From 3bee9f86ec9845fd17e329eddb9f03338f97fede Mon Sep 17 00:00:00 2001 From: Scott Cain Date: Fri, 19 Jul 2024 15:20:28 -0700 Subject: [PATCH 1/2] removing some gmod.org/mediawiki links --- wiki/AGS2011.md | 2 +- wiki/Apollo_Tutorial.md | 2 +- wiki/Artemis_Tutorial.md | 2 +- wiki/BioMart_Tutorial_2011.md | 2 +- wiki/Box.md | 2 +- .../Using_a_Database_With_JBrowse.md | 14 +- wiki/CVS.md | 2 +- wiki/Category%3ANews_Items.md | 4 +- wiki/Chado.md | 2 +- wiki/Chado_Natural_Diversity.md | 2 +- wiki/Chado_Tutorial.md | 2 +- wiki/Common_Download_URL.md | 2 +- wiki/Common_url.md | 2 +- wiki/DAS.md | 2 +- wiki/Ergatis.md | 2 +- wiki/GBrowse_2.0_Configuration_HOWTO.md | 2 +- wiki/GBrowse_2_Configuration_HOWTO.md | 2 +- wiki/GBrowse_Balloon_Tips.md | 2 +- .../GBrowse_Configuration_HOWTO/bullets2h3.md | 2 +- wiki/GBrowse_Linux_HOWTO.md | 2 +- wiki/GBrowse_syn_Tutorial.md | 2 +- wiki/GFF_Tutorial.md | 2 +- wiki/GMOD%3AAbout.md | 2 +- wiki/GMOD.md | 2 +- wiki/GMOD_REST_API.md | 2 +- wiki/GMOD_Summer_School.md | 2 +- ...MOD_Summer_School_Statement_of_Interest.md | 2 +- wiki/Galaxy_Tutorial.md | 2 +- wiki/Generic_Genome_Browser.md | 2 +- wiki/Genome.md | 2 +- wiki/Gmod_dbsf.md | 2 +- wiki/JBrowseDev/Current/Usage/ConfigFiles.md | 2 +- wiki/JBrowseDev/General_Usage.md | 2 +- wiki/JBrowseDev/Installation.md | 111 +------ wiki/JBrowseDev/Main.md | 4 +- wiki/JBrowseDev/Upcoming.md | 2 +- .../Using_Configuration_Files_With_JBrowse.md | 2 +- .../Using_a_Database_With_JBrowse.md | 2 +- wiki/JBrowse_Tutorial.md | 2 +- wiki/JBrowse_Tutorial_2012.md | 2 +- .../January_2010_GMOD_Meeting_Registration.md | 2 +- wiki/July_2008_GMOD_Meeting_Registration.md | 2 +- wiki/MAKER_Tutorial.md | 2 +- wiki/Mailing_Lists.md | 2 +- wiki/Mailing_list.md | 2 +- wiki/NGS.md | 2 +- wiki/Next_generation_sequencing.md | 2 +- wiki/PAG.md | 2 +- wiki/Plugin.md | 2 +- wiki/Plugins.md | 2 +- wiki/Postgres.md | 2 +- wiki/Property%3AHas_topic.md | 4 +- wiki/Property%3ALinktitle.md | 4 +- wiki/Property%3ALinktype.md | 4 +- wiki/Regionview_panel.md | 2 +- wiki/SOBA_Tutorial.md | 2 +- wiki/SVN.md | 2 +- wiki/Subversion.md | 2 +- wiki/Synteny.md | 2 +- wiki/TableEdit/IFALT.md | 2 +- wiki/Table_Editor.md | 2 +- wiki/Talk%3AGBrowse_Configuration_HOWTO.md | 2 +- wiki/Tripal_Tutorial.md | 2 +- wiki/User%3ARBuels.md | 2 +- wiki/Using_Existing_Databases_With_JBrowse.md | 303 ++++++------------ wiki/WebApollo_Tutorial.md | 2 +- 66 files changed, 178 insertions(+), 386 deletions(-) diff --git a/wiki/AGS2011.md b/wiki/AGS2011.md index ac15280e65..950870dd1b 100644 --- a/wiki/AGS2011.md +++ b/wiki/AGS2011.md @@ -14,7 +14,7 @@ (Redirected from -[AGS2011](http://gmod.org/mediawiki/index.php?title=AGS2011&redirect=no "AGS2011")) +[AGS2011](AGS2011) diff --git a/wiki/Apollo_Tutorial.md b/wiki/Apollo_Tutorial.md index b45310b7a6..a796f1b20e 100644 --- a/wiki/Apollo_Tutorial.md +++ b/wiki/Apollo_Tutorial.md @@ -14,7 +14,7 @@ (Redirected from [Apollo -Tutorial](http://gmod.org/mediawiki/index.php?title=Apollo_Tutorial&redirect=no "Apollo Tutorial")) +Tutorial](Apollo_Tutorial) diff --git a/wiki/Artemis_Tutorial.md b/wiki/Artemis_Tutorial.md index 6183b30174..28fe37a5a1 100644 --- a/wiki/Artemis_Tutorial.md +++ b/wiki/Artemis_Tutorial.md @@ -14,7 +14,7 @@ (Redirected from [Artemis -Tutorial](http://gmod.org/mediawiki/index.php?title=Artemis_Tutorial&redirect=no "Artemis Tutorial")) +Tutorial](Artemis_Tutorial) diff --git a/wiki/BioMart_Tutorial_2011.md b/wiki/BioMart_Tutorial_2011.md index d505c15d9a..8502ef1334 100644 --- a/wiki/BioMart_Tutorial_2011.md +++ b/wiki/BioMart_Tutorial_2011.md @@ -14,7 +14,7 @@ (Redirected from [BioMart Tutorial -2011](http://gmod.org/mediawiki/index.php?title=BioMart_Tutorial_2011&redirect=no "BioMart Tutorial 2011")) +2011](BioMart_Tutorial_2011) diff --git a/wiki/Box.md b/wiki/Box.md index 1920e55c2a..8b9761019d 100644 --- a/wiki/Box.md +++ b/wiki/Box.md @@ -14,7 +14,7 @@ (Redirected from -[Box](http://gmod.org/mediawiki/index.php?title=Box&redirect=no "Box")) +[Box](Box) diff --git a/wiki/BrowseDev/Using_a_Database_With_JBrowse.md b/wiki/BrowseDev/Using_a_Database_With_JBrowse.md index 8548f95d72..f9f227c979 100644 --- a/wiki/BrowseDev/Using_a_Database_With_JBrowse.md +++ b/wiki/BrowseDev/Using_a_Database_With_JBrowse.md @@ -2,21 +2,16 @@ - -# JBrowse Configuration Guide +# JBrowse Configuration Guide -(Redirected from [BrowseDev/Using a Database With -JBrowse](http://gmod.org/mediawiki/index.php?title=BrowseDev/Using_a_Database_With_JBrowse&redirect=no "BrowseDev/Using a Database With JBrowse")) - - @@ -41,12 +36,9 @@ want to do with your JBrowse. Check out the new [JBrowse FAQ](../JBrowse_FAQ "JBrowse FAQ") page for more tips on setup and configuration -http://gmod.org/wiki/JBrowse_FAQ Also see the [JBrowse Desktop](../JBrowse_Desktop "JBrowse Desktop") -guide here http://gmod.org/wiki/JBrowse_Desktop +guide here @@ -1447,7 +1439,7 @@ make it higher resolution Retrieved from -"[http://gmod.org/mediawiki/index.php?title=JBrowse_Configuration_Guide&oldid=27898#Using_JBrowse_with_Existing_Databases](http://gmod.org/mediawiki/index.php?title=JBrowse_Configuration_Guide&oldid=27898#Using_JBrowse_with_Existing_Databases#Using_JBrowse_with_Existing_Databases)" +"[http://gmod.org/mediawiki/index.php?title=JBrowse_Configuration_Guide&oldid=27898#Using_JBrowse_with_Existing_Databases](JBrowse_Configuration_Guide" diff --git a/wiki/CVS.md b/wiki/CVS.md index 116bdbb557..d0d69c9269 100644 --- a/wiki/CVS.md +++ b/wiki/CVS.md @@ -14,7 +14,7 @@ (Redirected from -[CVS](http://gmod.org/mediawiki/index.php?title=CVS&redirect=no "CVS")) +[CVS](CVS) diff --git a/wiki/Category%3ANews_Items.md b/wiki/Category%3ANews_Items.md index ab1b7bc36f..3cabf31081 100644 --- a/wiki/Category%3ANews_Items.md +++ b/wiki/Category%3ANews_Items.md @@ -32,7 +32,7 @@ Item](GMOD_News#Adding_a_News_Item "GMOD News") for details. The following 200 pages are in this category, out of 332 total. (previous 200) ([next -200](http://gmod.org/mediawiki/index.php?title=Category%253ANews_Items&pagefrom=News%2FJBrowse+1.10.0+released#mw-pages#mw-pages "Category%253ANews Items")) +200](Category%253ANews_Items) @@ -589,7 +589,7 @@ title="News/JBrowse 1.1 Released">News/JBrowse 1.1 Released (previous 200) ([next -200](http://gmod.org/mediawiki/index.php?title=Category%253ANews_Items&pagefrom=News%2FJBrowse+1.10.0+released#mw-pages#mw-pages "Category%253ANews Items")) +200](Category%253ANews_Items) diff --git a/wiki/Chado.md b/wiki/Chado.md index 4094a7ed91..05aefbd25b 100644 --- a/wiki/Chado.md +++ b/wiki/Chado.md @@ -14,7 +14,7 @@ (Redirected from -[Chado](http://gmod.org/mediawiki/index.php?title=Chado&redirect=no "Chado")) +[Chado](Chado) diff --git a/wiki/Chado_Natural_Diversity.md b/wiki/Chado_Natural_Diversity.md index 0f3b5cab65..f4770cc5f6 100644 --- a/wiki/Chado_Natural_Diversity.md +++ b/wiki/Chado_Natural_Diversity.md @@ -14,7 +14,7 @@ (Redirected from [Chado Natural -Diversity](http://gmod.org/mediawiki/index.php?title=Chado_Natural_Diversity&redirect=no "Chado Natural Diversity")) +Diversity](Chado_Natural_Diversity) diff --git a/wiki/Chado_Tutorial.md b/wiki/Chado_Tutorial.md index b3d0d619cf..36a04e5634 100644 --- a/wiki/Chado_Tutorial.md +++ b/wiki/Chado_Tutorial.md @@ -14,7 +14,7 @@ (Redirected from [Chado -Tutorial](http://gmod.org/mediawiki/index.php?title=Chado_Tutorial&redirect=no "Chado Tutorial")) +Tutorial](Chado_Tutorial) diff --git a/wiki/Common_Download_URL.md b/wiki/Common_Download_URL.md index c6fad1a5bd..dea36528b3 100644 --- a/wiki/Common_Download_URL.md +++ b/wiki/Common_Download_URL.md @@ -14,7 +14,7 @@ (Redirected from [Common Download -URL](http://gmod.org/mediawiki/index.php?title=Common_Download_URL&redirect=no "Common Download URL")) +URL](Common_Download_URL) diff --git a/wiki/Common_url.md b/wiki/Common_url.md index 9ee153234c..db5d0fb556 100644 --- a/wiki/Common_url.md +++ b/wiki/Common_url.md @@ -14,7 +14,7 @@ (Redirected from [Common -url](http://gmod.org/mediawiki/index.php?title=Common_url&redirect=no "Common url")) +url](Common_url) diff --git a/wiki/DAS.md b/wiki/DAS.md index e00a200e61..8d4cb4fbcf 100644 --- a/wiki/DAS.md +++ b/wiki/DAS.md @@ -14,7 +14,7 @@ (Redirected from -[DAS](http://gmod.org/mediawiki/index.php?title=DAS&redirect=no "DAS")) +[DAS](DAS) diff --git a/wiki/Ergatis.md b/wiki/Ergatis.md index bc94dfb3dc..d89207c371 100644 --- a/wiki/Ergatis.md +++ b/wiki/Ergatis.md @@ -14,7 +14,7 @@ (Redirected from -[Ergatis](http://gmod.org/mediawiki/index.php?title=Ergatis&redirect=no "Ergatis")) +[Ergatis](Ergatis) diff --git a/wiki/GBrowse_2.0_Configuration_HOWTO.md b/wiki/GBrowse_2.0_Configuration_HOWTO.md index 9355554d51..3d51f33751 100644 --- a/wiki/GBrowse_2.0_Configuration_HOWTO.md +++ b/wiki/GBrowse_2.0_Configuration_HOWTO.md @@ -14,7 +14,7 @@ (Redirected from [GBrowse 2.0 Configuration -HOWTO](http://gmod.org/mediawiki/index.php?title=GBrowse_2.0_Configuration_HOWTO&redirect=no "GBrowse 2.0 Configuration HOWTO")) +HOWTO](GBrowse_2.0_Configuration_HOWTO) diff --git a/wiki/GBrowse_2_Configuration_HOWTO.md b/wiki/GBrowse_2_Configuration_HOWTO.md index 935567194a..8821d5141a 100644 --- a/wiki/GBrowse_2_Configuration_HOWTO.md +++ b/wiki/GBrowse_2_Configuration_HOWTO.md @@ -14,7 +14,7 @@ (Redirected from [GBrowse 2 Configuration -HOWTO](http://gmod.org/mediawiki/index.php?title=GBrowse_2_Configuration_HOWTO&redirect=no "GBrowse 2 Configuration HOWTO")) +HOWTO](GBrowse_2_Configuration_HOWTO) diff --git a/wiki/GBrowse_Balloon_Tips.md b/wiki/GBrowse_Balloon_Tips.md index e9aac87efa..dbf8ae2313 100644 --- a/wiki/GBrowse_Balloon_Tips.md +++ b/wiki/GBrowse_Balloon_Tips.md @@ -14,7 +14,7 @@ (Redirected from [GBrowse Balloon -Tips](http://gmod.org/mediawiki/index.php?title=GBrowse_Balloon_Tips&redirect=no "GBrowse Balloon Tips")) +Tips](GBrowse_Balloon_Tips) diff --git a/wiki/GBrowse_Configuration_HOWTO/bullets2h3.md b/wiki/GBrowse_Configuration_HOWTO/bullets2h3.md index cf2ef26297..d9dd479d09 100644 --- a/wiki/GBrowse_Configuration_HOWTO/bullets2h3.md +++ b/wiki/GBrowse_Configuration_HOWTO/bullets2h3.md @@ -14,7 +14,7 @@ (Redirected from [GBrowse Configuration -HOWTO/bullets2h3](http://gmod.org/mediawiki/index.php?title=GBrowse_Configuration_HOWTO/bullets2h3&redirect=no "GBrowse Configuration HOWTO/bullets2h3")) +HOWTO/bullets2h3](GBrowse_Configuration_HOWTO/bullets2h3) diff --git a/wiki/GBrowse_Linux_HOWTO.md b/wiki/GBrowse_Linux_HOWTO.md index 6d82e471bc..7cebc7abc8 100644 --- a/wiki/GBrowse_Linux_HOWTO.md +++ b/wiki/GBrowse_Linux_HOWTO.md @@ -14,7 +14,7 @@ (Redirected from [GBrowse Linux -HOWTO](http://gmod.org/mediawiki/index.php?title=GBrowse_Linux_HOWTO&redirect=no "GBrowse Linux HOWTO")) +HOWTO](GBrowse_Linux_HOWTO) diff --git a/wiki/GBrowse_syn_Tutorial.md b/wiki/GBrowse_syn_Tutorial.md index f5e91a4f9d..e00fbf84e4 100644 --- a/wiki/GBrowse_syn_Tutorial.md +++ b/wiki/GBrowse_syn_Tutorial.md @@ -14,7 +14,7 @@ (Redirected from [GBrowse syn -Tutorial](http://gmod.org/mediawiki/index.php?title=GBrowse_syn_Tutorial&redirect=no "GBrowse syn Tutorial")) +Tutorial](GBrowse_syn_Tutorial) diff --git a/wiki/GFF_Tutorial.md b/wiki/GFF_Tutorial.md index 9c9b721d7d..c28cdd34ea 100644 --- a/wiki/GFF_Tutorial.md +++ b/wiki/GFF_Tutorial.md @@ -14,7 +14,7 @@ (Redirected from [GFF -Tutorial](http://gmod.org/mediawiki/index.php?title=GFF_Tutorial&redirect=no "GFF Tutorial")) +Tutorial](GFF_Tutorial) diff --git a/wiki/GMOD%3AAbout.md b/wiki/GMOD%3AAbout.md index 5183c0c9fc..007142ca40 100644 --- a/wiki/GMOD%3AAbout.md +++ b/wiki/GMOD%3AAbout.md @@ -14,7 +14,7 @@ (Redirected from -[GMOD%253AAbout](http://gmod.org/mediawiki/index.php?title=GMOD%253AAbout&redirect=no "GMOD%253AAbout")) +[GMOD%253AAbout](GMOD%253AAbout) diff --git a/wiki/GMOD.md b/wiki/GMOD.md index fa163bf22f..874e99c58d 100644 --- a/wiki/GMOD.md +++ b/wiki/GMOD.md @@ -14,7 +14,7 @@ (Redirected from -[GMOD](http://gmod.org/mediawiki/index.php?title=GMOD&redirect=no "GMOD")) +[GMOD](GMOD) diff --git a/wiki/GMOD_REST_API.md b/wiki/GMOD_REST_API.md index d2dcab4038..f9758c4bb0 100644 --- a/wiki/GMOD_REST_API.md +++ b/wiki/GMOD_REST_API.md @@ -14,7 +14,7 @@ (Redirected from [GMOD REST -API](http://gmod.org/mediawiki/index.php?title=GMOD_REST_API&redirect=no "GMOD REST API")) +API](GMOD_REST_API) diff --git a/wiki/GMOD_Summer_School.md b/wiki/GMOD_Summer_School.md index 093ce6a67f..0b840263d5 100644 --- a/wiki/GMOD_Summer_School.md +++ b/wiki/GMOD_Summer_School.md @@ -14,7 +14,7 @@ (Redirected from [GMOD Summer -School](http://gmod.org/mediawiki/index.php?title=GMOD_Summer_School&redirect=no "GMOD Summer School")) +School](GMOD_Summer_School) diff --git a/wiki/GMOD_Summer_School_Statement_of_Interest.md b/wiki/GMOD_Summer_School_Statement_of_Interest.md index b27b3ffd75..fbca3399b7 100644 --- a/wiki/GMOD_Summer_School_Statement_of_Interest.md +++ b/wiki/GMOD_Summer_School_Statement_of_Interest.md @@ -12,7 +12,7 @@ (Redirected from [GMOD Summer School Statement of -Interest](http://gmod.org/mediawiki/index.php?title=GMOD_Summer_School_Statement_of_Interest&redirect=no "GMOD Summer School Statement of Interest")) +Interest](GMOD_Summer_School_Statement_of_Interest) diff --git a/wiki/Galaxy_Tutorial.md b/wiki/Galaxy_Tutorial.md index 6c6f418a03..2498beeb93 100644 --- a/wiki/Galaxy_Tutorial.md +++ b/wiki/Galaxy_Tutorial.md @@ -14,7 +14,7 @@ (Redirected from [Galaxy -Tutorial](http://gmod.org/mediawiki/index.php?title=Galaxy_Tutorial&redirect=no "Galaxy Tutorial")) +Tutorial](Galaxy_Tutorial) diff --git a/wiki/Generic_Genome_Browser.md b/wiki/Generic_Genome_Browser.md index dbdf9ee26d..70165bd04f 100644 --- a/wiki/Generic_Genome_Browser.md +++ b/wiki/Generic_Genome_Browser.md @@ -14,7 +14,7 @@ (Redirected from [Generic Genome -Browser](http://gmod.org/mediawiki/index.php?title=Generic_Genome_Browser&redirect=no "Generic Genome Browser")) +Browser](Generic_Genome_Browser) diff --git a/wiki/Genome.md b/wiki/Genome.md index 079f55b475..9c3376b249 100644 --- a/wiki/Genome.md +++ b/wiki/Genome.md @@ -14,7 +14,7 @@ (Redirected from -[Genome](http://gmod.org/mediawiki/index.php?title=Genome&redirect=no "Genome")) +[Genome](Genome) diff --git a/wiki/Gmod_dbsf.md b/wiki/Gmod_dbsf.md index 8388bda931..d9a8585b57 100644 --- a/wiki/Gmod_dbsf.md +++ b/wiki/Gmod_dbsf.md @@ -14,7 +14,7 @@ (Redirected from [Gmod -dbsf](http://gmod.org/mediawiki/index.php?title=Gmod_dbsf&redirect=no "Gmod dbsf")) +dbsf](Gmod_dbsf) diff --git a/wiki/JBrowseDev/Current/Usage/ConfigFiles.md b/wiki/JBrowseDev/Current/Usage/ConfigFiles.md index c14dc229fb..0002b785c6 100644 --- a/wiki/JBrowseDev/Current/Usage/ConfigFiles.md +++ b/wiki/JBrowseDev/Current/Usage/ConfigFiles.md @@ -14,7 +14,7 @@ (Redirected from -[JBrowseDev/Current/Usage/ConfigFiles](http://gmod.org/mediawiki/index.php?title=JBrowseDev/Current/Usage/ConfigFiles&redirect=no "JBrowseDev/Current/Usage/ConfigFiles")) +[JBrowseDev/Current/Usage/ConfigFiles](JBrowseDev/Current/Usage/ConfigFiles) Redirect page diff --git a/wiki/JBrowseDev/General_Usage.md b/wiki/JBrowseDev/General_Usage.md index 651f57a524..0f11280202 100644 --- a/wiki/JBrowseDev/General_Usage.md +++ b/wiki/JBrowseDev/General_Usage.md @@ -14,7 +14,7 @@ (Redirected from [JBrowseDev/General -Usage](http://gmod.org/mediawiki/index.php?title=JBrowseDev/General_Usage&redirect=no "JBrowseDev/General Usage")) +Usage](JBrowseDev/General_Usage) diff --git a/wiki/JBrowseDev/Installation.md b/wiki/JBrowseDev/Installation.md index 6294849b76..5132d524d2 100644 --- a/wiki/JBrowseDev/Installation.md +++ b/wiki/JBrowseDev/Installation.md @@ -1,64 +1,30 @@ - - - - - - - - - -# JBrowse - - - - - -(Redirected from -[JBrowseDev/Installation](http://gmod.org/mediawiki/index.php?title=JBrowseDev/Installation&redirect=no "JBrowseDev/Installation")) - - - - - +# JBrowse JBrowse logo - - Status - - - Mature release - Development: active - Support: active - - Licence - } is open source - - LGPL, Artistic License 2.0 - - Resources - - - Home page @@ -77,15 +43,8 @@ Resources - Demo server - - - - - ## Contents - - - [1 About JBrowse](#About_JBrowse) - [1.1 @@ -127,8 +86,6 @@ Resources - [10 More on JBrowse](#More_on_JBrowse) - - ## About JBrowse JBrowse is a genome browser with a fully dynamic AJAX interface, being @@ -150,19 +107,16 @@ requirements for the server. directly over HTTP. Serve huge datasets from a single low-cost cloud instance. - Visit the JBrowse website. ### Screenshots - JBrowse alignment and coverage.png - ## Downloads - JBrowse Quick-Start Tutorial provides a basic step-by-step recipe for quickly getting up and running with JBrowse. - 1. Download JBrowse onto your web server. + rel="nofollow">Download JBrowse onto your web server. 2\. Unpack JBrowse into a directory that is served by your web browser. On many systems, this defaults to `/var/www`. @@ -343,18 +296,19 @@ rel="nofollow">150+ tomato genome resequencing project using JBrowse ## Contacts and Mailing Lists Please direct questions and inquiries regarding JBrowse to the mailing -lists below.*Requests for help should be directed to +lists below._Requests for help should be directed to gmod-ajax@lists.sourceforge.net.* +rel="nofollow">gmod-ajax@lists.sourceforge.net._ + +| | | | | +| -------------------------------------------------- | ---------------------------------------------------------------- | ----------------------------------------------------------------------- | ---------- | +| | Mailing List Link | Description | Archive(s) | +| **JBrowse** | gmod-ajax | **JBrowse** help and general questions. | gmod-ajax | **JBrowse** help and general questions. | Nabble (2010/05+), Sourceforge | -| | jbrowse-dev | **JBrowse** development discussions. | [↑](#cite_ref-PMID:19570905_1-0) \*JBrowse: a next-generation genome browser @@ -408,13 +360,10 @@ See [Category%253AJBrowse](../Category%253AJBrowse "Category%253AJBrowse") \* JBrowse: a dynamic web platform for genome visualization and analysis - [Available on platform](../Property%253AAvailable_on_platform "Property:Available on platform") - - web [+](../Special%253ASearchByProperty/Available-20on-20platform/web "Special%253ASearchByProperty/Available-20on-20platform/web") @@ -461,7 +410,7 @@ is javascript-based and does almost all of its work directly in the user's web browser, with minimal requirements for the server. -### Features\[[edit](http://gmod.org/mediawiki/index.php?title=JBrowse&action=edit§ion=1 "Edit section: Features")\] +### Features - Fast, smooth scrolling and zooming. Explore your genome with unparalleled speed. @@ -479,26 +428,14 @@ user's web browser, with minimal requirements for the server. genome of Ötzi the ice man [+](../Special%253ASearchByProperty/Has-20description/Browse-20the-20genome-20of-20%C3%96tzi-20the-20ice-20man "Special%253ASearchByProperty/Has-20description/Browse-20the-20genome-20of-20Ötzi-20the-20ice-20man") - - - ## Navigation menu - - - - - - - ### Navigation - - - [GMOD Home](../Main_Page) - [Software](../GMOD_Components) - [Categories / @@ -506,25 +443,15 @@ title="Visit the main page"> - [View all pages](../Special:AllPages) - - - ### Documentation - - - [Overview](../Overview) - [FAQs](../Category%253AFAQ) - [HOWTOs](../Category%253AHOWTO) - [Glossary](../Glossary) - - - ### Community - - - [GMOD News](../GMOD_News) - [Training / Outreach](../Training_and_Outreach) @@ -533,18 +460,12 @@ title="Visit the main page"> - [Meetings](../Meetings) - [Calendar](../Calendar) - - - ### Tools - Browse properties - - -- Last updated at 19:18 on 15 April - 2016. +- Last updated at 19:18 on 15 April 2016. - Content is available under - - - - - - diff --git a/wiki/JBrowseDev/Main.md b/wiki/JBrowseDev/Main.md index 23fc8940f3..3ec82f519d 100644 --- a/wiki/JBrowseDev/Main.md +++ b/wiki/JBrowseDev/Main.md @@ -14,7 +14,7 @@ (Redirected from -[JBrowseDev/Main](http://gmod.org/mediawiki/index.php?title=JBrowseDev/Main&redirect=no "JBrowseDev/Main")) +[JBrowseDev/Main](JBrowseDev/Main) @@ -120,7 +120,7 @@ is javascript-based and does almost all of its work directly in the user's web browser, with minimal requirements for the server. -### Features\[[edit](http://gmod.org/mediawiki/index.php?title=JBrowse&action=edit§ion=1 "Edit section: Features")\] +### Features - Fast, smooth scrolling and zooming. Explore your genome with unparalleled speed. diff --git a/wiki/JBrowseDev/Upcoming.md b/wiki/JBrowseDev/Upcoming.md index 0e30a75760..7ad965fc16 100644 --- a/wiki/JBrowseDev/Upcoming.md +++ b/wiki/JBrowseDev/Upcoming.md @@ -14,7 +14,7 @@ (Redirected from -[JBrowseDev/Upcoming](http://gmod.org/mediawiki/index.php?title=JBrowseDev/Upcoming&redirect=no "JBrowseDev/Upcoming")) +[JBrowseDev/Upcoming](JBrowseDev/Upcoming) diff --git a/wiki/JBrowseDev/Using_Configuration_Files_With_JBrowse.md b/wiki/JBrowseDev/Using_Configuration_Files_With_JBrowse.md index da83e8e3a9..3b3f96a080 100644 --- a/wiki/JBrowseDev/Using_Configuration_Files_With_JBrowse.md +++ b/wiki/JBrowseDev/Using_Configuration_Files_With_JBrowse.md @@ -14,7 +14,7 @@ (Redirected from [JBrowseDev/Using Configuration Files With -JBrowse](http://gmod.org/mediawiki/index.php?title=JBrowseDev/Using_Configuration_Files_With_JBrowse&redirect=no "JBrowseDev/Using Configuration Files With JBrowse")) +JBrowse](JBrowseDev/Using_Configuration_Files_With_JBrowse) Redirect page diff --git a/wiki/JBrowseDev/Using_a_Database_With_JBrowse.md b/wiki/JBrowseDev/Using_a_Database_With_JBrowse.md index 4c36b8f535..a110188451 100644 --- a/wiki/JBrowseDev/Using_a_Database_With_JBrowse.md +++ b/wiki/JBrowseDev/Using_a_Database_With_JBrowse.md @@ -14,7 +14,7 @@ (Redirected from [JBrowseDev/Using a Database With -JBrowse](http://gmod.org/mediawiki/index.php?title=JBrowseDev/Using_a_Database_With_JBrowse&redirect=no "JBrowseDev/Using a Database With JBrowse")) +JBrowse](JBrowseDev/Using_a_Database_With_JBrowse) Redirect page diff --git a/wiki/JBrowse_Tutorial.md b/wiki/JBrowse_Tutorial.md index 62517ffcee..edb77edf61 100644 --- a/wiki/JBrowse_Tutorial.md +++ b/wiki/JBrowse_Tutorial.md @@ -14,7 +14,7 @@ (Redirected from [JBrowse -Tutorial](http://gmod.org/mediawiki/index.php?title=JBrowse_Tutorial&redirect=no "JBrowse Tutorial")) +Tutorial](JBrowse_Tutorial) diff --git a/wiki/JBrowse_Tutorial_2012.md b/wiki/JBrowse_Tutorial_2012.md index 9771f808ba..9ea6c48f20 100644 --- a/wiki/JBrowse_Tutorial_2012.md +++ b/wiki/JBrowse_Tutorial_2012.md @@ -14,7 +14,7 @@ (Redirected from [JBrowse Tutorial -2012](http://gmod.org/mediawiki/index.php?title=JBrowse_Tutorial_2012&redirect=no "JBrowse Tutorial 2012")) +2012](JBrowse_Tutorial_2012) diff --git a/wiki/January_2010_GMOD_Meeting_Registration.md b/wiki/January_2010_GMOD_Meeting_Registration.md index e023e7d493..f09ee0589c 100644 --- a/wiki/January_2010_GMOD_Meeting_Registration.md +++ b/wiki/January_2010_GMOD_Meeting_Registration.md @@ -14,7 +14,7 @@ (Redirected from [January 2010 GMOD Meeting -Registration](http://gmod.org/mediawiki/index.php?title=January_2010_GMOD_Meeting_Registration&redirect=no "January 2010 GMOD Meeting Registration")) +Registration](January_2010_GMOD_Meeting_Registration) diff --git a/wiki/July_2008_GMOD_Meeting_Registration.md b/wiki/July_2008_GMOD_Meeting_Registration.md index 3d4a136635..2438e10661 100644 --- a/wiki/July_2008_GMOD_Meeting_Registration.md +++ b/wiki/July_2008_GMOD_Meeting_Registration.md @@ -14,7 +14,7 @@ (Redirected from [July 2008 GMOD Meeting -Registration](http://gmod.org/mediawiki/index.php?title=July_2008_GMOD_Meeting_Registration&redirect=no "July 2008 GMOD Meeting Registration")) +Registration](July_2008_GMOD_Meeting_Registration) diff --git a/wiki/MAKER_Tutorial.md b/wiki/MAKER_Tutorial.md index 949b88fa33..bfa1513993 100644 --- a/wiki/MAKER_Tutorial.md +++ b/wiki/MAKER_Tutorial.md @@ -14,7 +14,7 @@ (Redirected from [MAKER -Tutorial](http://gmod.org/mediawiki/index.php?title=MAKER_Tutorial&redirect=no "MAKER Tutorial")) +Tutorial](MAKER_Tutorial) diff --git a/wiki/Mailing_Lists.md b/wiki/Mailing_Lists.md index eeb7ff7fd7..94143e7083 100644 --- a/wiki/Mailing_Lists.md +++ b/wiki/Mailing_Lists.md @@ -14,7 +14,7 @@ (Redirected from [Mailing -Lists](http://gmod.org/mediawiki/index.php?title=Mailing_Lists&redirect=no "Mailing Lists")) +Lists](Mailing_Lists) diff --git a/wiki/Mailing_list.md b/wiki/Mailing_list.md index 2fa7812109..6c57a7e3e7 100644 --- a/wiki/Mailing_list.md +++ b/wiki/Mailing_list.md @@ -14,7 +14,7 @@ (Redirected from [Mailing -list](http://gmod.org/mediawiki/index.php?title=Mailing_list&redirect=no "Mailing list")) +list](Mailing_list) diff --git a/wiki/NGS.md b/wiki/NGS.md index df2360ed35..b3bea210e2 100644 --- a/wiki/NGS.md +++ b/wiki/NGS.md @@ -14,7 +14,7 @@ (Redirected from -[NGS](http://gmod.org/mediawiki/index.php?title=NGS&redirect=no "NGS")) +[NGS](NGS) diff --git a/wiki/Next_generation_sequencing.md b/wiki/Next_generation_sequencing.md index e4738734a5..02d9246dec 100644 --- a/wiki/Next_generation_sequencing.md +++ b/wiki/Next_generation_sequencing.md @@ -14,7 +14,7 @@ (Redirected from [Next generation -sequencing](http://gmod.org/mediawiki/index.php?title=Next_generation_sequencing&redirect=no "Next generation sequencing")) +sequencing](Next_generation_sequencing) diff --git a/wiki/PAG.md b/wiki/PAG.md index e60a5bfd35..ae202cc9d1 100644 --- a/wiki/PAG.md +++ b/wiki/PAG.md @@ -14,7 +14,7 @@ (Redirected from -[PAG](http://gmod.org/mediawiki/index.php?title=PAG&redirect=no "PAG")) +[PAG](PAG) diff --git a/wiki/Plugin.md b/wiki/Plugin.md index 8c6c75e17e..8e6ff353e5 100644 --- a/wiki/Plugin.md +++ b/wiki/Plugin.md @@ -14,7 +14,7 @@ (Redirected from -[Plugin](http://gmod.org/mediawiki/index.php?title=Plugin&redirect=no "Plugin")) +[Plugin](Plugin) diff --git a/wiki/Plugins.md b/wiki/Plugins.md index 9777ffac17..be064b3710 100644 --- a/wiki/Plugins.md +++ b/wiki/Plugins.md @@ -14,7 +14,7 @@ (Redirected from -[Plugins](http://gmod.org/mediawiki/index.php?title=Plugins&redirect=no "Plugins")) +[Plugins](Plugins) diff --git a/wiki/Postgres.md b/wiki/Postgres.md index 559bcd2c86..8ad802f256 100644 --- a/wiki/Postgres.md +++ b/wiki/Postgres.md @@ -14,7 +14,7 @@ (Redirected from -[Postgres](http://gmod.org/mediawiki/index.php?title=Postgres&redirect=no "Postgres")) +[Postgres](Postgres) diff --git a/wiki/Property%3AHas_topic.md b/wiki/Property%3AHas_topic.md index 457af2984a..7da2216d16 100644 --- a/wiki/Property%3AHas_topic.md +++ b/wiki/Property%3AHas_topic.md @@ -30,7 +30,7 @@ This is a property of type Showing 25 pages using this property. (previous 25) ([next -25](http://gmod.org/mediawiki/index.php?title=Property%253AHas_topic&from=GMOD+Malaysia+2014%2FMAKER+Tutorial#SMWResults#SMWResults "Property:Has topic")) +25](Property%253AHas_topic) @@ -318,7 +318,7 @@ title="Special%253ASearchByProperty/Has-20topic/JBrowse">+
