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Introduction to Galaxy
February 4 + February 5 2013

**Workshops for the Johns Hopkins community

Instructors: Dave Clements, Mo Heydarian

Rangos 490
725 North Wolfe Street**

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


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


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.


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


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.



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.


Contact [Mo Heydarian](mailto:mheydar1 AT jhmi DOT edu) or [Galaxy Outreach](mailto:outreach AT galaxyproject DOT org).