{bio,medical} informatics
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
(0) comments
Genetic Engineering News
NIH Awards Grant to Stanford to Launch Biomedical Computation Center
"The National Institutes of Health announced Sept. 29 that it has awarded the Stanford University School of Medicine a grant of $18.8 million to develop a National Center for Biomedical Ontology along with several other collaborating institutions. The goal of the center is to design and implement a new generation of computer systems that will enable researchers to share, compare and analyze data gathered from large biomedical experiments.
The center will be led by Mark Musen, MD, PhD, professor of medicine (medical informatics), whose Stanford research group created Protege, the most widely used ontology-development software in the world."
redux [05.01.00]"The National Center for Biomedical Ontology (cBiO) is a consortium of leading biologists, clinicians, informaticians, and ontologists who develop innovative technology and methods that allow scientists to create, disseminate, and manage biomedical information and knowledge in machine-processable form. The Center's resources include the Open Biomedical Ontologies (OBO) library, the Open Biomedical Data (OBD) repositories, and tools for accessing and using this biomedical information in research. The Center collaborates with biomedical researchers conducting Driving Biological Projects (DBPs) to enable their research and to stimulate technology development in cBiO. The Center is undertaking outreach and educational activities to train the future generation of researchers in using biomedical ontologies and cBiO tools to enhance scientific discovery."
"In the construction of both conventional software and intelligent systems, developers continue to seek higher level abstractions that both can aid in conceptual modeling and can assist in implementation and maintenance. In recent years, the artificial intelligence community has placed considerable attention on the notion of explicit ontologies -- shared conceptualizations of application areas that define the salient concepts and relationships among concepts. Such ontologies, when joined with well defined problem-solving methods, provide convenient formalisms for modeling and for implementing solutions to application tasks. This chapter reviews the motivation for seeking such high-level abstractions, and summarizes recent successes in building systems from reusable domain ontologies and problem-solving methods. As the environment for software execution moves from individual workstations to the Internet at large, casting new software applications in terms of these high-level abstractions may make complex systems both easier to build and easier to maintain."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
(0) comments
Nature Biotechnology
Are the current ontologies in biology good ontologies?
"The research histories of both biology and ontologies originate with the philosopher Aristotle. For 2,400 years, the two subjects have taken separate paths. Now, with the rise of bioinformatics, they are reunited in the 'hot' research topic of biological ontologies. So why are biological ontologies important? As more and more biological data are stored on computers, the problem of efficient retrieval and analysis of these data becomes the most important scientific bottleneck, and the problem is particularly acute in biology because biological data are notorious for their complex form and semantics. Ontologies can help because they embody the abstract knowledge required for data integration and analysis. The utility of ontologies has been clearly demonstrated in several biological domains (e.g., Gene Ontology1). However, within biology, the enthusiasm for ontologies has been accompanied by a general lack of awareness of what exactly ontologies are and how to use them. This lack of awareness is reflected in the fact that many, perhaps all, 'bio-ontologies' fail to follow international standards for ontology design and description. This failure is important because it places a serious restriction on their applicability to knowledge sharing, reuse and inference.
In this article, we analyze the current state of application of ontologies in biology, try to reveal the reasons for the existing difficulties, recommend a possible solution to the current problems and describe prospects and future challenges for the application of ontological engineering in biological domains."
[ via nodalpoint ]redux [03.17.02]
[requires 'free' registration]
"The great challenge in biological research today is how to turn data into knowledge. I have met people who think data is knowledge but these people are then striving for a means of turning knowledge into understanding. Knowledge and science are related words and to know, I believe, is to understand. Before rushing to convert genomics to 'genamics' and finding that it is another dead end, we should consider evacuating the Tower of Babel. We need a theoretical framework in which to embed biological data so that the endless stream of data, filled with the flotsam and jetsam of evolution, can be sifted and abstracted.