(previous 25) ([next -25](http://gmod.org/mediawiki/index.php?title=Property%253AHas_topic&from=GMOD+Malaysia+2014%2FMAKER+Tutorial#SMWResults#SMWResults "Property:Has topic")) +25](Property%253AHas_topic) diff --git a/wiki/Property%3ALinktitle.md b/wiki/Property%3ALinktitle.md index 348d6cb244..163dd86068 100644 --- a/wiki/Property%3ALinktitle.md +++ b/wiki/Property%3ALinktitle.md @@ -30,7 +30,7 @@ This is a property of type Showing 25 pages using this property. (previous 25) ([next -25](http://gmod.org/mediawiki/index.php?title=Property%253ALinktitle&from=GBrowse+syn#SMWResults#SMWResults "Property%253ALinktitle")) +25](Property%253ALinktitle) @@ -340,7 +340,7 @@ title="Special%253ASearchByProperty/Linktitle/The-20Arabidopsis-20Information-20
(previous 25) ([next -25](http://gmod.org/mediawiki/index.php?title=Property%253ALinktitle&from=GBrowse+syn#SMWResults#SMWResults "Property%253ALinktitle")) +25](Property%253ALinktitle) diff --git a/wiki/Property%3ALinktype.md b/wiki/Property%3ALinktype.md index aa5d63455f..d61f1634e1 100644 --- a/wiki/Property%3ALinktype.md +++ b/wiki/Property%3ALinktype.md @@ -30,7 +30,7 @@ This is a property of type Showing 25 pages using this property. (previous 25) ([next -25](http://gmod.org/mediawiki/index.php?title=Property%253ALinktype&from=Canto#SMWResults#SMWResults "Property%253ALinktype")) +25](Property%253ALinktype) @@ -330,7 +330,7 @@ title="Special%253ASearchByProperty/Linktype/wild-20URL">+
(previous 25) ([next -25](http://gmod.org/mediawiki/index.php?title=Property%253ALinktype&from=Canto#SMWResults#SMWResults "Property%253ALinktype")) +25](Property%253ALinktype) diff --git a/wiki/Regionview_panel.md b/wiki/Regionview_panel.md index 3fb20e267d..ae4c2a4045 100644 --- a/wiki/Regionview_panel.md +++ b/wiki/Regionview_panel.md @@ -14,7 +14,7 @@ (Redirected from [Regionview -panel](http://gmod.org/mediawiki/index.php?title=Regionview_panel&redirect=no "Regionview panel")) +panel](Regionview_panel) diff --git a/wiki/SOBA_Tutorial.md b/wiki/SOBA_Tutorial.md index bc9526a0b5..1e1f5d0443 100644 --- a/wiki/SOBA_Tutorial.md +++ b/wiki/SOBA_Tutorial.md @@ -14,7 +14,7 @@ (Redirected from [SOBA -Tutorial](http://gmod.org/mediawiki/index.php?title=SOBA_Tutorial&redirect=no "SOBA Tutorial")) +Tutorial](SOBA_Tutorial) diff --git a/wiki/SVN.md b/wiki/SVN.md index 3ed8503d07..c790c7ef17 100644 --- a/wiki/SVN.md +++ b/wiki/SVN.md @@ -14,7 +14,7 @@ (Redirected from -[SVN](http://gmod.org/mediawiki/index.php?title=SVN&redirect=no "SVN")) +[SVN](SVN) diff --git a/wiki/Subversion.md b/wiki/Subversion.md index 2017721e84..649748b7ff 100644 --- a/wiki/Subversion.md +++ b/wiki/Subversion.md @@ -14,7 +14,7 @@ (Redirected from -[Subversion](http://gmod.org/mediawiki/index.php?title=Subversion&redirect=no "Subversion")) +[Subversion](Subversion) diff --git a/wiki/Synteny.md b/wiki/Synteny.md index 2d1be76f4f..24ecda1b0b 100644 --- a/wiki/Synteny.md +++ b/wiki/Synteny.md @@ -14,7 +14,7 @@ (Redirected from -[Synteny](http://gmod.org/mediawiki/index.php?title=Synteny&redirect=no "Synteny")) +[Synteny](Synteny) diff --git a/wiki/TableEdit/IFALT.md b/wiki/TableEdit/IFALT.md index d97ef23dbc..54612c2fcf 100644 --- a/wiki/TableEdit/IFALT.md +++ b/wiki/TableEdit/IFALT.md @@ -14,7 +14,7 @@ (Redirected from -[TableEdit/IFALT](http://gmod.org/mediawiki/index.php?title=TableEdit/IFALT&redirect=no "TableEdit/IFALT")) +[TableEdit/IFALT](TableEdit/IFALT) diff --git a/wiki/Table_Editor.md b/wiki/Table_Editor.md index ccfef144c7..05f8a5931d 100644 --- a/wiki/Table_Editor.md +++ b/wiki/Table_Editor.md @@ -14,7 +14,7 @@ (Redirected from [Table -Editor](http://gmod.org/mediawiki/index.php?title=Table_Editor&redirect=no "Table Editor")) +Editor](Table_Editor) diff --git a/wiki/Talk%3AGBrowse_Configuration_HOWTO.md b/wiki/Talk%3AGBrowse_Configuration_HOWTO.md index 30468197f7..5ff3d886d4 100644 --- a/wiki/Talk%3AGBrowse_Configuration_HOWTO.md +++ b/wiki/Talk%3AGBrowse_Configuration_HOWTO.md @@ -12,7 +12,7 @@ (Redirected from [Talk%253AGBrowse Configuration -HOWTO](http://gmod.org/mediawiki/index.php?title=Talk%253AGBrowse_Configuration_HOWTO&redirect=no "Talk%253AGBrowse Configuration HOWTO")) +HOWTO](Talk%253AGBrowse_Configuration_HOWTO) diff --git a/wiki/Tripal_Tutorial.md b/wiki/Tripal_Tutorial.md index 8fc4bfbfd6..435dd988fe 100644 --- a/wiki/Tripal_Tutorial.md +++ b/wiki/Tripal_Tutorial.md @@ -14,7 +14,7 @@ (Redirected from [Tripal -Tutorial](http://gmod.org/mediawiki/index.php?title=Tripal_Tutorial&redirect=no "Tripal Tutorial")) +Tutorial](Tripal_Tutorial) diff --git a/wiki/User%3ARBuels.md b/wiki/User%3ARBuels.md index 950cdc8e67..9c8239f8ea 100644 --- a/wiki/User%3ARBuels.md +++ b/wiki/User%3ARBuels.md @@ -14,7 +14,7 @@ (Redirected from -[User%253ARBuels](http://gmod.org/mediawiki/index.php?title=User%253ARBuels&redirect=no "User%253ARBuels")) +[User%253ARBuels](User%253ARBuels) diff --git a/wiki/Using_Existing_Databases_With_JBrowse.md b/wiki/Using_Existing_Databases_With_JBrowse.md index 3a816c1055..080d3201c2 100644 --- a/wiki/Using_Existing_Databases_With_JBrowse.md +++ b/wiki/Using_Existing_Databases_With_JBrowse.md @@ -1,24 +1,4 @@ - - - - - - - - - -# JBrowse Configuration Guide - - - - - -(Redirected from [Using Existing Databases With -JBrowse](http://gmod.org/mediawiki/index.php?title=Using_Existing_Databases_With_JBrowse&redirect=no "Using Existing Databases With JBrowse")) - - - - +# JBrowse Configuration Guide **This page has been replaced with this page (Quick-start tutorial first, and then consult this guide when you need information on specific things you want to do with your JBrowse. - Check out the new [JBrowse FAQ](JBrowse_FAQ "JBrowse FAQ") page for more tips on setup and configuration -http://gmod.org/wiki/JBrowse_FAQ Also see the [JBrowse Desktop](JBrowse_Desktop "JBrowse Desktop") guide -here http://gmod.org/wiki/JBrowse_Desktop - - - +here. ## Contents - - - [1 Installation](#Installation) - [1.1 Making a @@ -434,8 +405,6 @@ rel="nofollow">http://gmod.org/wiki/JBrowse_Desktop - [27 External Links](#External_Links) - - # Installation At the most basic level, setting up JBrowse consists of: @@ -502,7 +471,6 @@ Tutorial provides a very basic step-by-step guide to formatting your own data, and in-depth configuration reference information can be found on this page. - Note: if there is an error installing the perl pre-requisites, and you get an error in your setup.log such as "/home.local/username/.cpanm/build.log: No such file or directory at @@ -546,8 +514,6 @@ The JSON configuration format was the first format supported by JBrowse, and is easy for software programs to read and modify. Before version 1.11.0, this was the only format supported by JBrowse. - - As an example, the trackList.json file might have something like this. Here is an example of a BAM track @@ -564,7 +530,6 @@ Here is an example of a BAM track ] } - The specifics of this config are not essential, we are specifying an array of tracks in a trackList.json style, and each track is an object that includes some parameters like the urlTemplate to refer to the @@ -721,10 +686,7 @@ to practically display in the dropdown selector, the first portion of the sequence list is shown in the dropdown selector, along with a message stating that there are more reference sequences than can be shown. The maximum number of reference sequences in the selector is set -by the `refSeqSelectorMaxSize` configuration variable, and defaults to -30. - - +by the `refSeqSelectorMaxSize` configuration variable, and defaults to 30. ### Reference Sequence Display Order @@ -785,7 +747,7 @@ character, as well as several other characters, may be used). Hence, it is possible to browse RNA and protein in addition to DNA. However, some characters should be avoided, because they will cause the sequence to "split" - part of the sequence will be cut off and and continue on the -next line. These characters are the *hyphen* and *question mark*. +next line. These characters are the _hyphen_ and _question mark_. Unfortunately, this prevents the use of hyphens to represent gaps in a reference sequence. @@ -801,7 +763,6 @@ Syntax used to import sequences with a config file: bin/prepare-refseqs.pl --conf --[refs|refid] [options] - Syntax used to import a indexed fasta(i.e. a fasta file where you run \`samtools faidx yourfile.fa\` which outputs yourfile.fa.fai) @@ -809,16 +770,15 @@ Syntax used to import a indexed fasta(i.e. a fasta file where you run This will copy yourfile.fa and yourfile.fa.fai to the data directory -| Option | Value | -|----|----| +| Option | Value | +| ------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | fasta, indexed_fasta, twobit, gff, sizes, or conf | Path to the file that JBrowse will use to import sequences. With the fasta and gff options, the sequence information is imported directly from the specified file. With the sizes option, a tab delimited file with chromosome names and lengths is used, but no sequence information is added. With the conf option, the specified config file includes the details necessary to access a database that contains the sequence information. Exactly one of these three options must be used. With indexed_fasta, the samtools faidx yourfile.fa must be run before hand. With twobit, the twobit file will automatically be copied into your data directory. | -| out | A path to the output directory (default is 'data' in the current directory) | -| seqdir | The directory where the reference sequences are stored (default: \/seq) | -| noseq | Causes no reference sequence track to be created. This is useful for reducing disk usage. | -| refs | A comma-delimited list of the names of sequences to be imported as reference sequences. This option (or refid) is required when using the conf option. It is not required when the fasta or gff options are used, but it can be useful with these options, since it can be used to select which sequences JBrowse will import. | -| refids | A comma-delimited list of the database identifiers of sequences to be imported as reference sequences. This option is useful when working with a Chado database that contains data from multiple different species, and those species have at least one chromosome with the same name (e.g. chrX). In this case, the desired chromosome cannot be uniquely identified by name, so it is instead identified by ID. This ID can be found in the 'feature_id' column of 'feature' table in a Chado database. | +| out | A path to the output directory (default is 'data' in the current directory) | +| seqdir | The directory where the reference sequences are stored (default: \/seq) | +| noseq | Causes no reference sequence track to be created. This is useful for reducing disk usage. | +| refs | A comma-delimited list of the names of sequences to be imported as reference sequences. This option (or refid) is required when using the conf option. It is not required when the fasta or gff options are used, but it can be useful with these options, since it can be used to select which sequences JBrowse will import. | +| refids | A comma-delimited list of the database identifiers of sequences to be imported as reference sequences. This option is useful when working with a Chado database that contains data from multiple different species, and those species have at least one chromosome with the same name (e.g. chrX). In this case, the desired chromosome cannot be uniquely identified by name, so it is instead identified by ID. This ID can be found in the 'feature_id' column of 'feature' table in a Chado database. | - Note: the \`prepare-refseqs.pl --sizes chrom.sizes\` option is maybe underappreciated. You can technically run jbrowse without any sequence data loaded, simply a set of chromosomes and their sizes. The @@ -843,8 +803,8 @@ of these tools also adds a track configuration stanza to the ### flatfile-to-json.pl -Each run of this script formats a single track for JBrowse. A *flat -file* is a data set that exists entirely in a single file. For this +Each run of this script formats a single track for JBrowse. A _flat +file_ is a data set that exists entirely in a single file. For this script, the file must be a [GFF3](GFF3 "GFF3"), BED, or GenBank text file. @@ -909,7 +869,6 @@ Basic usage: bin/biodb-to-json.pl --conf [options] - For a full list of the options supported by biodb-to-json.pl, run it with the --help option, like: @@ -966,30 +925,30 @@ Below is a comprehensive list of configuration options for HTMLFeatures tracks. HTMLFeatures tracks are also referred to as trackType: "FeatureTrack" or "type": "FeatureTrack". -| Option | Value | -|----|----| -| `yScalePosition` | Position of the y-axis scale indicator when the track is zoomed far enough out that density histograms are displayed. Can be "left", "right", or "center". Defaults to "center". | -| `maxFeatureScreenDensity` | Maximum density of features to display on the screen. If this is exceeded, will display either feature density histograms (if available), or a "too many features to show" message. The units of this number are features per screen width in pixels. Defaults to 0.5. | -| `description` | Comma-separated list of fields in which to look for the description of a feature. Case-insensitive. If set to `false` or `null`, no feature description will be shown. Defaults to 'note, description'. | -| `maxDescriptionLength` | Maximum length, in characters, for displayed feature descriptions. | -| `minSubfeatureWidth` | Minimum width, in pixels, of the *top-level* feature for JBrowse to attempt to display its subfeatures. Default 6. | -| `menuTemplate` | Optional menu configuration for right-click menus on features. Can be as large and complicated as you want. See [\#Customizing_Right-click_Context_Menus](#Customizing_Right-click_Context_Menus) below. If set to null or false, disables feature right-click menus. | -| `hooks→create` | JavaScript function that creates the parent feature HTML element and returns it. By default this is: `function(track,feature) { return document.createElement('div'); }`, which creates an HTML `div` element. | -| `hooks→modify` | JavaScript function that can be used to modify the feature HTML element in any way desired. If set, the function is called with the track object, feature object, and feature HTML element as arguments (signature: `function(track, feature, featDiv)`). | -| `style→featureScale` | Minimum zoom scale (pixels/basepair) for displaying individual features in the track. Not set by default, and overrides the `maxFeatureScreenDensity`. | -| `style→className` | CSS class for parent features. Defaults to "feature". | -| `style→subfeatureClasses` | Key-value pairs of CSS classes for subfeatures, organized by feature type. Example: { "CDS" : "transcript-CDS","UTR" : "transcript-UTR" } | -| `style→featureCss` | Text string of additional CSS rules to add to features. Example: "border-color: purple; background-color: yellow;" | -| `style→arrowheadClass` | CSS class of the strand arrowheads to show for this feature. Defaults to 'arrowhead'. If set to `null`, no arrowhead will be drawn. | -| `style→histScale` | Scale (pixels per basepair) below which the track will attempt to draw feature density histograms instead of features, if available. By default, this is set to 4 times the average feature density (features per basepair) of the track. | -| `style→label` | Comma-separated list of case-insensitive feature tags to use for showing the feature's label. The first one found will be used. Default 'name,id'. | -| `style→labelScale` | Scale (pixels per basepair) above which feature labels (names) will be shown. By default, this is set to 30 times the average feature density (features per basepair) of the track. | -| `style→descriptionScale` | Scale (pixels per basepair) above which long feature descriptions will be shown. By default, this is set to 170 times the average feature density (features per basepair) of the track. | -| `style→description` | Comma-separated list of case-insensitive feature tags to check for the feature's long description. The first one found will be used. Default 'note,description'. If blank no description is used. | -| `style→showLabels` | If set to true, feature labels may be shown. Defaults to true. Set this to false to disable display of feature labels. | -| `maxHeight` | Maximum height, in pixels, that the track is allowed to grow to. When it reaches this height, features that stack higher than this will not be shown, and a "Max height reached" message will be displayed. Default 600 pixels. | -| `showNoteInAttributes` | If set to true, show the feature's "Note" attribute as a regular attribute in the feature detail dialog. This is mostly useful for projects that want the blue description text on a feature to be different from the feature's Notes attribute, but still display the Notes attribute in the detail dialog | -| `topLevelFeatures` | Specifies which feature types should be considered "top-level" for this track. For example, if you have a track with gene-\>mRNA-\>CDS features, but for some reason want to only display the mRNA features, you can set topLevelFeatures=mRNA. Can also be an array of string types, or a function callback that returns an array of types. Default: all features are displayed. Added in 1.14.0 | +| Option | Value | +| ------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| `yScalePosition` | Position of the y-axis scale indicator when the track is zoomed far enough out that density histograms are displayed. Can be "left", "right", or "center". Defaults to "center". | +| `maxFeatureScreenDensity` | Maximum density of features to display on the screen. If this is exceeded, will display either feature density histograms (if available), or a "too many features to show" message. The units of this number are features per screen width in pixels. Defaults to 0.5. | +| `description` | Comma-separated list of fields in which to look for the description of a feature. Case-insensitive. If set to `false` or `null`, no feature description will be shown. Defaults to 'note, description'. | +| `maxDescriptionLength` | Maximum length, in characters, for displayed feature descriptions. | +| `minSubfeatureWidth` | Minimum width, in pixels, of the _top-level_ feature for JBrowse to attempt to display its subfeatures. Default 6. | +| `menuTemplate` | Optional menu configuration for right-click menus on features. Can be as large and complicated as you want. See [\#Customizing_Right-click_Context_Menus](#Customizing_Right-click_Context_Menus) below. If set to null or false, disables feature right-click menus. | +| `hooks→create` | JavaScript function that creates the parent feature HTML element and returns it. By default this is: `function(track,feature) { return document.createElement('div'); }`, which creates an HTML `div` element. | +| `hooks→modify` | JavaScript function that can be used to modify the feature HTML element in any way desired. If set, the function is called with the track object, feature object, and feature HTML element as arguments (signature: `function(track, feature, featDiv)`). | +| `style→featureScale` | Minimum zoom scale (pixels/basepair) for displaying individual features in the track. Not set by default, and overrides the `maxFeatureScreenDensity`. | +| `style→className` | CSS class for parent features. Defaults to "feature". | +| `style→subfeatureClasses` | Key-value pairs of CSS classes for subfeatures, organized by feature type. Example: { "CDS" : "transcript-CDS","UTR" : "transcript-UTR" } | +| `style→featureCss` | Text string of additional CSS rules to add to features. Example: "border-color: purple; background-color: yellow;" | +| `style→arrowheadClass` | CSS class of the strand arrowheads to show for this feature. Defaults to 'arrowhead'. If set to `null`, no arrowhead will be drawn. | +| `style→histScale` | Scale (pixels per basepair) below which the track will attempt to draw feature density histograms instead of features, if available. By default, this is set to 4 times the average feature density (features per basepair) of the track. | +| `style→label` | Comma-separated list of case-insensitive feature tags to use for showing the feature's label. The first one found will be used. Default 'name,id'. | +| `style→labelScale` | Scale (pixels per basepair) above which feature labels (names) will be shown. By default, this is set to 30 times the average feature density (features per basepair) of the track. | +| `style→descriptionScale` | Scale (pixels per basepair) above which long feature descriptions will be shown. By default, this is set to 170 times the average feature density (features per basepair) of the track. | +| `style→description` | Comma-separated list of case-insensitive feature tags to check for the feature's long description. The first one found will be used. Default 'note,description'. If blank no description is used. | +| `style→showLabels` | If set to true, feature labels may be shown. Defaults to true. Set this to false to disable display of feature labels. | +| `maxHeight` | Maximum height, in pixels, that the track is allowed to grow to. When it reaches this height, features that stack higher than this will not be shown, and a "Max height reached" message will be displayed. Default 600 pixels. | +| `showNoteInAttributes` | If set to true, show the feature's "Note" attribute as a regular attribute in the feature detail dialog. This is mostly useful for projects that want the blue description text on a feature to be different from the feature's Notes attribute, but still display the Notes attribute in the detail dialog | +| `topLevelFeatures` | Specifies which feature types should be considered "top-level" for this track. For example, if you have a track with gene-\>mRNA-\>CDS features, but for some reason want to only display the mRNA features, you can set topLevelFeatures=mRNA. Can also be an array of string types, or a function callback that returns an array of types. Default: all features are displayed. Added in 1.14.0 | `HTMLFeatures` track configuration options @@ -998,66 +957,61 @@ tracks. HTMLFeatures tracks are also referred to as trackType: Introduced in JBrowse 1.10.0, the new JBrowse CanvasFeatures tracks are faster and easier to configure than HTMLFeatures tracks. -| Option | Description | -|----|----| -| `maxHeight` | Maximum height, in pixels, that the track is allowed to grow to. When it reaches this height, features that stack higher than this will not be shown, and a "Max height reached" message will be displayed. Default 600 pixels. | -| `style→showLabels` | If true, allows feature labels to be shown if features are not too dense on the screen. Default `true`. | -| `style→showTooltips` | If true, allows feature name tooltips to be shown. Default true. | -| `displayMode` | 'normal', 'compact', or 'collapsed'. Sets the initial display mode of the track. Default 'normal'. | -| `style→featureScale` | Minimum zoom scale (pixels/basepair) for displaying individual features in the track. Not set by default, and overrides the `maxFeatureScreenDensity`. | -| `maxFeatureScreenDensity` | Maximum density of features to display on the screen. If this is exceeded, will display either feature density histograms (if available), or a "too many features to show" or "too much data to show" message. The units of this number are features per screen width in pixels. Defaults to 0.5. If increased to ~6 then it should pretty much always go away | -| `glyph` | JS class name of the glyph to use for each feature. By default, it tries to guess for each feature based on its `type` attribute, and uses JBrowse/View/FeatureGlyph/Box if it cannot find something better. Can be a callback with signature (feature), returning a string class name. | -| `menuTemplate` | Optional menu configuration for right-click menus on features. Can be as large and complicated as you want. See [\#Right-click_Context_Menus](#Right-click_Context_Menus) below. If set to null or false, disables feature right-click menus. | -| `style→maxDescriptionLength` | Maximum length, in characters, of long feature descriptions, for glyphs that support them. Default 70. | -| `style→color` | Basic color of features. Most glyphs interpret this as the fill color of the rectangle they draw. Color syntax is the same as that used for CSS, specified at http://dev.w3.org/csswg/css-color/. Default 'goldenrod'. | -| `style→mouseovercolor` | Color of the overlay drawn on top of features when the mouse hovers over them. Color syntax is the same as that used for CSS, specified at http://dev.w3.org/csswg/css-color/. Default rgba(0,0,0,0.3), which is semi-transparent black. | -| `style→borderColor` | Color