Bio Saga Blog - A Chronicle of Life Sciences & Informatics

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Lockheed Martin is working with researchers at Johns Hopkins University and medical informatics firm Sage Analytica to mine a "unique" set of medical records with the aim of integrating clinical and genomic data for prostate cancer research. The researchers are using Lockheed Martin's rule-based natural language processing platform, called ClinRead, to extract phenotypic descriptors from a set of clinical records tracking 33 men with metastatic prostate cancer for over 15 years before they succumbed to the disease. (Read Full Article)

The Small Business Administration has decided to raise the amount of Small Business Innovation Research program grants in both phases, with Phase I awards increasing from $100,000 to $150,000, and Phase II awards rising from $750,000 to $1 million. In 2008, SBA initially considered making the increases in the grants in order to catch up with inflation. Following a comments period and analysis, the administration has decided to implement the increases. The current award value of $100,000 and $750,000 was originally set in 1992. SBA has the authority to increase the amount of the award every five years. SBA said in an announcement in the Federal Register that adjusting the threshold of awards up to $150,000 and $1 million "adequately offsets the general effects of inflation, maintains a degree of stability and simplicity to the threshold levels, and continues to provide participating agencies with an appropriate degree of flexibility in award size." In determin...

DEPARTMENT OF BIOTECHNOLOGY Ministry of Science and Technology Govt of India TRANSLATIONAL HEALTH SCIENCE AND TECHNOLOGY INSTITUTE (Autonomous Institute and Part of NCR Bio-medical Science Cluster) Present location at the National Institute of Immunology JNU Complex, Aruna Asaf Ali Marg, New Delhi 110 067 EXECUTIVE DIRECTOR AND DEANS XTractor Premium - A Platform for discovery , knowledge sharing, analysis and modelling of published biomedical facts. The only Knowledgebase which provides "manually" annotated facts from PubMed on a weekly basis Innovative Features like Semantic Search , Concept Linking , Bibliographic search , Save, Export and Visualize Only Knowledgebase with daily updations from PubMed XTractor Premium now at an Special Introductory Offer. Subscribe now and save! Request for a Trial

This Pathways Compendium provides an index of Alzheimer disease pathway models contributed by researchers and companies. Probable Interaction Networks Involved in Pathology of Alzheimer Disease: Predicting Targets and Therapeutic Agents - NetPro™ based Study . Developed by researchers at Molecular Connections Private Limited, an in silico discovery services company. Users can click on a specific node (molecule) to get information on all interactions of the molecule in the given network. Click on the interaction arrows for information on the specific interaction. The Alzheimer Research Forum is a Pioneering Biomedical Web Community . Founded 13 years ago when the Web was still in its infancy, the "Alzforum" has more than 5,000 registered members and is familiar to most Alzheimer scientists in the world. XTractor Premium - A Platform for discovery , knowledge sharing, analysis and modelling of published biomedical facts. The only Knowledgebase which provides "manu...

More good news for Bio, more so for Bioinfo & CompBio while the end of Jyly say House Passes Proposed 3 Percent NIH Funding Increase now NIH is really promoting Bio Science research to bring in a economic turn. The best of times is now ! A National Institutes of Health funding program will support exploratory research and development projects in informatics and computational biology that explore a range of areas, including genomics , medical genetics, proteomics , biomedical imaging, and a wide variety of other approaches. Funded through the National Cancer Institute, the National Human Genome Research Institute, the other centers across NIH, the " Exploratory Innovations in Biomedical Computational Science and Technology " program will be coordinated by the NIH Biomedical Information Science and Technology Initiative committee. Under the program, NIH will grant up to $275,000 over two years to academic institutes, small businesses, non-profits, state governments, ...

"There does appear to be a distinction between the way curation is used in the bio-sciences, and elsewhere. In particular, the term "curated database" tends to mean a manually constructed database that links literature to data, curated by experts who provide authority (eg see the Wikipedia definition of Biocurator ). The earliest mention of the term "curated database" I can find is in the abstract (and only in the abstract) of Larsen et al (1993)." Chris Rusbridge Digital Curation Blog Since these database are hand curated by experts (manually curated), they always promise a accuracy & quality better than uncurated or NLP based databases. While NLP based databases follow a automated curation provide quick updates and tend to be large in terms of the quantum of data. While they may trade off in accuracy due to their automated curation process. While platforms like XTractor Premium follow a unique approach by trying to adopt the best of both worlds. A ...

