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Introduction to Galaxy February 27, 2015, 9:00-4:00Instructors: Dave Clements, Matt Schipma Galter Health Sciences Library, Learning Resources Center Northwestern University Feinberg School of Medicine campus Chicago, Illinois, United States |
Registration
This workshop is full.
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.
This hands-on workshop will 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
| Time | Topic |
|---|---|
| 8:30 | Arrival Arrival and coffee |
| 9:00 | Welcome Introductions and logistics |
| 9:30 | 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. |
| 11:20 | RNA-Seq Example Part I Review NGS data quality issues, quality control options in Galaxy, and Mapping and Splice Junction Calling |
| 12:20 | Lunch (on your own) |
| 1:35 | Galaxy Project Overview Introduction to Galaxy and the Galaxy community |
| 1:55 | RNA-Seq Example Part II Discuss and run differential gene expression analysis, and merging multiple experiments into a single picture; Visualization and Visual Analytics |
| 2:45 | Break |
| 3:00 | Sharing, Publishing, and Reproducibility with Galaxy Share and publish analysis, datasets, and workflows with Galaxy |
| 3:25 | 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 |
| 4:00 | Done |
Logistics
The workshop is being held in the Learning Resource Center of the Galter Health Sciences Library on the Northwestern University Feinberg School of Medicine campus in Chicago, Illinois.
The Learning Resources Center has 23 computers, and seating for up to 50. Participants are encouraged to bring their own wi-fi enabled laptops as there are fewer lab computers than there are participants. If you bring your own laptop, please install Firefox or Chrome beforehand.
Support
This workshop is generously supported by Northwestern University Research Computing Services, the Galter Health Sciences Library, the Northwestern University Clinical and Translational Sciences Institute (NUCATS), the Feinberg School of Medicine, an AWS in Education grant award, and the National Institutes of Health (NIH).
Slides
Feedback
Questions?
Contact [Pamela Shaw](mailto:p DASH shaw2@northwestern.edu) or [Galaxy Outreach](mailto:outreach AT galaxyproject DOT org).