of the borders drawn around boxes in glyphs. Color syntax is the same as that used for CSS, specified at http://dev.w3.org/csswg/css-color/. Default varies from glyph to glyph. | -| `style→borderWidth` | Width of the borders drawn around boxes in glyphs. Default 0.5 if borderColor specified | -| `style→height` | Height in pixels of glyphs. Default value varies from glyph to glyph. | -| `style→marginBottom` | Margin space to leave below each feature when arranging them in the view. Default 2 pixels. | -| `style→strandArrow` | If true, allow glyphs to draw strand arrowheads on features that are stranded. Default `true`. | -| `style→label` | Comma-separated list of case-insensitive feature tags to use for showing the feature's label. The first one found will be used. Default 'name,id'. | -| `style→textFont` | Font used for feature labels. Same format as CSS font rules. Default 'normal 12px Univers,Helvetica,Arial,sans-serif'. | -| `style→textColor` | Color of feature labels. Color syntax is the same as that used for CSS, specified at http://dev.w3.org/csswg/css-color/. Default 'black'. | -| `style→text2Color` | Color of feature descriptions. Color syntax is the same as that used for CSS, specified at http://dev.w3.org/csswg/css-color/. Default 'blue'. | -| `style→text2Font` | Font used for feature descriptions. Same format as CSS font rules. Default 'normal 12px Univers,Helvetica,Arial,sans-serif'. | -| `style→description` | Comma-separated list of case-insensitive feature tags to check for the feature's long description. The first one found will be used. Default 'note,description'. If blank no description is used. | -| `style→connectorColor` | Color of the connecting line drawn between boxes in glyphs that draw segments (like the Segments, ProcessedTranscript, and Gene glyphs). Color syntax is the same as that used for CSS, specified at http://dev.w3.org/csswg/css-color/. Default '#333'. | -| `style→connectorThickness` | Thickness in pixels of the connecting line drawn between boxes in glyphs that draw segments (like the Segments, ProcessedTranscript, and Gene glyphs). Default 1. | -| `style→utrColor` | Color of UTR regions drawn by ProcessedTranscript and Gene glyphs. Color syntax is the same as that used for CSS, specified at http://dev.w3.org/csswg/css-color/. Defaults to be a color that complements the current `style→color` value (calculated using a bit of color theory). | -| `subParts` | Comma-separated list of feature `type` tags that will be drawn as subparts of parent features. Defaults to all features for Segments glyphs, and 'CDS, UTR, five_prime_UTR, three_prime_UTR' for ProcessedTranscript glyphs. | -| `transcriptType` | For Gene glyphs, the feature `type` tag that indicates that a subfeature is a processed transcript. Defaults to 'mRNA'. | -| `labelTranscripts` | For Gene glyphs, if true, draw a label with the transcript's name beside each transcript, if space permits. Default true. | -| `style→transcriptLabelColor` | For Gene glyphs, the color of transcript name labels. Color syntax is the same as that used for CSS, specified at http://dev.w3.org/csswg/css-color/. Default 'black'. | -| `style→transcriptLabelFont` | For Gene glyphs, the font used for transcript name labels. Same format as CSS font rules. Default 'normal 10px Univers,Helvetica,Arial,sans-serif'. | -| `impliedUTRs` | Introduced in JBrowse 1.10.5. If true, indicates that UTRs are not present in the feature data, but should be inferred from the overlap of exon and CDS features in ProcessedTranscript and Gene glyphs. Default false. Can be a callback. | -| `maxFeatureGlyphExpansion` | A factor to expand the glyphs by so that if subfeatures go outside the bounds of the parent feature, they will still be rendered. Default: 500bp/current scale. | -| `inferCdsParts ` | If a single CDS span covers the whole gene except the UTRs, then it is drawn as though it only covers the exon parts (not the introns). Default: false. Added in 1.12.3 | -| `disableCollapsedClick` | Disables the click action when track is collapsed. Default: false. Added in 1.13.0 | -| `enableCollapsedMouseover` | Enables the mouseover action when track is collapsed. Default: false. Added in 1.13.0. See the ChromHMM track in volvox sample browser for example of mouseover on the collapsed track | -| `topLevelFeatures` | Specifies which feature types should be considered "top-level" for this track. For example, if you have a track with gene-\>mRNA-\>CDS features, but for some reason want to only display the mRNA features, you can set topLevelFeatures=mRNA. Can also be an array of string types, or a function callback that returns an array of types. Default: all features are displayed. Added in 1.14.0 | -| `ItemRgb` | If set to true, the RGB colors specified in BigBed or BED files will be used for the feature's background color. Default true. Added in 1.14.0 | +| Option | Description | +| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| `maxHeight` | Maximum height, in pixels, that the track is allowed to grow to. When it reaches this height, features that stack higher than this will not be shown, and a "Max height reached" message will be displayed. Default 600 pixels. | +| `style→showLabels` | If true, allows feature labels to be shown if features are not too dense on the screen. Default `true`. | +| `style→showTooltips` | If true, allows feature name tooltips to be shown. Default true. | +| `displayMode` | 'normal', 'compact', or 'collapsed'. Sets the initial display mode of the track. Default 'normal'. | +| `style→featureScale` | Minimum zoom scale (pixels/basepair) for displaying individual features in the track. Not set by default, and overrides the `maxFeatureScreenDensity`. | +| `maxFeatureScreenDensity` | Maximum density of features to display on the screen. If this is exceeded, will display either feature density histograms (if available), or a "too many features to show" or "too much data to show" message. The units of this number are features per screen width in pixels. Defaults to 0.5. If increased to ~6 then it should pretty much always go away | +| `glyph` | JS class name of the glyph to use for each feature. By default, it tries to guess for each feature based on its `type` attribute, and uses JBrowse/View/FeatureGlyph/Box if it cannot find something better. Can be a callback with signature (feature), returning a string class name. | +| `menuTemplate` | Optional menu configuration for right-click menus on features. Can be as large and complicated as you want. See [\#Right-click_Context_Menus](#Right-click_Context_Menus) below. If set to null or false, disables feature right-click menus. | +| `style→maxDescriptionLength` | Maximum length, in characters, of long feature descriptions, for glyphs that support them. Default 70. | +| `style→color` | Basic color of features. Most glyphs interpret this as the fill color of the rectangle they draw. Color syntax is the same as that used for CSS, specified at http://dev.w3.org/csswg/css-color/. Default 'goldenrod'. | +| `style→mouseovercolor` | Color of the overlay drawn on top of features when the mouse hovers over them. Color syntax is the same as that used for CSS, specified at http://dev.w3.org/csswg/css-color/. Default rgba(0,0,0,0.3), which is semi-transparent black. | +| `style→borderColor` | Color of the borders drawn around boxes in glyphs. Color syntax is the same as that used for CSS, specified at http://dev.w3.org/csswg/css-color/. Default varies from glyph to glyph. | +| `style→borderWidth` | Width of the borders drawn around boxes in glyphs. Default 0.5 if borderColor specified | +| `style→height` | Height in pixels of glyphs. Default value varies from glyph to glyph. | +| `style→marginBottom` | Margin space to leave below each feature when arranging them in the view. Default 2 pixels. | +| `style→strandArrow` | If true, allow glyphs to draw strand arrowheads on features that are stranded. Default `true`. | +| `style→label` | Comma-separated list of case-insensitive feature tags to use for showing the feature's label. The first one found will be used. Default 'name,id'. | +| `style→textFont` | Font used for feature labels. Same format as CSS font rules. Default 'normal 12px Univers,Helvetica,Arial,sans-serif'. | +| `style→textColor` | Color of feature labels. Color syntax is the same as that used for CSS, specified at http://dev.w3.org/csswg/css-color/. Default 'black'. | +| `style→text2Color` | Color of feature descriptions. Color syntax is the same as that used for CSS, specified at http://dev.w3.org/csswg/css-color/. Default 'blue'. | +| `style→text2Font` | Font used for feature descriptions. Same format as CSS font rules. Default 'normal 12px Univers,Helvetica,Arial,sans-serif'. | +| `style→description` | Comma-separated list of case-insensitive feature tags to check for the feature's long description. The first one found will be used. Default 'note,description'. If blank no description is used. | +| `style→connectorColor` | Color of the connecting line drawn between boxes in glyphs that draw segments (like the Segments, ProcessedTranscript, and Gene glyphs). Color syntax is the same as that used for CSS, specified at http://dev.w3.org/csswg/css-color/. Default '#333'. | +| `style→connectorThickness` | Thickness in pixels of the connecting line drawn between boxes in glyphs that draw segments (like the Segments, ProcessedTranscript, and Gene glyphs). Default 1. | +| `style→utrColor` | Color of UTR regions drawn by ProcessedTranscript and Gene glyphs. Color syntax is the same as that used for CSS, specified at http://dev.w3.org/csswg/css-color/. Defaults to be a color that complements the current `style→color` value (calculated using a bit of color theory). | +| `subParts` | Comma-separated list of feature `type` tags that will be drawn as subparts of parent features. Defaults to all features for Segments glyphs, and 'CDS, UTR, five_prime_UTR, three_prime_UTR' for ProcessedTranscript glyphs. | +| `transcriptType` | For Gene glyphs, the feature `type` tag that indicates that a subfeature is a processed transcript. Defaults to 'mRNA'. | +| `labelTranscripts` | For Gene glyphs, if true, draw a label with the transcript's name beside each transcript, if space permits. Default true. | +| `style→transcriptLabelColor` | For Gene glyphs, the color of transcript name labels. Color syntax is the same as that used for CSS, specified at http://dev.w3.org/csswg/css-color/. Default 'black'. | +| `style→transcriptLabelFont` | For Gene glyphs, the font used for transcript name labels. Same format as CSS font rules. Default 'normal 10px Univers,Helvetica,Arial,sans-serif'. | +| `impliedUTRs` | Introduced in JBrowse 1.10.5. If true, indicates that UTRs are not present in the feature data, but should be inferred from the overlap of exon and CDS features in ProcessedTranscript and Gene glyphs. Default false. Can be a callback. | +| `maxFeatureGlyphExpansion` | A factor to expand the glyphs by so that if subfeatures go outside the bounds of the parent feature, they will still be rendered. Default: 500bp/current scale. | +| `inferCdsParts ` | If a single CDS span covers the whole gene except the UTRs, then it is drawn as though it only covers the exon parts (not the introns). Default: false. Added in 1.12.3 | +| `disableCollapsedClick` | Disables the click action when track is collapsed. Default: false. Added in 1.13.0 | +| `enableCollapsedMouseover` | Enables the mouseover action when track is collapsed. Default: false. Added in 1.13.0. See the ChromHMM track in volvox sample browser for example of mouseover on the collapsed track | +| `topLevelFeatures` | Specifies which feature types should be considered "top-level" for this track. For example, if you have a track with gene-\>mRNA-\>CDS features, but for some reason want to only display the mRNA features, you can set topLevelFeatures=mRNA. Can also be an array of string types, or a function callback that returns an array of types. Default: all features are displayed. Added in 1.14.0 | +| `ItemRgb` | If set to true, the RGB colors specified in BigBed or BED files will be used for the feature's background color. Default true. Added in 1.14.0 | `CanvasFeatures` track configuration options - Note: the "compact" displayMode for CanvasFeatures tracks uses style-\>height and multiplies it by 0.35 to create the compact view. Therefore, if you adjust style-\>height to a smaller default value, then you can create "ultra compact" visualizations. - - - - ### Customizing CanvasFeatures tracks with callbacks Unlike HTML-based feature tracks, canvas-based feature tracks don't use @@ -1089,8 +1043,8 @@ you could set something like: } return false; } - style.color = function( feature, variableName, glyphObject, track ) { - return track.config.variantIsHeterozygous(feature) ? 'red' : 'blue'; + style.color = function( feature, variableName, glyphObject, track ) { + return track.config.variantIsHeterozygous(feature) ? 'red' : 'blue'; } Note: the multiline callbacks are only enabled in the tracks.conf form. @@ -1100,14 +1054,12 @@ about this format. ## Generic Track Configuration Options -| Option | Description | -|----|----| +| Option | Description | +| ------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | `subfeatureDetailLevel ` | Set the level of detail of the View details box. If set to 1, only displays one level of subfeatures for example. Default: 0 which displays all subfeature levels. Added in 1.12.3 | `Generic track` configuration options - - ## Customizing parts of the 'View details' Pop-ups with callbacks Starting in JBrowse version 1.11.3, the ability to customize parts of @@ -1116,7 +1068,6 @@ that have the format fmtDetailValue\_\* or fmtDetailField\_\* to either change the value section of an attribute in the config, or the fieldname of an attribute in the config. - Here is an example in tracks.conf format for formatting the "Name" field by adding a link to it: @@ -1138,7 +1089,6 @@ Note: It is also easy to specify these methods in trackList.json format. "fmtDetailValue_Name": "function(name) { return ''+name+''; }" } - Addendum: If the field has multiple values (e.g. multiple DBXrefs or GO terms), then the callback will receive an array as it's argument, and then you can also return an array which indicates that each element will @@ -1185,14 +1135,12 @@ tracks (both HTMLFeatures and CanvasFeatures) is highly configurable. To make something happen when left-clicking features on a track, add an onClick option to the feature track's configuration. - In the example configuration below, left-clicks on features will open an embedded popup window showing the results of searching for that feature's name in NCBI's global search, and "search at NCBI" will show in a tooltip when the user hovers over a feature with the mouse: - -``` de1 +```de1 "tracks": [ { "label" : "ReadingFrame", @@ -1207,7 +1155,6 @@ in a tooltip when the user hovers over a feature with the mouse: ... ``` - For details on all the options supported by **onClick**, see [Click Configuration Options](#Click_Configuration_Options). @@ -1224,14 +1171,10 @@ In JBrowse 1.11.6, the onClick-\>label attribute was extended further to allow the mouse-over description to be customized using callbacks and template strings. - Example for CanvasFeatures, allows full HTML tooltips. Here the {name} template is automatically filled in with the feature info: - - - -``` de1 +```de1 "onClick": { "label" : "Feature name: {name}", "title" : "{name} {type}", @@ -1239,13 +1182,11 @@ template is automatically filled in with the feature info: } ``` - Example for HTMLFeatures, which only allows plain text descriptions but can support newlines (essentially uses \ for mouseover). - -``` de1 +```de1 "onClick": { "label": "Feature name {name}\nFeature start {start}\nFeature end {end}", "title" : "{name} {type}", @@ -1253,15 +1194,10 @@ mouseover). } ``` - - Example using a callback (for either HMTLFeatures or CanvasFeatures), using this.feature to access the feature details - - - -``` de1 +```de1 "onClick": { "label": "function() { return 'Feature name: '+this.feature.get('name'); }", "title" : "{name} {type}", @@ -1269,8 +1205,6 @@ using this.feature to access the feature details } ``` - - Note: on CanvasFeatures, the action "defaultDialog" isn't necessary, but it is necessary for HTMLFeatures to keep the default dialog (as of writing, 1.11.6). @@ -1293,7 +1227,6 @@ the store's feature density divided by `maxFeatureScreenDensity`). This is often used for BAM coverage on Alignments2 tracks using the `histograms.urlTemplate` and `histograms.storeClass` arguments. - Example track [ tracks.mytrack ] @@ -1387,11 +1320,6 @@ This configuration results in a context menu like the one pictured below. For details on what each of the options supported by menu items does, see [\#Click Configuration Options](#Click_Configuration_Options). - - - - - ## Rendering high resolution screenshots using Puppeteer The Google Chrome headless browser "Puppeteer" is an alternative to @@ -1437,68 +1365,37 @@ needed. The third, fourth, fifth and sixth arguments are optional a) output filename b) output width c) output height and d) zoom factor to make it higher resolution - - # External Links - JBrowse: A Next Generation Genome Browser paper - Retrieved from -"[http://gmod.org/mediawiki/index.php?title=JBrowse_Configuration_Guide&oldid=27898#Using_JBrowse_with_Existing_Databases](http://gmod.org/mediawiki/index.php?title=JBrowse_Configuration_Guide&oldid=27898#Using_JBrowse_with_Existing_Databases#Using_JBrowse_with_Existing_Databases)" - - - +"[http://gmod.org/mediawiki/index.php?title=JBrowse_Configuration_Guide&oldid=27898#Using_JBrowse_with_Existing_Databases](JBrowse_Configuration_Guide" [Category](Special%253ACategories "Special%253ACategories"): - [JBrowse](Category%253AJBrowse "Category%253AJBrowse") - - - - - ## Navigation menu - - - - - - - - ### Navigation - - - [GMOD Home](Main_Page) - [Software](GMOD_Components) - [Categories / Tags](Categories) - - - ### Documentation - - - [Overview](Overview) - [FAQs](Category%253AFAQ) - [HOWTOs](Category%253AHOWTO) - [Glossary](Glossary) - - - ### Community - - - [GMOD News](GMOD_News) - [Training / Outreach](Training_and_Outreach) @@ -1507,18 +1404,12 @@ Retrieved from - [Meetings](Meetings) - [Calendar](Calendar) - - - ### Tools - Browse properties - - -- Last updated at 02:48 on 30 September - 2020. +- Last updated at 02:48 on 30 September 2020. - Content is available under - - - - - - diff --git a/wiki/WebApollo_Tutorial.md b/wiki/WebApollo_Tutorial.md index 41fa14ff78..365d8bb77e 100644 --- a/wiki/WebApollo_Tutorial.md +++ b/wiki/WebApollo_Tutorial.md @@ -14,7 +14,7 @@ (Redirected from [WebApollo -Tutorial](http://gmod.org/mediawiki/index.php?title=WebApollo_Tutorial&redirect=no "WebApollo Tutorial")) +Tutorial](WebApollo_Tutorial) From fe92b8211022c29a3f3e64b9178a8c92e4891fbd Mon Sep 17 00:00:00 2001 From: Scott Cain Date: Fri, 19 Jul 2024 16:19:51 -0700 Subject: [PATCH 2/2] removing several more gmod.org/mediawiki links --- wiki/Category%3A!FixAfterUpgrade.md | 7 +- wiki/Category%3A2013_Summer_School.md | 7 +- wiki/Category%3ABioDIG.md | 7 +- wiki/Category%3ACanto.md | 5 +- wiki/Category%3ACloud.md | 7 +- wiki/Category%3ADatabase.md | 7 +- wiki/Category%3ADeprecated.md | 7 +- wiki/Category%3AFile_Formats.md | 7 +- wiki/Category%3AGFF.md | 7 +- wiki/Category%3AGFF3.md | 7 +- wiki/Category%3AGMOD_Online_Training.md | 7 +- wiki/Category%3AGeneric_Gene_Pages.md | 7 +- wiki/Category%3AInstall.md | 7 +- wiki/Category%3AJobs.md | 7 +- wiki/Category%3ANGS.md | 7 +- ...ry%3APages_containing_blacklisted_links.md | 7 +- ...Category%3APages_with_broken_file_links.md | 7 +- wiki/Category%3APerformance.md | 7 +- wiki/Category%3AREST.md | 7 +- wiki/Category%3ARPC.md | 7 +- wiki/Category%3ARails.md | 7 +- wiki/Category%3AReactome.md | 7 +- wiki/Category%3ASAMtools.md | 7 +- wiki/Category%3ASemanticLink.md | 7 +- wiki/Category%3ASession.md | 7 +- wiki/Category%3ASocial_Media.md | 7 +- wiki/Category%3ASoftware_Engineer.md | 7 +- wiki/Category%3ATemplate.md | 7 +- wiki/Category%3ATools_using_GMOD.md | 7 +- wiki/Category%3ATutorial.md | 7 +- wiki/Category%3AUsers.md | 7 +- wiki/Category%3AVisualization.md | 7 +- wiki/Category%3AWebGBrowse.md | 7 +- wiki/Chado_Best_Practices.md | 285 +-- wiki/GBrowse_syn.1.md | 4 +- wiki/GO%3A%3ATermFinder.1.md | 4 +- wiki/GO_Graphic_Viewer.1.md | 4 +- wiki/Generic_Genome_Browser.md | 4 +- wiki/InterMine.md | 4 +- wiki/JBrowse.1.md | 4 +- wiki/JBrowse2.md | 4 +- wiki/JBrowseDev/Installation.md | 4 +- wiki/JBrowseDev/Main.md | 4 +- wiki/MAKER.1.md | 4 +- wiki/Pathway_Tools.1.md | 4 +- wiki/Special%3ASearch/!FixAfterUpgrade.md | 165 -- wiki/Special%3ASearch/2013_Summer_School.md | 1063 -------- wiki/Special%3ASearch/Database.md | 1483 ----------- wiki/Special%3ASearch/Deprecated.md | 863 ------- wiki/Special%3ASearch/File_Formats.md | 1232 --------- wiki/Special%3ASearch/GMOD_Online_Training.md | 932 ------- wiki/Special%3ASearch/GSOC.md | 1465 ----------- wiki/Special%3ASearch/Generic_Gene_Pages.md | 1218 --------- wiki/Special%3ASearch/Install.md | 1297 ---------- wiki/Special%3ASearch/Jobs.md | 842 ------- .../Pages_containing_blacklisted_links.md | 113 - .../Pages_with_broken_file_links.md | 222 -- wiki/Special%3ASearch/Performance.md | 1210 --------- wiki/Special%3ASearch/REST.md | 1219 --------- wiki/Special%3ASearch/RPC.md | 297 --- wiki/Special%3ASearch/Rails.md | 286 --- wiki/Special%3ASearch/Reactome.md | 776 ------ wiki/Special%3ASearch/SAMtools.md | 792 ------ wiki/Special%3ASearch/SemanticLink.md | 477 ---- wiki/Special%3ASearch/Session.md | 1181 --------- wiki/Special%3ASearch/Social_Media.md | 479 ---- wiki/Special%3ASearch/Software_Engineer.md | 429 ---- wiki/Special%3ASearch/Template.md | 1079 -------- wiki/Special%3ASearch/Tools_using_GMOD.md | 1230 --------- wiki/Special%3ASearch/Tutorial.md | 2227 ----------------- wiki/Special%3ASearch/Users.md | 1227 --------- wiki/Textpresso.md | 4 +- wiki/XORT.1.md | 4 +- 73 files changed, 93 insertions(+), 24277 deletions(-) delete mode 100644 wiki/Special%3ASearch/!FixAfterUpgrade.md delete mode 100644 wiki/Special%3ASearch/2013_Summer_School.md delete mode 100644 wiki/Special%3ASearch/Database.md delete mode 100644 wiki/Special%3ASearch/Deprecated.md delete mode 100644 wiki/Special%3ASearch/File_Formats.md delete mode 100644 wiki/Special%3ASearch/GMOD_Online_Training.md delete mode 100644 wiki/Special%3ASearch/GSOC.md delete mode 100644 wiki/Special%3ASearch/Generic_Gene_Pages.md delete mode 100644 wiki/Special%3ASearch/Install.md delete mode 100644 wiki/Special%3ASearch/Jobs.md delete mode 100644 wiki/Special%3ASearch/Pages_containing_blacklisted_links.md delete mode 100644 wiki/Special%3ASearch/Pages_with_broken_file_links.md delete mode 100644 wiki/Special%3ASearch/Performance.md delete mode 100644 wiki/Special%3ASearch/REST.md delete mode 100644 wiki/Special%3ASearch/RPC.md delete mode 100644 wiki/Special%3ASearch/Rails.md delete mode 100644 wiki/Special%3ASearch/Reactome.md delete mode 100644 wiki/Special%3ASearch/SAMtools.md delete mode 100644 wiki/Special%3ASearch/SemanticLink.md delete mode 100644 wiki/Special%3ASearch/Session.md delete mode 100644 wiki/Special%3ASearch/Social_Media.md delete mode 100644 wiki/Special%3ASearch/Software_Engineer.md delete mode 100644 wiki/Special%3ASearch/Template.md delete mode 100644 wiki/Special%3ASearch/Tools_using_GMOD.md delete mode 100644 wiki/Special%3ASearch/Tutorial.md delete mode 100644 wiki/Special%3ASearch/Users.md diff --git a/wiki/Category%3A!FixAfterUpgrade.md b/wiki/Category%3A!FixAfterUpgrade.md index c7d5d452d6..28524aab19 100644 --- a/wiki/Category%3A!FixAfterUpgrade.md +++ b/wiki/Category%3A!FixAfterUpgrade.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/!FixAfterUpgrade "Special%253ASearch/!FixAfterUpgrade") -in other pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3A2013_Summer_School.md b/wiki/Category%3A2013_Summer_School.md index ee1b19059a..c904cab987 100644 --- a/wiki/Category%3A2013_Summer_School.md +++ b/wiki/Category%3A2013_Summer_School.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/2013_Summer_School "Special:Search/2013 Summer School") -in other pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3ABioDIG.md b/wiki/Category%3ABioDIG.md index fdb57604ad..bfa5ec01b4 100644 --- a/wiki/Category%3ABioDIG.md +++ b/wiki/Category%3ABioDIG.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](http://gmod.org/wiki/Special:Search/BioDIG "Special:Search/BioDIG") -in other pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3ACanto.md b/wiki/Category%3ACanto.md index 2fd7b8bbc4..94488ec557 100644 --- a/wiki/Category%3ACanto.md +++ b/wiki/Category%3ACanto.md @@ -21,10 +21,7 @@ There is currently no text in this page. You can [search for this page title](http://gmod.org/wiki/Special:Search/Canto "Special:Search/Canto") -in other pages, or search the related logs, -but you do not have permission to create this page. +in other pages diff --git a/wiki/Category%3ACloud.md b/wiki/Category%3ACloud.md index fffcf1eab3..cdc53b84a6 100644 --- a/wiki/Category%3ACloud.md +++ b/wiki/Category%3ACloud.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](http://gmod.org/wiki/Special:Search/Cloud "Special:Search/Cloud") -in other pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3ADatabase.md b/wiki/Category%3ADatabase.md index 59af87b3b6..1852371432 100644 --- a/wiki/Category%3ADatabase.md +++ b/wiki/Category%3ADatabase.