Tuesday, February 29, 2000

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UAI-2000 Workshop on Fusion of Domain Knowledge with Data for Decision Support
"Statistics and inductive machine learning are data-oriented tasks in which domain models are induced from data, but databases are not the only resource from which models can be derived. Domain knowledge is still an important resource (whether in the form of deep knowledge or heuristics), and refinements in knowledge engineering have made the construction of knowledge-based systems more tractable. But when both data and domain knowledge are available, how can these two resources be used together for the construction of decision support systems? There is a growing interest in developing systems capable of both representing the knowledge pertaining to a domain and learning from the data available. Formal frameworks that enable some form of knowledge-data fusion (a.k.a. theory revision; theory refinement) to take place include probabilistic networks, possibilistic networks, neuro-fuzzy systems, and statistical inductive logic programming. A one-day workshop on knowledge-data fusion will be held on June 30, 2000, at Stanford University as part of The Sixteenth Conference on Uncertainty in Artificial Intelligence (UAI-2000). "

Monday, February 28, 2000

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The Times UK Gene chips are down in biotech patent battle
"It is a familiar British story. Ed Southern is an Oxford University professor, renowned for his work in developing tools for high-speed genetic analysis. Yet the lion's share of the commercial rewards of "gene chip" technology has gone not to Professor Southern or the university, but to Affymetrix, a Californian firm that is now one of the world's ten largest biotechnology companies.

Worse still, Professor Southern's faltering attempts to create his own business around his inventions risk being choked at birth by what he sees as corporate skullduggery. "

Saturday, February 26, 2000

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Science Daily Genome Scientists Muster Computer Software Tools For Handling The Flood Of Raw Data From The Human Genome Project And Related Efforts
"A new discipline has emerged at the intersection of computer science and biotechnology, bringing the power of advanced computational techniques to bear on complex problems in molecular biology. Called bioinformatics or computational biology, this new field is providing essential tools for scientists on the leading edge of research in genetics and other fundamental areas of biology."

Friday, February 25, 2000

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Science U.K. Plans Major Medical DNA Database
[summary - can be viewed for free once registered]
"Following the examples of Iceland, Sweden, and Estonia, the United Kingdom is drawing up plans to create a national database linking the DNA of 500,000 of its citizens to their medical records and lifestyle details. Its main goal is to tease apart the genetic and environmental components of conditions such as cardiovascular disease and cancer and, eventually, to come up with new drugs to treat--or even prevent--these conditions. An expert panel is currently hammering out a strategy for setting up the database and is due to report its recommendations next month.”

redux [02.13.00]
The Daily Davos Beyond the Genome
"By the spring of this year, the first draft of the human genome -- the sequence of all the genetic instructions needed to make up a human being -- will be published on the Web. But that is only the end of the beginning. Scientists still have very little idea of what most of the 100,000 or so human genes actually do, and finding out will take them into a very different area of research.

The raw material of the genome program has been anonymous samples of DNA, manipulated by complex laboratory machines that turn out information like a production line turns out widgets. But the new era of post-genome research involves analysing real people and their confidential medical records. The records are needed to match the genes that people carry with the diseases they may develop. Only then will gigabytes of genetic data into new treatments for cancer or heart disease. And that is why socialised healthcare is a vital part of post-genome research.

Countries such as the U.S., which provide healthcare through private enterprise, are useless for this sort of genetic inquiry. Only those countries which have organized the delivery of healthcare to their population in a way that is independent of the marketplace have built up the universal medical records necessary to make sense of the patterns of disease."

redux [02.06.00]
BBC News Iceland sells its genetic history
"It has never been done before and no-one really knows how successful it will be, but it has already divided the country and now the whole world is watching and waiting."

Thursday, February 24, 2000

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HMS Beagle Virtual Cures
[requires 'free' registration]
"For a brief period, supplying the data was enough. More genes meant more potential drug targets. But now the victims of the data flood are crying for help. Companies like Entelos, Inc. (Menlo Park, California) are coming to the rescue by building models that integrate all those data into a single, homeostatic, interconnected whole. The models allow researchers to run virtual drug trials to determine the best drug targets, treatment regimens, and patient populations."

Modelers feel that their time has come. "Leaders in the genomics field are all coming to this realization that model building is becoming the rate-limiting step," says Palsson. "There's a major shift taking place in the biological sciences." Math is back, he says, and "biology is going to become quantitative."

