Difference between revisions of "WebApollo/tool data"

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| support = active
 
| support = active
 
| type = Community annotation
 
| type = Community annotation
| os_web = y
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| platform = web
| logo = ApolloLogo.png
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| logo = WebApolloLogo.png
 
| home =  
 
| home =  
 
| about =  
 
| about =  
WebApollo is a browser-based sequence annotation application for distributed community annotation. It provides similar functionality to [[Apollo]] in a client-server web-based environment.
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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.
  
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:
+
The features of WebApollo include:
# a web-browser-based version of Apollo built on top of [[JBrowse]]
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*History tracking, including browsing of an annotation's edit history and full undo/redo functions
# full support for two-way client-server exchange of genome annotations  
+
*Real time updating: edits in one client are instantly pushed to all other clients
# an annotation tracking system designed to support collaborative genome research projects
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*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 http://genomearchitect.org/WebApolloDemo] (''Bos taurus'' genome).
  
This work is supported by an NIH grant (Lewis R01 GM080203).
 
 
| screenshot =  
 
| screenshot =  
 
| public_server =  
 
| public_server =  
 
| dl = <!-- text about where to download a tool -->
 
| dl = <!-- text about where to download a tool -->
| dl_url = http://icebox.lbl.gov/webapollo/releases/
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| dl_url = http://genomearchitect.org/webapollo/releases/
 
| dl_src =  
 
| dl_src =  
 
[https://github.com/berkeleybop/jbrowse JBrowse client source on github]
 
[https://github.com/berkeleybop/jbrowse JBrowse client source on github]
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| req =  
 
| req =  
 
| install =  
 
| install =  
Instructions for [[WebApollo_Installation|installation and configuration]] of WebApollo on a server.
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* [[WebApollo_Installation|Server installation guide]]
 
| config =  
 
| config =  
 
| doc =  
 
| doc =  
* [[Media:WebApollo User Guide.pdf | WebApollo User Guide (PDF)]]
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* [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]
  
 
| papers =  
 
| papers =  
| presentations =  
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| presentations = {{WebApolloPresentations}} <!-- edit Template:WebApolloPresentations -->
*WebApollo: A Web-based Sequence Annotation Editor for Distributed Community Annotation (poster) at [http://www.intlpag.org/2013/ PAG 2013], Jan 2013. [[Media:WebApollo PAG 2013 Poster.pdf | Download the poster]]
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*WebApollo demo, [http://www.k-state.edu/agc/symp2012/ i5K Community Workshop & Arthropod Genomics Symposium], June 2012. [[Media:WebApollo_Demo_i5K-AGS_2012.pdf | Tutorial]]; [[Media:WebApollo Arthropod Genomics 2012 poster.pdf | Poster]]
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*WebApollo: A Web-Based Sequence Annotation Editor for Distributed Community Annotation, [http://pir.georgetown.edu/biocuration2012/ Biocuration 2012], April 2012. [[Media:biocuration-abstract-v1-shortened.pdf | Biocuration abstract]]
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*[http://www.intl-pag.org/ PAG (Plant and Animal Genome) conference], Jan 2012.
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*WebApollo demo/tutorial, [http://www.entsoc.org/entomology2011 Entomological Society of America], Nov 2011. [[Media:WebApollo_at_ESA_Flyer.pdf | Flyer for tutorial]]
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*Manual Curation of Automated Gene Models, Workshop on Manual Annotation, Purdue University, Aug 2011. [[Media:NGS_workshop_annotation_AP-&-MMT.pdf | Slides]]
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*Talk: ''Biocuration, Best Practices'', [http://academy.nescent.org/wiki/Next-gen_sequencing Next-gen sequencing: Data acquisition, comparative genomics, design and analysis for population genetics, systematics and development (Course, National Evolutionary Synthesis Center (NESCent))], Aug 2011. [[Media:NESCent-NGS-Biocuration-MMT.pdf | T: Slides]]; [http://academy.nescent.org/wg/academy/images/7/76/Moni1.mp3 T: Audio].
+
*Workshop: ''Manual Curation of Automated Gene Models'', [http://academy.nescent.org/wiki/Next-gen_sequencing Next-gen sequencing: Data acquisition, comparative genomics, design and analysis for population genetics, systematics and development (NESCent course)], Aug 2011. [[Media:NGS_workshop_annotation_AP-&-MMT.pdf | W: Slides]]; [http://academy.nescent.org/wg/academy/images/e/e5/Moni2.mp3 W: Audio].
+
*WebApollo: A web-based sequence annotation editor for community annotation, [http://www.open-bio.org/wiki/BOSC_2011 Bioinformatics Open Source Conference (BOSC) 2011], July 2011. [[Media:BOSC2011-abstract.pdf | Abstract]]; [http://www.slideshare.net/bosc2011/webapollo-bosc2011 Slides]
+
 