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/Database "Special%253ASearch/Database") in other -pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3ADeprecated.md b/wiki/Category%3ADeprecated.md index 695e84e6c6..5913c01bc5 100644 --- a/wiki/Category%3ADeprecated.md +++ b/wiki/Category%3ADeprecated.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/Deprecated "Special%253ASearch/Deprecated") in other -pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3AFile_Formats.md b/wiki/Category%3AFile_Formats.md index 50efbf7ac6..b692666c67 100644 --- a/wiki/Category%3AFile_Formats.md +++ b/wiki/Category%3AFile_Formats.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/File_Formats "Special:Search/File Formats") in -other pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3AGFF.md b/wiki/Category%3AGFF.md index c8e2809dc0..80e9c98bf5 100644 --- a/wiki/Category%3AGFF.md +++ b/wiki/Category%3AGFF.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](http://gmod.org/wiki/Special:Search/GFF "Special:Search/GFF") in -other pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3AGFF3.md b/wiki/Category%3AGFF3.md index 37e45c55a5..1a99576948 100644 --- a/wiki/Category%3AGFF3.md +++ b/wiki/Category%3AGFF3.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](http://gmod.org/wiki/Special:Search/GFF3 "Special:Search/GFF3") -in other pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3AGMOD_Online_Training.md b/wiki/Category%3AGMOD_Online_Training.md index 5960e53a8d..0333e49f51 100644 --- a/wiki/Category%3AGMOD_Online_Training.md +++ b/wiki/Category%3AGMOD_Online_Training.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/GMOD_Online_Training "Special:Search/GMOD Online Training") -in other pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3AGeneric_Gene_Pages.md b/wiki/Category%3AGeneric_Gene_Pages.md index 71d7cb5797..0c76719efb 100644 --- a/wiki/Category%3AGeneric_Gene_Pages.md +++ b/wiki/Category%3AGeneric_Gene_Pages.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/Generic_Gene_Pages "Special:Search/Generic Gene Pages") -in other pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3AInstall.md b/wiki/Category%3AInstall.md index 01290c7f94..b97fad0ec3 100644 --- a/wiki/Category%3AInstall.md +++ b/wiki/Category%3AInstall.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/Install "Special%253ASearch/Install") in other pages, -or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3AJobs.md b/wiki/Category%3AJobs.md index 32095082c0..d3aa1fa4cc 100644 --- a/wiki/Category%3AJobs.md +++ b/wiki/Category%3AJobs.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/Jobs "Special%253ASearch/Jobs") in other pages, or -search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3ANGS.md b/wiki/Category%3ANGS.md index cad82a1f71..ec2c1ff466 100644 --- a/wiki/Category%3ANGS.md +++ b/wiki/Category%3ANGS.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](http://gmod.org/wiki/Special:Search/NGS "Special:Search/NGS") in -other pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3APages_containing_blacklisted_links.md b/wiki/Category%3APages_containing_blacklisted_links.md index 4c04eb041a..45e5ce446f 100644 --- a/wiki/Category%3APages_containing_blacklisted_links.md +++ b/wiki/Category%3APages_containing_blacklisted_links.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/Pages_containing_blacklisted_links "Special:Search/Pages containing blacklisted links") -in other pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3APages_with_broken_file_links.md b/wiki/Category%3APages_with_broken_file_links.md index f87e407acf..dc863760fd 100644 --- a/wiki/Category%3APages_with_broken_file_links.md +++ b/wiki/Category%3APages_with_broken_file_links.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/Pages_with_broken_file_links "Special:Search/Pages with broken file links") -in other pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3APerformance.md b/wiki/Category%3APerformance.md index b6d68f947b..350b07f2b8 100644 --- a/wiki/Category%3APerformance.md +++ b/wiki/Category%3APerformance.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/Performance "Special%253ASearch/Performance") in other -pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3AREST.md b/wiki/Category%3AREST.md index 1a39dad08a..e3936995b4 100644 --- a/wiki/Category%3AREST.md +++ b/wiki/Category%3AREST.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/REST "Special%253ASearch/REST") in other pages, or -search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3ARPC.md b/wiki/Category%3ARPC.md index 597f0c57c8..655fcd47c3 100644 --- a/wiki/Category%3ARPC.md +++ b/wiki/Category%3ARPC.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/RPC "Special%253ASearch/RPC") in other pages, or -search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3ARails.md b/wiki/Category%3ARails.md index 67611cc94e..5da48fbcb1 100644 --- a/wiki/Category%3ARails.md +++ b/wiki/Category%3ARails.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/Rails "Special%253ASearch/Rails") in other pages, or -search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3AReactome.md b/wiki/Category%3AReactome.md index d2b169968c..11a607d7f8 100644 --- a/wiki/Category%3AReactome.md +++ b/wiki/Category%3AReactome.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/Reactome "Special%253ASearch/Reactome") in other -pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3ASAMtools.md b/wiki/Category%3ASAMtools.md index 075f2fb384..00b6233ae7 100644 --- a/wiki/Category%3ASAMtools.md +++ b/wiki/Category%3ASAMtools.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/SAMtools "Special%253ASearch/SAMtools") in other -pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3ASemanticLink.md b/wiki/Category%3ASemanticLink.md index 35c517e77e..62e25125dd 100644 --- a/wiki/Category%3ASemanticLink.md +++ b/wiki/Category%3ASemanticLink.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/SemanticLink "Special%253ASearch/SemanticLink") in -other pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3ASession.md b/wiki/Category%3ASession.md index 7574e6abc6..64bb0f6d56 100644 --- a/wiki/Category%3ASession.md +++ b/wiki/Category%3ASession.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/Session "Special%253ASearch/Session") in other pages, -or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3ASocial_Media.md b/wiki/Category%3ASocial_Media.md index fe066d4a3c..2581dff776 100644 --- a/wiki/Category%3ASocial_Media.md +++ b/wiki/Category%3ASocial_Media.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/Social_Media "Special:Search/Social Media") in -other pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3ASoftware_Engineer.md b/wiki/Category%3ASoftware_Engineer.md index 9761d97599..5568235972 100644 --- a/wiki/Category%3ASoftware_Engineer.md +++ b/wiki/Category%3ASoftware_Engineer.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/Software_Engineer "Special:Search/Software Engineer") -in other pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3ATemplate.md b/wiki/Category%3ATemplate.md index feefe7f944..3641999c0c 100644 --- a/wiki/Category%3ATemplate.md +++ b/wiki/Category%3ATemplate.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/Template "Special%253ASearch/Template") in other -pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3ATools_using_GMOD.md b/wiki/Category%3ATools_using_GMOD.md index 9529464fda..2efc83671f 100644 --- a/wiki/Category%3ATools_using_GMOD.md +++ b/wiki/Category%3ATools_using_GMOD.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/Tools_using_GMOD "Special:Search/Tools using GMOD") -in other pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3ATutorial.md b/wiki/Category%3ATutorial.md index f5cb82eb27..6006c58d45 100644 --- a/wiki/Category%3ATutorial.md +++ b/wiki/Category%3ATutorial.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/Tutorial "Special%253ASearch/Tutorial") in other -pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3AUsers.md b/wiki/Category%3AUsers.md index 2d570b3538..9e533b7db2 100644 --- a/wiki/Category%3AUsers.md +++ b/wiki/Category%3AUsers.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](Special%253ASearch/Users "Special%253ASearch/Users") in other pages, or -search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3AVisualization.md b/wiki/Category%3AVisualization.md index bd7cac9e59..1db16abb97 100644 --- a/wiki/Category%3AVisualization.md +++ b/wiki/Category%3AVisualization.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](http://gmod.org/wiki/Special:Search/Visualization "Special:Search/Visualization") -in other pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Category%3AWebGBrowse.md b/wiki/Category%3AWebGBrowse.md index 9e6f1b2318..7e48608900 100644 --- a/wiki/Category%3AWebGBrowse.md +++ b/wiki/Category%3AWebGBrowse.md @@ -19,12 +19,7 @@ -There is currently no text in this page. You can [search for this page -title](http://gmod.org/wiki/Special:Search/WebGBrowse "Special:Search/WebGBrowse") -in other pages, or search the related logs, -but you do not have permission to create this page. + diff --git a/wiki/Chado_Best_Practices.md b/wiki/Chado_Best_Practices.md index 50c8c399ce..db2b25a9fb 100644 --- a/wiki/Chado_Best_Practices.md +++ b/wiki/Chado_Best_Practices.md @@ -1,22 +1,7 @@ - - - - - - - # Chado Best Practices - - - - - - - - Chado is a generic [schema](Glossary#Database_Schema "Glossary"), which means anyone writing software to query or write to chado (either [middleware](GMOD_Middleware "GMOD Middleware") or applications) should @@ -43,11 +28,8 @@ See also: further discussion on these conventions and how they were implemented at IGS (for comparison) - ## Contents - - - [1 Gene Models](#Gene_Models) - [1.1 Canonical @@ -157,15 +139,11 @@ See also: - [11 xxx Genome Versions](#xxx_Genome_Versions) - - ### Gene Models This section describes how one describes commonly encountered gene models in Chado. - - #### Canonical Gene Model The contig, a SO:Gene | 1 | The gene must always be provided | -| feature | SO:mRNA | 1 or more | One or more transcripts are required, and these are always of type SO:mRNA for protein-coding genes. | -| feature | exon | 1 or more | Exons are always required, even if the genome under consideration has no introns. | -| feature | polypeptide | At least 1 | A protein-coding gene always produces a polypeptide, by definition. The polypeptide is located relative to the same genomic feature as the exons, mRNAs and gene. A single featureloc is used, with *fmin* and *fmax* indicating the start and stop codon positions (location is inclusive of stop codon). The polypeptide sequence should be specified as an amino acid sequence. | - - +| Table | type_id | Number | Comments | +| -------------------------------------------------------------------------- | --------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| feature | SO:Gene | 1 | The gene must always be provided | +| feature | SO:mRNA | 1 or more | One or more transcripts are required, and these are always of type SO:mRNA for protein-coding genes. | +| feature | exon | 1 or more | Exons are always required, even if the genome under consideration has no introns. | +| feature | polypeptide | At least 1 | A protein-coding gene always produces a polypeptide, by definition. The polypeptide is located relative to the same genomic feature as the exons, mRNAs and gene. A single featureloc is used, with _fmin_ and _fmax_ indicating the start and stop codon positions (location is inclusive of stop codon). The polypeptide sequence should be specified as an amino acid sequence. | ##### Querying for Canonical Genes @@ -217,8 +191,7 @@ its [feature graph](Introduction_to_Chado#Feature_Graphs "Introduction to Chado") has 3 levels. If we follow this assumption: - -``` de1 +```de1 SELECT * FROM feature AS gene INNER JOIN feature_relationship AS feat0 ON (gene.feature_id = feat0.object_id) @@ -232,7 +205,6 @@ graph](Introduction_to_Chado#Feature_Graphs "Introduction to Chado") has gene.name = 'Dredd'; ``` - This query should fetch a 3-deep graph rooted at "Dredd". ##### Application Support @@ -240,8 +212,6 @@ This query should fetch a 3-deep graph rooted at "Dredd". - Supported by [Apollo](Apollo.1 "Apollo") - Supported by [GBrowse](GBrowse.1 "GBrowse") - - #### Noncoding Genes Similar to [canonical model](#Canonical_Gene_Model), except with @@ -253,8 +223,6 @@ model](#Canonical_Gene_Model), with the following exceptions: - Instead of an mRNA feature, there is a feature that is some other sub-type of RNA - - ##### Application Support - Supported by [Apollo](Apollo.1 "Apollo") @@ -285,8 +253,6 @@ no-one is using Chado to do this. There are currently two practices: a later date it becomes desirable to annotated the exon structure of a pseudogene, it will be compatible with this. - - ##### Application Support - [Apollo](Apollo.1 "Apollo"): status is unclear. @@ -309,8 +275,6 @@ located relative to other features (usually the genome, but once can have singletons that are located relative to other features - this may not be supported by all applications) - - ##### Application Support - Supported by [Apollo](Apollo.1 "Apollo") @@ -321,8 +285,6 @@ genome (singletons located relative to other features will be ignored). It may be necessary to configure apollo to make the feature type "1-level". - - #### Dicistronic Gene A dicistronic gene is a gene with a mRNA that codes for two distinct @@ -359,34 +321,19 @@ April 2007 (EDT)

- There are currently two proposals for handling dicistronic genes. The first is a hack and introduces redundancy, but works well with existing software and tools. The second is prefered from a modeling standpoint, but introduces a lot of complexity to software. - - - - - - #### xxx Operon -> **This page or section needs to be edited.** -> Please help by href="http://gmod.org/mediawiki/index.php?title=Chado_Best_Practices&action=edit" -> class="external text" rel="nofollow">editing this page to -> add your revisions or additions. - -Bacterial genes are often transcribed in groups; e.g. *lacZ*, *lacA* and -*lacY* make up the +Bacterial genes are often transcribed in groups; e.g. _lacZ_, _lacA_ and +_lacY_ make up the Lac operon. There are many similarities with [dicistronic genes](#Dicistronic_Gene) here. - - #### Trans-spliced Gene A trans-spliced gene has one or more transcripts in which that @@ -396,8 +343,8 @@ A trans-spliced transcript is spliced from exons coming from different parts of the genome. The distance between each trans-spliced part may be large, or it may be in the same location on the opposite strand. -Most *C. elegans* genes have a trans-spliced leader sequence. This is -different from the trans-splicing involved in *Drosophila*, where we +Most _C. elegans_ genes have a trans-spliced leader sequence. This is +different from the trans-splicing involved in _Drosophila_, where we observe what appears to be two transcripts on separate strands (both containing coding sequence) joining together in a single functional transcript. @@ -406,14 +353,14 @@ There are two proposals for dealing with this. One treats the trans-spliced transcript as a single transcripts, with exons coming from different locations. The other treats the trans-spliced transcript as a mature transcript created from two distinct primary transcripts. Note -that these proposals focus on the *Drosophila* example. A solution for -the *C. elegans* example has not been proposed. +that these proposals focus on the _Drosophila_ example. A solution for +the _C. elegans_ example has not been proposed. We treat this as an ordinary gene model, but relax our rules for exon -locations in a transcript. For example, for the canonical *Drosophila* +locations in a transcript. For example, for the canonical _Drosophila_ trans-spliced gene, we would allow transcripts to have exons on different strands. Note that in Chado, exon ordering comes from -*feature_relationship.rank* (between exon and transcript), **not** from +_feature_relationship.rank_ (between exon and transcript), **not** from the featureloc of the exon. Chado has no problem with this. However, some software may make assumptions that all exons are on the same strand, or may try to order exons by their location to get a transcript @@ -427,36 +374,18 @@ introduces a major departure from the [canonical gene model](#Canonical_Gene_Model). For this reason this proposal is unlikely to be adopted. - - ##### Application Support - [Apollo](Apollo.1 "Apollo"): status unclear. - [GBrowse](GBrowse.1 "GBrowse"): status unclear. - - #### xxx Gene with Regulatory Elements -> **This page or section needs to be edited.** -> Please help by href="http://gmod.org/mediawiki/index.php?title=Chado_Best_Practices&action=edit" -> class="external text" rel="nofollow">editing this page to -> add your revisions or additions. - Regulatory elements may be implicitly or explicitly associated with a gene. - - #### xxx Transposons -> **This page or section needs to be edited.** -> Please help by href="http://gmod.org/mediawiki/index.php?title=Chado_Best_Practices&action=edit" -> class="external text" rel="nofollow">editing this page to -> add your revisions or additions. - Transposons can be annotated as [singleton features](#Singleton_Feature) or as complex annotations. You would create a feature of type transposon insertion, with a loc of type 0 for insertion sites when the insertion @@ -479,7 +408,7 @@ uncharted water as far as both Chado and annotation tools are concerned (which is why this scenario is marked as being under discussion). One option would be to treat each transposon part as distinct singletons, but this may be unsatisfactory as one may desire to have the appropriate -*part_of* relations between the parts. +_part_of_ relations between the parts. #### Gene with Implicit Features Manifested @@ -489,8 +418,6 @@ consecutive exons. See for an example. Occasionally it may be desirable to store the introns as actual rows in the feature table - for example in a report database. - - #### Unlocalized Gene A gene without sequence based localization. @@ -528,7 +455,7 @@ distinct subfeatures (e.g. a transcript composes of exons), then it is **not** permitted to use multiple featurelocs to indicate this. Instead, there must be rows for the subfeatures, each with their own featureloc. -In a feature graph (i.e. a group of features connected *via* +In a feature graph (i.e. a group of features connected _via_ [feature_relationship](Chado_Tables#Table:_feature_relationship "Chado Tables") rows, all features will typically be localized relative to the same source feature (i.e. they will all have the same value for @@ -540,8 +467,6 @@ example, localizing features relative to a transcript or polypeptide or even exon is permitted, but unusual practices will most likely not be recognized by most software. - - #### Feature Localization to Contigs in Assembly In an assembled genome, it is common to locate relative to the top-level @@ -565,8 +490,6 @@ assembly feature. It may sometimes be desirable to have software that can perform location transformations, mapping features from contigs to top-level units and back. - - ##### Application Support - [Apollo](Apollo.1 "Apollo"): status unclear. @@ -587,7 +510,7 @@ such as chromosomes. Features can be located relative to both contigs and top-level assembly units. -Chado allows redundant feature localization using *featureloc.locgroup* +Chado allows redundant feature localization using _featureloc.locgroup_ \> 0. This allows a database to have primary locations for features relative to contigs, and secondary locations relative to top-level units such as chromosomes. The converse is also allowed. @@ -604,13 +527,13 @@ circumstances - [GBrowse](GBrowse.1 "GBrowse"): status unclear. - [GBrowse](GBrowse.1 "GBrowse"): status partial. -It is not clear if GBrowse uses *locgroup* in querying. If it constrains -by *locgroup*, then this is essentially the same as [feature +It is not clear if GBrowse uses _locgroup_ in querying. If it constrains +by _locgroup_, then this is essentially the same as [feature localization to contigs in assembly](#Feature_Localization_to_Contigs_in_Assembly). -Not clear if Apollo uses *locgroup* in querying. If it constrains by -*locgroup*, then this is essentially the same as [feature localization +Not clear if Apollo uses _locgroup_ in querying. If it constrains by +_locgroup_, then this is essentially the same as [feature localization to contigs in assembly](#Feature_Localization_to_Contigs_in_Assembly). Apollo will not preserve redundant *featureloc*s when writing back to the database. This could lead to the database getting out of sync. @@ -626,30 +549,18 @@ relative to chromosomes. Most software that interoperates with Chado will not be able to deal with this, so this scenario is discouraged except by advanced users who have no other option. - - #### Immature or Primary RNA Generally we do not explicitly represent primary RNA transcripts unless there is something useful to say about them. If one wants to instantiate these they would be represented as features, and the mature message -would be related to the primary message with *derived_from* as *type_id* +would be related to the primary message with _derived_from_ as _type_id_ in the [feature_relationship](Chado_Tables#Table:_feature_relationship "Chado Tables") table. - - ### xxx Genomic Rearrangements -> **This page or section needs to be edited.** -> Please help by href="http://gmod.org/mediawiki/index.php?title=Chado_Best_Practices&action=edit" -> class="external text" rel="nofollow">editing this page to -> add your revisions or additions. - - - #### Inversions Create a feature of type inversion with location spanning the inverted @@ -666,8 +577,6 @@ B' (post-rearrangement) and locate on B' and A', respectively. How to capture the fact that Afrag and Bfrag and A' and B' are part of same rearrangement? Use feature relations? - - #### Translocations Create a feature of type translocation with a location spanning the @@ -681,8 +590,6 @@ about this. Good point; we pondered adding a CV term to featureloc (I think it's still useful to have rank anyway - e.g. for multiple alignments). - - #### Deletions #### Copy Number Variations @@ -719,13 +626,13 @@ Here we would have one feature and two featurelocs. (locgroup 0))) The first location is on the chromosome arm (presumably wild type). The -second location has no *srcfeature* value (i.e. it is set to null). +second location has no _srcfeature_ value (i.e. it is set to null). However, it is effectively paired with the first location. if we later wished to instantiate the mutant chromosome arm feature, we would fill -in the second locgroup's *srcfeature*. +in the second locgroup's _srcfeature_. Let's take another example - a SNP that has only been characterised at -the protein level. This SNP changes an *I* to a *V*. +the protein level. This SNP changes an _I_ to a _V_. (feature (name "SNP_02") @@ -744,12 +651,11 @@ the protein level. This SNP changes an *I* to a *V*. Again, the second featureloc has no srcfeature. The mutant protein is implicit. The mutant protein sequence can be infered by taking the -sequence of *dpp-P1* and substituting the 24th residue with a *V*. +sequence of _dpp-P1_ and substituting the 24th residue with a _V_. To do a query for all SNPs that switch I to V or vice versa: - -``` de1 +```de1 SELECT snp.* FROM featureloc AS wildloc, @@ -766,7 +672,6 @@ WHERE mutloc.residue_info = 'I'; ``` - Note that this query remains the same even if mutant protein features are instantiated as opposed to left implicit. @@ -824,18 +729,15 @@ the residue is reverse complemented. (locgroup 2))) Here we have 6 locations for one SNP. The 6 locations can be imagined to -be in a 2-D matrix. The purpose of *rank* and *locgroup* is to specify +be in a 2-D matrix. The purpose of _rank_ and _locgroup_ is to specify the column and row in the matrix. - - | Allele | Genome | Transcript | Protein | -|-----------|--------|------------|---------| +| --------- | ------ | ---------- | ------- | | Wild-type | A | T | I | | Mutant | G | C | T | - -*rank* is used to group the strain and *locgroup* is used for the +_rank_ is used to group the strain and _locgroup_ is used for the grouping within that strain. rank=0 should be used for the wildtype, but this is not always possible; locgroup=0 should be used for primary (as opposed to derived) location, this is not always possible. The important @@ -848,14 +750,11 @@ different frames). Here we would want to add another locgroup, for the second protein. - - | Allele | Genome | Transcript | Protein1 | Protein2 | -|-----------|--------|------------|----------|----------| +| --------- | ------ | ---------- | -------- | -------- | | Wild-type | A | T | I | Y | | Mutant | G | C | T | H | - Again, if we don't need to instantiate the 2 mutant proteins, but their sequence can be reconstructed from the wild type proteins plus the corresponding mutation. @@ -867,11 +766,10 @@ and postgresql substring counts from 1. The following query dynamically constructs mutant feature residues based on the wild type feature and the mutant residue changes. this should work for a variety of variation features, not just SNPs. Note that we -need to use *locgroup* to properly group wild type/mutant pairs of +need to use _locgroup_ to properly group wild type/mutant pairs of locations, otherwise this query will give bad data. - -``` de1 +```de1 SELECT snp.name, wildfeat.name, @@ -896,9 +794,6 @@ WHERE wildloc.srcfeature = wildfeat ``` - - - #### Extensions The above will also work if we have a polymorphic site with a number of @@ -908,15 +803,13 @@ number of rows in the location matrix (i.e. we have rank \> 1). We could also instantiate multiple SNPs, one per strain, and keep the locations pairwise. - - #### Similarities to Alignments You should hopefully notice the parallels between modeling SNPs and modeling pairwise (e.g. BLAST) and multiple alignments. The difference is, alignments would always have locgroup=0, with the rank distinguishing query from subject. Also, with an HSP feature, the -*residue_info* is used to store the alignment string. +_residue_info_ is used to store the alignment string. #### Redundant Storage of Coordinates on Different Assembly Levels @@ -951,8 +844,8 @@ bp_search2gff.pl and gmod_bulk_load_gff3.pl where the featureloc entry for the query sequence has a featureloc.rank of 0 and the featureloc.rank of the target sequence is 1. The SO term is *match*. - - Note: *featureloc.locgroup* is not used. + rel="nofollow">SO term is _match_. + - Note: _featureloc.locgroup_ is not used. - Store the HSPs in both the [feature](Chado_Tables#Table:_feature "Chado Tables") and [analysisfeature](Chado_Tables#Table:_analysisfeature "Chado Tables") @@ -961,9 +854,9 @@ bp_search2gff.pl and gmod_bulk_load_gff3.pl where the featureloc entry for the query sequence has a featureloc.rank of 0 and the featureloc.rank of the target sequence is 1. The SO term is *match_part*. - - Note: *featureloc.locgroup* is not used. -- Map the hits and the HSPs to each other *via* entries in the + rel="nofollow">SO term is _match_part_. + - Note: _featureloc.locgroup_ is not used. +- Map the hits and the HSPs to each other _via_ entries in the [feature_relationship](Chado_Tables#Table:_feature_relationship "Chado Tables") tables. - Standard scores (rawscore, normscore, significance, identity) are @@ -974,60 +867,16 @@ bp_search2gff.pl and gmod_bulk_load_gff3.pl #### xxx Multiple Sequence Alignments -> **This page or section needs to be edited.