Bio Saga Blog - A Chronicle of Life Sciences & Informatics

GlaxoSmithKline Plc will buy a stake in Austria’s Intercell AG in a move that analysts said underscores drugmakers’ growing interest in vaccines. Glaxo will pay 33.6 million euros ($49.5 million) as part of the alliance to develop and market Intercell’s needle-free, patch-based immunizations for traveler’s diarrhea and pandemic influenza. The London-based drugmaker also will buy as much as 5 percent of Intercell for up to 84 million euros via a staggered shareholding option, the companies said in a statement today. 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! Re...

Indian Life Sciences Informatics Company, Molecular Connections announced today, that their XTractor Premium platform now has more that 503,985 " Expert " annotated biomedical facts from literature and is the fastest growing knowledgebase currently. XTractor Premium platform is Fast Becoming the definitive Semantic Knowledge discovery & Expert curated Knowledgebase for Life Science Researchers. The XTractor Premium Knowledgebase in addition to more than 503,985 relationships on proteins, drugs, biological process and diseases has advanced semantic search, concept linking analytics for effective knowledge discovery and modeling. XTractor Premium provides Precision based mining of the most relevant facts. Compared to natural language processing engines, manual annotation approach reduces false positives rate by 12-35%. XTractor premium serves as a platform to stay current with weekly updates from PubMed. Provides “Topic Tracking” with email alerts on spe...

In effort to make Karnataka Biotechnology Capital of Asia, the State government , on Wednesday, launched ‘Millennium Biotech policy II’ a successor to Biotech Policy issued of 2001. Releasing the policy, Principal Secretary IT, BT S&T Ashok Kumar Manoli said the new policy will provide all fiscal incentives and concessions under Karnataka Industry policy 2009-14 to bio technology industry and the R&D centres. Biotech organisations will get incentives including a subsidy of 50 per cent for setting up effluent treatment plants. The financial incentives includes assistance for patent tracking and patent registration. According to the new policy biotech will be treated as special industrial consumers and provided with dedicated power lines that are exempt from power cuts. It also assures power connection to biotech companies within 10 days of applications. Bioinforamtics companies that use up to 50 KVA power will be permitted to be established without any local restrict...

Canadian-based GPU maker Tycrid Platform Technologies has just announced the launch of the Prometheus Alliance , a collaborative effort aimed at developing cutting edge HPC applications for bioinformatics, with a specific emphasis on next-gen sequencing data and personalized genomics. Chris Heier, President of Tycrid Platform Technologies, stated in a release that "Alliance is being established to address a specific challenge that continues to impede the progress of scientific discovery – the lack of scalable, purpose-built appliances. I feel this is critical as we can virtually eliminate the need for scientists to become computer scientists. Our goal is to take a fresh, innovative approach to developing HPC solutions that do one thing really well – address specific computational challenges for bioinformatics .” XTractor Premium - A Platform for discovery , knowledge sharing, analysis and modelling of published biomedical facts. The only Knowledgebase which provides "...

The Oxford University Image Bioinformatics Research Group wishes to appoint a Computing Officer – Web Applications and Data Management to work on the JISC-funded ADMIRAL Project - A Data Management Infrastructure for Research Across the Life Sciences . This will involve interactive working with researchers to improve the management, archiving and Web Publication of their biological research data, undertaking Web application development, and system evaluation and maintenance of the data management infrastructure. Applicants should have a good B.Sc. or higher degree, probably in maths or science, and show evidence of creativity and research competence. Good programming and data management skills are required, as is familiarity with the standards and principles of modern Web application development. Experience with agile development techniques, Javascript, JQuery, Java, Python and RDF, and competence in Linux computer systems administration would be desirable. Further details about this...

The National Institutes of Health has granted $67.4 million in funding for trailblazing research that could reap great benefits but which are not guaranteeing immediate results, including genomics and proteomics studies, NIH said Monday. The Exceptional, Unconventional Research Enabling Knowledge Acceleration (EUREKA) program grants $200,000 per year for up to four years for researchers that test unconventional ideas or "tackle major methodological or technical challenges," according to NIH. Of the 56 grants, 10 researchers will receive a total of $10.6 million for two-year awards through the American Recovery and Reinvestment Act of 2009. "EUREKA awards reflect NIH's continued commitment to funding transformative research, even if it carries more than the usual degree of scientific risk," NIH Director Francis Collins said in a statement. "The grants seek to elicit those 'eureka moments' when scientists make major theoretical or technical advances...

