Difference between revisions of "Apollo"

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[[File:ApolloLogo.png|center|400px|alt=Apollo logo]]
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The Apollo genome editor is a Java-based application for browsing and annotating genomic sequences. There are currently two branches of Apollo, one primarily used for genome browsing and maintained at [http://www.ensembl.org Ensembl], and the other primarily used for genome annotation and maintained at the [http://berkeleybop.org/ Berkeley Bioinformatics and Open Source Projects]. The latter is part of the GMOD project. [[WebApollo]] is intended as a successor to Apollo, and is currently under development.
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<div class="componentBox">
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<div class="compBoxHdr">Status</div>
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*Mature release
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*development inactive
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*active support
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<div class="compBoxHdr">Resources</div>
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*[http://apollo.berkeleybop.org/ Home page]
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*[http://apollo.berkeleybop.org/current/install.html Download]
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*[http://gmod.org/extras/2008GMODCommunitySurvey.html#Apollo 2008 Survey]
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<div class="compBoxHdr">Events</div>
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{{SchoolBoxItem|Apollo}}
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[http://apollo.berkeleybop.org Apollo Homepage]
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==About Apollo==
  
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==Demo & Screenshots==
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Apollo is a GUI [graphical user interface]-based tool for editing genome annotations. Like [[GBrowse]], Apollo allows users to scroll and zoom in on areas of interest in a sequence; authorized users can edit annotations and write the changes back to the underlying database. Apollo can run off [[GFF3]] or a [[Chado]] database, and it can also integrate with remote services, such as BLAST and Primer BLAST analyses. Apollo is a standalone Java application.
  
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See [http://apollo.berkeleybop.org/current/images/mainwindow.jpg this screenshot].
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Visit the [http://apollo.berkeleybop.org/ Apollo website].
  
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==Requirements==
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==Downloads==
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Download Apollo: [http://apollo.berkeleybop.org/current/install.html http://apollo.berkeleybop.org/current/install.html]
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The source code for Apollo can be downloaded from https://sourceforge.net/projects/gmod/files/Apollo/.
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==Using Apollo==
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A comprehensive guide to installing and using Apollo is available from the [http://apollo.berkeleybop.org/current/userguide.html Apollo user guide].
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===System Requirements===
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Apollo requires JDK 1.5 or higher.
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===Installation===
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Installation instructions are available from the [http://apollo.berkeleybop.org/current/install.html Apollo website].
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===Documentation===
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* [http://apollo.berkeleybop.org/current/javadoc/ Apollo Javadocs]
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==Publications, Tutorials, and Presentations==
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===Publications on or mentioning Apollo===
  
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JDK 1.5 or higher.
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* [[Apollo]]: a community resource for genome annotation editing. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F19439563">PMID:19439563</span> <ref name=PMID:19439563/>
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* [[Apollo]]: a sequence annotation editor. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F12537571">PMID:12537571</span> <ref name=PMID:12537571/> [[Media:Gb-2002-3-12-research0082.pdf|PDF]]
  
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==Documentation==
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===Tutorials===
  
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; [http://apollo.berkeleybop.org/current/userguide.html Apollo user guide]
 
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: A comprehensive guide to installing and using Apollo.
 
 
; [[Apollo Tutorial]]
 
; [[Apollo Tutorial]]
 
: The Apollo session from the [[GMOD Schools|2009 GMOD Summer Schools]].
 
: The Apollo session from the [[GMOD Schools|2009 GMOD Summer Schools]].
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; [http://www.ncbi.nlm.nih.gov/pubmed/19439563 Apollo: a community resource for genome annotation editing.]
 
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: 2009 Apollo paper
 
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; [[:Image:Gb-2002-3-12-research0082.pdf|Apollo: a sequence annotation editor]]
 
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: The original 2002 Apollo publication.
 
 
; Apollo tutorials at the [http://dynamicgene.dnalc.org Dynamic Gene] web site.
 
; Apollo tutorials at the [http://dynamicgene.dnalc.org Dynamic Gene] web site.
 
: Flash based tutorials on how to use Apollo, using rice as an example.  Sections of particular interest are
 
: Flash based tutorials on how to use Apollo, using rice as an example.  Sections of particular interest are
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:* [http://dynamicgene.dnalc.org/resources/resources.html Resources] - how to download sample data and install Apollo on an MS Windows system.
 
:* [http://dynamicgene.dnalc.org/resources/resources.html Resources] - how to download sample data and install Apollo on an MS Windows system.
  
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=== Presentations ===
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===Presentations===
  
 
* [[Media:CommunityAnnotationNov2007.pdf|Community Annotation at ParameciumDB]] - [[User:Sperling|Linda Sperling's]] presentation on [[ParameciumDB|ParameciumDB's]] [[:Category:Community Annotation|Community Annotation]] process at the [[November 2007 GMOD Meeting]].
 
