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

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