One of my recent post discussed the dawn of the new era and new breed of search engines Search Wars . YEBOL a youngling from the the Stanford stable, a new search in the block. Yebol's mission is to build human-like world's knowledge base and provide knowledge based search (semantics) and services. Yebol utilizes a combination of patented algorithms paired with human knowledge to build a Web directory for each query and each user. Instead of the common “listing” of Web search queries, Yebol automatically clusters and categorizes search terms, Web sites, pages and contents. Yebol allows for a multi-dimensional search result instead of the normal one-dimensional search seen by most web search engines today. This provides a more accurate summary of top sites and categories; a wider array of related search terms; a longer and richer expansion for query results; and a deeper base of links and keywords in search result pages. Unlike ...

Indian Life Sciences Informatics Company, Molecular Connections announced today, that their XTractor Premium platform surpasses 200,000 "Expert" annotated facts from PubMed. XTractor Premium – is a platform for discovery, analysis and modeling of published biomedical facts. The application also comes with - XTractor Premium Knowledgebase - the only knowledgebase, which provides " Expert " annotated facts from PubMed on a daily basis. The XTractor Premium Knowledgebase now has more than 202,847 relationships on proteins, drugs, biological process and diseases and is ever growing with more than 600 relationships being added every single day. XTractor provides manually categorized updates on the latest published facts from PubMed for more than 20 categories which include : Biomarkers, clinical trials, dosage, pathways, toxicology, RNAi studies, mutations, knockouts, diseases mechanisms, protein- drug relationships and much more. Expert Annotated Facts make XTractor Pr...

The US House of Representatives on Friday passed a 2010 budget for the Departments of Labor, Health and Human Services, and Education that would increase funding for the National Institutes of Health by nearly $1 billion over its appropriation for 2009. The bill, which passed the house by a vote of 264 to 153, seeks an NIH appropriation for 2010 of $30.97 billion, which is an increase of $940 million over the 2009 level, excluding funding from the American Recovery and Reinvestment Act. That increase also would boost NIH funding by $500 million over the $30.5 million asked for by President Barack Obama in his budget request. The bill also seeks $6.8 billion for the Centers for Disease Control and Prevention, an increase of $67 million over the 2009 appropriation and $38.4 million over the White House's 2010 request. The Federation of American Societies for Experimental Biology, which supports increased funding for biomedical research , said passage of the bill makes it more like...

A not very long time ago, in a galaxy near, very near by.... SEARCH WARS Search, Search engines, While the Search engine big wigs fight for a niche in the search engines landscape .... The Google , Yahoo & now Micorsoft too (with their Bing ) There are the Wolfram | Alpha likes that are forming a separatist and slowly gaining power over the Google order. In fact google has managed to bring balance to both with its Google Squared . While platforms like XTractor , NextBio , Novoseek , GoPubMed , BioMedSearch have specialized in searching biomedical and biological knowledge are even more strengthening the separatists. Now to see and know who is more powerful, the galactic empire or the separatist? I leave it to the 'Republic' i.e. You users! to judge, in the form of your comments and experiences with such tools and searches! you could even voice your opinions here

Massachusetts Institute of Technology (MIT) researchers have demonstrated that a gel composed of small, woven protein fragments can successfully carry and release proteins of different sizes, potentially enabling the delivery of drugs such as insulin and trastuzumab (Herceptin). Researchers can control the rate of release by changing the density of the gel, allowing for continuous drug delivery over a specific period of time. The team is led by Shuguang Zhang, associate director of MIT's Center for Biomedical Engineering. The gel, known as a "nanofiber hydrogel scaffold," enables a gradual release of the proteins from the gel over hours, days or even months. The gel itself is eventually broken down into harmless amino acids - the building blocks of proteins. Peptide hydrogels are ideally suited for drug delivery as they are pure, easy to design and use, non-toxic, non-immunogenic, bio-absorbable, and can be locally applied to a particular tissue. Composed of self-assembli...

XTractor now has a ready reckoner on Drugs , Diseases , Proteins & Processes along with sample manually annotated sentences form PubMed available on each of those Drugs , Diseases , Proteins & Processes listed there. This is really going to be handy for any bench scientist. Be part of XTractor community. XTractor the first of its kind - Literature alert service , provides manually curated & annotated sentences for the Keywords of your choice XTractor maps, extracted entities (genes, processes, drugs, diseases etc) to multiple ontologies Enables customized report generation. With XTractor the sentences are categorized into biologically significant relationships The categorized sentences could then be tagged and shared across multiple users Provides users with the ability to create his own database for a set of Key terms Users could change the Keywords of preference from time to time, with changing research needs XTractor thus proves to be a platform for gett...

