Difference between revisions of "WebApollo"

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{{Tool data
 
{{Tool data
 
|name=WebApollo
 
|name=WebApollo
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|status=mature
 
|status=mature
 
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The public demo can be accessed at: [http://genomearchitect.org/WebApolloDemo http://genomearchitect.org/WebApolloDemo] (''Bos taurus'' genome).
 
The public demo can be accessed at: [http://genomearchitect.org/WebApolloDemo http://genomearchitect.org/WebApolloDemo] (''Bos taurus'' genome).
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|gmod date=
 
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|release date=2012
 
 
|open source=Yes
 
|open source=Yes
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|licence=
 
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|language=Javascript
 
 
|input=GFF3, BigWig, BAM
 
|input=GFF3, BigWig, BAM
 
|output=GFF3, others
 
|output=GFF3, others
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|audience=
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|language=Javascript, Java
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|release date=2012/01/01
 
|logo=WebApolloLogo.png
 
|logo=WebApolloLogo.png
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|screenshot=
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|contact=elee
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|public server=
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|survey link=
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|mail={{MailingListsFor|Apollo}}
 
|mail={{MailingListsFor|Apollo}}
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|contact email=elee@berkeleybop.org
 
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|integration=
 
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|papers=
 
 
|presentations={{WebApolloPresentations}}
 
|presentations={{WebApolloPresentations}}
 
|tutorials=;[[WebApollo Tutorial]]
 
|tutorials=;[[WebApollo Tutorial]]
 
:taught as part of the [[2013 GMOD Summer School]]
 
:taught as part of the [[2013 GMOD Summer School]]
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|getting started preamble=
 
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|req=
 
 
|install=*[[WebApollo_Installation|Server installation guide]]
 
|install=*[[WebApollo_Installation|Server installation guide]]
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|config=
 
 
|doc=* [http://genomearchitect.org/webapollo/docs/webapollo_user_guide.pdf WebApollo User Guide (PDF)]
 
|doc=* [http://genomearchitect.org/webapollo/docs/webapollo_user_guide.pdf WebApollo User Guide (PDF)]
 
* [http://apollo.berkeleybop.org/apollo_web/web_service_api.html Apollo Web service API]
 
* [http://apollo.berkeleybop.org/apollo_web/web_service_api.html Apollo Web service API]
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|dev ppl=The WebApollo project is a collaboration between Suzanna Lewis's group at LBNL (the Berkeley Bioinformatics Open-source Projects group, or [http://berkeleybop.org/ BBOP]), the JBrowse project in [http://biowiki.org/HolmesLab Ian Holmes' group] at Berkeley, and [http://genomes.arc.georgetown.edu/elsiklab/ Chris Elsik]'s group at University of Missouri.
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|gmod date=
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The personnel involved in WebApollo are: Suzanna Lewis (PI, LBNL); Ian Holmes (PI, UC Berkeley); Chris Elsik (PI, University of Missouri); [[User:Elee|Ed Lee]] (LBNL); [[User:GreggHelt2|Gregg Helt]] (LBNL); [[User:Justaddcoffee|Justin Reese]] (University of Missouri); [[User:Moni|Monica Munoz-Torres]] (LBNL); [[User:Childers|Chris Childers]] (University of Missouri); Rob Buels (UC Berkeley); [[User:MitchSkinner|Mitch Skinner]] (UC Berkeley) (Emeritus - developed first version of JBrowse); and Nomi Harris (LBNL) (emeritus).
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|survey link=
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|contact email=elee@berkeleybop.org
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{{ :WebApollo/tool_data | template = Template:ToolDisplay }}
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[[Category:Webapollo]]
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[[Category:AJAX]]
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[[Category:Community Annotation]]
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[[Category:Annotation]]
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[[Category:GMOD Components]]
 
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|linkurl=https://github.com/berkeleybop/jbrowse
 
|linkurl=https://github.com/berkeleybop/jbrowse
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[[Category:Webapollo]]
 
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Revision as of 23:57, 3 October 2013

WebApollo logo
Status
  • Mature release
  • Development: active
  • Support: active
Resources


Cloud component

Included in

Cloud component

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



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

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

Retrieved from "http://gmod.org/mediawiki/index.php?title=WebApollo&oldid=24623"
Facts about "WebApollo"RDF feed
Available on platformweb +
Has URLhttps://github.com/berkeleybop/jbrowse +, http://code.google.com/p/genomancer +, http://code.google.com/p/apollo-web +, http://code.google.com/p/gbol +, http://genomearchitect.org:8080/WebApolloDemo/ + and http://genomearchitect.org/webapollo/releases/ +
Has descriptionWebApollo is a browser-based tool for visu … 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).rg/WebApolloDemo] (Bos taurus genome). +
Has development statusactive +
Has download URLhttp://genomearchitect.org/webapollo/releases/ +
Has input formatGFF3 +, BigWig + and BAM +
Has logoWebApolloLogo.png +
Has output formatGFF3 + and others +
Has software maturity statusmature +
Has support statusactive +
Has titleJBrowse client +, Trellis server +, Annotation editing engine server +, Data model and I/O layer code used by editing engine +, WebApollo demo - Bos taurus genome + and WebApollo download +
Has topicWebApollo +
Interaction typereceives input from + and is based on +
InteractorWebApollo +
Interacts withMAKER + and JBrowse +
Is open sourceYes +
Link typesource code +, demo server + and download +
Release date1 January 2012 +
Tool functionality or classificationCommunity annotation + and Sequence annotation +
Written in languageJavascript + and Java +
Has subobjectThis property is a special property in this wiki.WebApollo#https://github.com/berkeleybop/jbrowse +, WebApollo#http://code.google.com/p/genomancer +, WebApollo#http://code.google.com/p/apollo-web +, WebApollo#http://code.google.com/p/gbol +, WebApollo#http://genomearchitect.org:8080/WebApolloDemo/ +, WebApollo#http://genomearchitect.org/webapollo/releases/ +, WebApollo + and WebApollo +