Very simply, the network we should be interested is not the network of names but the network of the objects themselves. The language of these objects is not the Oxford Dictionary of Molecular Biology--the Ontology Consortium's main source--but that of molecular recognition, the language of molecular biology itself."
redux [01.08.02]
"Research directed toward discovering how genetic factors influence a patient's response to drugs requires coordination of data produced from laboratory experiments, computational methods, and clinical studies. A public respository of pharmacogenetic data to which investigators from different centers can contribute will facilitate hypothesis generation for further research. We are developing a pharmacogenetics knowledge base (PharmGKB) that will support storage and retrieval of experimental data and conceptual knowledge. We are confronted with the challenge of designing an Internet-based resource that integrates complex biological, pharmacological, and clinical data in such a way that researchers can submit their data and users can retrieve information that supports genotype phenotype correlations. Successful management of the names, meaning, and organization of concepts used within the system is crucial. We have selected a frame-based knowledge-representation system for development of an ontology of concepts and relationships that represent the domain and that will permit storage of experimental data. Preliminary experience shows that the ontology we have developed for gene-sequence data submissions is appropriate for experimental data that researchers will enter."
redux [06.27.01]"Ontologies are specifications of the concepts in a given field and the relationships among those concepts. The development of ontologies for molecular-biology information and the sharing of those ontologies within the bioinformatics community are central problems in bioinformatics. If the bioinformatics community is to share ontologies effectively, ontologies must be exchanged in a form that uses standardized syntax and semantics. This paper reports on an effort among the authors to evaluate a number of alternative ontology-exchange languages, and to recommend one or more languages for use within the larger bioinformatics community. The study selected a set of candidate languages, and defined a set of capabilities that the ideal ontology-exchange language should satisfy. The study scored the languages according to the degree to which they provided each capability. In addition, the authors performed several ontology-exchange experiments with the two languages that received the highest scores: OML and Ontolingua. The result of those experiments, and the main conclusions of this study, was that the frame-based semantic model of Ontolingua is preferable to the conceptual graph model of OML, but that the XML-based syntax of OML is preferable to the Lisp-based syntax of Ontolingua."
"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.
redux [05.23.01]"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."
"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]
"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]
"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]
[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]
[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]
"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]
"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?"
"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."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
(0) comments
The Economist
The paperless library
"IT USED to be so straightforward. A team of researchers working together in the laboratory would submit the results of their research to a journal. A journal editor would then remove the authors' names and affiliations from the paper and send it to their peers for review. Depending on the comments received, the editor would accept the paper for publication or decline it. Copyright rested with the journal publisher, and researchers seeking knowledge of the results would have to subscribe to the journal.
No longer. The internet—and pressure from funding agencies, who are questioning why commercial publishers are making money from government-funded research by restricting access to it—is making free access to scientific results a reality. This week, the Organisation for Economic Co-operation and Development (OECD) issued a report describing the far-reaching consequences of this. The report, by John Houghton of Victoria University in Australia and Graham Vickery of the OECD, makes heavy reading for publishers who have, so far, made handsome profits. But it goes further than that. It signals a change in what has, until now, been a key element of scientific endeavour."
redux [08.15.05]
"Now, after a study that sent reverberations through the medical profession by finding that almost one-third of top research articles have been either contradicted or seriously questioned, some specialists are calling for radical changes in the system."
In advance of a world congress on peer review next month in Chicago, these specialists are suggesting that reviewers drop their anonymity and allow comments to be published."
""It would be lovely to start anew and to set up a trial of peer review against no peer review," Rennie said. "But no journal is willing to risk it.""
redux [06.25.04]
[requires 'free' registration]
"More than money and success is at stake. Free and widespread distribution of new research has the potential to redefine the way scientific and intellectual developments are recorded, circulated and preserved for years to come.
"Society pays for science," said Dr. Nicolelis, whose article in the October issue of PLoS got worldwide attention. "We have the technology, we have the expertise. Why is it that the only thing that has remained the same for 50 years is the way we publish our results? The whole system needs overhaul.""
redux [11.22.03]
"Science's Rocky-style publishing battle starts its second round Monday when a groundbreaking journal releases its latest issue.
The challenger, the upstart Public Library of Science: Biology, packed a strong punch last month with its first issue, which featured a headline-grabbing report of monkeys getting brain implants to control robot arms. The upcoming issue spotlights newly discovered genes for obesity and osteoporosis."
redux [10.14.03]
"There are lots of scientific journals, and the debut of another one normally would not raise many eyebrows.
But yesterday's online launch of Public Library of Science Biology drew so many curious browsers -- half-a-million Web hits in the first eight hours -- that the swamped site had to divert many to a backup site."
