NOTE: This document is provided for versions of Web Apollo 2014-04-03 and older.
- Mature release
- Development: active
- Support: active
WebApollo is a browser-based tool for visualization 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 (Apis mellifera genome).
Visit the WebApollo website.
Publications, Tutorials, and Presentations
Publications on or mentioning WebApollo
- Web Apollo: a web-based genomic annotation editing platform. 
|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 |
|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|
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.|
More on WebApollo
<ref>tag; no text was provided for refs named
Cite error: Invalid
|Available on platform||web +|
|Has URL||http://code.google.com/p/genomancer +, http://genomearchitect.org:8080/WebApolloDemo/ +, http://genomearchitect.org/webapollo/releases/ +, http://genomearchitect.org + and https://github.com/gmod/apollo +|
|Has description||WebApollo is a browser-based tool for visu … WebApollo is a browser-based tool for visualization 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:
|Has development status||active +|
|Has input format||GFF3 +, BigWig + and BAM +|
|Has logo||WebApolloLogo.png +|
|Has output format||GFF3 + and others +|
|Has software maturity status||mature +|
|Has support status||active +|
|Has title||Trellis server +, WebApollo demo - Bos taurus genome +, WebApollo download + and Client and server +|
|Has topic||WebApollo +|
|Interaction type||receives input from + and is based on +|
|Interacts with||MAKER + and JBrowse +|
|Is open source||Yes +|
|Link type||source code +, demo server +, download + and website +|
|Release date||2012 +|
|Tool functionality or classification||Community annotation + and Sequence annotation +|
|Has subobjectThis property is a special property in this wiki.||WebApollo#http://code.google.com/p/genomancer +, WebApollo#http://genomearchitect.org:8080/WebApolloDemo/ +, WebApollo#http://genomearchitect.org/webapollo/releases/ +, WebApollo#http://genomearchitect.org +, WebApollo#https://github.com/gmod/apollo +, WebApollo + and WebApollo +|