Icahn School of Medicine at Mount Sinai
    Introduction to Galaxy
    January 21, 2016, and
    January 22, 2016

    **Instructor: Dave Clements

    9:00-5:00

    Location: Large Classroom (Thursday), Small Classroom (Friday)
    Levy Library (11th floor)
    Annenberg Building. 1468 Madison Ave.
    Icahn School of Medicine at Mount Sinai (ISMMS), New York City **

    Registration

    Registration is free and open to any member of the ISMMS community. Space is available on a first-come, first served basis. Registration is now open. Please contact Andrew Sharp or Stuart Scott for the link.

    Audience

    Are you a life scientist who needs to do complex analysis on large datasets?

    Galaxy is an open, web-based platform for data intensive life science research that enables non-bioinformaticians to create, run, tune, and share their own bioinformatic analyses.

    Most of the workshop will be hands-on and teach participants how to integrate data, and perform simple and complex analysis within Galaxy. It will also cover data visualization and visual analytics, and how to share and reuse your bioinformatic analyses, all from within Galaxy.

    No programming or Linux command line experience is required.

    Agenda

    The agenda below is tentative and should be considered a work in progress.

    Time Topic
    9:00 Welcome
    Introductions and logistics
    9:20 Basic Analysis with Galaxy
    Walk through a worked, hands-on example demonstrating basic analysis with Galaxy
    10:45 Break
    11:00 Basic Analysis into Reusable Workflows
    Genericize our analysis into something we can use again.
    12:20 Lunch (on your own)
    1:20 RNA-Seq Example Part I
    Review 1) NGS data quality issues and some quality control options in Galaxy; and 2) Mapping and Splice Junction Calling
    2:50 Break
    3:05 RNA-Seq Example Part II
    Differential expression
    5:00 Done

    Icahn School of Medicine at Mount Sinai
    National Institutes of Health (NIH)

    Amazon Web Services

    Support

    This workshop is generously supported by an AWS in Education research grant award, the Icahn School of Medicine at Mount Sinai, and the National Institutes of Health (NIH).

    Slides

    Feedback

    We need it!

    Questions?

    Contact Andrew Sharp,Stuart Scott, or Galaxy Outreach.