"Led by heavyweights such as Nobel laureate Harold Varmus, former director of the National Institutes of Health, the PLoS project aims to shake up the world of scholarly publishing by freely sharing its monthly contents."
redux [10.10.03]
"In the highly lucrative world of cutting-edge scientific research, it is nothing short of a revolution. A group of leading scientists are to mount an unprecedented challenge to the publishers that lock away the valuable findings of research in expensive, subscription-only electronic databases by launching their own journal to give away results for free.
The control of information on everything from new cancer treatments to space exploration is at stake, while caught in the crossfire are the world's publicly funded scientists, some of whom will soon face a choice between their career and their conscience."
redux [08.22.03]
[requires 'free' registration]
"Debate over open access to scientific articles is steadily moving into the mainstream, with the publication this month of an editorial in The New York Times, a recently introduced Congressional bill to promote open access publishing, and a television commercial sponsored by the Public Library of Science (PLoS), a California-based group that plans to launch an open-access journal in October.
As enthusiasm grows, however, some skeptics wonder whether open-access journals will succeed financially, since they charge relatively small "article processing fees," paid upfront by the researcher, instead of substantial fees for institutional library subscriptions."
redux [07.01.03]
""It's ridiculous," Eisen said in this voice during a recent phone interview from Washington. "All these things we're so used to doing with information on the Internet, we're preventing clever entrepreneurial people from doing with works of science. The idea that a narrow profit motive would prevent the dissemination of this information -- it's insane!"
Eisen was in Washington to lend his support to a congressional effort he believes will make scientific publishing less insane and less ridiculous. Most scientific journals -- such as Science, Nature or the New England Journal of Medicine -- require researchers to turn over all rights to the reports selected for publication; the publications then charge institutions and individuals subscription fees to view these reports, a model that Eisen believes inhibits scientific progress. The approach is especially galling, Eisen says, when you consider that a great deal of the money that funds the research published in these journals comes from the federal government. The public is paying for science that it never gets to see, he says."
redux [12.16.02]
[requires 'free' registration]
"A group of prominent scientists is mounting an electronic challenge to the leading scientific journals, accusing them of holding back the progress of science by restricting online access to their articles so they can reap higher profits.
Supported by a $9 million grant from the Gordon and Betty Moore Foundation, the scientists say that this week they will announce the creation of two peer-reviewed online journals on biology and medicine, with the goal of cornering the best scientific papers and immediately depositing them in the public domain."
redux [11.15.02]
"Having persuaded the Energy Department to pull the plug on PubScience, a Web site that offered free access to scientific and technical articles, commercial publishers are taking aim at government-funded information services offering free legal and agricultural data.
"We're delighted with the decision [to shut down PubScience]," LeDuc said. "The administration has done a tremendous job of hearing our concerns and responding to what we've always considered to be our legitimate concern."
redux [09.24.02]
[requires 'free' registration]
"The UK's Office of Fair Trading says that the prices for scientific, technical, and medical (STM) journals are too high because normal competitive forces have been suspended. Libraries are paying too much. The prices of STMs are rising faster than inflation, and the disparity between for-profit and not-for-profit journals is obvious. Part of the problem is that the journals compete on quality, not price, so libraries are prone to skip the cheaper journals for the better, more expensive ones. Bundling journals also skews the market.
Goodman, S. 2002. "Unusual forces" are pushing journal market off course. Nature 419(6904):239.
redux [09.05.01]
[requires 'free' registration]
"Publishers of established scientific journals have thus far resisted demands for freer access. In its campaign to make biomedical research literature available free online, Public Library of Science is now taking a new tack: It hopes to publish peer-reviewed, electronic journals.
"If we really want to change the publication of scientific research, we must do the publishing ourselves," says an announcement posted Sept. 1 on the group's Web site. "It is time for us to work together to create the journals we have called for."
redux [04.24.01]
"When a molecular biologist or a biochemist has made a discovery - often after many months or even years of tedious experiments - they tell the rest of the world by publishing their results in a scientific journal. So far, these journals have controlled who can read them and who cannot - but maybe not for much longer.