* [[Media:CommunityAnnotationNov2007.pdf|Community Annotation at ParameciumDB]] - [[User:Sperling|Linda Sperling's]] presentation on [[ParameciumDB|ParameciumDB's]] [[:Category:Community Annotation|Community Annotation]] process at the [[November 2007 GMOD Meeting]].
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* [[Media:Apollo.GMOD.May2003.ppt|Progress Report]] - from [[May 2003 GMOD Meeting]]
 
* [[Media:Apollo.GMOD.May2003.ppt|Progress Report]] - from [[May 2003 GMOD Meeting]]
  
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=== Development / Bug Tracking ===
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==Contacts and Mailing Lists==
  
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* [http://apollo.berkeleybop.org/current/javadoc/ Apollo Javadocs]
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{| class="wikitable"
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* [http://sourceforge.net/tracker/?atid=462763&group_id=27707&func=browse Apollo bug tracker at Sourceforge]
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|
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! Mailing List Link
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! Description
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! Archive(s)
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[[:Template:MailingListsApollo]]
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|}
  
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== Mailing Lists ==
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Please submit bug reports to the [http://sourceforge.net/tracker/?atid=462763&group_id=27707&func=browse Apollo bug tracker at Sourceforge].
  
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{{MailingListsFor|Apollo}}
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==Apollo Development==
  
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==Downloads==
 
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Apollo executables for several platforms (Windows, Mac Os X, Linux, Solaris and generic Unix) are available from the [http://apollo.berkeleybop.org/current/index.html Apollo web site].
 
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The Apollo source code (which you need only if you want to modify Apollo) is available from {{SF_SVN|apollo|SourceForge}} via [[SVN]].
 
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==Users==
 
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Off the top of the heads of the attendees of the [[November 2007 GMOD Meeting]]. Sorted by version.
 
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* Triggers
 
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** VMWare
 
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** Dolan-Rice
 
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* Crabtree
 
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** Paramecium
 
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** INRA
 
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** SFSU (Smith)
 
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* cXML
 
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** FlyBase
 
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** BovineBase
 
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** VectorBase
 
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== Current Development ==
 
 
Apollo's functionality is being migrated to the Web as an extension to [[JBrowse]]. For further information please see the [[WebApollo]] pages.
 
Apollo's functionality is being migrated to the Web as an extension to [[JBrowse]]. For further information please see the [[WebApollo]] pages.
  
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== Logo ==
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==More on Apollo==
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See [[:Category:Apollo]]
  
 
The [[:Image:ApolloLogo.png|Apollo logo]] was created by [mailto:audra.radke@gmail.com Audra Radke], a participant in the [[Spring 2010 Logo Program]], while a design student at [http://www.linnbenton.edu Linn-Benton Community College].
 
The [[:Image:ApolloLogo.png|Apollo logo]] was created by [mailto:audra.radke@gmail.com Audra Radke], a participant in the [[Spring 2010 Logo Program]], while a design student at [http://www.linnbenton.edu Linn-Benton Community College].
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<references />
  
 
[[Category:Annotation]]
 
[[Category:Annotation]]

Revision as of 16:22, 24 August 2012

__NOTITLE__

Apollo logo
Status
  • Mature release
  • development inactive
  • active support
Resources
Events

2012 GMOD Summer School

About Apollo

Apollo is a GUI [graphical user interface]-based tool for editing genome annotations. Like GBrowse, Apollo allows users to scroll and zoom in on areas of interest in a sequence; authorized users can edit annotations and write the changes back to the underlying database. Apollo can run off GFF3 or a Chado database, and it can also integrate with remote services, such as BLAST and Primer BLAST analyses. Apollo is a standalone Java application.

Visit the Apollo website.

Downloads

Download Apollo: http://apollo.berkeleybop.org/current/install.html

The source code for Apollo can be downloaded from https://sourceforge.net/projects/gmod/files/Apollo/.

Using Apollo

A comprehensive guide to installing and using Apollo is available from the Apollo user guide.

System Requirements

Apollo requires JDK 1.5 or higher.

Installation

Installation instructions are available from the Apollo website.

Documentation

Publications, Tutorials, and Presentations

Publications on or mentioning Apollo

  • Apollo: a community resource for genome annotation editing. PMID:19439563 [1]
  • Apollo: a sequence annotation editor. PMID:12537571 [2] PDF

Tutorials

Apollo Tutorial
The Apollo session from the 2009 GMOD Summer Schools.
Apollo tutorials at the Dynamic Gene web site.
Flash based tutorials on how to use Apollo, using rice as an example. Sections of particular interest are
  • Annotation - how to use Apollo
  • Resources - how to download sample data and install Apollo on an MS Windows system.

Presentations

Contacts and Mailing Lists

Mailing List Link Description Archive(s)

Template:MailingListsApollo

Please submit bug reports to the Apollo bug tracker at Sourceforge.

Apollo Development

Apollo's functionality is being migrated to the Web as an extension to JBrowse. For further information please see the WebApollo pages.

More on Apollo

See Category:Apollo

The Apollo logo was created by Audra Radke, a participant in the Spring 2010 Logo Program, while a design student at Linn-Benton Community College.

  1. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:19439563
  2. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:12537571
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