WebApollo
WebApollo is a project that aims to provide similar functionality to Apollo in a client-server web-based environment.
Our overall goal is to develop a lightweight Web 2.0 infrastructure that will offer easy-to-use tools for collaborative genome annotation that allows users to view, create, and edit genomic annotations in a graphical environment. This includes the design and implementation of:
- a web-browser-based version of Apollo built on top of JBrowse
- full support for two-way client-server exchange of genome annotations (DAS2)
- an annotation tracking system designed to support collaborative genome research projects
The WebApollo project is a collaboration between Suzanna Lewis's group at LBNL (the Berkeley Bioinformatics Open-source Projects group, or BBOP), the JBrowse project in Ian Holmes' group at Berkeley, and Chris Elsik's group at University of Missouri.
Public Demo
Server Installation Instructions
Setting up a server for your organism's genome data [WebApollo release for setup]
This work is supported by an NIH grant (Lewis R01 GM080203).
Project members
- Suzanna Lewis (PI, LBNL)
- Ian Holmes (PI, UC Berkeley)
- Chris Elsik (PI, University of Missouri)
- Rob Buels (UC Berkeley)
- Chris Childers (University of Missouri)
- Gregg Helt (LBNL)
- Ed Lee (LBNL)
- Monica Munoz-Torres
- Justin Reese (University of Missouri)
- Mitch Skinner (Emeritus - developed first version of JBrowse)
- Nomi Harris (LBNL) (Emeritus)
Talks and Demos
Conference or Meeting | Date | Title | Speaker | Abstract and/or slides |
---|---|---|---|---|
Binformatics Open Source Conference (BOSC) 2011 | July 15, 2011 | WebApollo: A web-based sequence annotation editor for community annotation | Nomi Harris | Abstract Slides |
Next-gen sequencing: Data acquisition, comparative genomics, design and analysis for population genetics, systematics and development (Course, National Evolutionary Synthesis Center (NESCent)) | August 16-20, 2011 | Talk: Biocuration, Best Practices. Workshop: Manual Curation of Automated Gene Models. |
Mónica Muñoz-Torres | T: Slides T: Audio W: Slides W: Audio |
Workshop on Manual Annotation, Purdue University | August 26, 2011 | Manual Curation of Automated Gene Models | Mónica Muñoz-Torres | Slides |
Entomological Society of America | November 13-16, 2011 | WebApollo demo/tutorial | Gregg Helt, Ed Lee, Monica Muñoz-Torres | Flyer for tutorial |
PAG (Plant and Animal Genome) conference | January 14-18, 2012 | |||
Biocuration 2012 | April 2-4, 2012 | WebApollo: A Web-Based Sequence Annotation Editor for Distributed Community Annotation | Gregg Helt | Biocuration abstract |
i5K Community Workshop & Arthropod Genomics Symposium | May 30 - June 2, 2012 | WebApollo Demo | Gregg Helt, Ed Lee, Monica Muñoz-Torres | Tutorial Poster |
WebApollo Tutorial for the 2012 GMOD Summer School | August 25-29, 2012 | WebApollo Tutorial | Ed Lee |
Project Meetings
Project meetings normally take place on Mondays at 1:00pm California time (PDT). On the last Monday of the month we usually meet at 9am PDT.