** -> Please help by href="http://gmod.org/mediawiki/index.php?title=Chado_Best_Practices&action=edit" -> class="external text" rel="nofollow">editing this page to -> add your revisions or additions. - - - ### xxx Posttranslational Modifications -> **This page or section needs to be edited.** -> Please help by href="http://gmod.org/mediawiki/index.php?title=Chado_Best_Practices&action=edit" -> class="external text" rel="nofollow">editing this page to -> add your revisions or additions. - - - ### xxx Genotypes -> **This page or section needs to be edited.** -> Please help by href="http://gmod.org/mediawiki/index.php?title=Chado_Best_Practices&action=edit" -> class="external text" rel="nofollow">editing this page to -> add your revisions or additions. - - - ### xxx Phenotypes -> **This page or section needs to be edited.** -> Please help by href="http://gmod.org/mediawiki/index.php?title=Chado_Best_Practices&action=edit" -> class="external text" rel="nofollow">editing this page to -> add your revisions or additions. - ### xxx Cleavage -> **This page or section needs to be edited.** -> Please help by href="http://gmod.org/mediawiki/index.php?title=Chado_Best_Practices&action=edit" -> class="external text" rel="nofollow">editing this page to -> add your revisions or additions. - - - ### xxx Protein Complexes -> **This page or section needs to be edited.** -> Please help by href="http://gmod.org/mediawiki/index.php?title=Chado_Best_Practices&action=edit" -> class="external text" rel="nofollow">editing this page to -> add your revisions or additions. - ### GO annotations The details on GO annotation can be foind on the @@ -1053,9 +902,6 @@ dictyBase:DDB0185051 ### xxx Genome Versions - - - [Categories](Special%253ACategories "Special%253ACategories"): - [Pages with problems or @@ -1064,49 +910,24 @@ dictyBase:DDB0185051 - [BLAST](Category%253ABLAST "Category%253ABLAST") - [Chado](Category%253AChado "Category%253AChado") - - - - - ## Navigation menu - - - - - - - - ### Navigation - - - [GMOD Home](Main_Page) - [Software](GMOD_Components) - [Categories / Tags](Categories) - - - ### Documentation - - - [Overview](Overview) - [FAQs](Category%253AFAQ) - [HOWTOs](Category%253AHOWTO) - [Glossary](Glossary) - - - ### Community - - - [GMOD News](GMOD_News) - [Training / Outreach](Training_and_Outreach) @@ -1115,18 +936,12 @@ dictyBase:DDB0185051 - [Meetings](Meetings) - [Calendar](Calendar) - - - ### Tools - Browse properties - - -- Last updated at 08:47 on 16 April - 2013. +- Last updated at 08:47 on 16 April 2013. - Content is available under - - - - - - diff --git a/wiki/GBrowse_syn.1.md b/wiki/GBrowse_syn.1.md index c92d7c5b14..4574e78640 100644 --- a/wiki/GBrowse_syn.1.md +++ b/wiki/GBrowse_syn.1.md @@ -99,9 +99,7 @@ class="external free" rel="nofollow">http://dev.wormbase.org/db/seq/gbrowse_syn/compara?search_src=Cele%3Bname=X:1050001..1150000 [+](Special%253ASearchByProperty/Has-20URL/http%253A-2F-2Fdev.wormbase.org-2Fdb-2Fseq-2Fgbrowse_syn-2Fcompara-3Fsearch_src=Cele-253Bname=X%253A1050001..1150000 "Special%253ASearchByProperty/Has-20URL/http:-2F-2Fdev.wormbase.org-2Fdb-2Fseq-2Fgbrowse syn-2Fcompara-3Fsearch src=Cele-253Bname=X:1050001..1150000") and http://solgenomics.net/gbrowse2/bin/gbrowse_syn/sol3/ [+](Special%253ASearchByProperty/Has-20URL/http%253A-2F-2Fsolgenomics.net-2Fgbrowse2-2Fbin-2Fgbrowse_syn-2Fsol3-2F "Special%253ASearchByProperty/Has-20URL/http:-2F-2Fsolgenomics.net-2Fgbrowse2-2Fbin-2Fgbrowse syn-2Fsol3-2F") | -| [Has description](Property%253AHas_description "Property:Has description") | GBrowse_syn, or the Generic Synteny Browse … GBrowse_syn, or the Generic Synteny Browser, is a [GBrowse](GBrowse.1 "GBrowse")-based synteny browser designed to display multiple genomes, with a central reference species compared to two or more additional species. It can be used to view multiple sequence alignment data, synteny or co-linearity data from other sources against genome annotations provided by GBrowse. GBrowse_syn is included with the standard GBrowse package (version 1.69 and later). GBrowse package (version 1.69 and later). + | +| [Has description](Property%253AHas_description "Property:Has description") | GBrowse_syn, or the Generic Synteny Browse … GBrowse_syn, or the Generic Synteny Browser, is a [GBrowse](GBrowse.1 "GBrowse")-based synteny browser designed to display multiple genomes, with a central reference species compared to two or more additional species. It can be used to view multiple sequence alignment data, synteny or co-linearity data from other sources against genome annotations provided by GBrowse. GBrowse_syn is included with the standard GBrowse package (version 1.69 and later). GBrowse package (version 1.69 and later). | | [Has development status](Property%253AHas_development_status "Property:Has development status") | active [+](Special%253ASearchByProperty/Has-20development-20status/active "Special%253ASearchByProperty/Has-20development-20status/active") | | [Has download URL](Property%253AHas_download_URL "Property:Has download URL") | https://github.com/GMOD/GBrowse [+](Special%253ASearchByProperty/Has-20download-20URL/https%253A-2F-2Fgithub.com-2FGMOD-2FGBrowse "Special%253ASearchByProperty/Has-20download-20URL/https%253A-2F-2Fgithub.com-2FGMOD-2FGBrowse") | diff --git a/wiki/GO%3A%3ATermFinder.1.md b/wiki/GO%3A%3ATermFinder.1.md index 305adbe51d..fa95fe5492 100644 --- a/wiki/GO%3A%3ATermFinder.1.md +++ b/wiki/GO%3A%3ATermFinder.1.md @@ -58,9 +58,7 @@ rel="nofollow">http://search.cpan.org/dist/GO-TermFinder/ http://go.princeton.edu/cgi-bin/GOTermFinder/GOTermFinder [+](Special%253ASearchByProperty/Has-20URL/http%253A-2F-2Fgo.princeton.edu-2Fcgi-2Dbin-2FGOTermFinder-2FGOTermFinder "Special%253ASearchByProperty/Has-20URL/http%253A-2F-2Fgo.princeton.edu-2Fcgi-2Dbin-2FGOTermFinder-2FGOTermFinder") | | [Has description](Property%253AHas_description "Property:Has description") | GO TermFinder takes a list of genes as inp … GO TermFinder takes a list of genes as input, and determines whether there are enriched GO terms for that list. These modules provide an object oriented set of libraries for dealing with files produced by the Gene Ontology project. In particular, the GO TermFinder object allows a client program to provide a list of genes, from which it will determine p-values for the annotation associated with that list of genes. It does this using the hypergeometric distribution. In addition, a corrected p-value is calculated, to correct for multiple hypothesis testing. This distribution also contains a version of Shuai Weng's GO-View module (and associated classes), such that you can graphically display the output of the GO TermFinder. Some simple clients of these modules are provided in the examples directory of the download.in the examples directory of the download. + | +rel="nofollow">Gene Ontology project. In particular, the GO TermFinder object allows a client program to provide a list of genes, from which it will determine p-values for the annotation associated with that list of genes. It does this using the hypergeometric distribution. In addition, a corrected p-value is calculated, to correct for multiple hypothesis testing. This distribution also contains a version of Shuai Weng's GO-View module (and associated classes), such that you can graphically display the output of the GO TermFinder. Some simple clients of these modules are provided in the examples directory of the download.in the examples directory of the download. | | [Has development status](Property%253AHas_development_status "Property:Has development status") | maintenance [+](Special%253ASearchByProperty/Has-20development-20status/maintenance "Special%253ASearchByProperty/Has-20development-20status/maintenance") | | [Has input format](Property%253AHas_input_format "Property:Has input format") | gene list [+](Special%253ASearchByProperty/Has-20input-20format/gene-20list "Special%253ASearchByProperty/Has-20input-20format/gene-20list") | | [Has software maturity status](Property%253AHas_software_maturity_status "Property:Has software maturity status") | mature [+](Special%253ASearchByProperty/Has-20software-20maturity-20status/mature "Special%253ASearchByProperty/Has-20software-20maturity-20status/mature") | diff --git a/wiki/GO_Graphic_Viewer.1.md b/wiki/GO_Graphic_Viewer.1.md index 85951fa976..8df8b3f052 100644 --- a/wiki/GO_Graphic_Viewer.1.md +++ b/wiki/GO_Graphic_Viewer.1.md @@ -59,9 +59,7 @@ class="external free" rel="nofollow">http://sourceforge.net/projects/gmod/files/GOView/ [+](Special%253ASearchByProperty/Has-20URL/http%253A-2F-2Fsourceforge.net-2Fprojects-2Fgmod-2Ffiles-2FGOView-2F "Special%253ASearchByProperty/Has-20URL/http%253A-2F-2Fsourceforge.net-2Fprojects-2Fgmod-2Ffiles-2FGOView-2F") and http://www.yeastgenome.org/cgi-bin/GO/goTermFinder.pl [+](Special%253ASearchByProperty/Has-20URL/http%253A-2F-2Fwww.yeastgenome.org-2Fcgi-2Dbin-2FGO-2FgoTermFinder.pl "Special%253ASearchByProperty/Has-20URL/http%253A-2F-2Fwww.yeastgenome.org-2Fcgi-2Dbin-2FGO-2FgoTermFinder.pl") | -| [Has description](Property%253AHas_description "Property:Has description") | The GO Graphic Viewer module (Bio%253A%253AGMOD::G … The GO Graphic Viewer module (Bio%253A%253AGMOD::GO::View) generates a graphic that displays the parent and child relationships of a selected GO term. It also provides the visualization for the result from the GO::TermFinder Perl module created by the Stanford Microarray Database (SMD). This module is useful when analyzing experimental or computational results that produce a set of gene products that may have a common function or process. This distribution also includes two examples of its use in web browser-based user interfaces (goView.pl and goTermFinder.pl).nterfaces (goView.pl and goTermFinder.pl). + | +| [Has description](Property%253AHas_description "Property:Has description") | The GO Graphic Viewer module (Bio%253A%253AGMOD::G … The GO Graphic Viewer module (Bio%253A%253AGMOD::GO::View) generates a graphic that displays the parent and child relationships of a selected GO term. It also provides the visualization for the result from the GO::TermFinder Perl module created by the Stanford Microarray Database (SMD). This module is useful when analyzing experimental or computational results that produce a set of gene products that may have a common function or process. This distribution also includes two examples of its use in web browser-based user interfaces (goView.pl and goTermFinder.pl).nterfaces (goView.pl and goTermFinder.pl). | | [Has development status](Property%253AHas_development_status "Property:Has development status") | inactive [+](Special%253ASearchByProperty/Has-20development-20status/inactive "Special%253ASearchByProperty/Has-20development-20status/inactive") | | [Has input format](Property%253AHas_input_format "Property:Has input format") | gene or ORF names [+](Special%253ASearchByProperty/Has-20input-20format/gene-20or-20ORF-20names "Special%253ASearchByProperty/Has-20input-20format/gene-20or-20ORF-20names") and OBO ontology [+](Special%253ASearchByProperty/Has-20input-20format/OBO-20ontology "Special%253ASearchByProperty/Has-20input-20format/OBO-20ontology") | | [Has software maturity status](Property%253AHas_software_maturity_status "Property:Has software maturity status") | mature [+](Special%253ASearchByProperty/Has-20software-20maturity-20status/mature "Special%253ASearchByProperty/Has-20software-20maturity-20status/mature") | diff --git a/wiki/Generic_Genome_Browser.md b/wiki/Generic_Genome_Browser.md index 70165bd04f..408f9bdf56 100644 --- a/wiki/Generic_Genome_Browser.md +++ b/wiki/Generic_Genome_Browser.md @@ -156,9 +156,7 @@ edit features) Note that the information on this page refers to GBrowse 2; GBrowse 1.x is recommended only for applications where legacy browser support is required and a single database is used.is required and a single database -is used. + +is used. http://www.mousemine.org/ [+](Special rel="nofollow">http://ratmine.mcw.edu/ [+](Special%253ASearchByProperty/Has-20URL/http%253A-2F-2Fratmine.mcw.edu-2F "Special%253ASearchByProperty/Has-20URL/http%253A-2F-2Fratmine.mcw.edu-2F"), http://zmine.zfin.org/ [+](Special%253ASearchByProperty/Has-20URL/http%253A-2F-2Fzmine.zfin.org-2F "Special%253ASearchByProperty/Has-20URL/http%253A-2F-2Fzmine.zfin.org-2F") and http://www.wormbase.org/tools/wormmine [+](Special%253ASearchByProperty/Has-20URL/http%253A-2F-2Fwww.wormbase.org-2Ftools-2Fwormmine "Special%253ASearchByProperty/Has-20URL/http%253A-2F-2Fwww.wormbase.org-2Ftools-2Fwormmine") | -| [Has description](Property%253AHas_description "Property:Has description") | InterMine makes it easy to integrate multi … InterMine makes it easy to integrate multiple data sources into a single data warehouse. It has a core data model based on the Sequence Ontology and supports several biological data formats, just configure which organisms or data files are required. It is easy to extend the data model and integrate your own data, Java and Perl APIs and an XML format to help import custom data. Currently supported formats include Chado, GFF3, FASTA, GO and gene association files, UniProt XML, PSI XML (protein interactions), InParanoid orthologs, Ensembl, UniProt, and many others. A web application allows creation of custom queries, includes template queries (web forms to run 'canned' queries) and can upload and operate on lists of data. It is possible to configure/create widgets to analyse lists with graphs and enrichment statistics. An admin user can publish new template queries, change report pages and create public lists at any time without any programming. Many aspects of the web app can be configured and branded.the web app can be configured and branded. + and InterMine should always be checked out in source code form [+](Special%253ASearchByProperty/Has-20description/InterMine-20should-20always-20be-20checked-20out-20in-20source-20code-20form "Special%253ASearchByProperty/Has-20description/InterMine-20should-20always-20be-20checked-20out-20in-20source-20code-20form") | +| [Has description](Property%253AHas_description "Property:Has description") | InterMine makes it easy to integrate multi … InterMine makes it easy to integrate multiple data sources into a single data warehouse. It has a core data model based on the Sequence Ontology and supports several biological data formats, just configure which organisms or data files are required. It is easy to extend the data model and integrate your own data, Java and Perl APIs and an XML format to help import custom data. Currently supported formats include Chado, GFF3, FASTA, GO and gene association files, UniProt XML, PSI XML (protein interactions), InParanoid orthologs, Ensembl, UniProt, and many others. A web application allows creation of custom queries, includes template queries (web forms to run 'canned' queries) and can upload and operate on lists of data. It is possible to configure/create widgets to analyse lists with graphs and enrichment statistics. An admin user can publish new template queries, change report pages and create public lists at any time without any programming. Many aspects of the web app can be configured and branded.the web app can be configured and branded. and InterMine should always be checked out in source code form [+](Special%253ASearchByProperty/Has-20description/InterMine-20should-20always-20be-20checked-20out-20in-20source-20code-20form "Special%253ASearchByProperty/Has-20description/InterMine-20should-20always-20be-20checked-20out-20in-20source-20code-20form") | | [Has development status](Property%253AHas_development_status "Property:Has development status") | active [+](Special%253ASearchByProperty/Has-20development-20status/active "Special%253ASearchByProperty/Has-20development-20status/active") | | [Has input format](Property%253AHas_input_format "Property:Has input format") | Chado [+](Special%253ASearchByProperty/Has-20input-20format/Chado "Special%253ASearchByProperty/Has-20input-20format/Chado"), [GFF3](GFF3 "GFF3") [+](Special%253ASearchByProperty/Has-20input-20format/-5B-5BGFF3-5D-5D "Special%253ASearchByProperty/Has-20input-20format/-5B-5BGFF3-5D-5D"), FASTA [+](Special%253ASearchByProperty/Has-20input-20format/-5B-5BFASTA-5D-5D "Special%253ASearchByProperty/Has-20input-20format/-5B-5BFASTA-5D-5D"), GO ontology files [+](Special%253ASearchByProperty/Has-20input-20format/GO-20ontology-20files "Special%253ASearchByProperty/Has-20input-20format/GO-20ontology-20files"), GO gene association files [+](Special%253ASearchByProperty/Has-20input-20format/GO-20gene-20association-20files "Special%253ASearchByProperty/Has-20input-20format/GO-20gene-20association-20files"), UniProt XML [+](Special%253ASearchByProperty/Has-20input-20format/UniProt-20XML "Special%253ASearchByProperty/Has-20input-20format/UniProt-20XML"), PSI XML (protein interactions) [+](Special%253ASearchByProperty/Has-20input-20format/PSI-20XML-20(protein-20interactions) "Special%253ASearchByProperty/Has-20input-20format/PSI-20XML-20(protein-20interactions)"), InParanoid orthologs [+](Special%253ASearchByProperty/Has-20input-20format/InParanoid-20orthologs "Special%253ASearchByProperty/Has-20input-20format/InParanoid-20orthologs"), Ensembl [+](Special%253ASearchByProperty/Has-20input-20format/Ensembl "Special%253ASearchByProperty/Has-20input-20format/Ensembl"), Uniprot [+](Special%253ASearchByProperty/Has-20input-20format/Uniprot "Special%253ASearchByProperty/Has-20input-20format/Uniprot") and and many others. Custom formats can be supported through the data-source framework. [+](Special%253ASearchByProperty/Has-20input-20format/and-20many-20others.-20Custom-20formats-20can-20be-20supported-20through-20the-20data-2Dsource-20framework. "Special%253ASearchByProperty/Has-20input-20format/and-20many-20others.-20Custom-20formats-20can-20be-20supported-20through-20the-20data-2Dsource-20framework.") | | [Has licence](Property%253AHas_licence "Property:Has licence") | + and Browse the + and Browse the genome of Ötzi the ice man [+](Special%253ASearchByProperty/Has-20description/Browse-20the-20genome-20of-20%C3%96tzi-20the-20ice-20man "Special%253ASearchByProperty/Has-20description/Browse-20the-20genome-20of-20Ötzi-20the-20ice-20man") diff --git a/wiki/JBrowse2.md b/wiki/JBrowse2.md index c225df7ac8..f4247e13d2 100644 --- a/wiki/JBrowse2.md +++ b/wiki/JBrowse2.md @@ -74,9 +74,7 @@ rel="nofollow">https://github.com/GMOD/jbrowse-components/ http://jbrowse.org/demos [+](Special%253ASearchByProperty/Has-20URL/http%253A-2F-2Fjbrowse.org-2Fdemos "Special%253ASearchByProperty/Has-20URL/http%253A-2F-2Fjbrowse.org-2Fdemos") | | [Has description](Property%253AHas_description "Property:Has description") | JBrowse 2 is a multi-modal genome browser … JBrowse 2 is a multi-modal genome browser that can view data in linear, circular, dotplot, and syntenic modes, in order to better serve the needs of structural variant visualization and comparative genomics. It is coded using React and follows in the footsteps of JBrowse 1 in being highly pluggable. Users can write plugins to create custom data adapters, track types, and even entirely new view types. See https://jbrowse.org/jb2/ for more infoSee https://jbrowse.org/jb2/ for more info + | +rel="nofollow">https://jbrowse.org/jb2/ for more info | | [Has development status](Property%253AHas_development_status "Property:Has development status") | active [+](Special%253ASearchByProperty/Has-20development-20status/active "Special%253ASearchByProperty/Has-20development-20status/active") | | [Has input format](Property%253AHas_input_format "Property:Has input format") | [GFF3](GFF3 "GFF3") [+](Special%253ASearchByProperty/Has-20input-20format/-5B-5BGFF3-5D-5D "Special%253ASearchByProperty/Has-20input-20format/-5B-5BGFF3-5D-5D"), Indexed FASTA [+](Special%253ASearchByProperty/Has-20input-20format/Indexed-20FASTA "Special%253ASearchByProperty/Has-20input-20format/Indexed-20FASTA"), BigWig [+](Special%253ASearchByProperty/Has-20input-20format/BigWig "Special%253ASearchByProperty/Has-20input-20format/BigWig"), BAM [+](Special%253ASearchByProperty/Has-20input-20format/BAM "Special%253ASearchByProperty/Has-20input-20format/BAM"), CRAM [+](Special%253ASearchByProperty/Has-20input-20format/CRAM "Special%253ASearchByProperty/Has-20input-20format/CRAM"), VCF/GFF/BED tabixed files [+](Special%253ASearchByProperty/Has-20input-20format/VCF-2FGFF-2FBED-20tabixed-20files "Special%253ASearchByProperty/Has-20input-20format/VCF-2FGFF-2FBED-20tabixed-20files"), .hic files [+](Special%253ASearchByProperty/Has-20input-20format/.hic-20files "Special%253ASearchByProperty/Has-20input-20format/.hic-20files") and and more [+](Special%253ASearchByProperty/Has-20input-20format/and-20more "Special%253ASearchByProperty/Has-20input-20format/and-20more") | | [Has licence](Property%253AHas_licence "Property:Has licence") | + and Browse the + and Browse the genome of Ötzi the ice man [+](../Special%253ASearchByProperty/Has-20description/Browse-20the-20genome-20of-20%C3%96tzi-20the-20ice-20man "Special%253ASearchByProperty/Has-20description/Browse-20the-20genome-20of-20Ötzi-20the-20ice-20man") diff --git a/wiki/JBrowseDev/Main.md b/wiki/JBrowseDev/Main.md index 3ec82f519d..31fb446da0 100644 --- a/wiki/JBrowseDev/Main.md +++ b/wiki/JBrowseDev/Main.md @@ -132,9 +132,7 @@ user's web browser, with minimal requirements for the server. back-end server code, just tools for formatting data files to be read directly over HTTP. Serve huge datasets from a single low-cost cloud instance.ets from a single low-cost cloud instance. - + and Browse the + and Browse the genome of Ötzi the ice man [+](../Special%253ASearchByProperty/Has-20description/Browse-20the-20genome-20of-20%C3%96tzi-20the-20ice-20man "Special%253ASearchByProperty/Has-20description/Browse-20the-20genome-20of-20Ötzi-20the-20ice-20man") diff --git a/wiki/MAKER.1.md b/wiki/MAKER.1.md index 144238445b..9dcaf10a41 100644 --- a/wiki/MAKER.1.md +++ b/wiki/MAKER.1.md @@ -186,9 +186,7 @@ title="Apollo">Apollo. MAKER comes with sample data for testing purposes. See the /data directory in the download. /data -directory in the download. +, Review article on +directory in the download. , Review article on eukaryotic genome annotation from the MAKER team. + and list of PGDBs + and list of PGDBs hosted elsewhere [+](Special%253ASearchByProperty/Has-20description/list-20of-20PGDBs-20hosted-20elsewhere "Special%253ASearchByProperty/Has-20description/list-20of-20PGDBs-20hosted-20elsewhere") diff --git a/wiki/Special%3ASearch/!FixAfterUpgrade.md b/wiki/Special%3ASearch/!FixAfterUpgrade.md deleted file mode 100644 index f3ee33bff3..0000000000 --- a/wiki/Special%3ASearch/!FixAfterUpgrade.md +++ /dev/null @@ -1,165 +0,0 @@ - - - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=%21FixAfterUpgrade&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=%21FixAfterUpgrade&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=%21FixAfterUpgrade&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=%21FixAfterUpgrade&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=%21FixAfterUpgrade&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below **2** results starting with \#**1**. - - - -**Create the page "!FixAfterUpgrade" on -this wiki!