Becton Dickinson has signed a definitive agreement to acquire molecular diagnostics firm HandyLab for an undisclosed sum. HandyLab sells the Jaguar molecular diagnostics system, which incorporates clinical sample preparation, nucleic acid extraction, microfluidic real-time PCR amplification and detection. The Ann Arbor, Mich.-based firm launched the system in November 2008. BD said that it plans to place its BD GeneOhm assays for methicillin-resistant Staphylococcus aureus , Clostridium difficile , and vancomycin-resistant Enterococcus on the HandyLab platform and market them as the new BD Max system. The acquisition follows an alliance between the firms begun earlier this year aimed at placing the GeneOhm tests on the Jaguar system. "We believe this new platform enables both our healthcare-associated infections offering and future expansion into other molecular opportunities," BD President Vincent Forlenza said in a statement. BD said that it will provide more informati...

Was going through a recent blog on indiblogger about the NASSCOM Product Conclave . Where this time is themed and focused on SAAS & related services. In the recent times SAAS or Software as a Service has even captured the attention of Life Science and biomedical community globally. Indian Life Sciences Informatics Company, Molecular Connections' year old SAAS product startup is www.XTractor.in . In July 2008 came of with a commercial version of the product XTractor Premium- expert curated biomedical discovery, analysis and knowledge modeling platform, based on semantic curation and annotation of biomedical facts from PubMed . Has very handy analytics to search and narrow down the most relevant facts, build and discover relationships between biomedical facts check out some of the user CaseStudies . XTractor Premium knowledgebase currently contains 302,269 relationships categorized on 24 categories Gene-Gene , Gene-Drug , Gene-Disease , Gene-Process , Gene-Mutation/Polymorphis...

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

Entrez gene is the most widely used data resource for Gene based information worldwide. To enable researchers to obtain high quality manually annotated information from XTractor when they search for a Gene on Entrez Gene, we are now providing direct links from Entrez Gene records to corresponding Gene Reports in XTractor. To use this outlinked option- when in Entrez Gene, for any human gene select the “Link Out” option from the Display menu in Entrez Gene and click on the XTractor link. You will be taken directly to the XTractor graphical report for the Gene of interest and also manually annotated facts on the associated Diseases, Drugs and the Biological Processes for the Gene. http://www.xtractor.in/ncbiSearch.do?xid=XT_15377&symbol=BRCA1 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 Innovati...

The National Institutes of Health has awarded 970 stimulus grants worth more than $625 million — around 14 percent of total NIH stimulus grant funding to date — to projects that fall within the broad family of 'omics disciplines, according to a preliminary analysis of the NIH funding database conducted by GenomeWeb Daily News . As of Sept. 30, the close of the fiscal year, the National Institutes of Health had awarded a total of $5 billion in stimulus funding — nearly half of the $10 billion appropriation that NIH will disburse over two years under the American Recovery and Reinvestment Act of 2009 . The $5 billion figure includes both grants and contracts, however. For grants alone, NIH had awarded approximately $4.4 billion via 12,789 ARRA grants as of Oct. 7, according to the database. The 970 grants awarded to 'omics projects comprise 7.5 percent of the stimulus grants awarded so far, but the total funding awarded to these projects makes up 14 percent of NIH ARRA grant ...

The National Institutes of Health has awarded more than 12,000 grants totaling around $5 billion so far under the economic recovery and stimulus package, the White House said today. President Barack Obama commuted to Bethesda this morning to announce the funding as a milestone, to unveil a $175 million grant for cancer genomics, and to tour the NIH campus. In late-morning speeches before a crowd of NIH staff, President Obama, Health and Human Services Secretary Kathleen Sebelius, and NIH Director Francis Collins loosely outlined how the $5 billion in grants over two years — nearly half of NIH’s total $10 billion appropriation under the American Recovery and Reinvestment Act — will stimulate research and create jobs. A number of genomics-focused programs will be funded under the stimulus package, including $175 million over two years for The Cancer Genome Atlas, a joint effort between the National Human Genome Research Institute and the National Cancer Institute, according to a fact...

