Difference between revisions of "WebApollo/tool data"

From GMOD
Jump to: navigation, search
m
m
Line 10: Line 10:
 
| 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.
+
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]]
+
*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
+
*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
  
This work is supported by an NIH grant (Lewis R01 GM080203).
 
 
| screenshot =  
 
| screenshot =  
 
| public_server =  
 
| public_server =  
Line 51: Line 62:
 
*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].
 
*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]
 
*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 =  
Line 65: Line 75:
 
| 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://icebox.lbl.gov:8080/WebApolloDemo/ Demo (Bos taurus genome)]

Revision as of 00:52, 9 February 2013

{{ {{{template}}} | name = WebApollo | full_name = | status = mature | dev = active | support = active | type = Community annotation | os_web = y | logo = ApolloLogo.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

| screenshot = | public_server = | dl = | dl_url = http://icebox.lbl.gov/webapollo/releases/ | dl_src = JBrowse client source on github

| dl_src_url = | dl_dev = | dl_dev_url = | getting_started_preamble = | req = | install = Instructions for installation and configuration of WebApollo on a server. | config = | doc =

| papers = | presentations =

| tutorials =

| 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); Rob Buels (UC Berkeley); Chris Childers (University of Missouri); Gregg Helt (LBNL); Ed Lee (LBNL); Monica Munoz-Torres (LBNL); Justin Reese (University of Missouri); 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 = }}