** See also the search results found. - -- - - [GMOD News Archives](/wiki/GMOD_News_Archives "GMOD News Archives") - - - - - - \[\[Category%253A\!FixAfterUpgrade\]\] - - - - - - 2 KB (234 words) - 11:12, 22 August 2013 - - - -- - - [Widget:GoogleCalendar](/wiki/Widget:GoogleCalendar "Widget:GoogleCalendar") - - - - - - \[\[Category%253A\!FixAfterUpgrade\]\] - - - - - - 5 KB (883 words) - 22:27, 4 October 2012 - - - - - -View (previous 50 \| next 50) (20 \| 50 \| 100 \| 250 \| 500) - - - - - - - - -## Navigation menu - - - -### Namespaces - -- [Special - page](/wiki/Special%253ASearch/!FixAfterUpgrade "This is a special page, you cannot edit the page itself") - - - - - - -### Navigation - - - -- [GMOD Home](/wiki/Main_Page) -- [Software](/wiki/GMOD_Components) -- [Categories / - Tags](/wiki/Categories) -- [View all - pages](/wiki/Special:AllPages) - - - - -### Documentation - - - -- [Overview](/wiki/Overview) -- [FAQs](/wiki/Category%253AFAQ) -- [HOWTOs](/wiki/Category%253AHOWTO) -- [Glossary](/wiki/Glossary) - - - - -### Community - - - -- [GMOD News](/wiki/GMOD_News) -- [Training / - Outreach](/wiki/Training_and_Outreach) -- [Support](/wiki/Support) -- [GMOD - Promotion](/wiki/GMOD_Promotion) -- [Meetings](/wiki/Meetings) -- [Calendar](/wiki/Calendar) - - - - -### Tools - - - - - - - - - - - - - - - - - diff --git a/wiki/Special%3ASearch/2013_Summer_School.md b/wiki/Special%3ASearch/2013_Summer_School.md deleted file mode 100644 index f059fddd17..0000000000 --- a/wiki/Special%3ASearch/2013_Summer_School.md +++ /dev/null @@ -1,1063 +0,0 @@ - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=2013+Summer+School&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=2013+Summer+School&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=2013+Summer+School&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=2013+Summer+School&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=2013+Summer+School&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below **42** results starting with \#**1**. - - - - -**Create the page "2013 Summer -School" on this wiki!** See also the search results found. - -## Page title matches - -- - - [2013 GMOD Summer - School](/wiki/2013_GMOD_Summer_School "2013 GMOD Summer School") - - - - - - \[\[File:2013-summer-school.png\|right\|300px\|2013 - GMOD Summer - School\]\] Dates: Friday July 19th - - Tuesday July 23rd 2013 - - - - - - 5 KB (638 words) - 21:52, 22 January 2014 - - - -- - - [News/Accepting Applications For GMOD Summer School - 2013](/wiki/News/Accepting_Applications_For_GMOD_Summer_School_2013 "News/Accepting Applications For GMOD Summer School 2013") - - - - - - \[\[File:2013-summer-school.png\|right\|300px\|link=2013_GMOD_Summer_School\]\] - '''Applications are now open for the - 2013 GMOD - Summer - School!''' - - - - - - 1 KB (158 words) - 18:24, 17 April 2013 - - - -- - - [News/2013 Summer School Tutorials - Available](/wiki/News/2013_Summer_School_Tutorials_Available "News/2013 Summer School Tutorials Available") - - - - - - \[\[File:2013-summer-school.png\|right\|300px\|2013 - GMOD Summer - School\]\] ...arly those where new - software releases have occurred since the last - summer - school; these include: - - - - - - 865 B (115 words) - 23:41, 5 August 2013 - - - -## Page text matches - -- - - [Chado Tutorial 2012](/wiki/Chado_Tutorial_2012 "Chado Tutorial 2012") - - - - - - ...s presented by \[\[User%253AScott\|Scott Cain\]\] as part of the - \[\[2012 GMOD Summer - School\]\]. - - - - - - 50 KB (7,599 words) - 16:26, 2 September 2018 - - - -- - - [Site Guidelines](/wiki/Site_Guidelines "Site Guidelines") - - - - - - \# These guidelines were first developed for the \[\[GMOD - Summer - School\|GMOD Courses\]\], where these - were used to format the \[\[Training_and_Outreach The - 2013 paper by Leite ''et al.'' on the - grooved shell carpet clam \2013 GMOD - Summer - School\]\] - - - - - - 6 KB (800 words) - 21:39, 15 October 2013 - - - -- - - [MAKER](/wiki/MAKER "MAKER") - - - - - - :taught as part of the \[\[2013 GMOD - Summer - School\]\] - - - - - - 9 KB (1,211 words) - 21:53, 2 February 2014 - - - -- - - [GBrowse Tutorial](/wiki/GBrowse_Tutorial "GBrowse Tutorial") - - - - - - ; \[\[GBrowse Tutorial 2012\|GBrowse tutorial from - 2013 GMOD - Summer - School\]\] ...Scott Cain\]\] at the - \[\[2013 GMOD - Summer - School\]\] and the \[\[2012 GMOD - Summer - School\]\]. It demonstrates setting - up, configuring and using \[\[GBrowse\]\] with some - - - - - - 2 KB (236 words) - 17:10, 18 December 2013 - - - -- - - [GMOD Schools](/wiki/GMOD_Schools "GMOD Schools") - - - - - - \[\[File:2013-summer-school.png\|180px\|2013 - GMOD Summer - School\]\] - \[\[File:2012SummerSchool400.png\|140px\|2012 GMOD - Summer - School\]\] - - - - - - 2 KB (250 words) - 22:22, 16 April 2014 - - - -- - - [JBrowse](/wiki/JBrowse "JBrowse") - - - - - - \* Visualizing next-generation sequencing data with JBrowse - (2013)\\* - Visualizing next-generation sequencing data wit \|presentations=\* - April 2013 - Bio-IT World, Robert - Buels: \[\[Media:JBrowse_bioit_world_apr2013.pdf\|PDF\]\] - - - - - - 8 KB (1,157 words) - 19:18, 15 April 2016 - - - -- - - [Meetings](/wiki/Meetings "Meetings") - - - - - - \[\[File:gmod-2013-mtg.png\|right\|100px\|link=April - 2013 GMOD Meeting\]\] ! rowspan="1" - \| 2013 - - - - - - 6 KB (720 words) - 19:49, 24 January 2020 - - - -- - - [JBrowse Tutorial - 2012](/wiki/JBrowse_Tutorial_2012 "JBrowse Tutorial 2012") - - - - - - \#REDIRECT \[\[JBrowse Tutorial - 2013\]\] \[\[Category%253A2012 - Summer - School\]\] - - - - - - 112 B (10 words) - 16:02, 22 July 2013 - - - -- - - [WebApollo](/wiki/WebApollo "WebApollo") - - - - - - :taught as part of the \[\[2013 GMOD - Summer - School\]\] - - - - - - 4 KB (536 words) - 20:37, 6 April 2015 - - - -- - - [Project Statistics](/wiki/Project_Statistics "Project Statistics") - - - - - - \| 2013-01 \|\| 23,935 \|\| 30,951 - \|\| 57,497\|\| 22,733 \| 2013-02 - \|\| 19,651 \|\| 25,633 \|\| 48,077 \|\| 18,301 - - - - - - 12 KB (1,301 words) - 18:39, 2 May 2014 - - - -- - - [WebApollo/tool data](/wiki/WebApollo/tool_data "WebApollo/tool data") - - - - - - :taught as part of the \[\[2013 GMOD - Summer - School\]\] - - - - - - 5 KB (636 words) - 20:34, 15 October 2013 - - - -- - - [GFF3](/wiki/GFF3 "GFF3") - - - - - - \[\[2013 GMOD - Summer - School\]\]\
19-23 July - 2013\
- - - - - - 16 KB (2,350 words) - 20:25, 12 July 2016 - - - -- - - [Tripal Tutorial - v1.1](/wiki/Tripal_Tutorial_v1.1 "Tripal Tutorial v1.1") - - - - - - \| where = \[\[2013 GMOD - Summer - School\]\] \| when = July - 2013 - - - - - - 131 KB (21,091 words) - 21:53, 2 January 2014 - - - -- - - [JBrowse Tutorial - 2013](/wiki/JBrowse_Tutorial_2013 "JBrowse Tutorial 2013") - - - - - - ...User%253ARobertBuels\|Robert Buels\]\] at the - \[\[2013 GMOD - Summer - School\]\] in July - 2013 using JBrowse 1.9.8. This - tutorial uses the AWS AMI '''ami-d2c8b1bb''' named - '''2013 GMOD start day 3''' in the - US-East region. - - - - - - 14 KB (1,948 words) - 20:48, 27 August 2013 - - - -- - - [2013 GMOD Summer - School](/wiki/2013_GMOD_Summer_School "2013 GMOD Summer School") - - - - - - \[\[File:2013-summer-school.png\|right\|300px\|2013 - GMOD Summer - School\]\] Dates: Friday July 19th - - Tuesday July 23rd 2013 - - - - - - 5 KB (638 words) - 21:52, 22 January 2014 - - - -- - - [News/Accepting Applications For GMOD Summer School - 2013](/wiki/News/Accepting_Applications_For_GMOD_Summer_School_2013 "News/Accepting Applications For GMOD Summer School 2013") - - - - - - \[\[File:2013-summer-school.png\|right\|300px\|link=2013_GMOD_Summer_School\]\] - '''Applications are now open for the - 2013 GMOD - Summer - School!''' - - - - - - 1 KB (158 words) - 18:24, 17 April 2013 - - - -- - - [AWS walkthrough](/wiki/AWS_walkthrough "AWS walkthrough") - - - - - - \[\[Category%253A2012 Summer - School\]\] - \[\[Category%253A2013 - Summer - School\]\] - - - - - - 2 KB (380 words) - 22:14, 30 July 2013 - - - -- - - [MAKER Tutorial 2010](/wiki/MAKER_Tutorial_2010 "MAKER Tutorial 2010") - - - - - - \| where = \[\[2010 GMOD Summer - School - Americas\]\] - ...cificbiosciences.com/assets/files/1-23439884-eprint.pdf fifteen - minutes by 2013\]. If the hype is to - be believed, then whole genome sequencing will become - - - - - - 62 KB (9,933 words) - 22:41, 14 February 2013 - - - -- - - [GBrowse syn Tutorial - 2012](/wiki/GBrowse_syn_Tutorial_2012 "GBrowse syn Tutorial 2012") - - - - - - If you are 2013 GMOD - Summer - School, you are on the wrong - tutorial.\ ...taught by \[\[User%253AMckays\|Sheldon McKay\]\] as - part of the \[\[2013 GMOD - Summer - School\]\]. - - - - - - 19 KB (2,685 words) - 17:23, 22 July 2013 - - - -- - - [SOBA Tutorial 2012](/wiki/SOBA_Tutorial_2012 "SOBA Tutorial 2012") - - - - - - ...ught as part of the \[\[2012 GMOD - Summer - School\]\] and the - \[\[2013 GMOD - Summer - School\]\]. \[\[Category%253A2012 - Summer - School\]\] - - - - - - 15 KB (1,830 words) - 20:52, 27 August 2013 - - - -- - - [News/Last Call For Summer School - Apps](/wiki/News/Last_Call_For_Summer_School_Apps "News/Last Call For Summer School Apps") - - - - - - \[\[File:2013-summer-school.png\|right\|200px\|2013 - GMOD Summer - School\]\] The deadline to apply for - the \[\[2013 GMOD - Summer - School\]\] is rapidly approaching! - Please submit your application by June 10th to en - - - - - - 694 B (103 words) - 22:45, 7 June 2013 - - - -- - - [JBrowse/tool data](/wiki/JBrowse/tool_data "JBrowse/tool data") - - - - - - \* April 2013 - Bio-IT World, Robert - Buels: \[\[Media:JBrowse_bioit_world_apr2013.pdf\|PDF\]\] \* August - 2012 - presentation given as part of the \[\[2012 GMOD - Summer - School\]\]: - \[\[Media:JBrowse_gmod_aug2012.pdf\|PDF\]\] - - - - - - 8 KB (1,143 words) - 08:09, 28 January 2014 - - - -- - - [Tripal/tool data](/wiki/Tripal/tool_data "Tripal/tool data") - - - - - - : used during the \[\[2013 GMOD - Summer - School\]\] : used during the \[\[2012 - GMOD Summer - School\]\] - - - - - - 5 KB (734 words) - 18:39, 10 September 2013 - - - -- - - [MAKER/tool data](/wiki/MAKER/tool_data "MAKER/tool data") - - - - - - :taught as part of the \[\[2013 GMOD - Summer - School\]\] - - - - - - 7 KB (963 words) - 18:29, 10 September 2013 - - - -- - - [SOBA/tool data](/wiki/SOBA/tool_data "SOBA/tool data") - - - - - - :taught as part of the \[\[2013 GMOD - Summer - School\]\] - - - - - - 4 KB (669 words) - 03:35, 24 June 2014 - - - -- - - [GBrowse syn/tool - data](/wiki/GBrowse_syn/tool_data "GBrowse syn/tool data") - - - - - - :Installing and configuring GBrowse_syn; from the - \[\[2013 GMOD - Summer - School\]\] - - - - - - 5 KB (748 words) - 18:33, 10 September 2013 - - - -- - - [Galaxy/tool data](/wiki/Galaxy/tool_data "Galaxy/tool data") - - - - - - :As taught at the \[\[2013 GMOD - Summer - School\]\] - - - - - - 6 KB (839 words) - 00:12, 3 October 2013 - - - -- - - [Galaxy Tutorial - 2013](/wiki/Galaxy_Tutorial_2013 "Galaxy Tutorial 2013") - - - - - - ...ill be taught by \[\[User%253AClements\|Dave Clements\]\] at the - \[\[2013 GMOD - Summer - School\]\]. Get the starting image - for this tutorial - '''GMOD 2013 - Galaxy Install Training Instance (ami-f1a1d998)'''. It needs to be run - as - - - - - - 23 KB (3,328 words) - 23:33, 10 June 2014 - - - -- - - [Chado Tutorial 2013](/wiki/Chado_Tutorial_2013 "Chado Tutorial 2013") - - - - - - ...s presented by \[\[User%253AScott\|Scott Cain\]\] as part of the - \[\[2013 GMOD - Summer - School\]\]. Or six years of - school in 15 minutes or less. - - - - - - 50 KB (7,599 words) - 12:36, 20 May 2014 - - - -- - - [GMOD Online Training 2014/Chado - Tutorial](/wiki/GMOD_Online_Training_2014/Chado_Tutorial "GMOD Online Training 2014/Chado Tutorial") - - - - - - ...s presented by \[\[User%253AScott\|Scott Cain\]\] as part of the - \[\[2013 GMOD - Summer - School\]\]. Or six years of - school in 15 minutes or less. - - - - - - 50 KB (7,595 words) - 12:53, 20 May 2014 - - - -- - - [WebApollo Tutorial - 2013](/wiki/WebApollo_Tutorial_2013 "WebApollo Tutorial 2013") - - - - - - ...The guide below details the steps I used to set up the GMOD - Summer - School - 2013 AMI. wget - https://apollo-web.googlecode.com/files/WebApollo-2013-05-16.tgz - - - - - - 12 KB (1,839 words) - 00:11, 20 February 2014 - - - -- - - [GBrowse syn Tutorial - 2013](/wiki/GBrowse_syn_Tutorial_2013 "GBrowse syn Tutorial 2013") - - - - - - ...taught by \[\[User%253AMckays\|Sheldon McKay\]\] as part of the - \[\[2013 GMOD - Summer - School\]\]. The starting image for - this tutorial is '''2013 GMOD start - day 4 (ami-3f7c0456)'''. It can be run as a micro or small inst - - - - - - 20 KB (2,714 words) - 10:44, 22 May 2014 - - - -- - - [News/2013 Summer School Tutorials - Available](/wiki/News/2013_Summer_School_Tutorials_Available "News/2013 Summer School Tutorials Available") - - - - - - \[\[File:2013-summer-school.png\|right\|300px\|2013 - GMOD Summer - School\]\] ...arly those where new - software releases have occurred since the last - summer - school; these include: - - - - - - 865 B (115 words) - 23:41, 5 August 2013 - - - -- - - [JBrowse Tutorial Programming for Biology - 2014](/wiki/JBrowse_Tutorial_Programming_for_Biology_2014 "JBrowse Tutorial Programming for Biology 2014") - - - - - - "description": "GMOD Summer - School - 2013 P. ultima Example", - - - - - - 13 KB (1,909 words) - 19:41, 23 October 2014 - - - -- - - [GMOD Malaysia 2014/JBrowse - Tutorial](/wiki/GMOD_Malaysia_2014/JBrowse_Tutorial "GMOD Malaysia 2014/JBrowse Tutorial") - - - - - - "description": "GMOD Summer - School - 2013 P. ultima Example", - - - - - - 14 KB (1,931 words) - 00:01, 20 February 2014 - - - -- - - [GMOD Malaysia 2014/WebApollo - Tutorial](/wiki/GMOD_Malaysia_2014/WebApollo_Tutorial "GMOD Malaysia 2014/WebApollo Tutorial") - - - - - - ...The guide below details the steps I used to set up the GMOD - Summer - School - 2013 AMI. wget - https://apollo-web.googlecode.com/files/WebApollo-2013-05-16.tgz - - - - - - 12 KB (1,863 words) - 00:15, 20 February 2014 - - - -- - - [GMOD Online Training 2014/JBrowse - Tutorial](/wiki/GMOD_Online_Training_2014/JBrowse_Tutorial "GMOD Online Training 2014/JBrowse Tutorial") - - - - - - "description": "GMOD Summer - School - 2013 P. ultima Example", - - - - - - 13 KB (1,905 words) - 14:21, 21 May 2014 - - - -- - - [JBrowse Tutorial PAG - 2015](/wiki/JBrowse_Tutorial_PAG_2015 "JBrowse Tutorial PAG 2015") - - - - - - "description": "GMOD Summer - School - 2013 P. ultima Example", - - - - - - 19 KB (2,615 words) - 16:21, 11 January 2015 - - - - - -View (previous 50 \| next 50) (20 \| 50 \| 100 \| 250 \| 500) - - - - - - - - -## Navigation menu - - - - -### Namespaces - -- [Special - page](/wiki/Special%253ASearch/2013_Summer_School "This is a special page, you cannot edit the page itself") - - - -### Navigation - - - -- [GMOD Home](/wiki/Main_Page) -- [Software](/wiki/GMOD_Components) -- [Categories / - Tags](/wiki/Categories) -- [View all - pages](/wiki/Special:AllPages) - - - - -### Documentation - - - -- [Overview](/wiki/Overview) -- [FAQs](/wiki/Category%253AFAQ) -- [HOWTOs](/wiki/Category%253AHOWTO) -- [Glossary](/wiki/Glossary) - - - - -### Community - - - -- [GMOD News](/wiki/GMOD_News) -- [Training / - Outreach](/wiki/Training_and_Outreach) -- [Support](/wiki/Support) -- [GMOD - Promotion](/wiki/GMOD_Promotion) -- [Meetings](/wiki/Meetings) -- [Calendar](/wiki/Calendar) - - - - -### Tools - - - - - - - - - - - - - - - diff --git a/wiki/Special%3ASearch/Database.md b/wiki/Special%3ASearch/Database.md deleted file mode 100644 index 7c2a744c09..0000000000 --- a/wiki/Special%3ASearch/Database.md +++ /dev/null @@ -1,1483 +0,0 @@ - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=Database&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=Database&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=Database&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=Database&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=Database&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below up to **50** results starting with \#**1**. - - - - -**Create the page "Database" on this -wiki!** See also the search results found. - -## Page title matches - -- - - [Apollo-Chado example - database](/wiki/Apollo-Chado_example_database "Apollo-Chado example database") - - - - - - - - - - 587 B (98 words) - 21:08, 15 September 2009 - - - -- - - [Insertional Mutagenesis Database - (IMDB)]( "Insertional Mutagenesis Database (IMDB)") - - - - - - ...This project was developed from ATIDB, the Arabidopsis thaliana - insertion database. : See - \[http://atidb.cshl.org/ http://atidb.cshl.org\] for a - database of Arabidopsis insertional - mutants. - - - - - - 1 KB (150 words) - 07:22, 30 January 2008 - - - -- - - [News/Virtual Issue in Journal - Database](/wiki/News/Virtual_Issue_in_Journal_Database "News/Virtual Issue in Journal Database") - - - - - - ...e:DatabaseJournal.jpg\|link=http://database.oxfordjournals.org/\|300px\|right\|Database: - The Journal of Biological Databases and Curation\]\] ...h one of the - editors of the journal - \[http://database.oxfordjournals.org/ - ''Database''\], an open access - journal whose aim for publications lines up very nicely - - - - - - 2 KB (282 words) - 23:08, 9 October 2012 - - - -- - - [News/Sea Urchin Genome - Database](/wiki/News/Sea_Urchin_Genome_Database "News/Sea Urchin Genome Database") - - - - - - \[\[File:SpBaseLogo.png\|link=http://spbase.org/\|right\|Sea Urchin - Genome Database\]\] Today, Tuesday - April 4th, the \[http://spbase.org Sea Urchin Genome - Database\] went public. Based on the - GMOD tools and applications the site organizes - - - - - - 787 B (118 words) - 23:09, 9 October 2012 - - - -- - - [News/Long Term Database - Funding](/wiki/News/Long_Term_Database_Funding "News/Long Term Database Funding") - - - - - - ...tabases and resources\]" appeared in - ''\[http://database.oxfordjournals.org/ - Database: The Journal of Biological - Databases and Curation\]''. - ...proboards.com/index.cgi?board=fundingissues discussion thread on - long term database funding\] has now - been started on the \[http://biocurator.org International S - - - - - - 3 KB (395 words) - 23:09, 9 October 2012 - - - -- - - [GBrowse syn - Database](/wiki/GBrowse_syn_Database "GBrowse syn Database") - - - - - - ...the database that GBrowse_syn - uses, and how to get syntenic data into that - database. =Loading the alignment - database= - - - - - - 7 KB (897 words) - 21:27, 14 August 2012 - - - -- - - [JBrowseDev/Using a Database With - JBrowse](/wiki/JBrowseDev/Using_a_Database_With_JBrowse "JBrowseDev/Using a Database With JBrowse") - - - - - - - - - - 51 B (6 words) - 14:27, 29 March 2013 - - - -- - - [GBrowse User - Database](/wiki/GBrowse_User_Database "GBrowse User Database") - - - - - - \[\[GBrowse\]\] has the option to use a - database to manage users, so that a - user may save their session for use on multiple To use the user - database, you will need to install - the \[http://search.cpan.org/~gbarr/libnet-1.22/Ne - - - - - - 7 KB (1,094 words) - 22:41, 29 December 2010 - - - -- - - [BrowseDev/Using a Database With - JBrowse](/wiki/BrowseDev/Using_a_Database_With_JBrowse "BrowseDev/Using a Database With JBrowse") - - - - - - - - - - 101 B (11 words) - 15:54, 1 April 2013 - - - -- - - [JBrowseDev/Current/Usage/Database](/wiki/JBrowseDev/Current/Usage/Database "JBrowseDev/Current/Usage/Database") - - - - - - \#REDIRECT \[\[JBrowseDev/Using a - Database With JBrowse\]\] - - - - - - 54 B (7 words) - 17:31, 29 July 2011 - - - -- - - [News/BioMart Special Issue in - Database](/wiki/News/BioMart_Special_Issue_in_Database "News/BioMart Special Issue in Database") - - - - - - I am very pleased to announce the publication of the - DATABASE special issue dedicated to - the \[http://www.biomart.org/ BioMart\] project ...ast ten years to - become what it is today, a collaboration between numerous - database projects on five continents: - Asia, Australia, Europe, North America and Sou - - - - - - 949 B (135 words) - 04:25, 19 November 2011 - - - -- - - [Example ChIP - database](/wiki/Example_ChIP_database "Example ChIP database") - - - - - - - - - - 40 B (6 words) - 19:41, 17 April 2012 - - - -- - - [News/Xenbase Hiring Database - Manager](/wiki/News/Xenbase_Hiring_Database_Manager "News/Xenbase Hiring Database Manager") - - - - - - '''\[http://www.xenbase.org Xenbase\] is looking for a new - database manager.''' We need an - experienced software developer / designer looking fo Xenbase is the - model organism database for Xenopus, - a frog used extensively in biomedical research for understandi - - - - - - 4 KB (523 words) - 00:27, 21 August 2012 - - - -## Page text matches - -- - - [GMOD Middleware](/wiki/GMOD_Middleware "GMOD Middleware") - - - - - - ...ough GMOD uses the \[\[Chado\]\] \[\[Glossary#Schema\|schema\]\] - for its underlying database, each - group has developed a separate interface to their databases. This mee - ...approaches and components that it supports. This applies to - applications, database schemas, as - well as to middleware, a software ''layer'' that mediates the e - - - - - - 40 KB (5,672 words) - 21:27, 15 August 2013 - - - -- - - [PSU Presentation](/wiki/PSU_Presentation "PSU Presentation") - - - - - - \* GeneDB is the organism data and annotation - database for the Pathogen Sequencing - Unit (PSU) at the Sanger Institute, UK \* Connection to the - database is specified graphically, so - the '''iBatis''' configuration file has varia - - - - - - 4 KB (513 words) - 21:16, 9 October 2012 - - - -- - - [Hibernate - Presentation](/wiki/Hibernate_Presentation "Hibernate Presentation") - - - - - - \*\* Wrote Ensembl API Database - adaptor for Chado... Not maintainable. \* Need API for - Database I/O - - - - - - 12 KB (1,477 words) - 21:16, 9 October 2012 - - - -- - - [IBatis Presentation](/wiki/IBatis_Presentation "IBatis Presentation") - - - - - - \* iBatis does not create your - database in memory as objects \* - Generates ibatis CRUD objects by introspecting - database tables - - - - - - 12 KB (1,304 words) - 21:10, 9 October 2012 - - - -- - - [GBrowse (DasI) - Presentation]( "GBrowse (DasI) Presentation") - - - - - - =====Create the database===== \*\* - Database connection object - - - - - - 3 KB (415 words) - 20:05, 8 October 2012 - - - -- - - [Modware - Presentation](/wiki/Modware_Presentation "Modware Presentation") - - - - - - \* Database transactions supported \# - Inserts chromosome into database - - - - - - 13 KB (1,574 words) - 21:24, 15 August 2013 - - - -- - - [Main Page](/wiki/Main_Page "Main Page") - - - - - - ...ratory database of genome - annotations, or a large web-accessible community - database. GMOD tools are in use at - \[\[MOD\|many large and small community databases\]\]. - \[\[File:ChadoLogo.png\|250px\|thumb\|none\|link=Chado\|Chado: - Biological database schema\]\] - - - - - - 5 KB (651 words) - 18:39, 1 June 2024 - - - -- - - [GMOD Developer's - Guide](/wiki/GMOD_Developer%27s_Guide "GMOD Developer's Guide") - - - - - - ...tional database, it should be able - to interact with a Chado database via - a database adaptor. - - - - - - 6 KB (985 words) - 05:18, 28 January 2008 - - - -- - - [Chado - Getting - Started](/wiki/Chado_-_Getting_Started "Chado - Getting Started") - - - - - - Chado is a \[\[Glossary#Database - Schema\|relational database - schema\]\] that underlies \[\[GMOD_Users\|many GMOD installations\]\]. - It is capab First you will need - database software, or Relational - Database Management System (RDBMS). - The recommended RDBMS for Chado currently is \[ht - - - - - - 3 KB (469 words) - 18:08, 13 February 2014 - - - -- - - [Chado FAQ](/wiki/Chado_FAQ "Chado FAQ") - - - - - - ...called DBIx::DBStag, which does the actual writing of ontology data - to the database. When it loads the - Gene Ontology (and possibly other ontologies), it destr : Instead, you - must run a SQL command to repair the - database: - - - - - - 6 KB (1,058 words) - 17:50, 5 February 2014 - - - -- - - [Apollo-Chado](/wiki/Apollo-Chado "Apollo-Chado") - - - - - - Reading and Writing to a Chado - database with Apollo vocabulary terms - that Apollo expects to be in the - database. This - - - - - - 4 KB (635 words) - 18:06, 28 December 2007 - - - -- - - [CMap](/wiki/CMap "CMap") - - - - - - \|type=Genome Visualization & Editing, Comparative Genome - Visualization, Database schema \* A - relational database, e.g. - \[http://www.mysql.com MySQL (4.0+)\], Sybase Adaptive Server - Enterpris - - - - - - 7 KB (996 words) - 23:40, 17 October 2013 - - - -- - - [TIGR-Workflow / - Ergatis](/wiki/TIGR-Workflow_/_Ergatis "TIGR-Workflow / Ergatis") - - - - - - ...database instance. In the past, - due to its primary use at TIGR/JCVI, the - database support was limited to - Sybase, though flat-files could also be generated. - - - - - - 2 KB (354 words) - 23:49, 25 July 2012 - - - -- - - [Flash GViewer - Documentation](/wiki/Flash_GViewer_Documentation "Flash GViewer Documentation") - - - - - - The Rat Genome Database has an - SVG-based genome viewer that shows the location of genes and QTLs ag - ...tation XML files or create a CGI/JSP script that retrieves the data - from a database. Details of the - various file formats are given below. - - - - - - 30 KB (4,819 words) - 21:16, 9 October 2012 - - - -- - - [GBrowse](/wiki/GBrowse "GBrowse") - - - - - - \|about=GBrowse is a combination of - database and interactive web pages - for manipulating and displaying annotations on ge ...nly for - applications where legacy browser support is required and a single - database is used. - - - - - - 11 KB (1,422 words) - 16:47, 10 April 2023 - - - -- - - [GMOD - Getting - Started](/wiki/GMOD_-_Getting_Started "GMOD - Getting Started") - - - - - - ...