Difference between revisions of "Apollo"

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{{ImageCenter|ApolloLogo.png||300|http://gmod.org/wiki/Apollo#Logo|}}
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Apollo documentation, mailing lists, is now actively maintained at [http://genomearchitect.org Genome Architect].
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Source code, releases, and issues can be found on [https://github.com/gmod/apollo/ GitHub].
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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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[http://apollo.berkeleybop.org Apollo Homepage]
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==Demo & Screenshots==
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See [http://apollo.berkeleybop.org/current/images/mainwindow.jpg this screenshot].
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==Requirements==
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JDK 1.5 or higher.
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==Documentation==
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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.
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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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; [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.
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; Apollo tutorials at the [http://www.dynamicgene.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://www.dynamicgene.org/annotation/annotation.html Annotation] - how to use Apollo
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:* [http://www.dynamicgene.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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=== Development / Bug Tracking ===
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* [http://apollo.berkeleybop.org/current/javadoc/ Apollo Javadocs]
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* [http://sourceforge.net/tracker/?atid=462763&group_id=27707&func=browse Apollo bug tracker at Sourceforge]
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== Mailing Lists ==
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{{MailingListsFor|Apollo}}
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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 ==
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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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== Logo ==
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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.linn-benton.edu Linn-Benton Community College].
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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.