Dr. Justin Sanchez discusses technologies that enable direct brain to computer interfacing, Dr. Justin C. Sanchez , Director of the Neuroprosthetics Research Group, Assistant Professor, Department of Pediatrics, Division of Neurology, Department of Neuroscience, Department of Biomedical Engineering, University of Florida. I really had no idea that the technologies that Justin has developed existed other than in science fiction. The possibilities are endless, and could change everything from computing, to flying planes, to simply changing the channel… Do you want to know more? Listen to Dr. Justin Sanchez! Be a part of the XTractor community. XTractor is the first of its kind - Literature alert service , that provides manually curated and annotated sentences for the Keywords of user preference. XTractor maps the extracted entities (genes, processes, drugs, diseases etc) to multiple ontologies and enables customized report generation. With XTractor the sentences are categorized into ...

Blogging about curation in the past several issues have been discussed but here is something very critical. To thrive, the field that links biologists and their data urgently needs structure, recognition and support. Biocuration , the activity of organizing, representing and making biological information accessible to both humans and computers, has become an essential part of biological discovery and biomedical research. But curation increasingly lags behind data generation in funding, development and recognition. Three urgent actions to advance this key field. First, authors, journals and curators should immediately begin to work together to facilitate the exchange of data between journal publications and databases. Second, in the next five years, curators, researchers and university administrations should develop an accepted recognition structure to facilitate community-based curation efforts . Third, curators, researchers, academic institutions and funding agencies should, in the ...

XTractor now has over Over 150 registered users from FDA , NIH , NCI , Astra Zeneca , Wyeth , MD Anderson Cancer Institute , Washington university , Scripps institute , Max Planck , Harvard Medical school and many more in less than 3 weeks !!! More than 600 annotated facts added everyday. A total of 25,000 facts added till date!!! Be a part of the XTractor community. XTractor is the first of its kind - Literature alert service , that provides manually curated and annotated sentences for the Keywords of user preference. XTractor maps the extracted entities (genes, processes, drugs, diseases etc) to multiple ontologies and enables customized report generation. With XTractor the sentences are categorized into biological significant relationships and it also provides the user with the ability to create his own database for a set of Key terms. Also the user could change the Keywords of preference from time to time, with changing research needs. The categorized sentences could the...

“For example, the presence of a specific protein in the blood or in any body fluid might indicate a specific infection. Once an association between a biomarker and a disease is clearly established, the one can be used to signal the other, and to a high degree of certainty. As well, changes in the prevalence of a biomarker in the organism can immediately and reliably signpost a patient’s response to treatment” Some pharmaceutical companies are already advancing their research and harnessing the power of biomarkers, which can: Be used to detect the predisposition for disease in a population, screen for its presence, confirm its diagnosis, assess its severity, predict its response to available therapies and measure its clinical course Be used as targets to discover new drugs Be a decisive factor in determining whether or not to continue research on an entity Show early in the development phase whether an entity could lead to side effects that should terminate further research Help to mak...

The Protein Data Bank Japan (PDBj) curates , edits and distributes protein structural data as a member of the worldwide Protein Data Bank (wwPDB) and currently processes 25–30% of all deposited data in the world. Structural information is enhanced by the addition of biological and biochemical functional data as well as experimental details extracted from the literature and other databases. Several applications have been developed at PDBj for structural biology and biomedical studies : (i) a Java-based molecular graphics viewer, j V; (ii) display of electron density maps for the evaluation of structure quality; (iii) an extensive database of molecular surfaces for functional sites, e F-site, as well as a search service for similar molecular surfaces, e F-seek; (iv) identification of sequence and structural neighbors; (v) a graphical user interface to all known protein folds with links to the above applications, Protein Globe. Recent examples are shown that highlight the...

Videos in Biosciences

Leading scientists discuss DNA database at April 7-8 Meeting For a quarter century, GenBank has helped advance scientific discovery worldwide. Established by the National Institutes of Health (NIH) in 1982, the database of nucleic acid sequences is one of the key tools that scientists use to conduct biomedical and biologic research. Since its creation, GenBank has grown at an exponential rate, doubling in size every 18 months. In celebration of this vital resource and its contribution to science over the last 25 years, the National Center for Biotechnology Information, National Library of Medicine (NLM), NIH, is holding a two-day conference on GenBank. The conference will take place April 7-8, 2008 at the Natcher Conference Center on the main NIH campus in Bethesda, Maryland. For details on the meeting, see the conference Web site, at http://www.tech-res.com/GenBank25 . The conference is open to the public and also will be available via live and archived webcast; the April 7 proceedin...