Difference between revisions of "Apollo/tool data"

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This page stores the data that populates the [[Apollo]] wiki page.
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</noinclude>
 
{{ {{{template}}}
 
{{ {{{template}}}
 
| name = Apollo
 
| name = Apollo
 
| full_name =  
 
| full_name =  
| status = Mature release
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| status = mature
| dev = development inactive
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| dev = inactive
| os = mac, win, linux, unix
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| support = active
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| platform = linux, os x, unix, win
 
| logo = ApolloLogo.png
 
| logo = ApolloLogo.png
 
| home = http://apollo.berkeleybop.org/
 
| home = http://apollo.berkeleybop.org/
| about = 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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| about = 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.
 
| screenshot =  
 
| screenshot =  
 
| public_server =  
 
| public_server =  
 
| dl = 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].
 
| dl = 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].
 
The Apollo source code (only needed if you plan to modify Apollo) is available from {{SF_SVN|apollo|SourceForge}} via [[SVN]].
 
 
 
| dl_url = http://apollo.berkeleybop.org/current/install.html
 
| dl_url = http://apollo.berkeleybop.org/current/install.html
| dl_src =  
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| dl_src = The Apollo source code (only needed if you plan to modify Apollo) is available from {{SF_SVN|apollo|SourceForge}} via [[SVN]].
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| dl_src_url = https://sourceforge.net/projects/gmod/files/Apollo/
 
| dl_dev =  
 
| dl_dev =  
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| dl_dev_url =
 
| getting_started_preamble = A comprehensive guide to installing and using Apollo is available from the [http://apollo.berkeleybop.org/current/userguide.html Apollo user guide].
 
| getting_started_preamble = A comprehensive guide to installing and using Apollo is available from the [http://apollo.berkeleybop.org/current/userguide.html Apollo user guide].
 
| req = Apollo requires JDK 1.5 or higher.
 
| req = Apollo requires JDK 1.5 or higher.
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| config =  
 
| config =  
 
| doc = * [http://apollo.berkeleybop.org/current/javadoc/ Apollo Javadocs]
 
| doc = * [http://apollo.berkeleybop.org/current/javadoc/ Apollo Javadocs]
 
 
| papers = * [[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/>
 
| papers = * [[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/>
 
* [[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]]
 
* [[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]]
 
 
| 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]].
 
| 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:Apollo.ppt|Progress Report]] - from [[May 2005 GMOD Meeting]]
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* [[Media:Apollo.GMOD.ppt|Progress Report]] - from [[September 2003 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]]
 
* [[Media:Apollo.GMOD.May2003.ppt|Progress Report]] - from [[May 2003 GMOD Meeting]]
 
+
| tutorials =
| tutorials = ; [[Apollo Tutorial]]
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; [[Apollo Tutorial 2011]]
: The Apollo session from the [[GMOD Schools|2009 GMOD Summer Schools]].
+
: 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.
 
; 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
 
:* [http://dynamicgene.dnalc.org/annotation/annotation.html Annotation] - how to use Apollo
 
:* [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://dynamicgene.dnalc.org/resources/resources.html Resources] - how to download sample data and install Apollo on an MS Windows system.
 
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; [http://apollo.berkeleybop.org/current/userguide.html Apollo user guide]
 +
: The current user guide, which has comprehensive instructions for installation and usage of Apollo.
 
| wild_urls =  
 
| wild_urls =  
 
| mail = {{MailingListsFor|Apollo}}
 
| mail = {{MailingListsFor|Apollo}}
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| dev_ppl =  
 
| dev_ppl =  
| dev_status = 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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| dev_status = Active development of Apollo has ceased; the focus has shifted to [[WebApollo]], a web-based version of the tool.
  
 
| contact_email =  
 
| contact_email =  
| formats =  
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| input =
 +
| output =  
 
| see_also =  
 
| see_also =  
| dl_src_url = https://sourceforge.net/projects/gmod/files/Apollo/
 
| dl_dev_url =
 
 
| demo_server =  
 
| demo_server =  
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|release date=2002
 
| survey_link = Apollo
 
| survey_link = Apollo
 
}}
 
}}
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[[Category:Tool data]]
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[[Category:GMOD Components]]
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[[Category:Apollo]]

Latest revision as of 18:44, 10 September 2013


This page stores the data that populates the Apollo wiki page.


{{ {{{template}}} | name = Apollo | full_name = | status = mature | dev = inactive | support = active | platform = linux, os x, unix, win | logo = ApolloLogo.png | home = http://apollo.berkeleybop.org/ | about = 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. | screenshot = | public_server = | dl = Apollo executables for several platforms (Windows, Mac OS X, Linux, Solaris and generic Unix) are available from the Apollo web site. | dl_url = http://apollo.berkeleybop.org/current/install.html | dl_src = The Apollo source code (only needed if you plan to modify Apollo) is available from SourceForge via SVN. | dl_src_url = https://sourceforge.net/projects/gmod/files/Apollo/ | dl_dev = | dl_dev_url = | getting_started_preamble = A comprehensive guide to installing and using Apollo is available from the Apollo user guide. | req = Apollo requires JDK 1.5 or higher. | install = Installation instructions are available from the Apollo website. | config = | doc = * Apollo Javadocs | papers = * Apollo: a community resource for genome annotation editing. PMID:19439563 [1]

  • Apollo: a sequence annotation editor. PMID:12537571 [2] PDF

| presentations = * Community Annotation at ParameciumDB - Linda Sperling's presentation on ParameciumDB's Community Annotation process at the November 2007 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 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.
Apollo user guide
The current user guide, which has comprehensive instructions for installation and usage of Apollo.

| 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.

Please submit bug reports to the Apollo bug tracker at Sourceforge. | logo_info = 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.

| dev_ppl = | dev_status = Active development of Apollo has ceased; the focus has shifted to WebApollo, a web-based version of the tool.

| contact_email = | input = | output = | see_also = | demo_server = |release date=2002 | survey_link = Apollo }}
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