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Collaborative Genomic Data Analyses in the Cloud

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Talk from eScience in the Cloud 2014

Talk from eScience in the Cloud 2014

Published in: Education, Technology

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  • 1. Collaborative Genomic Data Analyses in the Cloud Steven B. Roberts Associate Professor School of Aquatic and Fishery Sciences University of Washington robertslab.info
  • 2. Open Science • You are free to Share! • Our lab practices open notebook science robertslab.info sr320@uw.edu
  • 3. Stochastic Variation 10.1093/bfgp/elt054 10.6084/m9.figshare.880763
  • 4. raw - 70G mapping - 60G tables - 40G ........ big, big, compute intensive, education Why cloud?
  • 5. }
  • 6. Use Cases • Joining on Annotations • File Conversion • Querying Gene Tables
  • 7. github.com/sr320/qdod/wiki
  • 8. Sharing Collaboration*
  • 9. Reproducible OpenCollaboration Open Notebook Science
  • 10. Open Notebook Science ... there is a URL to a laboratory notebook that is freely available and indexed on common search engines. It does not necessarily have to look like a paper notebook but it is essential that all of the information available to the researchers to make their conclusions is equally available to the rest of the world. —Jean-Claude Bradley
  • 11. Open Notebook Science genefish.wikispaces.com
  • 12. Open Notebook Science Set some variables blast convert file format upload to SQLShare (python client) join in SQLShare - download read in pandas matplotlib generates graph of GOsllim
  • 13. Open Notebook Science Wiki - collaboration, versioning, search, publishing Evernote - simple, multi-platform IPython - executable, versioning* Comparison no perfection solution
  • 14. Challenges: versioning, provenance, collaboration, simple sharing, discoverability
  • 15. Reproducible ScienceOpen
  • 16. Acknowledgements Mackenzie Gavery Claire Olson Sam White Brent Vadopalas Jake Heare Bill Howe Dan Halperin EPA STAR Aquaculture Program DNA methylation