Biospace Virtual Drug Development: Start-ups Put Biology in Motion
"One way of animating our growing store of static information is through computer simulation. It is an area that is beginning to emerge slowly in the life sciences, with only a handful of academic and commercial players active in the area. But for a fledging discipline, there is a great variety in the scope of work being undertaken. While academic labs try to create accurate simulations of red blood cells and simple bacteria, the private companies are taking on bolder projects--simulating human organs and even human diseases in their entirety."

Science Revealing Uncertainties in Computer Models
[summary - can be viewed for free once registered]
"Computer simulations give the impression of precision, but they are founded on a raft of assumptions, simplifications, and outright errors. New tools are needed, scientists say, to quantify the uncertainties inherent in calculations and to evaluate the validity of the models. But making uncertainties evident is a tough challenge, as evidenced by several recent workshops.”

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individual.com Cambridge Healthtech Institute Survey Shows Oncologists Are Eager and Optimistic Regarding Genomics
"Almost half those polled in the Cambridge Healthtech Institute (CHI) survey described themselves as "very enthusiastic" about genomics cancer research, while another 42% were "somewhat enthusiastic."

"One interesting fact," says Ms. Branca, "was that many of the respondents believe genomic research will lead to increased application of pharmacogenomics. But more than 30% of the respondents are still unsure that this trend will, in turn, lead to more individualized cancer therapy."

Wednesday, February 23, 2000

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Cambridge Healthtech Institute Beyond Genome 2000
"Beyond Genome 2000 is a five-day event covering a number of computational tools used in the analysis and correlation of genomic data. The first two days are dedicated to Bioinformatics and Genome Research, focusing on the computational advances necessary to comprehend the vast amount of information gathered through the Human Genome Project. Next is a two-day conference on In Silico Biology that explores tools being developed to translate raw data into workable models that will provide guidance for target selection. The final portion of Beyond Genome concentrates on Proteomics, which will provide in-depth coverage of recent developments in the field of high-throughput protein expression analysis and its impact on diagnostic and therapeutic product development."

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AAAI 2000 Workshop Learning Statistical Models From Relational Data
"Researchers from a variety of backgrounds (including machine learning, statistics, inductive logic programming, databases, and reasoning under uncertainty) are beginning to develop techniques to learn statistical models from relational data. This work diverges from traditional approaches in these fields that assume data instances are structurally identical and statistically independent or assume that relationships are deterministic. New developments in this area are vital because of the growing interest in mining information in relational databases, object-oriented databases, XML and other structured and semi-structured formats. The workshop will focus on learning models that represent statistical correlations between the properties of related entities directly from relational data."

Tuesday, February 22, 2000

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MIT Technology Review The Bell Labs of Biology
"The sequence of the human genome is determined once in the history of mankind. It’s a unique time in biology and chemistry—equivalent to the advent of quantum mechanics in physics. The question is—how do we begin to understand and assimilate the huge amount of information encoded in the genome? The other revolution that has occurred during the last 10 years in the biological and physical sciences is in the way in which we carry out experimental science. There’s been a tremendous increase in our ability to design, implement and analyze experiments—to carry them out not one at a time but thousands or millions at a time. That has been made possible by combinatorial technologies, computational tools and advances in engineering and miniaturization—the kind of tools and processes that revolutionized the semiconductor industry are being moved over into the biological and physical sciences. The bottom line is that without that set of tools it would be damn near impossible to deal with the huge amount of information related to the human genome."

Monday, February 21, 2000

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Science Bioinformatics in the Information Age
[summary - can be viewed for free once registered]
"The vast amounts of data generated by genome sequencing, gene chip technology and genome data mining have to be carefully analysed and interpreted. Such analysis and interpretation is the domain of the burgeoning field of bioinformatics. In her TechView article, Spengler looks at the progress and problems besetting the bioinformatics age. ”

Sunday, February 20, 2000

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ABCNews.Com Fruit Fly Genome Decoded
"Scientists at last have deciphered virtually the entire genetic code of the fruit fly, an important dry run in figuring out all the genes that make humans tick."

"To those who have spent their careers studying the fruit fly, the data are likely to offer many insights as well as possibilities for new experiments. Among other things, Dr. Edward Lewis said it will mean scientists may spend as much time scrutinizing newly available genetic code on computer screens as they now do in lab experiments."

