Difference between revisions of "WebApollo/tool data"
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| − | WebApollo is a | + | 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. |
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: | 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: | ||
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| dl_url = http://icebox.lbl.gov/webapollo/releases/ | | dl_url = http://icebox.lbl.gov/webapollo/releases/ | ||
| dl_src = | | dl_src = | ||
| − | + | [https://github.com/berkeleybop/jbrowse JBrowse client source on github] | |
* [http://code.google.com/p/apollo-web Annotation editing engine server source code on Google Code] | * [http://code.google.com/p/apollo-web Annotation editing engine server source code on Google Code] | ||
* [http://code.google.com/p/gbol Data model and I/O layer code used by editing engine on Google Code] | * [http://code.google.com/p/gbol Data model and I/O layer code used by editing engine on Google Code] | ||
* [http://code.google.com/p/genomancer Trellis server code on Google Code] | * [http://code.google.com/p/genomancer Trellis server code on Google Code] | ||
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| dl_src_url = | | dl_src_url = | ||
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| dl_dev_url = | | dl_dev_url = | ||
| getting_started_preamble = | | getting_started_preamble = | ||
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| req = | | req = | ||
| install = | | install = | ||
| + | Instructions for [[WebApollo_Installation|installation and configuration]] of WebApollo on a server. | ||
| config = | | config = | ||
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| doc = | | doc = | ||
| − | + | * [[Media: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] | ||
Revision as of 00:45, 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 sequence annotation application for distributed community annotation. It provides similar functionality to Apollo in a client-server web-based environment.
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:
- a web-browser-based version of Apollo built on top of JBrowse
- full support for two-way client-server exchange of genome annotations
- an annotation tracking system designed to support collaborative genome research projects
This work is supported by an NIH grant (Lewis R01 GM080203). | screenshot = | public_server = | dl = | dl_url = http://icebox.lbl.gov/webapollo/releases/ | dl_src = 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
| 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 =
- WebApollo: A Web-based Sequence Annotation Editor for Distributed Community Annotation (poster) at PAG 2013, Jan 2013. Download the poster
- WebApollo demo, i5K Community Workshop & Arthropod Genomics Symposium, June 2012. Tutorial; Poster
- WebApollo: A Web-Based Sequence Annotation Editor for Distributed Community Annotation, Biocuration 2012, April 2012. Biocuration abstract
- PAG (Plant and Animal Genome) conference, Jan 2012.
- WebApollo demo/tutorial, Entomological Society of America, Nov 2011. Flyer for tutorial
- Manual Curation of Automated Gene Models, Workshop on Manual Annotation, Purdue University, Aug 2011. Slides
- Talk: Biocuration, Best Practices, Next-gen sequencing: Data acquisition, comparative genomics, design and analysis for population genetics, systematics and development (Course, National Evolutionary Synthesis Center (NESCent)), Aug 2011. T: Slides; T: Audio.
- Workshop: Manual Curation of Automated Gene Models, Next-gen sequencing: Data acquisition, comparative genomics, design and analysis for population genetics, systematics and development (NESCent course), Aug 2011. W: Slides; W: Audio.
- WebApollo: A web-based sequence annotation editor for community annotation, Bioinformatics Open Source Conference (BOSC) 2011, July 2011. Abstract; Slides
| tutorials =
- WebApollo Tutorial for the 2012 GMOD Summer School - uses a prerelease version of WebApollo
| 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 = | output = | see_also = | demo_server = *Demo (Bos taurus genome) | survey_link = }}
