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  1. Article: Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring.

    Maier, Wolfgang / Bray, Simon / van den Beek, Marius / Bouvier, Dave / Coraor, Nathaniel / Miladi, Milad / Singh, Babita / De Argila, Jordi Rambla / Baker, Dannon / Roach, Nathan / Gladman, Simon / Coppens, Frederik / Martin, Darren P / Lonie, Andrew / Grüning, Björn / Kosakovsky Pond, Sergei L / Nekrutenko, Anton

    bioRxiv : the preprint server for biology

    2021  

    Abstract: The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data.Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is ... ...

    Abstract The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data.Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is necessary to pull together global computational resources and deliver the best open source tools and analysis workflows within a ready to use, universally accessible resource. Such a resource should not be controlled by a single research group, institution, or country. Instead it should be maintained by a community of users and developers who ensure that the system remains operational and populated with current tools. A community is also essential for facilitating the types of discourse needed to establish best analytical practices. Bringing together public computational research infrastructure from the USA, Europe, and Australia, we developed a distributed data analysis platform that accomplishes these goals. It is immediately accessible to anyone in the world and is designed for the analysis of rapidly growing collections of deep sequencing datasets. We demonstrate its utility by detecting allelic variants in high-quality existing SARS-CoV-2 sequencing datasets and by continuous reanalysis of COG-UK data. All workflows, data, and documentation is available at https://covid19.galaxyproject.org .
    Language English
    Publishing date 2021-03-25
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2021.03.25.437046
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring

    Maier, Wolfgang / Bray, Simon / van den Beek, Marius / Bouvier, Dave / Coraor, Nathaniel / Miladi, Milad / Singh, Babita / Rambla De Argila, Jordi / Baker, Dannon / Roach, Nathan / Gladman, Simon / Coppens, Frederik / Martin, Darren / Lonie, Andrew / Gruning, Bjorn / Kosakovsky Pond, Sergei / Nekrutenko, Anton

    bioRxiv

    Abstract: The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data. Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is ... ...

    Abstract The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data. Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is necessary to pull together global computational resources and deliver the best open source tools and analysis workflows within a ready to use, universally accessible resource. Such a resource should not be controlled by a single research group, institution, or country. Instead it should be maintained by a community of users and developers who ensure that the system remains operational and populated with current tools. A community is also essential for facilitating the types of discourse needed to establish best analytical practices. Bringing together public computational research infrastructure from the USA, Europe, and Australia, we developed a distributed data analysis platform that accomplishes these goals. It is immediately accessible to anyone in the world and is designed for the analysis of rapidly growing collections of deep sequencing datasets. We demonstrate its utility by detecting allelic variants in high-quality existing SARS-CoV-2 sequencing datasets and by continuous reanalysis of COG-UK data. All workflows, data, and documentation is available at https://covid19.galaxyproject.org.
    Keywords covid19
    Language English
    Publishing date 2021-03-25
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2021.03.25.437046
    Database COVID19

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  3. Article ; Online: Galaxy: a web-based genome analysis tool for experimentalists.

    Blankenberg, Daniel / Von Kuster, Gregory / Coraor, Nathaniel / Ananda, Guruprasad / Lazarus, Ross / Mangan, Mary / Nekrutenko, Anton / Taylor, James

    Current protocols in molecular biology

    2010  Volume Chapter 19, Page(s) Unit 19.10.1–21

    Abstract: High-throughput data production has revolutionized molecular biology. However, massive increases in data generation capacity require analysis approaches that are more sophisticated, and often very computationally intensive. Thus, making sense of high- ... ...

    Abstract High-throughput data production has revolutionized molecular biology. However, massive increases in data generation capacity require analysis approaches that are more sophisticated, and often very computationally intensive. Thus, making sense of high-throughput data requires informatics support. Galaxy (http://galaxyproject.org) is a software system that provides this support through a framework that gives experimentalists simple interfaces to powerful tools, while automatically managing the computational details. Galaxy is distributed both as a publicly available Web service, which provides tools for the analysis of genomic, comparative genomic, and functional genomic data, or a downloadable package that can be deployed in individual laboratories. Either way, it allows experimentalists without informatics or programming expertise to perform complex large-scale analysis with just a Web browser.
    MeSH term(s) Animals ; Computational Biology/methods ; Genetic Techniques ; Genome ; Humans ; Internet ; Software Design
    Language English
    Publishing date 2010-01-13
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1934-3647
    ISSN (online) 1934-3647
    DOI 10.1002/0471142727.mb1910s89
    Database MEDical Literature Analysis and Retrieval System OnLINE

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