Tuesday, February 15, 2000

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SF Gate Biologists, Engineers Teaming Up to Unravel Genomic Thread DNA sequencing instruments evolved in Silicon Valley
"The data pouring off this sequencing assembly line flows into an air-conditioned computer center. There, in the quiet chill, an array of 1,500 PCs takes these raw gene fragments, matches them to known sequences or marks them as novel, and deposits the data in storage systems that are the information-equivalent of bank vaults... the data massaging work doesn't require a very powerfulcomputer. There's just so much data spewing off the sequencing line that Incyte needed a cheaper way to do it.

So engineers wrote a program, based on the free Linux operating system, that allows those humble PCs to divvy up the processing chores. By using free Linux, and buying generic computers, Francis estimates that Incyte gets the job done at 10 percent of what it used to cost when the company used powerful workstations running the Unix operating system."

Monday, February 14, 2000

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Yahoo! Finance Gemini Launches New Genetics Initiative In Newfoundland & Labrador
"Gemini Holdings plc, the clinical genomics company, today announced the signing of an agreement with Lineage Biomedical Inc., of St. John's, Newfoundland, to establish a joint venture for the purpose of identifying genes for common diseases using the unique population resources of Newfoundland. The joint venture, Newfound Genomics, will establish a genetics based research facility in Newfoundland and Labrador with the aim to identify disease-causing genes."

"The Canadian province of Newfoundland and Labrador has a population of around 550,000 people, primarily descended from a small 'founder' population of English, Scottish and Irish immigrants that populated the islands between the 1600s and the 1840s. The unique population history of Newfoundland and Labrador and the increased prevalence of certain diseases, such as psoriasis, rheumatoid arthritis and diabetes, represent a powerful resource for geneticists to identify genes that predispose to these diseases."

Sunday, February 13, 2000

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The Daily Davos Beyond the Genome
"By the spring of this year, the first draft of the human genome -- the sequence of all the genetic instructions needed to make up a human being -- will be published on the Web. But that is only the end of the beginning. Scientists still have very little idea of what most of the 100,000 or so human genes actually do, and finding out will take them into a very different area of research.

The raw material of the genome program has been anonymous samples of DNA, manipulated by complex laboratory machines that turn out information like a production line turns out widgets. But the new era of post-genome research involves analysing real people and their confidential medical records. The records are needed to match the genes that people carry with the diseases they may develop. Only then will gigabytes of genetic data into new treatments for cancer or heart disease. And that is why socialised healthcare is a vital part of post-genome research.

Countries such as the U.S., which provide healthcare through private enterprise, are useless for this sort of genetic inquiry. Only those countries which have organized the delivery of healthcare to their population in a way that is independent of the marketplace have built up the universal medical records necessary to make sense of the patterns of disease."

Saturday, February 12, 2000

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msnbc Robots speed up gene exploration
"Scientists have used robots to record the interactions between proteins in a single cell in a technical tour de force that will help researchers learn about the function of unknown genes"

Dr. Stanley Fields of the University of Washington in Seattle and the drug development company CuraGen Corporation of New Haven, Conn., have automated the process and used robots to test the simultaneous interactions of roughly a thousand molecules inside a yeast cell. In addition to determining what an unknown gene does, the research published in the science journal Nature will also help scientists figure out more about known genes."

dow jones business news CuraGen's Shares Soar On News It Completed Protein Map Of Genome
"CuraGen (CRGN), a drug discovery and development company, said it expects it will take 24 months to identify the protein interactions for the human genome, once the sequence is publicly available."

The Bump: CURAGEN CORP [ NASDAQ : CRGN]

Wednesday, February 09, 2000

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BioNews Bioinformatics Forum Bioinformatics & Data Integration conference
"Featured Presentations & Case Studies:

*Bristol-Myers Squibb Pharmaceutical Research Institute - Gain an overview of the d2-cluster program and understand the technology underlying EST clustering

*Procter & Gamble Pharmaceuticals - Build a rigorous project management system to increase the effectiveness and efficiency in deploying bioinformatics

*National Cancer Institute - Learn how the color-coded clustered image map (CIM) has been used for application to molecular data on cells used in the National Cancer Institute's drug discovery program

*Roche Biosciences - See how chem-informatics, bioinformatics, biomedical informatics and medical informatics describe the spectrum of experimental and computational data essential for optimizing the drug development process

*SmithKline Beecham Pharmaceuticals - Hear about the work of the Object Management Group and the Bio-Ontologies Consortium in establishing standards for object software interoperability and building shareable ontologies for molecular biology "

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pharmaceuticalonline.com Spotfire Delivers Spotfire Pro, Related Services Through the Web
"Spotfire Forum is a free, Web-based collaborative portal for scientific and technical decision-makers. The portal leverages the open nature of the Web to facilitate the exchange of ideas and encourage innovative approaches to discovery, development, manufacture, marketing of chemical products. The Forum offers users free downloadable plug-ins, free downloadable analytical methodologies and templates, and threaded discussion capabilities."