+
 
+
 
| tutorials =  
 
| tutorials =  
*[[WebApollo Tutorial 2012 | WebApollo Tutorial for the 2012 GMOD Summer School]] - uses a prerelease version of WebApollo
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;[[WebApollo Tutorial]]
 +
:taught as part of the [[2013 GMOD Summer School]]
 
| wild_urls =  
 
| wild_urls =  
 
| mail = {{MailingListsFor|Apollo}}
 
| mail = {{MailingListsFor|Apollo}}
Line 61: Line 64:
 
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.
 
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.
  
The personnel involved in WebApollo are: Suzanna Lewis (PI, LBNL); Ian Holmes (PI, UC Berkeley); Chris Elsik (PI, University of Missouri); Rob Buels (UC Berkeley); [[User:Childers|Chris Childers]] (University of Missouri); [[User:GreggHelt2|Gregg Helt]] (LBNL); [[User:Elee|Ed Lee]] (LBNL); [[User:Moni|Monica Munoz-Torres]] (LBNL); [[User:Justaddcoffee|Justin Reese]] (University of Missouri); [[User:MitchSkinner|Mitch Skinner]] (UC Berkeley) (Emeritus - developed first version of JBrowse); and Nomi Harris (LBNL) (Emeritus).
+
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).
  
 
| dev_status = <!-- what's going on, development-wise -->
 
| dev_status = <!-- what's going on, development-wise -->
 
| contact_email = elee@berkeleybop.org
 
| contact_email = elee@berkeleybop.org
| input = <!-- input formats -->
+
| input = GFF3, BigWig, BAM
| output = <!-- output formats -->
+
| output = GFF3, others
 
| see_also =  
 
| see_also =  
| demo_server = *[http://icebox.lbl.gov:8080/WebApolloDemo/ Demo (Bos taurus genome)]
+
| demo_server = *[http://genomearchitect.org:8080/WebApolloDemo/ Demo (Bos taurus genome)]
| survey_link =  
+
| survey_link =
 +
|release date=2012
 +
| extras =
 +
{{GitcComponent}}
 
}}
 
}}
  

Latest revision as of 20:34, 15 October 2013

{{ {{{template}}} | name = WebApollo | full_name = | status = mature | dev = active | support = active | type = Community annotation | platform = web | logo = WebApolloLogo.png | home = | about = 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).

| screenshot = | public_server = | dl = | dl_url = http://genomearchitect.org/webapollo/releases/ | dl_src = JBrowse client source on github

| dl_src_url = | dl_dev = | dl_dev_url = | getting_started_preamble = | req = | install =

| config = | doc =

| papers = | 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

| tutorials =

WebApollo Tutorial
taught as part of the 2013 GMOD Summer School

| wild_urls = | mail =

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.

| logo_info = 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. | dev_ppl = 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).

| dev_status = | contact_email = elee@berkeleybop.org | input = GFF3, BigWig, BAM | output = GFF3, others | see_also = | demo_server = *Demo (Bos taurus genome) | survey_link = |release date=2012 | extras =

Included in

Cloud component

}}