C03-Visualization-Webapollo
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WebApollo is a web-based genome annotation editor that allows multiple users to collaboratively edit annotations in real-time. It uses a client-server model where the web-based client communicates with an annotation editing engine and data server through a framework called Trellis. This allows annotations to be accessed and edited without installing software by running in a web browser.
C03-Visualization-Webapollo
- 1. WebApollo: A Web-Based Sequence Annotation Editor for Community AnnotationEd Lee, Gregg Helt, Nomi Harris, Mitch Skinner, Christopher Childers, Justin Reese, Jay Sandaram, Christine Elsik, Ian Holmes, Suzanna LewisBioinformatics Open Source Conference (BOSC 2011)July 15, 2011
- 2. “Old” ApolloPopular open source genome annotation editing toolLets biologists view computational analyses and experimental evidence for genomic features and build a manually-curated consensusStandalone Java application
- 3. In The Old DaysUsers had to download and install ApolloAnnotations saved locally in flat filesSharing done by emailing filesOnly one person could edit a region at a time
- 4. Apollo in the Old Days(Flat file)
- 5. Starting To Get BetterAnnotations saved directly to a centralized databaseEdits made by other users not visible until you actively reloadedPotential issues with stale annotation dataApollo software downloaded more transparently by Java Web StartUsers still needed to install Java
- 6. Starting To Get Better
- 7. WebApollo:Collaborative AnnotationWeb-based (runs in browser)No software download requiredAnnotations saved to centralized databaseEdit server mediates annotation changes made by multiple usersReal-time annotation updating
- 9. Web-based ClientUses JBrowseJavascript annotation browserFastHighly interactiveWebApollo extensions to JBrowseGestures for editing annotationsCommunication with the annotation editing engine and data providing serviceHTML5 Canvas quantitative data rendering
- 10. Multiple Client SynchronizationComet modelServer pushes annotation updates to all clients in real time
- 11. Annotation Editing EngineJavaHandles all the logic for editingEdits stored persistently in the serverBerkeleyDB JE for fast accessAble to restore data if either client or server crashesPer-sequence (contig, chromosome, etc.) user permissions (none/read/write)
- 12. Enabling WebApollo to access as many types of genomic data as possibleEfficient 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. TrellisTrellis Framework ServletPokaPluginJBrowse JSON PluginWebApollo ClientDAS Data ModelUCSC MySQLGenome databaseDAS Model to UCSC MySQLDAS HTTP Request with format modifierMySQL response to DAS Model Model to JBrowse JSON
- 14. WebApollo DemoTry it yourself: http://icebox.lbl.gov:8080/ApolloWebDemoAnnotations you make on demo server are:Not kept privateNot guaranteed to persist
- 16. Source Code(BSD License)Client source codehttps://github.com/berkeleybop/jbrowseAnnotation editing enginehttp://code.google.com/p/apollo-webData model and I/O layerhttp://code.google.com/p/gbolTrellis server codehttp://code.google.com/p/genomancer
- 17. AcknowledgementsLBNLEd LeeGregg HeltNomi HarrisSuzanna LewisUC BerkeleyMitch SkinnerIan HolmesGeorgetown UniversityChristopher ChildersJustin ReeseJay SundaramChristine ElsikDemo: http://icebox.lbl.gov:8080/ApolloWebDemo
Editor's Notes
- #13: 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).