Bio Saga Blog - A Chronicle of Life Sciences & Informatics

Cognizant, a leading provider of consulting, technology, and business process outsourcing services, and Eagle Genomics Ltd., a bioinformatics software company specializing in genomic data management and integration, has announced they are working with the Pistoia Alliance, Inc., a nonprofit, precompetitive alliance of life science companies and vendors, as one of the groups engaged to develop a conceptual cloud-based platform to facilitate access to public and proprietary sources of gene sequence data. The Pistoia Alliance’s sequence services working group aims to define and document an externally hosted service for securely storing and mining both proprietary derived gene/sequence information and public domain gene databases. This conceptual platform developed by Cognizant and Eagle Genomics, as part of this piloting stage, will enable working group companies to securely share their bioinformatics resources among simultaneous, registered users in a secure, encrypted environment, while...

A Workshop on Computational Approaches in Biological Data mining is being organised by the Unit Of Simulation and Informatics, Indian Agricultural Research Institute, New Delhi. The topics to be discussed are:- Introduction to Biological databases  Biological data mining  Concept and application of machine learning techniques in bioinformatics  Tools and techniques for bio-molecular prediction  Future directions in biological data mining.  Dates:- March 23rd-25th, 2011. Application deadline:- February 25th, 2011. Do you wish to know more?

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Courtesy Bioclues Are you a skilled bioinformatician? Do you have experience with analysis and integration  of large data sets? Would you like to work with leading experts and constantly improve  your skills? Then you may be Intomics’ next bioinformatician. We are expanding our bioinformatics team and are seeking a skilled bioinformatician to  help the team provide innovative solutions for our clients in the pharmaceutical industry.  You will play an important role in implementing data mining strategies for projects in  areas such as target identification, biomarker identification, disease systems biology, and  translation research. Our preferred candidate has the following profile: Bioinformatics or computational biology background Experience with large-scale data mining Strong experience with programming (e.g.  Perl,  Python,  Java),  databases (e.g.  MySQL, PostgreSQL), and Unix Excellent communication skills and the abi...

e-LICO multi-omics prediction challenge with background knowledge on Obstructive Nephropathy We present a biological data-mining problem that poses a number of significant challenges: The available data are of high dimensionality but of extre... Time Left:  90 days Teams:  84 Prize:  2500 EUR Share |

Pfizer UK-Kent-Sandwich Computational Biologist Computational Sciences are integral to Pfizer’s strategy to accelerate the discovery of important new medicines. This is your opportunity to join a dynamic, innovative team, focusing on the development and use of novel computational methods and algorithms to enhance the efficiency and effectiveness of drug discovery. We are looking for a Computational Biologist with skills in working with genomics data, developing novel algorithms and generating new biological hypotheses to join our Computational Sciences Center of Emphasis in Sandwich, UK. Specific areas of interest include: • Identification of new datasets and data mining techniques relevant to drug discovery • Developing and testing novel methods and algorithms, working with academic collaborators where opportunities arise • Building and testing prototype systems (both interfaces and algorithm libraries) • Working with scientists to apply tools to every day problems • Awarded or...

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...

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...

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 ...

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...

There's a great deal of wisdom in a crowd, but how do you listen to a thousand people talking at once? Identifying the wants, needs, and knowledge of internet users can be like listening to a mob. In the Web 2.0 era, leveraging the collective power of user contributions, interactions, and feedback is the key to market dominance. A new category of powerful programs and web based technology lets you discover the patterns, inter-relationships, and individual profiles-the collective intelligence, locked in the data people leave behind as they surf websites, post blogs, and interact with other users. XTractor Premium is one such initiative, epitome of Collective Intelligence in Action for bio medical data. Implemens collective intelligence concepts of vital data gathering and mining techniques like analyzing trends, discovering relationships, and making predictions. It provides a pragmatic approach to personalization by combining content-based analysis with collaborative approaches ...

Here is a hand picked item, one of my favorites among the recent blogs that came across. This articles reflects and talks about many things which i have appreciated in the recent times and have blogged in the past web 2.0 .... Why should a (bioinformatics) scientist learn web development ? Up to now bioinformatics research with genomics datasets, has been happening like that: you download the data from a website of a big-iron institution ( NCBI , TAIR ), set them up locally, BLAST ‘em, MySQL’em, parse them with Perl script, and do all other sorts of un-imaginable things. Even though bioinformaticians might be un-aware of the term, part of the local processing that happens with the data is a mashup. This term translates to the combination of pieces of data from different sources, something akin to what has been happening on the web (see also Web 2.0 or programmable web ). In no way this is close to the myriad of Web 2.0 mashups that exist out there, created using APIs offered openly...

Biomedical Data mining happens to be a long-standing problem in scientific research. Scientists are constantly in search of newer and innovative means to mine biomedical data. 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 then be tagged and shared across multiple users. Thus XTractor proves to be a platform for getting real-time highly accurate data along with the ability to Share and ...

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...

XTractor - Discovering Newer Scientific Relations Across Abstracts http://www.xtractor.in/ 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 then be tagged and shared across multiple users. Thus XTractor proves to be a platform for getting real-time highly accurate data along with the ability to Share and collaborate. This has been added to Biological Informatics Subject Tracer Information Blog. This has been added to the tools section of Research Resources Subjec...

Atrium Research has published the 2008 Electronic Laboratory Notebook Survey . This study contains the results and analysis of a survey of information technology, management, and scientific personnel in the life sciences, chemical, academic, government and food markets. Comprehensive data and analysis are reported on dozens of questions answered by 527 professionals from more than 20 countries. The report highlights user and prospective user opinions on data management challenges, technology interest, motivations, project goals, purchase timing, integration needs, and supplier product and brand perception. According to the report, the market for ELNs is exploding, with more than 30 suppliers offering commercial solutions. One of the fastest growing informatics markets with a growth rate of nearly 20 per cent per year, ELNs are radically improving the effectiveness of laboratory operations. ELNs enable new approaches to knowledge management, collaboration, and data integration. 'We ...

A report in the August issue of Behavioral Neuroscience, published by the American Psychological Association, describes how this novel use of data mining may enable investigators to test therapies to delay or even prevent disease, starting with hereditary forms. Data mining to detect the subtle behavioral expression of mutations could conceivably allow investigators to test therapies aimed at preventing, slowing or stopping disease. By being able to predict more accurately which carriers may express the disease before they experience symptoms (the "premorbid" state), researchers could test medicines that might prevent symptoms from emerging. Methods such as data mining can be therapeutically useful even before science understands how disease begins. The authors wrote, "The discovery of reliable behavioral endpoints with predictive validity, even before a good understanding of their etiology is achieved, can significantly improve intervention research." Do you want ...

Bangalore, India — Indian Life Sciences Informatics Company, Molecular Connections announced today, the release of XTractor™, a first of its kind manually curated literature alert service. XTractor™ can be accessed free of charge by the scientific community world wide. XTractor™ acts as a literature alert service, which provides scientists with manually annotated scientific facts from literature. It enables researchers to be up-to-date with the latest scientific publications in the STM arena, as and when they are published. Once registered the scientists have the freedom to choose their keywords of choice and also set the frequency at which they wish to receive these alerts. Mining scientific literature to retrieve accurate hits or extract entity relationship has always been a long-standing problem in research. It is a daunting task to identify the right gene name or the right drug name and extract relations/association with diseases, processes; pathways etc accurately fo...