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Viaken.com Viaken Systems and InforMax Forge Alliance
"Viaken’s ASP model will offer InforMax customers an additional channel to access our bioinformatics software, providing ease of use and dedicated servers in a highly secure environment."

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individual.com Incyte Supports President's Initiative to Guarantee Genetic Privacy
"Incyte Pharmaceuticals, Inc. (Nasdaq: INCY), the world's leading provider of genomic information, announced today its full support for President Clinton's effort to protect the privacy of federal employees' genetic testing results.

"We believe the race to discover new genes and the underlying cause of disease is bringing a new era of creativity to drug discovery and health care," said Roy A. Whitfield, chief executive officer of Incyte. "For genomics to deliver on its promise of revolutionizing health care, consumers need to be certain that the information generated by these medical advances is not used in a discriminatory fashion."

Tuesday, February 08, 2000

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JAMA Life Expectancy Gains From Cancer Prevention Strategies for Women With Breast Cancer and BRCA1or BRCA2 Mutations
"We developed a Markov state transition model to compare the survival benefits of secondary cancer prevention strategies for women with BRCA-associated breast cancer. The model simulates the natural history of hypothetical cohorts of women with newly diagnosed, unilateral BRCA-associated breast cancer who elect 1 of 8 strategies for prevention of second cancers"

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KDNuggets Self-organising Data Mining
"This book covers several areas of knowledge discovery and describes a spectrum of parametric and nonparametric self-organizing modeling methods. It introduces principles of evolution - inheritance, mutation and selection - for generating a network structure systematically enabling automatic model structure synthesis and model validation."

Preface to Self-Organising Data Mining

Monday, February 07, 2000

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prnewswire Guidelines Reference GART and VIRADAPT Studies in Supporting Clinical Utility of Genotypic Drug Resistance Testing
"'The guidelines support the use of genotyping resistance tests as a rapid means to assist in the selection of the appropriate antiviral drug regimen in the treatment of HIV infected patients, especially in cases of virologic failure', said Richard Daly, CEO of Visible Genetics."

The Bump: VGIN bumped up 26.5% [as of 02.07.00]

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enVision Bioinformatics Infrastructure for Large-Scale Analyses
"The Bioinformatics Infrastructure alpha project is making a three-pronged assault on the problem: analysis, access, and movement of data. In the analysis component, participants are developing molecular scanning and comparison algorithms for various collections, and the Legion metasystem will recruit the computing resources required for large-scale analyses."

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IBM.com IBM Joins Group to Create Library of Genetic Markers
"IBM has pledged to contribute about $3 million to the SNP Consortium, a group dedicated to creating a public database of single nucleotide polymorphisms (SNPs) patterns, which can indicate whether individuals are predisposed to certain diseases. IBM will also develop software, computers, and services to be sold to pharmaceutical companies engaged in the study of SNP patterns."

SNP Consortium Overview
"Its mission is to develop up to 300,000 SNPs distributed evenly throughout the human genome and to make the information related to these SNPs available to the public without intellectual property restrictions. The project started in April 1999 and is anticipated to continue until the end of 2001."

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Individual.com Rosetta Inpharmatics Publishes Approach to Link Genomics To Protein Function in Science
"This research is the first to combine innovative DNA microarray and bioinformatics strategies to track signal transduction pathways...The study examined the full spectrum of genes that regulate important cell signaling pathways in a model system..."This work illustrates the potential to identify the time course of all transcriptional responses resulting from activation of a signaling pathway, thereby identifying many previously unknown candidate genes for the biological process under study," stated Leland H. Hartwell, Ph.D., President of the Fred Hutchinson Cancer Research Center, and Chairperson of Rosetta's Scientific Advisory Board."