E-mail, Internet discussion groups, electronic databases and pre- or e-print servers have already transformed the way scientists openly exchange their results. And in the life sciences, researchers are now demanding that their work be included in at least one free central electronic archive of published literature, challenging the traditional ownership of publishers. The demand has sparked widespread discussions among scientists, publishers, scientific societies and librarians about the future of scientific publishing. The outcome may be nothing short of a revolution in the scientific publishing world."
redux [09.20.00]
"How should biomedical research be communicated? How should research be assessed and validated?"
"Below are abstracts, transcripts, and biographies from the conference. Some presentations did not lend themselves to transcription. Where possible we have supplemented them with editorials from the speakers.
We have also commissioned editorial articles from several speakers and delagates at the meeting."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
(0) comments
The Washington Post
New Analyses Bolster Central Tenets of Evolution Theory
"When scientists announced last month they had determined the exact order of all 3 billion bits of genetic code that go into making a chimpanzee, it was no surprise that the sequence was more than 96 percent identical to the human genome. Charles Darwin had deduced more than a century ago that chimps were among humans' closest cousins.
ut decoding chimpanzees' DNA allowed scientists to do more than just refine their estimates of how similar humans and chimps are. It let them put the very theory of evolution to some tough new tests."
redux [08.31.05]
"Scientists unleashed a torrent of studies comparing the genetic coding for humans and chimpanzees on Wednesday, reporting that 96 percent of our DNA sequences are identical. Even more intriguingly, the other 4 percent appears to contain clues to how we became different from our closest relatives in the animal kingdom, they said."
"The researchers said the results confirmed the common evolutionary origin of humans and chimpanzees. Out of the 3 billion base pairs in the DNA coding for chimps and humans, about 35 million show single-base differences, and another 5 million DNA sites are different because of insertions or deletions of genetic code. Waterston estimated that 1 million of those coding changes are responsible for the functional differences between humans and chimps — thus defining our humanness."
redux [05.26.04]
"What is the difference between a chimp and a human? There could be a lot more to the answer than scientists thought, according to the first accurate DNA sequence of a chimp chromosome."
"Because chimps and humans appear broadly similar, some have assumed that most of the differences would occur in the large regions of DNA that do not appear to have any obvious function. But that was not the case."
redux [04.05.04]
"A comparison of the chimp and human genomes casts new light on why the two species are so different despite having very similar genetic code."
"One of the leading scientists on the project says the answer lies in the process that orchestrates the genes as the chimpanzee is developing."
"The latest experimental results have solidified evidence of a roughly 10% difference in gene expression from several regions of the brain."
"The researchers have confirmed their findings in four regions of the cerebral cortex, and in the cerebellum and the caudate nucleus. On the other hand, evidence relating to the linear accumulation of differences over time means "we are coming to believe that these are not all functionally relevant," Paabo added."
redux [12.12.03]
[requires 'free' registration]
"In a preliminary screen, Dr. Clark and his colleagues have found that a large number of genes shows signs of accelerated evolution in the human lineage. Those are genes that, by a statistical test applied to changes in their DNA, appear to be under strong recent pressure of natural selection and so are likely to be those that make humans differ from chimpanzees.
A prominent set of accelerated human genes are those involved in hearing, particularly the gene that makes a protein called alpha-tectorin, a component of the tectorial membrane of the inner ear."
"Another group of selected genes is involved in brain development."
redux [12.10.03]
"Researchers today released a draft version of the genetic sequence of our closest relative, the chimpanzee Pan troglodytes .
The differences between the chimp's genetic code and ours should reveal what makes us human, scientists hope. The disparities might, for example, lie in genes that control the development of the brain and language, or of human-specific diseases such as Alzheimer's, AIDS and malaria."
redux [05.20.03]
"Scientists from the Wayne State University, School of Medicine, Detroit, US, examined key genes in humans and several ape species and found our "life code" to be 99.4% the same as chimps.
They propose moving common chimps and another very closely related ape, bonobos, into the genus, Homo, the taxonomic grouping researchers use to classify people in the animal kingdom."
redux [04.29.03]
"By studying chimpanzees, scientists are honing their genetic view of humanity, researchers told this week's meeting of the Human Genome Organisation in Cancun, Mexico."
