The Apollo genome annotation editor, which is a stand-alone Java application, allows users to view, create, and edit genomic annotations in a graphical environment. Apollo has been used for years by many genome projects. WebApollo is a new project that aims to provide similar functionality 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. 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 Georgetown.
This work is supported by an NIH grant (Lewis R01 GM080203).
- Suzanna Lewis (PI, LBNL)
- Ian Holmes (PI, UC Berkeley)
- Chris Elsik (PI, Georgetown)
- Rob Buels (UC Berkeley)
- Chris Childers (Georgetown)
- Nomi Harris (LBNL)
- Gregg Helt (LBNL)
- Ed Lee (LBNL)
- Monica Munoz-Torres (Georgetown)
- Justin Reese (Georgetown)
- (Mitch Skinner (Developed first version of JBrowse--no longer at UC Berkeley))
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|
|Workshop on Manual Annotation, Purdue University||September, 2011||Best Practices in Biocuration||Mónica Cecilia Muñoz-Torres|
|Entomological Society of America||November 13-16, 2011||WebApollo demo/tutorial||Gregg Helt, Ed Lee, Monica Cecilia Muñoz-Torres||Flyer for tutorial|
|Next-gen sequencing: Data acquisition, comparative genomics, design and analysis for population genetics, systematics and development (Course, National Evolutionary Synthesis Center (NESCent))||Biocuration, Best Practices||Mónica Cecilia Muñoz-Torres|
|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||May 30 - June 2, 2012||WebApollo Demo||Gregg Helt, Ed Lee, Monica Cecilia Muñoz-Torres|
Project meetings normally take place on Mondays at 1:00pm California time. On the last Monday of the month we usually meet at 9am California time.