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[[Category:Webapollo]] | [[Category:Webapollo]] | ||
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[[Category:AJAX]] | [[Category:AJAX]] | ||
| − | [[Category: | + | [[Category:Community Annotation]] |
| + | [[Category:Annotation]] | ||
| + | [[Category:GMOD Components]] | ||
Revision as of 00:54, 9 February 2013
Status
- Mature release
- Development: active
- Support: active
Resources
Included in
Contents
About WebApollo
WebApollo is a browser-based tool for visualisation and editing of sequence annotations. It is designed for distributed community annotation efforts, where numerous people may be working on the same sequences in geographically different locations; real-time updating keeps all users in sync during the editing process.
The features of WebApollo include:
- History tracking, including browsing of an annotation's edit history and full undo/redo functions
- Real time updating: edits in one client are instantly pushed to all other clients
- Convenient management of user login, authentication, and edit permissions
- Two-stage curation process: edit within a temporary workspace, then publish to a curated database
- Ability to add comments, either chosen from a pre-defined set of comments or as freeform text.
- Ability to add dbxrefs [database crossreferences] -- e.g. for GO functional annotation
- Can set start of translation for a transcript or let server determine automatically
- Flagging of non-canonical splice sites in curated annotations
- Edge matching to selected feature: matching edges across annotations and evidence tracks are highlighted
- Option to color transcript CDS by reading frame
- Loading of data directly from GFF3, BigWig, and BAM files, both remotely and from user's local machine.
- Configurable heat map rendering of BigWig data
- Per-session track configuration to set annotation colors, height, and other properties
- Export of annotation tracks as GFF3 and optionally other formats
- Search by sequence residues using server-side interface to BLAT or other sequence search programs
The public demo can be accessed at: http://genomearchitect.org/WebApolloDemo (Bos taurus genome).
Downloads
- Download WebApollo: http://genomearchitect.org/webapollo/releases/
- JBrowse client source on github
- Annotation editing engine server source code on Google Code
- Data model and I/O layer code used by editing engine on Google Code
- Trellis server code on Google Code
Using WebApollo
Installation
Documentation
Publications, Tutorials, and Presentations
Tutorials
- WebApollo Tutorial
- taught as part of the 2013 GMOD Summer School
Presentations
| Date (YYYY-MM-DD) | Event | Title | Speaker/Authors | Abstract/Slides |
|---|---|---|---|---|
| 2013-01-12 - 2013-01-16 | PAG 2013 (International Plant & Animal Genome XXI) | WebApollo: A Web-based Sequence Annotation Editor for Distributed Community Annotation | Gregg Helt, Ed Lee, Robert Buels, Christopher Childers, Justin Reese, Mónica Muñoz-Torres, Christine Elsik, Ian Holmes, and Suzanna Lewis | Poster |
| 2012-08-25 - 2012-08-29 | WebApollo Tutorial for the 2012 GMOD Summer School | WebApollo Tutorial | Ed Lee | |
| 2012-05-30 - 2012-06-02 | i5K Community Workshop & Arthropod Genomics Symposium | WebApollo Demo | Gregg Helt, Ed Lee, Monica Muñoz-Torres | Tutorial Poster |
| 2012-04-02 - 2012-04-04 | Biocuration 2012 | WebApollo: A Web-Based Sequence Annotation Editor for Distributed Community Annotation | Gregg Helt | Biocuration abstract |
| 2012-01-14 - 2012-01-18 | PAG (Plant and Animal Genome) conference | |||
| 2011-11-13 - 2011-11-16 | Entomological Society of America | WebApollo demo/tutorial | Gregg Helt, Ed Lee, Monica Muñoz-Torres | Flyer for tutorial |
| 2011-08-26 | Workshop on Manual Annotation, Purdue University | Manual Curation of Automated Gene Models | Mónica Muñoz-Torres | Slides |
| 2011-08-16 - 2011-08-20 | Next-gen sequencing: Data acquisition, comparative genomics, design and analysis for population genetics, systematics and development (Course, National Evolutionary Synthesis Center (NESCent)) | Talk: Biocuration, Best Practices. Workshop: Manual Curation of Automated Gene Models. |
Mónica Muñoz-Torres | T: Slides T: Audio W: Slides W: Audio |
| 2011-07-15 | Bioinformatics Open Source Conference (BOSC) 2011 | 'WebApollo: A web-based sequence annotation editor for community annotation' | Nomi Harris | Abstract Slides |
Contacts and Mailing Lists
| Mailing List Link | Description | Archive(s) | |
|---|---|---|---|
| Apollo and WebApollo | apollo | Apollo and WebApollo mailing list | Gmane (2008/04-2010/10), Nabble (2010/05+) |
| gmod-apollo-cmts | Apollo and WebApollo code updates. |
WebApollo Development
Development team
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.
The personnel involved in WebApollo are: Suzanna Lewis (PI, LBNL); Ian Holmes (PI, UC Berkeley); Chris Elsik (PI, University of Missouri); Ed Lee (LBNL); Gregg Helt (LBNL); Justin Reese (University of Missouri); Monica Munoz-Torres (LBNL); Chris Childers (University of Missouri); Rob Buels (UC Berkeley); Mitch Skinner (UC Berkeley) (Emeritus - developed first version of JBrowse); and Nomi Harris (LBNL) (Emeritus).
More on WebApollo
WebApollo Logo
The WebApollo logo was created by Audra Radke, a participant in the Spring 2010 Logo Program, while a design student at Linn-Benton Community College.
Raw tool data at WebApollo/tool data
