to seek consensus on the best approach to genome sequencing."

?The goal is to try to look forward and understand what common ground we have, and how to best move forward into the future,? said Gene Myers, Celera?s vice president for informatics research.

?In what appeared to be a move to offset any tension, researchers arriving at the meeting, which was held in neutral territory on the bucolic campus of the Howard Hughes Medical Institute, received nametags that conspicuously omitted organizational affiliations. The meeting was marked by an atmosphere that was collegial, yet cautious."

redux [03.08.01]
BioMedNet Evolution and scientific literature: towards a decentralized adaptive web
[requires 'free' registration]

"The February issues of Science and Nature, in which competing groups of scientists published their versions of the human genome, have settled nothing in the competitive battle. The Human Genome Project and Celera Corporation, which took different approaches to mapping the human genome, are still fighting. Officials of the public genome project seem to be exclaiming that the technique used by Celera failed, while Celera executives claim that the competition has no clue what it is talking about. At least one ethicist thinks that the battle is a case study of all the things besides science that go into scientific research and publication."

redux [07.05.00]
The Chicago Tribune BEHIND THE SCENES OF THE GENOME PROJECT

"On its surface, the genome story seems designed to illustrate one of the oldest of all American homilies: the virtues of extreme decentralization. An entrepreneur here is free to go into business for him or herself, over the objections of the chain of command, even in competition with the government.

In fact, the story points to a deeper moral, in an opposite direction. Last week's ceremony...in which Venter appeared at center stage with arch-rival Francis Collins of the NIH's Human Genome Research Institute, didn't just happen. There had to be some cooperation and knuckling-under.

?The White House gala was brokered by the elders of the scientific establishment. The lever presumably was a piece of a Nobel Prize. The intense behind-the-scenes diplomatic effort ended with the benediction pronounced last week by President Clinton:

"When we get all this worked out and we are all living to be 150--young people will still fall in love, old people will still fight about things that should have been resolved 50 years ago--we will all, on occasion, do stupid things, and we will all see the unbelievable capacity of humanity to be noble. This is a great day.""

Tuesday, June 05, 2001

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"In an effort to boost the supply of scientists literate in bioinformatics, the Global Genomics and Bioinformatics Unified Learning Environment (GLOBULE) is offering free bioinformatics courses for credit online. The courses will be designed for undergraduates at third-year level and above. Students will be able to interact with teachers and each other. Video lectures are already available, and formal courseware modules are planned. GLOBULE is backed by an international consortium of major institutions: Stanford University, Uppsala University, the Karolinska Institute, the National University of Singapore, the University of Sydney, and the University of the Western Cape.

Reference: Butler, D. 2001. Bioinformatics to be nurtured online. Nature 411(6837):513."

Monday, June 04, 2001

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"What both the Blueprint and DoubleTwist efforts point to is an era in which scientific discoveries are just as likely to come from parsing trillions of bits of data that already exist somewhere in a computer as they are to be discovered through finely tuned experiments in a wet lab. The efforts also signal a much more collaborative type of science than has ever before existed. As Kovac put it, "Biology is no longer about researchers in their laboratories, but a more dynamic community living and breathing in an age of interconnectedness." If Kovac, Couch, and others can pull off their grand bioinformatics projects of connecting the most brilliant minds in biology, they might turn out to be right that the impact of this new technology during the next decade will be greater than what we have seen so far from the Internet."

redux [05.19.01]
Nature: Web Debates Evolution and scientific literature: towards a decentralized adaptive web

"As our systems grow more sophisticated, we will see applications that support not just links between authors and papers but relationships between users and information repositories, and users and communities. What is required is a mechanism to enable communication between these relationships that leads to information exchange, adaptation and recombination. A new generation of information-retrieval tools and applications are being designed that will support self-organizing knowledge on distributed networks driven by human interaction (see Active Recommendation Project at Los Alamos. For example, to support trans-disciplinary science we stimulate different databases to learn new terms and adapt existing keywords to the categories recognized by different communities. This capability would allow a physicist or chemist to collaborate with colleagues in the life sciences without having to learn an entirely new vocabulary."

"Through the use of these new tools, we will derive a shared knowledge structure that is based on users and usage in addition to that provided by author citations. Thus, the aggregated connections that readers make between papers and concepts will provide an alternative conceptualization of a given knowledge space. Such techniques will be coupled with classical search and retrieval methods, and these capabilities have an obvious utility for discovering and supporting evolving knowledge from these networks."

Friday, June 01, 2001

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redux [04.01.01]
BusinessWeek Bioinformatics
"The reason for this sudden feeding frenzy? Sales growth. Although analysts estimate that bioinformatics will grow into a $2 billion dollar industry in the next five years, most IT companies believe the payoffs will be much higher. An internal study commissioned by IBM, for instance, predicts that when the markets for high-performance computing, storage, and e-commerce combine with that of data management, the worldwide market for IT products and services in the life-sciences sector will swell to $43 billion by 2004. Looking at these kinds of numbers, "now is not the time to think small,'' says Caroline A. Kovac, vice-president of IBM's Global Life Sciences Business Unit."

redux [06.26.00]
Oscar Gruss & Son Trends in Commercial Bioinformatics
""The purpose of this document is to provide an overview of the rapidly emerging field of "commercial bioinformatics."

"For the purposes of this review, we define bioinformatics as the backbone computational tools and databases that support genomic and related research, which broadly encompasses the study of DNA structure/function, gene expression and protein production/structure/function.""