C03-Visualization-Webapollo

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

“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

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

Apollo in the Old Days
(Flat file)

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

Starting To Get Better

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

WebApollo Framework

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

Multiple Client Synchronization
Comet model
Server pushes annotation updates to all clients in real time

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)

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

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

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

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

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

C03-Visualization-Webapollo

by Bioinformatics Open Source Conference

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