“ … LigerCat is a search tool for NCBI’s PubMed that uses tag clouds to provide an overview of important concepts and trends. LigerCat aggregates multiple articles in PubMed , summing their MeSH descriptors and presenting them in a cloud, weighted by frequency “. LigerCat is an abbreviation for Literature and Genomics Resource Catalog , which is a free PubMed search tool developed in 2009 as part of the Biology of Aging project at the MBLWHOI Library at the Woods Hole Marine Biological Laboratory . LigerCat is great news for geneticists or anyone involved in translational research, a fairly effortless means of data mining for dynamic links to a very complex literature. LigerCat can be used to search in several ways: 1) to locate and select a list of individual journal titles indexed in PubMed , 2) search using terms from the National Library of Medicine’s Medical Subject Heading (MeSH) list , 3) search using keywords, 4) search on Genes found in the NCBI database...

The National Institutes of Health has pledged $45 million in grants to establish two new genomics centers at the University of North Carolina at Chapel Hill and at the Medical College of Wisconsin (MCW), as well as to continue funding existing centers at Johns Hopkins University and at the University of Southern California. The two new Centers of Excellence in Genomic Science at UNC and MCW will pursue genomics studies of mental health and gene regulation , respectively. Under the new grants, MCW will receive around $8 million over three years and UNC will reap around $8.6 million over five years from the National Human Genome Research Institute and the National Institute of Mental Health. Johns Hopkins' genomics center will receive around $16.8 million over five years to continue epigenetics of disease studies and USC will use around $12 million over the same period to conduct computational and informatics-based research of genetic variation and disease . "Our aim is to ...

Mutations in the protein tyrosine kinase gene ERBB4 contribute to — and may provide hints about treating — a subset of melanoma, according to a paper by researchers from the National Institutes of Health and Johns Hopkins University that appeared in the advanced, online edition of Nature Genetics this week. The team sequenced protein tyrosine kinase or PTK genes in 29 individuals with melanoma. Their search uncovered dozens of somatic mutations affecting the kinase domain of 19 different PTK genes. When they looked at the same 19 genes in another 79 melanoma patients, the researchers found that almost a fifth of those tested harbored mutations in ERBB4 . And, they reported, knocking down the mutated form of ERBB4 or using a drug that targeted the gene slowed the growth of melanoma cell lines, suggesting it might be useful to evaluate ERBB4 status in melanoma patients. Researchers at the NIH Intramural Sequencing Center sequenced all 86 PTK family genes in tumor samples from 29 ...

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 ...

BioFocus DPI has partnered with the cancer drug candidate and biomarker company Oncodesign to offer an integrated service platform, Galapagos division BioFocus DPI said today. The agreement will create a service that combines BioFocus DPI's target discovery and screening capabilities with Oncodesign's biomarker and pharmacological services to offer target validation and clinical candidate selection services, the company said. BioFocus DPI offers gene-to-drug candidate discovery services, including in vitro and cell-based screening, chemogenomic and informatics offerings , storage, distribution, and other structural biology and medicinal chemistry services. 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, ...

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...

Accelrys ACD/Labs (Advanced Chemistry Development, Inc.) Afferent Systems Inc. Agilent Technologies Aureus Pharma Barnard Chemical Information Ltd. (John Barnard and Geoff Downs) SEE: digital chemistry Bio-Rad Laboratories BioReason BioSolveIT BlueObelisk.org Bruker Daltonics Inc. Cambridge Crystallographic Data Centre CambridgeSoft Corporation CARB Center for Advanced Research in Biotechnology (NIST/University of Maryland) Cengent Therapeutics (Genes to Leads). Acquired by Inncardio, Inc. Center for Molecular Modeling (NIH) Centre for Molecular and Biomolecular Informatics CMBI (formerly: CAOS/CAMM: Dutch National Center for Computer-Assisted Chemistry and Molecular Modelling) Cerep ChemAxon ChemDiv, Inc. (Chemical Diversity) Chemical Abstracts Service Chemical Computing Group, Inc. Chemical Simulations Group ChemInnovation Software ChemNavigator ChemSW (Chemistry Software for Windows, formerly: WindowChem) Chenomx Inc. CIS Chemical Information System CombiChem.net CompuChem C...