"The data call for some revision of the estimated genetic similarity between us and our closest relatives. Previously, human and chimp genetic sequences were quoted as being nearly 99% identical, with a difference of only a few DNA's letters. In fact, the similarity may be as low as 94-95%, says Todd Taylor of the RIKEN Genomic Sciences Center in Yokohama, Japan.
redux [03.04.03]
"Chimpanzees seem almost human, and scientists have maintained for decades that chimps are, in fact, 98.5 percent genetically identical to humans.
But the results of a new study call that figure into question, with a finding that there are actually large chunks of the human and chimp genomes that are vastly different."
"It involves sampling data from select regions of many different related species, and then comparing them within the context of their phylogenetic relationships. In the research described in the Science paper, Rubin and colleagues sampled 17 primate species closely related to human and spanning 40 million years of evolution -- insufficient time for significant genetic divergence to have taken place.
According to Rubin, phylogenetic shadowing compensates for the failure of traditional comparative genomics techniques, which "invariably miss recent changes in DNA sequence that account for primate-specific biological traits." The approach overcomes the primary challenge of comparing genomes of closely related species: the difficulty in distinguishing functional from nonfunctional sequences."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
(0) comments
news.telegraph
Brain image lie detector could trap terrorists
"Brain-imaging techniques are now reliable enough to detect whether a person is lying, scientists report today. They could provide a valuable tool in questioning criminals and terrorists."
""We can't predict if someone will one day use a bomb," Dr Daniel Langleben tells the journal Nature. "But we can use fMRI to distinguish true and false responses and detect concealed information about past events. Either approach or a combination of both could tell us whether X is in terrorist organisation Y.""
"Medical imaging and brain research are among the most challenging and fascinating topics of contemporary science. Exciting possibilities exist to improve both the state of the art in medicine and our understanding of the human brain. These opportunities have motivated many researchers to use powerful computational methods to analyze images of brain structure and function, applying them to key questions in medicine and neuroscience. Algorithms can now uncover disease-specific patterns of brain structure and function in whole populations. These tools now chart how the brain grows in childhood, detect abnormalities in disease, and visualize how genes, medication, and demographic factors affect the brain. Image analysis methods can also identify and monitor systematic patterns of altered anatomy in diseases such as Alzheimer's, tumor growth, epilepsy, and multiple sclerosis, and psychiatric disorders such as schizophrenia, autism, and dyslexia.
We briefly review recent developments in brain image analysis, focusing on (1) some of the main concepts and tools used when analyzing brain images, and (2) how to apply these tools to study key neuroscience questions relating to disease, development, and genetic influences on the brain. We describe a range of new tools that compare, contrast, and average imaging data in large human populations. We describe our construction of statistical brain atlases that store detailed information on how the brain varies across age and gender, across time, in health and disease, and over time. We also discuss some common mathematical methods that are currently being used to analyze variations in brain organization, cortical patterning, asymmetry and tissue distribution in several collaborative studies of brain development and disease (N=1000 scans)."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
(0) comments
SciDev.Net
Personalised medicine 'overhyped'
"The promise of personalised medicines — tailored to a person's genes — have been "overhyped", particularly for developing countries, according to the UK's national science academy.
Healthcare based on 'pharmacogenetics' is likely to be decades away, especially in developing countries, due to gaps in scientific knowledge and a shortage of researchers equipped to study the link between genes and disease, says a report published by the Royal Society yesterday."
redux [08.04.05]
"Wolfgang Sadee, director of the pharmacogenomics programme at Ohio State University in Columbus, adds that it will be five years until drug companies fully embrace the field. "If we train people now," he says, "in five years they will be in the right position to help out."
The earlier approach of pharmacogenetics, which targets a single gene, has already scored some successes. Herceptin (trastuzumab), for example, treats breast cancer by targeting a single receptor on tumour cells that is overabundant in women who inherit a specific gene mutation. And the analysis of individual genes that affect drug metabolism has helped to improve efficacy.
With its emphasis on multiple genes and their expression patterns, pharmacogenomics extends the reach of its predecessor."
redux [02.12.03]
[requires 'free' registration]
""The need to incorporate the teaching of pharmacogenomics into the medical curriculum is quite urgent," said Gurwitz, who this academic year has launched such a course at Tel-Aviv University, which he hopes will stimulate other medical schools to follow. "Pharmacogenomics must be incorporated within a few years ... into the general MD curriculum," he said.
