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C03-Visualization-Webapollo

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  • Q: Doesn’t UCSC already have a DAS server?A: Yes, but the way we’re doing it is faster and preserves more information.Q: DAS1 or DAS2?A: Trellis mediates between the two (so it can support either).
  • Transcript

    • 1. WebApollo: A Web-Based Sequence Annotation Editor for Community Annotation
      Ed Lee, Gregg Helt, Nomi Harris, Mitch Skinner, Christopher Childers, Justin Reese, Jay Sandaram, Christine Elsik, Ian Holmes, Suzanna Lewis
      Bioinformatics Open Source Conference (BOSC 2011)
      July 15, 2011
    • 2. “Old” Apollo
      Popular open source genome annotation editing tool
      Lets biologists view computational analyses and experimental evidence for genomic features and build a manually-curated consensus
      Standalone Java application
    • 3. In The Old Days
      Users had to download and install Apollo
      Annotations saved locally in flat files
      Sharing done by emailing files
      Only one person could edit a region at a time
    • 4. Apollo in the Old Days
      (Flat file)
    • 5. Starting To Get Better
      Annotations saved directly to a centralized database
      Edits made by other users not visible until you actively reloaded
      Potential issues with stale annotation data
      Apollo software downloaded more transparently by Java Web Start
      Users still needed to install Java
    • 6. Starting To Get Better
    • 7. WebApollo:Collaborative Annotation
      Web-based (runs in browser)
      No software download required
      Annotations saved to centralized database
      Edit server mediates annotation changes made by multiple users
      Real-time annotation updating
    • 8. WebApollo Framework
    • 9. Web-based Client
      Uses JBrowse
      Javascript annotation browser
      Fast
      Highly interactive
      WebApollo extensions to JBrowse
      Gestures for editing annotations
      Communication with the annotation editing engine and data providing service
      HTML5 Canvas quantitative data rendering
    • 10. Multiple Client Synchronization
      Comet model
      Server pushes annotation updates to all clients in real time
    • 11. Annotation Editing Engine
      Java
      Handles all the logic for editing
      Edits stored persistently in the server
      BerkeleyDB JE for fast access
      Able to restore data if either client or server crashes
      Per-sequence (contig, chromosome, etc.) user permissions (none/read/write)
    • 12. Enabling WebApollo to access as many types of genomic data as possible
      Efficient access to public data from UCSC, Ensembl, and GMOD Chado databases
      Unified strategy (like DAS) is preferred
      Solution: Trellis, a DAS server framework that:
      Supports modular back-end plugins, e.g.,
      Poka Trellis plugin for UCSC database access
      DAS plugin for Ensembl servers
      Supports modular front-end content formats, e.g.,
      JBrowse JSON plugin
    • 13. Trellis
      Trellis Framework Servlet
      PokaPlugin
      JBrowse JSON Plugin
      WebApollo Client
      DAS Data Model
      UCSC
      MySQL
      Genome database
      DAS Model to UCSC MySQL
      DAS HTTP Request
      with format modifier
      MySQL response to DAS Model
      Model to
      JBrowse JSON
    • 14. WebApollo Demo
      Try it yourself: http://icebox.lbl.gov:8080/ApolloWebDemo
      Annotations you make on demo server are:
      Not kept private
      Not guaranteed to persist
    • 15.
    • 16. Source Code(BSD License)
      Client source code
      https://github.com/berkeleybop/jbrowse
      Annotation editing engine
      http://code.google.com/p/apollo-web
      Data model and I/O layer
      http://code.google.com/p/gbol
      Trellis server code
      http://code.google.com/p/genomancer
    • 17. Acknowledgements
      LBNL
      Ed Lee
      Gregg Helt
      Nomi Harris
      Suzanna Lewis
      UC Berkeley
      Mitch Skinner
      Ian Holmes
      Georgetown University
      Christopher Childers
      Justin Reese
      Jay Sundaram
      Christine Elsik
      Demo: http://icebox.lbl.gov:8080/ApolloWebDemo