-\_Getting_Started\|Getting Started with Chado\]\] discusses GMOD's - relational database schema. Chado is - useful for organizing your data and is also integrated wi - - - - - - 1 KB (240 words) - 20:32, 15 September 2009 - - - -- - - [Community](/wiki/Community "Community") - - - - - - A proposed database module for Chado. \* The community module uses a relational - database, a Servlets and JSP engine, - and the Struts Web application framework. - - - - - - 2 KB (254 words) - 00:52, 18 November 2010 - - - -- - - [GMODTools](/wiki/GMODTools "GMODTools") - - - - - - ...rom several Chado dbs, and add other sources that may not be in - your Chado database. \* each genome - Chado database has different policy - and choices with respect to feature, vocabulary and ot - - - - - - 10 KB (1,496 words) - 23:00, 15 August 2013 - - - -- - - [Summary of Fall 2005 CHSL - Meeting](/wiki/Summary_of_Fall_2005_CHSL_Meeting "Summary of Fall 2005 CHSL Meeting") - - - - - - '''During the meeting it was suggested that we have a common - database against which to test - software. A first step would be to provide Postgres d Allen Day - suggested that he will provide a Postgres dump of the - database for human, yeast and mouse. - - - - - - 2 KB (257 words) - 15:02, 13 February 2007 - - - -- - - [Comparison of XORT and Hibernate for Chado - reporting](/wiki/Comparison_of_XORT_and_Hibernate_for_Chado_reporting "Comparison of XORT and Hibernate for Chado reporting") - - - - - - ...t up by hand but the JBOSS Eclipse IDE has a nice tool that will - read your database schema and - generate them for you. This is also the first place we encounter ...s - file that describes your schema matches the actual schema that is in - the database. Once that is done all - you need to do is write a dumpspec to dump the data - - - - - - 9 KB (1,641 words) - 15:48, 12 September 2011 - - - -- - - [Apollo-Chado example - database](/wiki/Apollo-Chado_example_database "Apollo-Chado example database") - - - - - - - - - - 587 B (98 words) - 21:08, 15 September 2009 - - - -- - - [GeneXplorer](/wiki/GeneXplorer "GeneXplorer") - - - - - - ...al web supplements for papers arising from data in the Stanford - Microarray Database. As an example, - see: - - - - - - 2 KB (364 words) - 18:57, 13 July 2012 - - - -- - - [GO Graphic Viewer](/wiki/GO_Graphic_Viewer "GO Graphic Viewer") - - - - - - ...ult from the GO::TermFinder Perl module created by the Stanford - Microarray Database (SMD). This - module is useful when analyzing experimental or computational r - - - - - - 2 KB (264 words) - 23:44, 3 December 2013 - - - -- - - [Pathway Tools](/wiki/Pathway_Tools "Pathway Tools") - - - - - - ...=Community Annotation, Comparative Genome Visualization , - Database schema, - Database tools, Gene Expression - Visualization, Genome Visualization & Editing, Molec - - - - - - 5 KB (650 words) - 00:07, 16 October 2013 - - - -- - - [PubSearch](/wiki/PubSearch "PubSearch") - - - - - - ...h and annotate genes to keywords from articles. It has a simple, - \[\[MySQL\]\] database backend and - uses a set of \[\[:Category%253AJava\|Java\]\] Servlets and JSPs for que - - - - - - 1 KB (178 words) - 00:52, 18 November 2010 - - - -- - - [Restriction Graphic - Viewer](/wiki/Restriction_Graphic_Viewer "Restriction Graphic Viewer") - - - - - - ...ite analysis tool. It is a component of the Generic Model Organism - Systems Database project. - - - - - - 595 B (80 words) - 22:36, 11 September 2009 - - - -- - - [BioMart](/wiki/BioMart "BioMart") - - - - - - \|type=Community Annotation, Database - schema, Database tools, Genome - Annotation, Middleware, Tool Integration, Data federation sof - \|about=BioMart is a freely available, open source, federated - database system that provides unified - access to disparate, geographically distribute - - - - - - 2 KB (228 words) - 22:26, 15 October 2013 - - - -- - - [Argos](/wiki/Argos "Argos") - - - - - - ...implemented common - database/information service tools - needed for organism database systems, - which can be automatically distributed and updated to any computer - ...others are well developed tools but don't quite meet the needs of - this bio-database distribution. - - - - - - 12 KB (1,641 words) - 15:41, 16 July 2012 - - - -- - - [Citrina](/wiki/Citrina "Citrina") - - - - - - ...o SQL dumps between organism sites and automatically populate the - postgres database via Ant's SQL - tasks. Ant can also execute external scripts so Citrina can t - - - - - - 2 KB (397 words) - 22:19, 11 September 2009 - - - -- - - [Insertional Mutagenesis Database - (IMDB)]( "Insertional Mutagenesis Database (IMDB)") - - - - - - ...This project was developed from ATIDB, the Arabidopsis thaliana - insertion database. : See - \[http://atidb.cshl.org/ http://atidb.cshl.org\] for a - database of Arabidopsis insertional - mutants. - - - - - - 1 KB (150 words) - 07:22, 30 January 2008 - - - -- - - [LuceGene](/wiki/LuceGene "LuceGene") - - - - - - ...d retrieval with LuceGene is 10x to 20x faster than using a - Postgres Chado database. ...orts, or - other complex data, can be quite slow. Chado is a good management - database, but lacks efficiency for - web access to support many customers. Lucene has - - - - - - 6 KB (792 words) - 15:09, 6 September 2010 - - - -- - - [PubFetch](/wiki/PubFetch "PubFetch") - - - - - - ...psis.org/ TAIR\]. A standard API and data format will be created to - provide database queries and return - results, popular existing formats and protocols will be ...be reviewed - and adapted to create the main PubFetch module and appropriate - database interace modules. Figure 2 - below is a schematic diagram of the exising RGD - - - - - - 3 KB (467 words) - 16:31, 15 October 2008 - - - -- - - [Textpresso](/wiki/Textpresso "Textpresso") - - - - - - ...dual sentences, and the implementation of semantic categories, for - which a database of articles and - individual sentences can be searched. The source of the ful - ...publicly (via WWW) accessible - database, while the other half is - needed for database preparation and - maintenance. If necessary, the latter can be reduced. - - - - - - 5 KB (697 words) - 17:56, 17 October 2013 - - - -- - - [Publications](/wiki/Publications "Publications") - - - - - - ...se join the - \[http://www.mendeley.com/groups/2472261/generic-model-organism-database-gmod-project/ - GMOD group\] and contribute GMOD and GMOD-related papers to th - ...ywidget - src="http://www.mendeley.com/groups/2472261/generic-model-organism-database-gmod-project/" - width="100%" height="400px" n_papers="50" /\> - - - - - - 21 KB (3,298 words) - 22:22, 9 February 2015 - - - -- - - [GMOD Components](/wiki/GMOD_Components "GMOD Components") - - - - - - The diagram below represents a model organism - database (MOD) and its typical - components. The ''top ten'' types of functionality ar - - - - - - 3 KB (425 words) - 19:55, 2 December 2013 - - - -- - - [GBrowse FAQ](/wiki/GBrowse_FAQ "GBrowse FAQ") - - - - - - \* Connect to your database using the - mysql command-line client and run the command: ...ure from end to end. - When using \[\[GFF3\]\] and a Bio::DB::SeqFeature::Store - database (see \[\[GBrowse - Adaptors\]\]), that is all you have to do. For example, using - - - - - - 11 KB (1,733 words) - 14:48, 18 May 2013 - - - -- - - [CMap FAQ](/wiki/CMap_FAQ "CMap FAQ") - - - - - - ...t them, you have to write a Perl code in the config file that - accesses the database through the - sql() object. ...ing \$self-\>sql(). The resulting object has methods - that interact with the database. For - more information about the methods that can be called execute "perldo - - - - - - 7 KB (1,071 words) - 13:01, 14 October 2010 - - - -- - - [GMOD FAQ](/wiki/GMOD_FAQ "GMOD FAQ") - - - - - - ...ally any sort of organism or group of organisms can be the focus of - a GMOD database (see - \[\[GMOD_Users\|the GMOD users list\]\] for many examples). It's been - sugge ...popular components include the genome browser - \[\[GBrowse\]\], the relational - database - \[\[Chado\_-_Getting_Started\|Chado\]\], and the comparative map - viewer \[\[CMap\]\]. - - - - - - 2 KB (238 words) - 18:17, 24 September 2008 - - - -- - - [XORT](/wiki/XORT "XORT") - - - - - - \|type=Database tools, Middleware - ...ata output and data debug system. Because it originates from the - \[\[Chado\]\] database, we denote the - corresponding XML "Chado XML." - - - - - - 1 KB (221 words) - 21:22, 16 October 2013 - - - -- - - [Chado Manual](/wiki/Chado_Manual "Chado Manual") - - - - - - ;Database ...oftware is an example of - a DBMS. The documentation rarely uses the term - ''database'' in this sense. - - - - - - 17 KB (2,655 words) - 13:43, 14 March 2014 - - - -- - - [Chado%253A%253AAutoDBI - Presentation](/wiki/Chado%253A%253AAutoDBI_Presentation "Chado%253A%253AAutoDBI Presentation") - - - - - - \* Database connection: use a base - class - - - - - - 6 KB (795 words) - 23:33, 8 October 2012 - - - -- - - [June 2006 GMOD - Meeting](/wiki/June_2006_GMOD_Meeting "June 2006 GMOD Meeting") - - - - - - GMOD Generic Model Organism Database - - - - - - 3 KB (426 words) - 19:30, 23 January 2008 - - - -- - - [Chado Update via - GFF](/wiki/Chado_Update_via_GFF "Chado Update via GFF") - - - - - - There has frequently been interest in updating a \[\[Chado\]\] - database using a \[\[GFF\]\] file, - and I've finally gotten around to trying to implement ...ld be able to - trigger updates to an existing feature, where CRUDop is your - database Create/Replace/Update/Drop - operation. - - - - - - 3 KB (459 words) - 19:23, 30 December 2008 - - - -- - - [Questions on - Testing](/wiki/Questions_on_Testing "Questions on Testing") - - - - - - \* load test file into test database \* use API to fetch objects from - database - - - - - - 2 KB (361 words) - 17:16, 5 April 2007 - - - -- - - [GMOD Project Page](/wiki/GMOD_Project_Page "GMOD Project Page") - - - - - - \* database processing of '''high - throughput genomics analyses''' with input, output, i - - - - - - 2 KB (274 words) - 22:07, 29 October 2010 - - - -- - - [MOD](/wiki/MOD "MOD") - - - - - - ...ism databases, so that the MOD in GMOD can apply to any organism or - genome database projects. - - - - - - 1 KB (155 words) - 20:21, 6 March 2013 - - - -- - - [Face Caucus SGN: Associating Solanaceae loci with - phenotype](/wiki/Face_Caucus_SGN%253A_Associating_Solanaceae_loci_with_phenotype "Face Caucus SGN: Associating Solanaceae loci with phenotype") - - - - - - ...k (\[\[:Category%253ASGN\|SGN\]\], http://www.sgn.cornell.edu/) is a - Clade Oriented Database (COD) - containing genomic, genetic and taxonomic information for species in - ...permissions vary according to the user-type. The framework for - editing the database is now being - extended for developing an online ontology annotation tool, an - - - - - - 2 KB (259 words) - 01:15, 19 August 2009 - - - -- - - [January 2007 GMOD meeting - agenda](/wiki/January_2007_GMOD_meeting_agenda "January 2007 GMOD meeting agenda") - - - - - - \| tentative Chado database - discussion/tutorial session - - - - - - 2 KB (295 words) - 15:02, 13 February 2007 - - - -- - - [NIH 2002 Workshop on Model Organism - Databases](/wiki/NIH_2002_Workshop_on_Model_Organism_Databases "NIH 2002 Workshop on Model Organism Databases") - - - - - - ...n broader meaning in recent years, and now signifies any curated - community database that is dedicated - to a single species or related clade of species. ...se resources - include management structures, standard operating procedures, - database models and software. Such - reuse of existing resources will result in higher - - - - - - 26 KB (3,975 words) - 05:03, 28 January 2008 - - - -- - - [MOD User Interface - Caucus](/wiki/MOD_User_Interface_Caucus "MOD User Interface Caucus") - - - - - - ...ne, searching with broader concepts, extracting focused answers, - and cross-database facilitation. We - hope most presenters can touch on these to give the audien \[\*\]\] - MOD in the generic sense of an organism/genome-related - database,\
defining the M as - you would: Model, Many, or My organism. - - - - - - 4 KB (599 words) - 01:32, 29 March 2007 - - - - - -View (previous 50 \| next 50) (20 \| 50 \| 100 \| 250 \| 500) - - - - - - - - -## Navigation menu - - - - -### Namespaces - -- [Special - page](/wiki/Special%253ASearch/Database "This is a special page, you cannot edit the page itself") - - - -### Navigation - - - -- [GMOD Home](/wiki/Main_Page) -- [Software](/wiki/GMOD_Components) -- [Categories / - Tags](/wiki/Categories) -- [View all - pages](/wiki/Special:AllPages) - - - - -### Documentation - - - -- [Overview](/wiki/Overview) -- [FAQs](/wiki/Category%253AFAQ) -- [HOWTOs](/wiki/Category%253AHOWTO) -- [Glossary](/wiki/Glossary) - - - - -### Community - - - -- [GMOD News](/wiki/GMOD_News) -- [Training / - Outreach](/wiki/Training_and_Outreach) -- [Support](/wiki/Support) -- [GMOD - Promotion](/wiki/GMOD_Promotion) -- [Meetings](/wiki/Meetings) -- [Calendar](/wiki/Calendar) - - - - -### Tools - - - - - - - - - - - - - - - diff --git a/wiki/Special%3ASearch/Deprecated.md b/wiki/Special%3ASearch/Deprecated.md deleted file mode 100644 index f111c2b4d1..0000000000 --- a/wiki/Special%3ASearch/Deprecated.md +++ /dev/null @@ -1,863 +0,0 @@ - - - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=Deprecated&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=Deprecated&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=Deprecated&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=Deprecated&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=Deprecated&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below **36** results starting with \#**1**. - - - -**Create the page "Deprecated" on -this wiki!** See also the search results found. - -- - - [Textpresso](/wiki/Textpresso "Textpresso") - - - - - - ...m/~brill/blog.htm blog\], \[http://research.microsoft.com/~brill/ - homepage\]''deprecated''). RBT seems - to be no longer available at JHU. A copy appears to be avai - - - - - - 5 KB (697 words) - 17:56, 17 October 2013 - - - -- - - [Chado New Users](/wiki/Chado_New_Users "Chado New Users") - - - - - - \* Parenting a CDS/polypeptide directly on a gene is - deprecated because the gene (sensu - eukaryota) includes nontranscribed regions - - - - - - 4 KB (611 words) - 19:58, 22 April 2008 - - - -- - - [GBrowse Ubuntu - HOWTO](/wiki/GBrowse_Ubuntu_HOWTO "GBrowse Ubuntu HOWTO") - - - - - - \The information below is - deprecated.\ - - - - - - 8 KB (799 words) - 20:37, 8 August 2018 - - - -- - - [Glossary](/wiki/Glossary "Glossary") - - - - - - ...f GFF supported in GMOD: \[\[#GFF3\|GFF3\]\] and - \[\[#GFF2\|GFF2\]\]. GFF2 is now - ''deprecated''. \[\[GFF2\]\] is a - supported \[\[#GFF\|GFF\]\] format in GMOD, '''but it is now - deprecated and if you have a choice - you should use \[\[#GFF3\|GFF3\]\]'''. Unfortunately, - - - - - - 14 KB (2,081 words) - 02:50, 14 March 2014 - - - -- - - [GBrowse 1 Configuration - HOWTO](/wiki/GBrowse_1_Configuration_HOWTO "GBrowse 1 Configuration HOWTO") - - - - - - ...han one level of nesting, and several other common situations. - '''GFF2 is deprecated and if possible - you are strongly encouraged to use \[\[GFF3\]\].''' ...he same as - providing the \-user\ option to \db_args\, and - is deprecated. - - - - - - 79 KB (12,563 words) - 16:45, 15 August 2011 - - - -- - - [GBrowse Adaptors](/wiki/GBrowse_Adaptors "GBrowse Adaptors") - - - - - - \| Quite fast; large user base; Have to use this if your data is in - the (now deprecated) \[\[GFF2\]\] - format. - - - - - - 3 KB (443 words) - 16:22, 7 August 2012 - - - -- - - [GBrowse 2.0 HOWTO](/wiki/GBrowse_2.0_HOWTO "GBrowse 2.0 HOWTO") - - - - - - description = Zebrafish genome, build 1 - (deprecated) description = Zebrafish - genome, build 1 (deprecated) - - - - - - 101 KB (15,507 words) - 04:44, 9 January 2014 - - - -- - - [GFF](/wiki/GFF "GFF") - - - - - - \[\[GFF2\]\] is a supported format in GMOD, '''but it is now - deprecated and if you have a choice - you should use GFF3'''. Unfortunately, data is so - - - - - - 16 KB (2,336 words) - 19:49, 10 September 2012 - - - -- - - [GFF3 2011 tutorial](/wiki/GFF3_2011_tutorial "GFF3 2011 tutorial") - - - - - - \[\[gmod:GFF2\|GFF2\]\] is a supported format in GMOD, '''but it is - now deprecated and if you have a - choice you should use GFF3'''. Unfortunately, data is so - - - - - - 16 KB (2,387 words) - 22:13, 11 February 2014 - - - -- - - [GFF2](/wiki/GFF2 "GFF2") - - - - - - ...s/GFF/GFF_Spec.shtml GFF2\] is a supported format in GMOD, '''but - it is now deprecated and if you have - a choice you should use \[\[GFF3\]\]'''. Unfortunately, data i == GFF2 - is Deprecated! == - - - - - - 17 KB (2,719 words) - 13:27, 21 April 2017 - - - -- - - [MAKER Tutorial 2013](/wiki/MAKER_Tutorial_2013 "MAKER Tutorial 2013") - - - - - - \*''fix_fasta'' - Deprecated, use - fasta_tool - - - - - - 80 KB (12,961 words) - 23:47, 29 July 2013 - - - -- - - [GBrowse syn Scripts](/wiki/GBrowse_syn_Scripts "GBrowse syn Scripts") - - - - - - :This script is deprecated. You can - use the \[\[GBrowse_syn_Scripts#load_alignments_msa.pl\|load_alignme - :This script is deprecated. You can - use the \[\[GBrowse_syn_Scripts#load_alignments_msa.pl\|load_alignme - - - - - - 6 KB (931 words) - 22:39, 21 February 2013 - - - -- - - [Chado Post-Composed - Phenotypes](/wiki/Chado_Post-Composed_Phenotypes "Chado Post-Composed Phenotypes") - - - - - - == Recommended Deprecated Fields == - are deprecated to break the - connection between the phenotype value and the - - - - - - 4 KB (680 words) - 23:12, 19 August 2015 - - - -- - - [Chado Phenotype Module - - Staging](/wiki/Chado_Phenotype_Module_-_Staging "Chado Phenotype Module - Staging") - - - - - - Deprecated and superceded by - phenotypeprop. - - - - - - 5 KB (680 words) - 22:10, 10 December 2010 - - - -- - - [Web-apollo-meeting-2011-1-6](/wiki/Web-apollo-meeting-2011-1-6 "Web-apollo-meeting-2011-1-6") - - - - - - \*\* Caching functionality (firebug report too?): Has - deprecated as a priority as current - solution is adequate. Speed is - - - - - - 2 KB (320 words) - 23:24, 6 January 2011 - - - -- - - [Chado Natural Diversity Module/natdiv schema changes - call](/wiki/Chado_Natural_Diversity_Module/natdiv_schema_changes_call "Chado Natural Diversity Module/natdiv schema changes call") - - - - - - ....uniquename. 2) Added phenotype.units_id. 3) Added phenotypeprop - table. 4) Deprecated phenotype_cvterm - table. - - - - - - 11 KB (1,777 words) - 15:05, 4 February 2012 - - - -- - - [GFF3](/wiki/GFF3 "GFF3") - - - - - - \[\[GFF2\]\] is a supported format in GMOD, '''but it is now - deprecated and if you have a choice - you should use GFF3'''. Unfortunately, data is so - - - - - - 16 KB (2,350 words) - 20:25, 12 July 2016 - - - -- - - [BioGraphics:anchored arrow - glyph](/wiki/BioGraphics:anchored_arrow_glyph "BioGraphics:anchored arrow glyph") - - - - - - \| Deprecated option; do not use. - - - - - - 13 KB (2,003 words) - 16:05, 19 April 2012 - - - -- - - [BioGraphics:arrow - glyph](/wiki/BioGraphics:arrow_glyph "BioGraphics:arrow glyph") - - - - - - \| Deprecated option; do not use. - - - - - - 12 KB (1,878 words) - 16:05, 19 April 2012 - - - -- - - [BioGraphics:extending arrow - glyph](/wiki/BioGraphics:extending_arrow_glyph "BioGraphics:extending arrow glyph") - - - - - - \| Deprecated option; do not use. - - - - - - 13 KB (2,033 words) - 16:05, 19 April 2012 - - - -- - - [BioGraphics:hybrid plot - glyph](/wiki/BioGraphics:hybrid_plot_glyph "BioGraphics:hybrid plot glyph") - - - - - - ...ph to generate. Options are "boxes", "line","points", or - "linepoints". The deprecated "boxes" - subtype is equivalent to "histogram". - - - - - - 17 KB (2,698 words) - 16:05, 19 April 2012 - - - -- - - [BioGraphics:phylo align - glyph](/wiki/BioGraphics:phylo_align_glyph "BioGraphics:phylo align glyph") - - - - - - ...ph to generate. Options are "boxes", "line","points", or - "linepoints". The deprecated "boxes" - subtype is equivalent to "histogram". - - - - - - 15 KB (2,325 words) - 16:05, 19 April 2012 - - - -- - - [BioGraphics:scale - glyph](/wiki/BioGraphics:scale_glyph "BioGraphics:scale glyph") - - - - - - ...ph to generate. Options are "boxes", "line","points", or - "linepoints". The deprecated "boxes" - subtype is equivalent to "histogram". - - - - - - 15 KB (2,284 words) - 16:06, 19 April 2012 - - - -- - - [BioGraphics:span - glyph](/wiki/BioGraphics:span_glyph "BioGraphics:span glyph") - - - - - - \| Deprecated option; do not use. - - - - - - 12 KB (1,914 words) - 16:06, 19 April 2012 - - - -- - - [BioGraphics:vista plot - glyph](/wiki/BioGraphics%253Avista_plot_glyph "BioGraphics:vista plot glyph") - - - - - - ...or "whiskers" (for a whiskerplot showing mean, +/- stdev and - max/min. The deprecated "boxes" - subtype is a synonym for "histogram." - - - - - - 20 KB (3,072 words) - 16:06, 19 April 2012 - - - -- - - [BioGraphics:whiskerplot - glyph](/wiki/BioGraphics:whiskerplot_glyph "BioGraphics:whiskerplot glyph") - - - - - - ...ph to generate. Options are "boxes", "line","points", or - "linepoints". The deprecated "boxes" - subtype is equivalent to "histogram". - - - - - - 15 KB (2,351 words) - 16:06, 19 April 2012 - - - -- - - [BioGraphics:wiggle density - glyph](/wiki/BioGraphics:wiggle_density_glyph "BioGraphics:wiggle density glyph") - - - - - - ...ph to generate. Options are "boxes", "line","points", or - "linepoints". The deprecated "boxes" - subtype is equivalent to "histogram". - - - - - - 17 KB (2,633 words) - 16:06, 19 April 2012 - - - -- - - [BioGraphics:wiggle xyplot - glyph](/wiki/BioGraphics:wiggle_xyplot_glyph "BioGraphics:wiggle xyplot glyph") - - - - - - ...ph to generate. Options are "boxes", "line","points", or - "linepoints". The deprecated "boxes" - subtype is equivalent to "histogram". - - - - - - 17 KB (2,680 words) - 16:06, 19 April 2012 - - - -- - - [BioGraphics:xyplot - glyph](/wiki/BioGraphics:xyplot_glyph "BioGraphics:xyplot glyph") - - - - - - ...ph to generate. Options are "boxes", "line","points", or - "linepoints". The deprecated "boxes" - subtype is equivalent to "histogram". - - - - - - 15 KB (2,348 words) - 16:06, 19 April 2012 - - - -- - - [GFF Tutorial 2012](/wiki/GFF_Tutorial_2012 "GFF Tutorial 2012") - - - - - - \[\[GFF2\]\] is a supported format in GMOD, '''but it is now - deprecated and if you have a choice - you should use GFF3'''. Unfortunately, data is so - - - - - - 16 KB (2,352 words) - 21:54, 11 September 2012 - - - -- - - [MAKER Tutorial 2012](/wiki/MAKER_Tutorial_2012 "MAKER Tutorial 2012") - - - - - - \*''fix_fasta'' - Deprecated, use - fasta_tool - - - - - - 80 KB (12,923 words) - 20:52, 27 August 2013 - - - -- - - [GFF3 Tutorial 2011](/wiki/GFF3_Tutorial_2011 "GFF3 Tutorial 2011") - - - - - - \[\[GFF2\|GFF2\]\] is a supported format in GMOD, '''but it is now - deprecated and if you have a choice - you should use GFF3'''. Unfortunately, data is so - - - - - - 16 KB (2,345 words) - 00:23, 14 February 2013 - - - -- - - [MAKER Tutorial 2011](/wiki/MAKER_Tutorial_2011 "MAKER Tutorial 2011") - - - - - - \*''fix_fasta'' - Deprecated, use - fasta_tool - - - - - - 69 KB (11,026 words) - 20:52, 27 August 2013 - - - -- - - [GMOD Malaysia 2014/MAKER - Tutorial](/wiki/GMOD_Malaysia_2014/MAKER_Tutorial "GMOD Malaysia 2014/MAKER Tutorial") - - - - - - \*''fix_fasta'' - Deprecated, use - fasta_tool \*''gff3_preds2models'' - - Deprecated pass the predictions to - MAKER in the \maker_opts.ctl\ in gff3 format - - - - - - 85 KB (13,463 words) - 00:56, 27 February 2014 - - - -- - - [GMOD Online Training 2014/GFF3 - Tutorial](/wiki/GMOD_Online_Training_2014/GFF3_Tutorial "GMOD Online Training 2014/GFF3 Tutorial") - - - - - - \[\[GFF2\]\] is a supported format in GMOD, '''but it is now - deprecated and if you have a choice - you should use GFF3'''. Unfortunately, data is so - - - - - - 16 KB (2,318 words) - 04:56, 19 May 2014 - - - -- - - [GMOD Online Training 2014/MAKER - Tutorial](/wiki/GMOD_Online_Training_2014/MAKER_Tutorial "GMOD Online Training 2014/MAKER Tutorial") - - - - - - \*''fix_fasta'' - Deprecated, use - fasta_tool - - - - - - 80 KB (12,952 words) - 03:53, 19 May 2014 - - - - - -View (previous 50 \| next 50) (20 \| 50 \| 100 \| 250 \| 500) - - - - - - - - -## Navigation menu - - - -### Namespaces - -- [Special - page](/wiki/Special%253ASearch/Deprecated "This is a special page, you cannot edit the page itself") - - - - - - -### Navigation - - - -- [GMOD Home](/wiki/Main_Page) -- [Software](/wiki/GMOD_Components) -- [Categories / - Tags](/wiki/Categories) -- [View all - pages](/wiki/Special:AllPages) - - - - -### Documentation - - - -- [Overview](/wiki/Overview) -- [FAQs](/wiki/Category%253AFAQ) -- [HOWTOs](/wiki/Category%253AHOWTO) -- [Glossary](/wiki/Glossary) - - - - -### Community - - - -- [GMOD News](/wiki/GMOD_News) -- [Training / - Outreach](/wiki/Training_and_Outreach) -- [Support](/wiki/Support) -- [GMOD - Promotion](/wiki/GMOD_Promotion) -- [Meetings](/wiki/Meetings) -- [Calendar](/wiki/Calendar) - - - - -### Tools - - - - - - - - - - - - - - - - - diff --git a/wiki/Special%3ASearch/File_Formats.md b/wiki/Special%3ASearch/File_Formats.md deleted file mode 100644 index a2e50fc858..0000000000 --- a/wiki/Special%3ASearch/File_Formats.md +++ /dev/null @@ -1,1232 +0,0 @@ - - - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=File+Formats&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=File+Formats&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=File+Formats&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=File+Formats&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=File+Formats&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below up to **50** results starting with \#**1**. - - - -**Create the page "File Formats" -on this wiki!