Difference between revisions of "Apollo"

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Apollo documentation, mailing lists, is now actively maintained at [http://genomearchitect.org Genome Architect].
  
[[File:ApolloLogo.png|center|400px|alt=Apollo logo]]
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Source code, releases, and issues can be found on [https://github.com/gmod/apollo/ GitHub].
 
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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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*[[Apollo Tutorial]]
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</div>
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==About Apollo==
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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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Visit the [http://apollo.berkeleybop.org/ Apollo website].
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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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* [[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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===Tutorials===
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; [[Apollo Tutorial]]
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: The Apollo session from the [[GMOD Schools|2009 GMOD Summer Schools]].
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; Apollo tutorials at the [http://dynamicgene.dnalc.org Dynamic Gene] web site.
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: 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/annotation/annotation.html Annotation] - how to use Apollo
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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.
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===Presentations===
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* [[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.ppt|Progress Report]] - from [[May 2005 GMOD Meeting]]
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* [[Media:Harris 040527.ppt|Future Plans]] - from [[April 2004 GMOD Meeting]]
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* [[Media:Apollo.GMOD.ppt|Progress Report]] - from [[September 2003 GMOD Meeting]]
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* [[Media:Apollo.GMOD.May2003.ppt|Progress Report]] - from [[May 2003 GMOD Meeting]]
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==Contacts and Mailing Lists==
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{| class="wikitable"
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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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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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==Apollo Development==
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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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==More on Apollo==
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See [[:Category:Apollo]]
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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 />
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[[Category:Annotation]]
 
[[Category:Annotation]]
 
[[Category:Apollo]]
 
[[Category:Apollo]]
[[Category:Webapollo]]
 
[[Category:GMOD Components]]
 
 
[[Category:Java]]
 
[[Category:Java]]
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[[Category:GMOD_Components]]
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[[Category:GMOD_Component]]
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[[Category:WebApollo]]

Latest revision as of 22:45, 16 February 2017

Apollo documentation, mailing lists, is now actively maintained at Genome Architect.

Source code, releases, and issues can be found on GitHub.