The consequence of not doing so, he says, could be that any therapeutic benefits of the Human Genome Project will be severely delayed. The next generation of doctors will not have an adequate understanding of the interplay between genetics and drug metabolism, he warns."
redux [01.07.03]
"Much like the giant Homer Simpson Pez dispenser in his office, John Quackenbush, PhD, dispenses tasty tidbits when he opens his mouth."
" I think if you review the microarray literature, everybody in the early days was saying, oh, we're going to find out what all the pathways are. And now I think everyone is realizing that what comes out of the arrays are associations. It's the whole link, the disjunction between correlation and causality. I may discover that mass murderers drink more milk than anybody else but that doesn't mean drinking milk makes you a mass murderer."
redux [12.17.02]
"Investors may have stopped watching, but drug companies are finally beginning to wrench tangible benefits from the human genome. Two years after a boom fed by hype, a revolution finally is starting to take hold not in how drugs are invented, but in how they are tested.
Merck (nyse: MRK - news - people ), the world's third-largest drug company, is using gene expression arrays, also known as DNA chips, to keep clinical duds from reaching expensive animal or human trials. Separately, Millennium Pharmaceuticals (nasdaq: MLNM - news - people ) used similar chips in its late-stage clinical studies of its cancer drug, Velcade. Millennium's work is a big step toward so-called personalized medicine, in which treatment would be tailored toward individual patients based on genetic makeup."
redux [10.07.02]
[requires 'free' registration]
"Pharmacogenomics holds the promise of delivering safer, better designer drugs--and profits--to pharmaceutical manufacturers. But the technology also poses a challenge to the industry's current, highly successful business model that relies on one-size-fits-all blockbuster drugs.
For small biotech companies and large drug manufacturers alike, pharmacogenomics remains only one component of genome-based research and consumes only a small part of the $30 billion (US) in annual pharmaceutical research and development funding, according to the Pharmaceutical Research and Manufacturers of America (PhRMA). "It's an area where we are seeing movement, but it's not there yet," says Gillian Woollett, associate vice president for biologics and biotechnology at PhRMA."
redux [09.10.02]
"Collins is unimpressed by the hubbub that has shaken the industry lately. "In some quarters there was a misunderstanding, or naivete, about how having the sequence was going to solve everything. And there were some business models built solely upon the notion of quick profits, particularly selling subscription databases."
He dismisses talk about a foundering industry. "I think that every pharmaceutical company is still expecting that genomics will be the platform upon which they will build the next generation of drugs," says Collins. Others echo Collins' perspective. "We will change the treatment of cancer," says Variagenics' Adams. And there is no hint of doubt in his voice."
redux [08.08.01]
"Pharmacogenomics requires the integration and analysis of genomic, molecular, cellular, and clinical data, and thus offers a remarkable set of challenges to biomedical informatics. These include infrastructural challenges such as the creation of data models and data bases for storing this data, the integration of these data with external databases, the extraction of information from natural language text, and the protection of databases with sensitive information. There are also scientific challenge in creating tools to support gene expression analysis, three-dimensional structural analysis, and comparative genomic analysis. In this review, we summarize the current uses of informatics within pharmacogenomics, and show how the technical challenges that remain for biomedical informatics are typical of those that will be confronted in the post-genomic era."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
(0) comments
The University of Chicago Chronicle
AgentCell simulation allows for study on three biological levels
"Scientists at the University and Argonne National Laboratory have constructed a computer simulation that allows them to study the relationship between biochemical fluctuations within a single cell and the cell’s behavior as it interacts with other cells and its environment.
The simulation, called AgentCell, has possible applications in cancer research, drug development and combating bioterrorism. Other simulations of biological systems are limited to the molecular level, the single-cell level or the level of bacterial populations. AgentCell can simultaneously simulate activity on all three scales, something its creators believe no other software can do."
"In recent years, single-cell biology has focused on the relationship between the stochastic nature of molecular interactions and variability of cellular behavior. To describe this relationship, it is necessary to develop new computational approaches at the single cell level.
