Difference between revisions of "Apollo"

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{{Tool data
 
{{Tool data
 
|name=Apollo
 
|name=Apollo
 +
|full name=
 
|status=mature
 
|status=mature
−
|dev=active
+
|dev=inactive
 
|support=active
 
|support=active
−
|type=Genome annotation, manual sequence annotation
+
|type=
−
|platform=linux, unix, os x, windows
+
|platform=linux, os x, unix, win
 +
|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.
 +
|gmod date=
 +
|release date=2002
 +
|open source=Yes
 +
|licence=
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|language=Java
 +
|input=
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|output=
 +
|audience=
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|logo=ApolloLogo.png
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|screenshot=
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|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 src=The Apollo source code (only needed if you plan to modify Apollo) is available from {{SF_SVN|apollo|SourceForge}} via [[SVN]].
 +
|survey link=Apollo
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|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].
 +
|contact email=elee@berkeleybop.org
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|integration=
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|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]]
 +
|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]]
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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]]
 +
|tutorials=; [[Apollo Tutorial 2011]]
 +
: The Apollo session from the [[2011 GMOD Spring Training]]
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; [[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.
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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.
 +
|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.
 +
|install=Installation instructions are available from the [http://apollo.berkeleybop.org/current/install.html Apollo website].
 +
|config=
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|doc=* [http://apollo.berkeleybop.org/current/javadoc/ Apollo Javadocs]
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|dev ppl=
 +
|dev status=Active development of Apollo has ceased; the focus has shifted to [[WebApollo]], a web-based version of the tool.
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|dl tracking=
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|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=
 
}}
 
}}
 +
{{SemanticLink
 +
|linkurl=http://apollo.berkeleybop.org/current/install.html
 +
|linktype=dl url
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}}
 +
{{SemanticLink
 +
|linkurl=https://sourceforge.net/projects/gmod/files/Apollo/
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|linktype=dl src url
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}}
 +
{{SemanticLink
 +
|linkurl=http://apollo.berkeleybop.org/
 +
|linktype=home
 +
}}
 +
 +
 +
 
<!-- to alter this page, please edit the raw data, which is stored at http://gmod.org/wiki/Apollo/tool_data -->
 
<!-- to alter this page, please edit the raw data, which is stored at http://gmod.org/wiki/Apollo/tool_data -->
  

Revision as of 23:47, 3 October 2013







"win" is not in the list of possible values (web, linux, os x, unix, windows, vm, cloud) for this property.


"win" is not in the list of possible values (web, linux, os x, unix, windows, vm, cloud) for this property.

  • "dl url" is not in the list of possible values (website, download, source code, public server, demo server, wild URL, documentation, publication, social media, other) for this property.
  • "win" is not in the list of possible values (web, linux, os x, unix, windows, vm, cloud) for this property.
  • "dl src url" is not in the list of possible values (website, download, source code, public server, demo server, wild URL, documentation, publication, social media, other) for this property.
  • "dl url" is not in the list of possible values (website, download, source code, public server, demo server, wild URL, documentation, publication, social media, other) for this property.
  • "win" is not in the list of possible values (web, linux, os x, unix, windows, vm, cloud) for this property.
  • "home" is not in the list of possible values (website, download, source code, public server, demo server, wild URL, documentation, publication, social media, other) for this property.
  • "dl src url" is not in the list of possible values (website, download, source code, public server, demo server, wild URL, documentation, publication, social media, other) for this property.
  • "dl url" is not in the list of possible values (website, download, source code, public server, demo server, wild URL, documentation, publication, social media, other) for this property.
  • "win" is not in the list of possible values (web, linux, os x, unix, windows, vm, cloud) for this property.
Apollo logo
Status
  • Mature release
  • Development: inactive
  • Support: active
Resources


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


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 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.

Presentations

Contacts and Mailing Lists

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.


Apollo Development

Current status

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

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

Raw tool data at Apollo/tool data

Retrieved from "http://gmod.org/mediawiki/index.php?title=Apollo&oldid=24619"
Facts about "Apollo"RDF feed
Available on platformlinux +, os x + and unix +
Has URLhttp://apollo.berkeleybop.org/current/install.html +, https://sourceforge.net/projects/gmod/files/Apollo/ + and http://apollo.berkeleybop.org/ +
Has descriptionApollo is a GUI (graphical user interface) … 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.. Apollo is a standalone Java application. +
Has development statusinactive +
Has download URLhttp://apollo.berkeleybop.org/current/install.html +
Has logoApolloLogo.png +
Has software maturity statusmature +
Has support statusactive +
Has topicApollo +
Has websitehttp://apollo.berkeleybop.org/ +
Is open sourceYes +
Release date2002 +
Written in languageJava +
Has subobjectThis property is a special property in this wiki.Apollo#http://apollo.berkeleybop.org/current/install.html +, Apollo#https://sourceforge.net/projects/gmod/files/Apollo/ + and Apollo#http://apollo.berkeleybop.org/ +