1. Articles from Oxford Journals

    bioinformatics.oxfordjournals.org

    1-6 of 6

    1. A Database Of Global Events For Epidemic Intelligence

      Explore Oxford Journals (Apr 6 2012)

      Summary: We present a novel public health database (GENI-DB) in which news events on the topic of over 176 infectious diseases and chemicals affecting human and animal health are compiled from surveillance of the global online news media in 10 languages. News event frequency data were gathered systematically through the BioCaster public health surveillance system from July 2009 to the present and is available to download by the research community for purposes of analyzing trends in the global burden of infectious diseases. Database search can be conducted by year, country, disease and language. Availability: The GENI-DB is freely available via ... (Read Full Article)

    2. toolkit for rapid, customized LIMS development

      Explore Oxford Journals (Jan 30 2011) Pharmaceuticals

      Summary: Workflow Information Storage Toolkit (WIST) is a set of application programming interfaces and web applications that allow for the rapid development of customized laboratory information management systems (LIMS). WIST provides common LIMS input components, and allows them to be arranged and configured using a flexible language that specifies each component's visual and semantic characteristics. WIST includes a complete set of web applications for adding, editing and viewing data, as well as a powerful setup tool that can build new LIMS modules by analyzing existing database schema. Availability and implementation: WIST is implemented in Perl and may be obtained ... (Read Full Article)

    3. A sample storage management system for biobanks

      Explore Oxford Journals (Oct 21 2010) Biobanking

      Summary: Establishment of large-scale biobanks of human specimens is essential to conduct molecular pathological or epidemiological studies. This requires automation of procedures for specimen cataloguing and tracking through complex analytical processes. The International Agency for Research on Cancer (IARC) develops a large portfolio of studies broadly aimed at cancer prevention and including cohort, case–control and case-only studies in various parts of the world. This diversity of study designs, structure, annotations and specimen collections is extremely difficult to accommodate into a single sample management system (SMS). Current commercial or academic SMS are often restricted to a few sample types and ... (Read Full Article)

    4. Collaborative Annotation Toolkit For Massive Amounts Of Image Data

      Explore Oxford Journals (Jul 16 2009)

      Summary: High-resolution, three-dimensional (3D) imaging of large biological specimens generates massive image datasets that are difficult to navigate, annotate and share effectively. Inspired by online mapping applications like GoogleMapsTM, we developed a decentralized web interface that allows seamless navigation of arbitrarily large image stacks. Our interface provides means for online, collaborative annotation of the biological image data and seamless sharing of regions of interest by bookmarking. The CATMAID interface enables synchronized navigation through multiple registered datasets even at vastly different scales such as in comparisons between optical and electron microscopy. Availability: http://fly.mpi-cbg.de/catmaid Contact: tomancak@mpi-cbg.de (Read Full Article)

    5. Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlated molecular changes

      Explore Oxford Journals (Jun 16 2009)

      Motivation: According to current consistency metrics such as percentage of overlapping genes (POG), lists of differentially expressed genes (DEGs) detected from different microarray studies for a complex disease are often highly inconsistent. This irreproducibility problem also exists in other high-throughput post-genomic areas such as proteomics and metabolism. A complex disease is often characterized with many coordinated molecular changes, which should be considered when evaluating the reproducibility of discovery lists from different studies. Results: We proposed metrics percentage of overlapping genes-related (POGR) and normalized POGR (nPOGR) to evaluate the consistency between two DEG lists for a complex disease, considering correlated molecular ... (Read Full Article)

    6. A Laboratory Information Management System (LIMS) for a high throughput genetic platform aimed at candidate gene mutation screening

      Explore Oxford Journals (Sep 16 2007) Pharmaceuticals

      Summary: High throughput mutation screening in an automated environment generates large data sets that have to be organized and stored reliably. Complex multistep workflows require strict process management and careful data tracking. We have developed a Laboratory Information Management Systems (LIMS) tailored to high throughput candidate gene mutation scanning and resequencing that respects these requirements. Designed with a client/server architecture, our system is platform independent and based on open-source tools from the database to the web application development strategy. Flexible, expandable and secure, the LIMS, by communicating with most of the laboratory instruments and robots, tracks samples and laboratory ... (Read Full Article)