Resources: Publications

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  1. eScience initiatives over the world

    15 Mar 2013 | Publications | Contributor(s): Yvan Le Bras

    Présentation des initiatives e-Science recensées à l'international.

  2. EMME publication : an Experimental Metadata Management Environment (JOBIM 2013)

    11 Jul 2013 | Publications | Contributor(s): Cyril Monjeaud, Yvan Le Bras, Olivier Collin

    The EMME project (Experimental Metadata Management Environment) carried out by the GenOuest bioinformatic facility, aims at developing a metadata tracking platform for the technical facilities in the Western France. The EMME environment is based on ISA tools in association with some analysis tools. …

  3. HUB eBiogenouest : Wiki Formatting

    08 Apr 2013 | Publications | Contributor(s): Yvan Le Bras

    Guide to inform user how to edit a wiki page on the HUB-eBGO

  4. Refactoring HUBzero for Linked Data : The paper

    17 Apr 2013 | Publications | Contributor(s): Michael Witt, Yongyang Yu

    The HUBzero cyberinfrastructure provides a virtual research environment that includes a set of tools for web-based, sci- enti c collaboration and a platform for publishing and using resources such as executable software, source code, im- ages, learning modules, videos, documents, and datasets. …

  5. An e-IRG overview on cloud computing for research and science

    17 Apr 2013 | Publications | Contributor(s): e-IRG group

    e-IRG has published a report which presents cloud computing in a holistic way, elaborates its applicability for research and science, investigates related policy aspects and provides policy recommendations. The future of cloud computing for research and science appears to be hybrid: the first …

  6. e-IRG Blue Paper

    17 Apr 2013 | Publications | Contributor(s): e-IRG group

    The Blue Paper identifies the most important areas of data management addressing following topics: • Data e-Infrastructure • Reliability and Replications • Metadata • Unified Access and interoperability • Security

  7. A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data

    23 Apr 2013 | Publications | Contributor(s): C. Titus Brown, Adina Howe, Qingpeng Zhang, Alexis B. Pyrkosz, Timothy H. Brom

    Deep shotgun sequencing and analysis of genomes, transcriptomes, ampli ed single-cell genomes, and metagenomes has enabled investigation of a wide range of organisms and ecosystems. However, sampling variation in short-read data sets and high sequencing error rates of modern sequencers present …

  8. De novo genome assembly: what every biologist should know

    23 Apr 2013 | Publications | Contributor(s): Monya Baker

    PDF link

  9. Review : A beginner's guide to eukaryotic genome annotation

    23 Apr 2013 | Publications | Contributor(s): Mark Yandell, Daniel Ence

    The falling cost of genome sequencing is having a marked impact on the research community with respect to which genomes are sequenced and how and where they are annotated. Genome annotation projects have generally become small-scale affairs that are often carried out by an individual laboratory. …

  10. Efficient Clustering of Metagenomic Sequences using Locality Sensitive Hashing

    23 Apr 2013 | Publications | Contributor(s): Zeehasham Rasheed, Huzefa Rangwala, Daniel Barbar

    The new generation of genomic technologies have allowed researchers to determine the collective DNA of organisms (e.g., microbes) co-existing as communities across the ecosystem (e.g., within the human host). There is a need for the computational approaches to analyze and annotate the large volumes …