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prnewswire LION Bioscience AG and Tripos, Inc. Build Strategic Alliance in Life Science Informatics
"Under the alliance the two companies are integrating LION's bioinformatics with Tripos' cheminformatics expertise, pioneering the development of a unified platform for managing the many diverse information systems in Life Sciences. As part of the extension agreement, LION has made an equity investment in Tripos on terms that Tripos will disclose separately.

The first product being jointly developed under the alliance is "GenChem," a powerful software tool that aids in integrating and processing genetic, molecular, cellular, tissue, high throughput screening and chemical data, on one single IT-platform.”

Friday, February 04, 2000

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HMS Beagle Cancer's fingerprints
[requires 'free' registration]
"Diffuse large B-cell lymphoma (DLBCL) is not one disease, but many. Around 40% of patients respond to chemotherapy, and the rest usually succumb to the disease. The clinical differences are manifested in differing progression rates, host responses, and differentiation states of the tumors. Researchers have now used genetic screening to identify two distinct categories of the disease, each with unique gene expression profiles. One type expressed genes typical of germinal center B cells, the other had a profile similar to that seen during in vitro activation of peripheral blood B cells. Patients with a germinal centerlike disease had a significantly better prognosis than patients with cancers falling in the latter category. This work could lead to improved classification of cancers and implementation of more targeted therapy. ”

Reference: Alizadeh, A.A., Eisen, M.B., Davis, R.E. et al. 2000. Distinct types of diffuse large B-cell lymphoma identified by gene expression profile. Nature 403(6769):503-511.

Update: NIH News Release Scientists Discover Common Cancer is Two Distinct Diseases
"Louis Staudt, M.D., Ph.D., a scientist at the National Cancer Institute (NCI) and a senior author on the paper, said this finding helps to explain why about 40 percent of patients with this type of [non-Hodgkin's lymphoma (NHL)] can be cured with standard chemotherapy regimens, while other patients who seemingly have the same disease often relapse. "It's a case of mistaken identity," said Staudt. "The tumor cells might look very similar, but this study offers strong evidence that their molecular engines work very differently. ”

"We arrayed on a specialized glass-slide chip more than 15,000 of these unique genes with about 3,000 other genes that are involved in various cancers or in the immune system," said Ash Alizadeh, a scientist at Stanford University School of Medicine and one of the lead authors on the study. "This customized microarray, which is slightly larger than a penny and contains over 18,000 genes in all, is known as a 'Lymphochip.'" The principal members of the Stanford laboratory team are Brown, Alizadeh, Michael Eisen, Ph.D. (a lead author), and David Botstein, Ph.D. ”

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Individual.com AlphaGene Announces the Award of a Major New Patent in Bioinformatics
"The patent covers the use of agents that implement continuous, selective database updates to proceed asynchronously with respect to the addition of new data into the database. These agents keep large and dynamic databases well annotated and up-to-date, while allowing users to keep long-running searches alive for entries meeting certain specific annotation criteria. Changes in methods of annotation or amount of data in the databases do not limit users who continue utilizing and researching the databases. ”

Wednesday, February 02, 2000

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EE Times RNA computer clears 10-bit hurdle
"Princeton University researchers claim to have reached a new level of complexity in DNA computing. The group has demonstrated an RNA-based computer capable of solving mathematical problems that were encoded as 10-bit strings. Strands of RNA containing 1,024 base pairs were encoded with every possible solution to a specific chess problem. Ribonuclease digestion progressively narrowed down the possible solutions until only the 43 correct solutions — plus one incorrect one — remained. ”

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silicon.com Cancer researchers pioneer data mining techniques
"Medical researchers at the University of Leeds are pioneering the latest data mining techniques in their fight against Leukaemia...The Disease Registry Application is designed to allow researchers to map, analyse and display data on the distribution of the disease nationwide.”

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Individual.com Blackstone Builds Compute Farm for Celera Genomics for Rapid Mapping of Human Genome
"Blackstone Technology Group today announced that Celera Genomics (NYSE:CRA), a PE Corporation business, has selected Blackstone to assist the company with configuration and roll-out of one of the world's largest compute farms.”

"Prior to the computer farm, computers at Celera were organized by function. While one group of computers at Celera's headquarters was processing data, another group would remain idle waiting for data. This downtime meant that Celera's computers were not being tapped to their full potential. Now, with their compute farm in place, Celera is able to use all of its processors, all the time as they move forward quickly in their quest to map the human genome.”

Tuesday, February 01, 2000

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first post!