We have developed AgentCell, a model using agent-based technology to study the relationship between stochastic intracellular processes and behavior of individual cells. As a test-bed for our approach we use bacterial chemotaxis, one of the best-characterized biological systems. In this model, each bacterium is an agent equipped with its own chemotaxis network, motors and flagella. Swimming cells are free to move in a 3D environment. Digital chemotaxis assays reproduce experimental data obtained from both single cells and bacterial populations."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
(0) comments
connected.telegraph
Cracked: the puzzle of protein origami
"Scientists are close to cracking the code of life with an advance that has far-reaching implications for the understanding, diagnosis and treatment of disease. They have known for more than 40 years how the genetic code held in DNA describes the sequence of molecular building blocks - amino acids - that make up proteins, the complex molecules used to build and run our bodies.
But it has not been possible to predict the shape of proteins, which is crucial for understanding how these biological machines work. Solving this three-dimensional puzzle has been one of the grand challenges of biology, one that could speed the development of new drugs to treat cancer, heart disease and all other ailments.
Now Prof David Baker, Dr Philip Bradley and Dr Kira Misura of the University of Washington, Seattle, report in the latest issue of the journal Science that they have managed the feat to high accuracy for a handful of small proteins, providing the first hope that it is possible."
"Rosetta@home is a scientific research project that uses internet-connected computers to predict and design protein structures, and protein-protein and protein-ligand interactions. Our goal is to develop methods that accurately predict and design protein structures and complexes, an endeavor that may ultimately help researchers develop cures for human diseases (See the Human Proteome Folding Project, a collaborative effort to apply our software on the human genome). Our project relies on individuals, like you, who donate time on their computers to collectively provide the computing power necessary to further develop, test, and improve our methods."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
(0) comments
foodconsumer
The Shape of Food Allergenicity
"Scientists once thought that any protein could potentially become an allergen. In the current study, however, using a computer program to categorize 129 common plant food allergens, structural biologist John Jenkins of the British Institute of Food Research (IFR) and colleagues found that 65% of these proteins fell into just four structural families. The study used the protein families defined by Pfam, a database of protein structures housed at the Wellcome Trust Sanger Institute in the United Kingdom.
The results suggest that certain protein structures contribute to plants' allergenicity, says coauthor Clare Mills, head of the allergy research team at IFR. The next step is finding out which structures contribute, and how they do so."
redux [08.25.05]
"A team of UK scientists will analyse and demonstrate how bioinformatics could help food companies improve their products, from pin-pointing allergy-causing proteins to identifying the cause of batch spoilage."
"Such techniques offer obvious opportunities for product development, but could also help producers meet upcoming EU regulations on allergens in food. From 25 November this year, the Commission will require firms to declare on labels whether the product inside contains potential food allergens."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
(0) comments
The Chart
New degree first of kind in state
"Although the [Human Genome Project] itself is completed, the data collected will take years to analyze, providing several career opportunities for students interested in studying and recording all the data that has been collected.
Missouri Southern saw this as an opportunity and is the first university in the state to offer a bachelor's degree specifically for such an interest. Bioinformatics is a new career field that unites biology and computer information science and applies it to the study of DNA. "
"Because of the difficulty of the program, it is slowly gaining interest.
"It's a difficult major to market because it being heavily involved in mathematics, computers and science makes this a limited type of program to sell, so it's not for everyone," said Dr. Gerald Schlink, professor of biology."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
(0) comments
UCSD News
Computer Modeling Reveals Hidden Conversations Within Cells
"UCSD biochemists have developed a computer program that helps explain a long-standing mystery: how the same proteins can play different roles in a wide range of cellular processes, including those leading to immune responses and cancer.
Prior to the UCSD team’s findings, which are published in the September 16 issue of the journal Science, many scientists expressed doubts that a computational approach could represent the intricate mechanisms through which cells respond to outside signals. However, the researchers report that their computer model accurately predicts particular behaviors of living cells."
