WebApollo: A Web-Based Sequence Annotation Editor for Community Annotation<br />Ed Lee, Gregg Helt, Nomi Harris, Mitch Ski...
“Old” Apollo<br />Popular open source genome annotation editing tool<br />Lets biologists view computational analyses and ...
In The Old Days<br />Users had to download and install Apollo<br />Annotations saved locally in flat files<br />Sharing do...
Apollo in the Old Days<br />(Flat file)<br />
Starting To Get Better<br />Annotations saved directly to a centralized database<br />Edits made by other users not visibl...
Starting To Get Better<br />
WebApollo:Collaborative Annotation<br />Web-based (runs in browser)<br />No software download required<br />Annotations sa...
WebApollo Framework<br />
Web-based Client<br />Uses JBrowse<br />Javascript annotation browser<br />Fast<br />Highly interactive<br />WebApollo ext...
Multiple Client Synchronization<br />Comet model<br />Server pushes annotation updates to all clients in real time<br />
Annotation Editing Engine<br />Java<br />Handles all the logic for editing<br />Edits stored persistently in the server<br...
Enabling WebApollo to access as many types of genomic data as possible<br />Efficient access to public data from UCSC, Ens...
Trellis<br />Trellis Framework Servlet<br />PokaPlugin<br />JBrowse JSON Plugin<br />WebApollo Client<br />DAS Data Model<...
WebApollo Demo<br />Try it yourself:                                               http://icebox.lbl.gov:8080/ApolloWebDem...
Source Code(BSD License)<br />Client source code<br />https://github.com/berkeleybop/jbrowse<br />Annotation editing engin...
Acknowledgements<br />LBNL<br />Ed Lee<br />Gregg Helt<br />Nomi Harris<br />Suzanna Lewis<br />UC Berkeley<br />Mitch Ski...
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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).
  • C03-Visualization-Webapollo

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

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