S Cain - GMOD in the cloud

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Presentation at BOSC2012 by S Cain - GMOD in the cloud

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S Cain - GMOD in the cloud

  1. 1. GMOD in the CloudScott CainGMOD Project CoordinatorOntario Institute for Cancer Researchscott@scottcain.netBOSCJuly 14, 2012
  2. 2. Introduction: GMOD is … Click to edit the title text format• A set of interoperable open-source software components for visualizing, annotating, and managing biological data.• An active community of developers and users asking diverse questions, and facing common challenges, with their biological data.
  3. 3. Who uses GMOD? Click to edit the title text format Plus hundreds of others
  4. 4. GMOD in the Cloud Click to edit the title text formatWhat GMOD in the cloud isnt: Clouds Guy getting blown up Garrys MOD (aka gmod.com)
  5. 5. cloud.gmod.org Click to edit the title text format GMOD tools preinstalled: Tripal Drupal-based web frontend Chado Generic organism DB schema GBrowse Venerable genome browser JBrowse Fast, AJAX genome browser Sample data Saccharomyces cerevisiae WebApollo* *Coming soon! Can be run as a micro machine (albeit slowly)
  6. 6. cloud.gmod.org Click to edit the title text format AMI GMOD Your data Software and configs
  7. 7. WebApollo Click to edit the title text format
  8. 8. A little more on Tripal Click to edit the title text formatBased on the popular CMS Drupal.Several modules written to serve as an interface for Chado: Controlled Vocabularies Features Analyses Libraries StocksIntegrated job management
  9. 9. Click to edit the title text format
  10. 10. Click to edit the title text format
  11. 11. Click to edit the title text format
  12. 12. Click to edit the title text format
  13. 13. Potential use case for Cloud GMOD Click to edit the title text formatCommunity annotation jamboree: - Clone GitC image - Load in computational annotations (MAKER) - Configure GBrowse, JBrowse, WebApollo - Unleash the wisdom of the masses (or trained spider monkeys, or undergrads-- whatever you have) - When the jamboree is over, dump out as GFF and shutdown the instance.
  14. 14. Why use the cloud? Click to edit the title text formatAvoid installation related issues (saves you time and frustration (and me for that matter)!)Save money (how much, of course, depends)Availability of common genomic data sets (several projects already make these available at AWS)
  15. 15. Acknowlegements Click to edit the title text format • Funding agencies: NIH, USDA ARS, NSF, Ontario government • Lincoln Stein • Stephen Ficklin and the Tripal group • Rob Buels, Mitch Skinner and JBrowse developers • The rest of the GMOD community--many bug reports, fixes, users

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