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| − | {{Tool data
| + | Apollo documentation is now actively maintained at [http://genomearchitect.org Genome Architect]. |
| − | |name=Apollo
| + | |
| − | |full name=
| + | Source code and issues can be found on [https://github.com/gmod/apollo/ GitHub]. |
| − | |status=mature
| + | |
| − | |dev=inactive
| + | |
| − | |support=active
| + | |
| − | |type=
| + | |
| − | |platform=linux, unix, os x, windows, web, vm, cloud
| + | |
| − | |about=<span style="color:red">'''Please be aware that Berkeley Bioinformatics Open-Source Projects (BBOP) is no longer developing the desktop version of Apollo and that support for its use has been discontinued.'''</span> 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.
| + | |
| − | |open source=Yes
| + | |
| − | |licence=open source
| + | |
| − | |input data type=
| + | |
| − | |input=FASTA, GFF3, BED, BAM, VCF, etc. JBrowse
| + | |
| − | |output=
| + | |
| − | |language=Java, JavaScript
| + | |
| − | |audience=genome annotation
| + | |
| − | |release date=2002
| + | |
| − | |use template=Yes
| + | |
| − | |logo=ApolloLogo.png
| + | |
| − | |screenshot=
| + | |
| − | |contact=
| + | |
| − | |mail={{MailingListsFor|Apollo}}Please submit bug reports to the [http://sourceforge.net/tracker/?atid=462763&group_id=27707&func=browse Apollo bug tracker at Sourceforge].
| + | |
| − | |dl=Apollo executables for several platforms (Windows, Mac OS X, Linux, Solaris and generic Unix) are available from the [http://genomearchitect.org/desktop-apollo Apollo web site].
| + | |
| − | |dl src=The Apollo source code (only needed if you plan to modify Apollo) is available from {{SF_SVN|apollo|SourceForge}} via [[SVN]].
| + | |
| − | |papers=* [[Apollo]]: a community resource for genome annotation editing. <span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rfr_id=info%3Asid%2Focoins.info%3Agenerator&rft.genre=article&rft_id=info%3Apmid%2F19439563">PMID:19439563</span> <ref name=PMID:19439563/>
| + | |
| − | * [[Apollo]]: a sequence annotation editor. <span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rfr_id=info%3Asid%2Focoins.info%3Agenerator&rft.genre=article&rft_id=info%3Apmid%2F12537571">PMID:12537571</span> <ref name=PMID:12537571/> [[Media:Gb-2002-3-12-research0082.pdf|PDF]]
| + | |
| − | |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:Apollo.ppt|Progress Report]] - from [[May 2005 GMOD Meeting]]
| + | |
| − | * [[Media:Harris 040527.ppt|Future Plans]] - from [[April 2004 GMOD Meeting]]
| + | |
| − | * [[Media:Apollo.GMOD.ppt|Progress Report]] - from [[September 2003 GMOD Meeting]]
| + | |
| − | * [[Media:Apollo.GMOD.May2003.ppt|Progress Report]] - from [[May 2003 GMOD Meeting]]
| + | |
| − | |tutorials=; [[Apollo Tutorial 2011]]
| + | |
| − | : The Apollo session from the [[2011 GMOD Spring Training]]
| + | |
| − | ; [[Apollo Tutorial 2010]]
| + | |
| − | : The Apollo session from the [[2010 GMOD Summer School - Americas]].
| + | |
| − | ; 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
| + | |
| − | :* [http://dynamicgene.dnalc.org/annotation/annotation.html Annotation] - how to use Apollo
| + | |
| − | :* [http://dynamicgene.dnalc.org/resources/resources.html Resources] - how to download sample data and install Apollo on an MS Windows system.
| + | |
| − | ; [http://genomearchitect.org/desktop-apollo Apollo user guide]
| + | |
| − | : The current user guide, which has comprehensive instructions for installation and usage of Apollo.
| + | |
| − | |getting started preamble=A comprehensive guide to installing and using Apollo is available from the [http://genomearchitect.org/desktop-apollo Apollo user guide].
| + | |
| − | |req=Apollo requires JDK 1.5 or higher.
| + | |
| − | |install=Installation instructions are available from the [http://genomearchitect.org/desktop-apollo Apollo website].
| + | |
| − | |config=
| + | |
| − | |doc=* [http://genomearchitect.org/desktop-apollo Apollo Javadocs]
| + | |
| − | |dev ppl=
| + | |
| − | |dev ppl=
| + | |
| − | |dl tracking=
| + | |
| − | |logo info=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].
| + | |
| − | |see also=
| + | |
| − | |extra=
| + | |
| − | |survey link=Apollo
| + | |
| − | |contact email=elee@berkeleybop.org
| + | |
| − | |dev status=Active development of Apollo has ceased; the focus has shifted to [[WebApollo]], a web-based version of the tool.
| + | |
| − | }}
| + | |
| | [[Category:Annotation]] | | [[Category:Annotation]] |
| | [[Category:Apollo]] | | [[Category:Apollo]] |
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| | [[Category:GMOD_Component]] | | [[Category:GMOD_Component]] |
| | [[Category:WebApollo]] | | [[Category:WebApollo]] |
| − | {{SemanticLink
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| − | |linkurl=http://genomearchitect.org/desktop-apollo
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| − | |linktitle=
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| − | |linktype=download
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| − | }}
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| − | {{SemanticLink
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| − | |linkurl=https://sourceforge.net/projects/gmod/files/Apollo/
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| − | |linktitle=
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| − | |linktype=source code
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| − | |linkdesc=
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| − | }}
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| − | {{SemanticLink
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| − | |linkurl=http://genomearchitect.org/desktop-apollo
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| − | |linktitle=
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| − | |linktype=website
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