Introduction to Galaxy
    February 4 + February 5 2013

    **Workshops for the Johns Hopkins community

    Instructors: Dave Clements, Mo Heydarian

    9:00am-4:30pm
    Rangos 490
    725 North Wolfe Street**

    Biological Chemistry @ Johns Hopkins
    Reddy and Sollner-Webb Labs
    Center for Computational Biology
    Salzberg Lab
    Johns Hopkins

    Registration

    Registration was free, and open to anyone in the Johns Hopkins community. Both workshops were full and had waiting lists.

    Audience

    Are you a biomedical researcher who needs to do complex analysis on large datasets?

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

    These hands-on workshops will teach participants how to integrate data, and perform simple and complex analysis within Galaxy. They 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

    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
    10:20 Basic Analysis into Reusable Workflows
    Genericize our analysis into something we can use again.
    10:40 Break
    11:00 RNA-Seq Example Part I
    Review NGS data quality issues and some quality control options in Galaxy; Mapping and Splice Junction Calling with Tophat
    12:00 Galaxy Project Overview
    Introduction to Galaxy and the Galaxy community
    12:20 Lunch (catered)
    1:05 RNA-Seq Example Part II
    Cufflinks, Visualization, and Visual Analytics
    1:55 Sharing, Publishing, and Reproducibility with Galaxy
    Share and publish analysis, datasets, and workflows with Galaxy
    2:15 Break
    2:35 Setting up your own Galaxy Cluster on the Amazon Cloud
    Every participant will set up their own functional and populated (but short-lived) Galaxy server on the cloud
    4:30 Done

    Support

    Amazon Web Services

    This workshop is generously supported by an AWS in Education grant award, and the Department of Biological Chemistry @ Johns Hopkins and the Center for Computational Biology.

    Slides

    Flyer

    Please distribute to parts of Johns Hopkins that might be interested. You are also encouraged to print a post a copy of the workshop flyer.

    Questions?

    Contact Mo Heydarian or Galaxy Outreach.