Difference between revisions of "Apollo/tool data"
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+ | <noinclude> | ||
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+ | This page stores the data that populates the [[Apollo]] wiki page. | ||
+ | |||
+ | </noinclude> | ||
{{ {{{template}}} | {{ {{{template}}} | ||
| name = Apollo | | name = Apollo | ||
| full_name = | | full_name = | ||
− | | status = | + | | status = mature |
− | | dev = | + | | dev = inactive |
− | | | + | | support = active |
+ | | 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 | + | | 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]. | ||
− | |||
− | |||
− | |||
| dl_url = http://apollo.berkeleybop.org/current/install.html | | dl_url = http://apollo.berkeleybop.org/current/install.html | ||
− | | dl_src = | + | | dl_src = The Apollo source code (only needed if you plan to modify Apollo) is available from {{SF_SVN|apollo|SourceForge}} via [[SVN]]. |
+ | | dl_src_url = https://sourceforge.net/projects/gmod/files/Apollo/ | ||
| dl_dev = | | dl_dev = | ||
+ | | 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. | ||
Line 22: | Line 27: | ||
| 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&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/> | | 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]] | * [[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]]. | | 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]] | ||
Line 31: | Line 34: | ||
* [[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]] | + | ; [[Apollo Tutorial 2011]] |
− | : The Apollo session from the [[GMOD | + | : 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. | ||
− | + | ; [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}} | ||
Line 46: | Line 52: | ||
| dev_ppl = | | dev_ppl = | ||
− | | dev_status = Apollo | + | | 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 = | ||
− | | | + | | input = |
+ | | output = | ||
| see_also = | | see_also = | ||
− | |||
− | |||
| demo_server = | | demo_server = | ||
+ | |release date=2002 | ||
| survey_link = Apollo | | survey_link = Apollo | ||
}} | }} | ||
+ | |||
+ | [[Category:Tool data]] | ||
+ | [[Category:GMOD Components]] | ||
+ | [[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]
| presentations = * Community Annotation at ParameciumDB - Linda Sperling's presentation on ParameciumDB's Community Annotation process at the November 2007 GMOD Meeting.
- Progress Report - from May 2005 GMOD Meeting
- Future Plans - from April 2004 GMOD Meeting
- Progress Report - from September 2003 GMOD Meeting
- 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 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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