"The computer model comprises 70 equations to account for the behavior of five proteins and three RNA molecules in the “NF-kappaB signaling pathway,” which regulates genes involved in cancer, inflammation, immune function and cell death. Each equation takes into account a different parameter, such as how quickly a protein is synthesized, or how quickly it is degraded."
redux [07.24.05]
"So if what we’re doing is going to become anything more than a kind of niche activity for a small group of computational biologists and become part of working practice then I think we have to solve a number of problems. One, of course, is we have to explain to people what they get out of this that’s different. That’s a very important thing, but let’s leave it for a second. One of the things we have to move away from is this idea that every time I want to study a particular system, I have to build from scratch a kind of monolithic model of it, and not take advantage of the fact that lots of other people will have actually bitten off various different parts of it."
redux [03.01.04]
[requires 'free' registration]
"Imagine being able to discover the latest blockbuster drug using nothing but a PC and some highly sophisticated software. It's not as far-fetched as it sounds. A growing number of labs--both industrial and academic--are going "in silico," simulating everything from cells to clinical trials. The result is a sea change in pharmaceutical research, with resources once earmarked for bench work now being shunted into central processing unit clock cycles."
redux [09.09.02]
"Consistent with his lifelong reputation as a visionary and provocateur, Brenner challenged a crowd of over 250 bioinformaticists gathered at the Wellcome Trust Genome Campus in Hinxton, UK, to "forget the genome."
"The more you annotate the genome, the more you make it opaque," he warned in a keynote speech delivered at the joint Cold Spring Harbor Laboratory/Wellcome Trust Genome Informatics conference on Saturday. "We need to focus on our cells."
Brenner questioned the ability of computational approaches to derive functional knowledge from genomic sequence alone--a "hideously difficult task," he said--because some problems are simply "not soluble or computable." The future, according to Brenner, requires going back to the bench. Old-fashioned data on the biochemistry of the cell would then be used to flesh out the cell map, which would serve as "a framework to think of genomes and their products.""
redux [07.29.02]
"Colin Hill, president and CEO of GNS, said the adoption of modeling will be slow, but even the largest and most stubborn pharmas will soon realize they have to adopt it if they want to compete.
He has seen more success selling pharmas the baby steps toward modeling: tools, such as its Diagrammatic Cell Language, software and database information, rather than actual models."
redux [11.27.00]
"What do a Boeing 777 and the human body have in common? Both are complex systems, dependent on millions of complex parts, whether they be a jet-propelled engine or a pumping organ such as the heart. The big difference: Engineers can design and build highly accurate computer models of the way a Boeing 777 will behave in flight. The human heart? Its complexity has long stymied efforts by researchers intent on turning drug development into a predictive science, much like building airplanes.
But that's changing. A handful of companies are developing software that can model single cells, whole organs, cellular metabolism and toxicology, diseases throughout a patient's body, and even an entire clinical trial."
redux [02.16.01]
"Computers capable of mimicking life have long been the stuff of sci-fi nightmares - think The Terminator or 2001's HAL 9000. But for researchers struggling to make sense of vast amounts of new biological data, and for drug companies anxious to cut costs and speed development, having accurate computer simulations of living systems is still a dream. To make that dream come true, they are turning to "in silico biology," building computer models of the intricate processes that take place inside cells, organs, and even people. The ultimate goal: an entire organism modeled in silicon, allowing researchers to test new therapies much as engineers "fly" new airplane designs on supercomputers."
redux [05.15.01]
[requires 'free' registration]
""We in physics are used to studying complex systems, but the level of complexity inherent in biological systems ... is way beyond what we have experience dealing with," said Rajagopal, assistant director of research at the Cavendish Laboratory in the University of Cambridge. "Biological systems are much harder to model as they are in highly non-equilibrium states and you not only have to take into account the flow of matter and energy, but also the flow of information!"
He added: "In biology, the whole is greater than the sum of its parts. We have to move on from the "reductionist" towards an "integrationist" approach."
redux [05.15.01]
[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."
bookmark:
connotea
::
del.icio.us
::digg
::furl
::reddit
::yahoo::
(0) comments
Bio-IT World
‘Proximity Communication’ May Speed Drug Simulations
"Medical researchers imagine a day when gene-mapping simulations will take an hour or two to compute instead of a week, on systems that process data up to 100 times faster than they do today. That dream could become a reality in the next five years with technology called proximity communication that's under development at Sun Microsystems Laboratories in Menlo Park, Calif."
"In 2003, the U.S. government awarded Sun Labs a US$50 million Defense Advanced Research Projects Agency contract to help design next-generation supercomput