** See also the search results found. - -- - - [GMOD Middleware](/wiki/GMOD_Middleware "GMOD Middleware") - - - - - - Update the gene '''xfile''': change the name symbol to - '''x-file''' and retrieve the changed - record. Regenerate the report from Problem 1. T symbol: - x-file - - - - - - 40 KB (5,672 words) - 21:27, 15 August 2013 - - - -- - - [GMOD Developer's - Guide](/wiki/GMOD_Developer%27s_Guide "GMOD Developer's Guide") - - - - - - \*\* db=short symbolic name of datasource (MOD), used to look up conf - file \*\* Sequence feature apps - should read/write GenBank & EMBL - formats (BioPerl and BioJava handle - this). GFF? GTF? BED? GAME? BSML? TIGR add BSML - - - - - - 6 KB (985 words) - 05:18, 28 January 2008 - - - -- - - [CMap](/wiki/CMap "CMap") - - - - - - File:Cmap_sample1.jpg - File:Cmap_sample2.jpg - - - - - - 7 KB (996 words) - 23:40, 17 October 2013 - - - -- - - [Flash GViewer](/wiki/Flash_GViewer "Flash GViewer") - - - - - - \[\[File:Flash gviewer - title.jpg\|center\|Flash GViewer Logo\]\] ...ckwaveFlash&promoid=BIOW - here\]. To edit the source code (the \.fla\ - file in \[\[SVN\]\]) and publish - modified versions of the \.swf\ requires Mac - - - - - - 2 KB (339 words) - 19:41, 26 February 2014 - - - -- - - [Flash GViewer - Documentation](/wiki/Flash_GViewer_Documentation "Flash GViewer Documentation") - - - - - - \* Annotations can come from a static XML - file or can be dynamically generated - by a server-side script ...cript that retrieves the data from a - database. Details of the various file - formats are given below. - - - - - - 30 KB (4,819 words) - 21:16, 9 October 2012 - - - -- - - [GBrowse](/wiki/GBrowse "GBrowse") - - - - - - \* Supports third party annotation using \[\[GFF\]\] - formats. ...ns\|plug-in\]\] - architecture (e.g. run \[\[wp:BLAST\|BLAST\]\], dump & import many - formats, find oligonucleotides, - \[\[PrimerDesigner.pm\|design primers\]\], create restri - - - - - - 11 KB (1,422 words) - 16:47, 10 April 2023 - - - -- - - [GMODTools](/wiki/GMODTools "GMODTools") - - - - - - \* DNA files (full chromosomes) in raw and fasta - formats \* Gene Ontology association - file - - - - - - 10 KB (1,496 words) - 23:00, 15 August 2013 - - - -- - - [BLAST Graphic Viewer/tool - data](/wiki/BLAST_Graphic_Viewer/tool_data "BLAST Graphic Viewer/tool data") - - - - - - \| install = See the INSTALL file in - the \[http://sourceforge.net/projects/gmod/files/blastGraphic/ - blastGraph \| input = \ - - - - diff --git a/wiki/Special%3ASearch/GMOD_Online_Training.md b/wiki/Special%3ASearch/GMOD_Online_Training.md deleted file mode 100644 index c15b5d6cc4..0000000000 --- a/wiki/Special%3ASearch/GMOD_Online_Training.md +++ /dev/null @@ -1,932 +0,0 @@ - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=GMOD+Online+Training&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=GMOD+Online+Training&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=GMOD+Online+Training&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=GMOD+Online+Training&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=GMOD+Online+Training&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below **35** results starting with \#**1**. - - - - -**Create the page "GMOD -Online Training" on this wiki!** See also the search results found. - -## Page title matches - -- - - [GMOD Online Training 2014/WebApollo - Tutorial](/wiki/GMOD_Online_Training_2014/WebApollo_Tutorial "GMOD Online Training 2014/WebApollo Tutorial") - - - - - - \$ wget - icebox.lbl.gov/webapollo/gmod/2014/summer_school/new_config.tgz - ...ou can get more information about the Chado at - \[http://gmod.org/wiki/Chado - GMOD Chado page\]. The configuration - is stored in \/var/lib/tomcat7/webapps/W - - - - - - 77 KB (11,812 words) - 00:39, 21 May 2014 - - - -- - - [GMOD Online Training - 2014/Schedule](/wiki/GMOD_Online_Training_2014/Schedule "GMOD Online Training 2014/Schedule") - - - - - - ! Affiliation; GMOD role ...tt - Cain\]\] \|\| \[http://oicr.on.ca/ Ontario Institute for Cancer - Research\]\GMOD Project - Coordinator; \[\[Chado\]\], \[\[GBrowse\]\] - - - - - - 3 KB (382 words) - 07:42, 22 May 2014 - - - -- - - [GMOD Online Training 2014/Chado - Tutorial](/wiki/GMOD_Online_Training_2014/Chado_Tutorial "GMOD Online Training 2014/Chado Tutorial") - - - - - - ...tutorial was presented by \[\[User%253AScott\|Scott Cain\]\] as part of - the \[\[2013 GMOD Summer School\]\]. - Chado is the database schema of the - GMOD project. This session introduces - database concepts, and then provides an o - - - - - - 50 KB (7,595 words) - 12:53, 20 May 2014 - - - -- - - [GMOD Online Training 2014//SOBA - Tutorial](/wiki/GMOD_Online_Training_2014//SOBA_Tutorial "GMOD Online Training 2014//SOBA Tutorial") - - - - - - \* NAME: GMOD Summer 2014 - SOBA/GAL - ...ibution in the \[GAL/docs/html/GAL.html GAL/docs/html/GAL.html\] - document or online at: - - - - - - 19 KB (2,557 words) - 14:38, 19 May 2014 - - - -- - - [GMOD Online Training - 2014](/wiki/GMOD_Online_Training_2014 "GMOD Online Training 2014") - - - - - - \[\[File:Gmod-online-training.png\|left\|300px\]\] - \[\[File:GitcLogo.png\|150px\|right\|link=Cloud\|GMOD - in the Cloud toolset\]\] - - - - - - 3 KB (445 words) - 16:12, 29 April 2014 - - - -- - - [News/Applications Open for GMOD Online - Training](/wiki/News/Applications_Open_for_GMOD_Online_Training "News/Applications Open for GMOD Online Training") - - - - - - ...first online - training course for those interested - in the set up and use of GMOD - components. ...ld from '''Monday 19th May to Friday 23rd May 2014''', - and will cover core GMOD software, - including \[\[GBrowse\]\] and \[\[JBrowse\]\], \[\[Galaxy\]\], - \[\[MAKER\]\], \[\[T - - - - - - 563 B (82 words) - 20:18, 1 April 2014 - - - -- - - [GMOD Online Training 2014/GFF3 - Tutorial](/wiki/GMOD_Online_Training_2014/GFF3_Tutorial "GMOD Online Training 2014/GFF3 Tutorial") - - - - - - ...tom built to represent GFF data. GFF is \[\[#GFF in - GMOD\|frequently used in - GMOD\]\] for data exchange and - representation of genomic data. ...n its predecessor, - ''\[\[#GFF2\|GFF2\]\]''. '''GFF3 is the preferred format in - GMOD''', but data is not always - available in GFF3 format, so you may have to use - - - - - - 16 KB (2,318 words) - 04:56, 19 May 2014 - - - -- - - [GMOD Online Training 2014/MAKER - Tutorial](/wiki/GMOD_Online_Training_2014/MAKER_Tutorial "GMOD Online Training 2014/MAKER Tutorial") - - - - - - ...e annotations, evidence, and quality control statistics for use - with other GMOD programs like - \[\[GBrowse\]\], \[\[JBrowse\]\], \[\[Chado\]\], and \[\[Apollo\]\]. - \| Output is compatible with popular - GMOD annotation tools like - \[\[Apollo\]\], \[\[GBrowse\]\] \[\[JBrowse\]\] - - - - - - 80 KB (12,952 words) - 03:53, 19 May 2014 - - - -- - - [GMOD Online Training 2014/JBrowse - Tutorial](/wiki/GMOD_Online_Training_2014/JBrowse_Tutorial "GMOD Online Training 2014/JBrowse Tutorial") - - - - - - \wget - https://s3.amazonaws.com/gmod-online-2014/GMOD_Summer_School_2014_JBrowse.tar.gz\ - "description": "GMOD Summer School - 2013 P. ultima Example", - - - - - - 13 KB (1,905 words) - 14:21, 21 May 2014 - - - -- - - [GMOD Online Training 2014/GBrowse syn - Tutorial](/wiki/GMOD_Online_Training_2014/GBrowse_syn_Tutorial "GMOD Online Training 2014/GBrowse syn Tutorial") - - - - - - The starting image for this tutorial is - '''GMOD 2014 - online school - ami-907e97f8'''. It - can be run as a micro or small instance. \$ \git - clone - https://github.com/GMOD/GBrowse.git\ - - - - - - 20 KB (2,751 words) - 19:05, 22 May 2014 - - - -## Page text matches - -- - - [April 2004 GMOD - Meeting](/wiki/April_2004_GMOD_Meeting "April 2004 GMOD Meeting") - - - - - - GMOD Meeting April, 2004 - \GMOD/Turnkey web demo\ - - - - - - 42 KB (6,309 words) - 20:37, 30 November 2010 - - - -- - - [2009 GMOD Summer School - - Europe](/wiki/2009_GMOD_Summer_School_-_Europe "2009 GMOD Summer School - Europe") - - - - - - \| - \[\[File:GMOD2009Europe300.png\|link=GMOD - Europe 2009\|GMOD Europe 2009\]\] \| - \\2009 - GMOD Summer School - Europe\\
3-6 August, 2009\
Oxford UK\ - - - - - - 10 KB (1,210 words) - 22:13, 16 April 2014 - - - -- - - [August 2009 GMOD - Meeting](/wiki/August_2009_GMOD_Meeting "August 2009 GMOD Meeting") - - - - - - ...e 2009\]\], five days of GMOD - including a \[\[2009 GMOD Summer - School - Europe\|GMOD Summer - School\]\]\ \\[\[File:Aug2009MeetingPhoto.JPG\|August - 2009 GMOD Meeting\]\] - - - - - - 59 KB (8,741 words) - 19:37, 4 September 2013 - - - -- - - [2009 GMOD Summer School - - Americas](/wiki/2009_GMOD_Summer_School_-_Americas "2009 GMOD Summer School - Americas") - - - - - - \| \\2009 - GMOD Summer School - - Americas\\
16-19 July, 2009\
\[http://www.nescent - ..., this course focused on installing, configuring and integrating - popular \[\[GMOD Components\]\]. - - - - - - 11 KB (1,433 words) - 22:13, 16 April 2014 - - - -- - - [Training and - Outreach](/wiki/Training_and_Outreach "Training and Outreach") - - - - - - ...ing and outreach activities. See \[\[Support\]\] for other support - options in GMOD. - ...\[\[GMOD Help Desk\]\], - \[\[GMOD - Components\|GMOD component\]\] - developers, and by GMOD users. - - - - - - 2 KB (250 words) - 21:09, 6 August 2013 - - - -- - - [News/GMOD Tutorials! GMOD - Training!](/wiki/News/GMOD_Tutorials!_GMOD_Training! "News/GMOD Tutorials! GMOD Training!") - - - - - - \[\[File:GMOD2009Europe170.png\|link=http://gmod.org/wiki/Training_and_Outreach#Online_Tutorials\|120px\|right\|Summer - School - - \[\[File:2009SummerSchoolAmericas170.png\|link=http://gmod.org/wiki/Training_and_Outreach#Online_Tutorials\|120px\|right\|Summer - School - - - - - - - 4 KB (542 words) - 23:11, 9 October 2012 - - - -- - - [News/New GMOD - Tutorials](/wiki/News/New_GMOD_Tutorials "News/New GMOD Tutorials") - - - - - - \[\[File:2010SummerSchoolAmericas170.png\|link=http://gmod.org/wiki/Training_and_Outreach#Online_Tutorials\|right\|Summer - School - Ameri ...now available for the - \[\[GMOD Components\]\] that were - covered at the \[\[2010 GMOD Summer - School - Americas\]\]. Each tutorial includes a \[\[VMware\]\] system - ima - - - - - - 1 KB (223 words) - 23:09, 9 October 2012 - - - -- - - [GMOD Schools](/wiki/GMOD_Schools "GMOD Schools") - - - - - - \[\[File:Gmod-online-training.png\|150px\|GMOD - Online - Training 2014\]\] - \[\[File:GMOD-malaysia.png\|150px\|GMOD - Malaysia 2014\]\] - - - - - - 2 KB (250 words) - 22:22, 16 April 2014 - - - -- - - [PAG 2009](/wiki/PAG_2009 "PAG 2009") - - - - - - ...PAG was also immediately before the \[\[January 2009 - GMOD Meeting\]\] and many - GMOD members attended both meetings. - ...ng \[\[GMOD Components\]\]. This - page lists only those items that mentioned - \[\[GMOD Components\]\] in their - abstracts. - - - - - - 10 KB (1,390 words) - 18:16, 2 October 2012 - - - -- - - [PAG 2010](/wiki/PAG_2010 "PAG 2010") - - - - - - ...using GMOD components. This page - lists the subset that mentioned GMOD - or GMOD components in the abstract. - == About GMOD Components == - - - - - - 13 KB (1,711 words) - 18:17, 2 October 2012 - - - -- - - [MWAS Tutorial](/wiki/MWAS_Tutorial "MWAS Tutorial") - - - - - - ...se include difficulties associated with Repeat identification, gene - finder training, and other complex - analyses. Unfortunately emerging model organisms are of ...state of - the art annotation pipelines, and the truth is that, with enough - training data, they do. However, it - is important to keep in mind that ''ab initio'' - - - - - - 34 KB (5,308 words) - 22:03, 3 October 2012 - - - -- - - [2010 GMOD Summer School - - Americas](/wiki/2010_GMOD_Summer_School_-_Americas "2010 GMOD Summer School - Americas") - - - - - - \| \\2010 - GMOD Summer School - - Americas\\
6-9 May, 2010\
\[http://www.nescent.or - ...\[GMOD Components\]\]. Sessions - were taught by GMOD Component - developers and GMOD staff. There was - space in the course for 25 participants, and admission wa - - - - - - 13 KB (1,782 words) - 22:14, 16 April 2014 - - - -- - - [September 2010 GMOD - Meeting](/wiki/September_2010_GMOD_Meeting "September 2010 GMOD Meeting") - - - - - - \| style="font-size: 180%; line-height: 120%" \|\September 2010 - GMOD Meeting\\
13-14 - September 2010\
Cambridge, UK \
\
\[\[File - ...center" \| - \[\[File:GMOD2010Europe300.png\|200px\|link=GMOD - Europe 2010\|Part of GMOD Europe - 2010\]\] - - - - - - 100 KB (14,725 words) - 17:31, 30 November 2012 - - - -- - - [GMOD Promotion](/wiki/GMOD_Promotion "GMOD Promotion") - - - - - - \[\[File:PoweredByGMOD.png\|310px\|center\|Powered by - GMOD\]\] There are a number of - resources available to help spread the word about the - GMOD project. This serves (at least) - three interrelated purposes. - - - - - - 7 KB (1,003 words) - 18:14, 8 January 2013 - - - -- - - [PAG 2011](/wiki/PAG_2011 "PAG 2011") - - - - - - ...er demos, and posters, either about - GMOD and - \[\[GMOD Components\]\], or using - GMOD components. == About - GMOD Components == - - - - - - 11 KB (1,443 words) - 19:19, 4 September 2013 - - - -- - - [Community Annotation - September 2010 - Satellite](/wiki/Community_Annotation_-_September_2010_Satellite "Community Annotation - September 2010 Satellite") - - - - - - ...pt2010MtgLogo300.png\|link=September 2010 - GMOD Meeting\|220px\|September 2010 - GMOD Meeting\]\] ...e: 200%; - line-height: 120%"\>\Community Annotation \[\[Satellite Meetings - - GMOD Europe 2010\|Satellite - Meeting\]\]\\
\
\ - - - - - - 20 KB (3,079 words) - 18:52, 8 October 2012 - - - -- - - [2011 GMOD Spring - Training](/wiki/2011_GMOD_Spring_Training "2011 GMOD Spring Training") - - - - - - \[\[File:2011GMODSpringTrainingLogo.png\|center\|600px\|2011 - GMOD Spring - Training March 8-12, 2011\]\] - \[\[File:2011GMODSpringTraining.jpg\|center\|600px\|March 2011 - GMOD Spring - Training Participants, minus a - few\]\] - - - - - - 11 KB (1,481 words) - 23:28, 11 February 2020 - - - -- - - [Tripal Tutorial (pre version - 0.3b)]( "Tripal Tutorial (pre version 0.3b)") - - - - - - \| where = \[\[2011 GMOD Spring - Training\]\] ...of PHP5 modules that - bridges the Drupal Content Managment System (CMS) and - GMOD Chado. - - - - - - 80 KB (12,830 words) - 20:41, 2 October 2012 - - - -- - - [PAG 2012](/wiki/PAG_2012 "PAG 2012") - - - - - - ...er demos, and posters, either about - GMOD and - \[\[GMOD Components\]\], or using - GMOD components. == About - GMOD Components == - - - - - - 5 KB (616 words) - 18:18, 2 October 2012 - - - -- - - [GMOD Online Training - 2014/Schedule](/wiki/GMOD_Online_Training_2014/Schedule "GMOD Online Training 2014/Schedule") - - - - - - ! Affiliation; GMOD role ...tt - Cain\]\] \|\| \[http://oicr.on.ca/ Ontario Institute for Cancer - Research\]\GMOD Project - Coordinator; \[\[Chado\]\], \[\[GBrowse\]\] - - - - - - 3 KB (382 words) - 07:42, 22 May 2014 - - - -- - - [Galaxy Tutorial - 2013](/wiki/Galaxy_Tutorial_2013 "Galaxy Tutorial 2013") - - - - - - ...s tutorial will be taught by \[\[User%253AClements\|Dave Clements\]\] - at the \[\[2013 GMOD Summer - School\]\]. Get the starting image for this tutorial - - '''GMOD 2013 Galaxy Install - Training Instance (ami-f1a1d998)'''. - It needs to be run as GalaxyWikiLink\|CloudMa - - - - - - 23 KB (3,328 words) - 23:33, 10 June 2014 - - - -- - - [InterMine Tutorial - 2011](/wiki/InterMine_Tutorial_2011 "InterMine Tutorial 2011") - - - - - - ...ocuments/Software/intermine/bio/sources/example-sources/malaria-gff - /home/gmod/Documents/Software/intermine/bio/sources/ - You should now have a directory of data available at - \/home/gmod/Documents/Data/intermine/malaria\ - - - - - - 43 KB (6,258 words) - 17:56, 14 February 2013 - - - -- - - [Tripal Tutorial - 2011](/wiki/Tripal_Tutorial_2011 "Tripal Tutorial 2011") - - - - - - \| where = \[\[2011 GMOD Spring - Training\]\] ...of PHP5 modules that - bridges the Drupal Content Managment System (CMS) and - GMOD Chado. - - - - - - 80 KB (12,788 words) - 22:37, 14 February 2013 - - - -- - - [GMOD Online Training - 2014](/wiki/GMOD_Online_Training_2014 "GMOD Online Training 2014") - - - - - - \[\[File:Gmod-online-training.png\|left\|300px\]\] - \[\[File:GitcLogo.png\|150px\|right\|link=Cloud\|GMOD - in the Cloud toolset\]\] - - - - - - 3 KB (445 words) - 16:12, 29 April 2014 - - - -- - - [News/Applications Open for GMOD Online - Training](/wiki/News/Applications_Open_for_GMOD_Online_Training "News/Applications Open for GMOD Online Training") - - - - - - ...first online - training course for those interested - in the set up and use of GMOD - components. ...ld from '''Monday 19th May to Friday 23rd May 2014''', - and will cover core GMOD software, - including \[\[GBrowse\]\] and \[\[JBrowse\]\], \[\[Galaxy\]\], - \[\[MAKER\]\], \[\[T - - - - - - 563 B (82 words) - 20:18, 1 April 2014 - - - - - -View (previous 50 \| next 50) (20 \| 50 \| 100 \| 250 \| 500) - - - - - - - - -## Navigation menu - - - - -### Namespaces - -- [Special - page](/wiki/Special%253ASearch/GMOD_Online_Training "This is a special page, you cannot edit the page itself") - - - -### Navigation - - - -- [GMOD Home](/wiki/Main_Page) -- [Software](/wiki/GMOD_Components) -- [Categories / - Tags](/wiki/Categories) -- [View all - pages](/wiki/Special:AllPages) - - - - -### Documentation - - - -- [Overview](/wiki/Overview) -- [FAQs](/wiki/Category%253AFAQ) -- [HOWTOs](/wiki/Category%253AHOWTO) -- [Glossary](/wiki/Glossary) - - - - -### Community - - - -- [GMOD News](/wiki/GMOD_News) -- [Training / - Outreach](/wiki/Training_and_Outreach) -- [Support](/wiki/Support) -- [GMOD - Promotion](/wiki/GMOD_Promotion) -- [Meetings](/wiki/Meetings) -- [Calendar](/wiki/Calendar) - - - - -### Tools - - - - - - - - - - - - - - - diff --git a/wiki/Special%3ASearch/GSOC.md b/wiki/Special%3ASearch/GSOC.md deleted file mode 100644 index e02173418c..0000000000 --- a/wiki/Special%3ASearch/GSOC.md +++ /dev/null @@ -1,1465 +0,0 @@ - - - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=GSOC&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=GSOC&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=GSOC&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=GSOC&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=GSOC&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below up to **50** results starting with \#**1**. - - - -**Create the page -"GSOC" on this wiki!** -See also the search results found. - -## Page title matches - -- - - [GSoC](/wiki/GSoC "GSoC") - - - - - - \[\[File:GoogleSummer_2016logo.jpg\|373px\|right\|link=GSoC\]\] - ...GSoC works, please refer to the - \[https://developers.google.com/open-source/gsoc/faq - FAQ\]. - - - - - - 5 KB (719 words) - 16:07, 12 February 2024 - - - -- - - [News/News/Prospecting for Proposals for GSoC - 2015](/wiki/News/News/Prospecting_for_Proposals_for_GSoC_2015 "News/News/Prospecting for Proposals for GSoC 2015") - - - - - - \[\[File:GoogleSummer_2015logo.jpg\|200px\|right\|link=GSoC\]\] - ...tting an application for \[http://google-melange.com Google Summer - of Code (GSoC)\] this year, and we - are soliciting project ideas from people and groups inv - - - - - - 1 KB (208 words) - 21:59, 10 February 2015 - - - -- - - [News/Prospecting for Proposals for GSoC - 2015](/wiki/News/Prospecting_for_Proposals_for_GSoC_2015 "News/Prospecting for Proposals for GSoC 2015") - - - - - - \[\[File:GoogleSummer_2015logo.jpg\|200px\|right\|link=GSoC\]\] - ...tting an application for \[http://google-melange.com Google Summer - of Code (GSoC)\] this year, and we - are soliciting project ideas from people and groups inv - - - - - - 1 KB (206 words) - 17:01, 5 February 2020 - - - -- - - [GSOC Project Ideas - 2015](/wiki/GSOC_Project_Ideas_2015 "GSOC Project Ideas 2015") - - - - - - \[\[Category%253AGSoC\]\] - \[\[Category%253AGSOC\]\] - - - - - - 16 KB (2,455 words) - 09:10, 23 February 2015 - - - -- - - [GSOC Mentoring - Guide](/wiki/GSOC_Mentoring_Guide "GSOC Mentoring Guide") - - - - - - \*\[https://developers.google.com/open-source/gsoc/resources/manual - GSoC Mentoring Guide\] - \*\[https://developers.google.com/open-source/gsoc/help/responsibilities#student_responsibilities - Mentor Responsibilities\] - - - - - - 3 KB (457 words) - 03:07, 25 January 2023 - - - -- - - [GSOC Applications - Guide](/wiki/GSOC_Applications_Guide "GSOC Applications Guide") - - - - - - ...\] are described in the - \[https://developers.google.com/open-source/gsoc/faq - GSoC FAQ\]: \*You have not been - accepted as a GSoC - Contributor/Student in GSoC more than - once. - - - - - - 2 KB (294 words) - 15:31, 12 February 2024 - - - -- - - [GSOC Groups](/wiki/GSOC_Groups "GSOC Groups") - - - - - - \[\[Category%253AGSOC\]\] - - - - - - 4 KB (561 words) - 18:02, 19 February 2016 - - - -- - - [GSoC/IDEA 10](/wiki/GSoC/IDEA_10 "GSoC/IDEA 10") - - - - - - \\<-- ''Back to \[\[GSoC - 2011\]\]''\ - - - - - - 8 KB (1,297 words) - 21:55, 27 February 2014 - - - -- - - [GSoC/IDEA 9](/wiki/GSoC/IDEA_9 "GSoC/IDEA 9") - - - - - - \\<-- Back to - \[\[GSoC\]\]\ \* - irc://irc.freenode.net/#gsoc - - - - - - 12 KB (1,905 words) - 20:08, 5 April 2011 - - - -- - - [News/Apply For GSoC 2013 - Now!](/wiki/News/Apply_For_GSoC_2013_Now! "News/Apply For GSoC 2013 Now!") - - - - - - \[\[Image:soc-logo-google-blue.jpg\|right\|250px\|link=GSoC\]\] - ...tics group is now accepting applications from students to - participate in \[\[GSoC\|Google - Summer of Code 2013\]\]. - - - - - - 1 KB (144 words) - 21:19, 24 April 2013 - - - -- - - [GSoC 2011](/wiki/GSoC_2011 "GSoC 2011") - - - - - - ==Welcome to the Genome Informatics - GSoC== ''“Google Summer of Code - (GSoC) is a global program that - offers student developers stipends to write code - - - - - - 20 KB (2,895 words) - 23:51, 25 July 2012 - - - -- - - [News/GMOD's GSoC Going Great - Guns!](/wiki/News/GMOD%27s_GSoC_Going_Great_Guns! "News/GMOD's GSoC Going Great Guns!") - - - - - - If you have any thoughts or suggestions on the - GSoC project, please send them along - to \[mailto:help@gmod.org the GMOD helpdesk\] - \[\[Category%253AGSoC\]\] - - - - - - 1,017 B (164 words) - 21:31, 9 July 2013 - - - -- - - [News/GSoC 2013 Mentors - Wanted!](/wiki/News/GSoC_2013_Mentors_Wanted! "News/GSoC 2013 Mentors Wanted!") - - - - - - ...-melange.com/gsoc/org/google/gsoc2013/genomeinformatics - Genome Informatics GSoC page\]. ...ou - have one, or you are interested in being a mentor, please post on the - \[\[GSoC\|Google Summer of Code - page\]\]. - - - - - - 1 KB (180 words) - 13:26, 15 April 2013 - - - -- - - [GSOC Project Ideas - 2016](/wiki/GSOC_Project_Ideas_2016 "GSOC Project Ideas 2016") - - - - - - ..., JBrowse track, and visualisations implemented in GeneValidator (a - former GSoC project - - http://wurmlab.github.io/tools/genevalidator/) and potentially ot - ...nteractively explore analyse these SNVs in human genomes. The goal - of this GSoC project is to develop an - interactive visualisation platform to better under - - - - - - 28 KB (4,153 words) - 14:34, 8 March 2016 - - - -- - - [News/Prospecting for Proposals for GSoC - 2016](/wiki/News/Prospecting_for_Proposals_for_GSoC_2016 "News/Prospecting for Proposals for GSoC 2016") - - - - - - \[\[File:GoogleSummer_2016logo.jpg\|272px\|right\|link=GSoC\]\] - ...or - \[https://developers.google.com/open-source/gsoc/ - Google Summer of Code (GSoC)\] this - year, and we are soliciting project ideas from people and groups inv - - - - - - 1 KB (209 words) - 16:38, 5 February 2020 - - - -- - - [GSoC 2013](/wiki/GSoC_2013 "GSoC 2013") - - - - - - ...ge:soc-logo-google-blue.jpg\|right\|480px\|link=http://www.google-melange.com/gsoc/homepage/google/gsoc2013\]\] - GSoC has several goals: - - - - - - 17 KB (2,555 words) - 19:59, 12 February 2014 - - - -- - - [News/Prospecting for Proposals for GSoC - 2014](/wiki/News/Prospecting_for_Proposals_for_GSoC_2014 "News/Prospecting for Proposals for GSoC 2014") - - - - - - \[\[File:Landing-page-gsoc2014.png\|200px\|right\|link=GSoC\]\] - GMOD is participating in \[http://google-melange.com Google Summer of - Code (GSoC)\] this year, and we are - soliciting project ideas from people and groups inv - - - - - - 1 KB (180 words) - 03:56, 23 January 2014 - - - -- - - [News/Prospecting for Proposals for GSoC - 2017](/wiki/News/Prospecting_for_Proposals_for_GSoC_2017 "News/Prospecting for Proposals for GSoC 2017") - - - - - - \[\[Image:GoogleSummer_2016logo.jpg\|272px\|right\|link=GSoC\]\] - ...or - \[https://developers.google.com/open-source/gsoc/ - Google Summer of Code (GSoC)\] this - year, and we are soliciting project ideas from people and groups inv - - - - - - 1 KB (209 words) - 16:38, 5 February 2020 - - - -- - - [GSOC Project Ideas - 2017](/wiki/GSOC_Project_Ideas_2017 "GSOC Project Ideas 2017") - - - - - - ...using JBrowse and WebApollo, is completely browser based. The goal - of this GSoC project is to a) migrate - to latest JBrowse for improved performance (and la ...l pull-requests, - that will be merged and deployed throughout the course of - GSoC. - - - - - - 18 KB (2,646 words) - 05:18, 16 March 2017 - - - -- - - [GSOC Project Ideas - 2018](/wiki/GSOC_Project_Ideas_2018 "GSOC Project Ideas 2018") - - - - - - \[\[Category%253AGSOC\]\] - \[\[Category%253AGSoC\]\] - - - - - - 12 KB (1,846 words) - 18:55, 29 January 2018 - - - -- - - [GSOC Project Ideas - 2019](/wiki/GSOC_Project_Ideas_2019 "GSOC Project Ideas 2019") - - - - - - '''Got an idea for - \[\[GSoC\|GSOC - 2019\]\]?''' \# Describe it in the - '''\[http://bit.ly/gsoc-2019-ogi-propose - online form\]''' and ''we'll'' post it here. - - - - - - 7 KB (1,064 words) - 15:52, 19 February 2019 - - - -- - - [GSOC Project Ideas - 2020](/wiki/GSOC_Project_Ideas_2020 "GSOC Project Ideas 2020") - - - - - - '''Got an idea for - \[\[GSoC\|GSOC - 2020\]\]?''' - - - - - - 20 KB (3,057 words) - 02:14, 19 March 2020 - - - -- - - [News/Prospecting for Proposals for GSoC - 2020](/wiki/News/Prospecting_for_Proposals_for_GSoC_2020 "News/Prospecting for Proposals for GSoC 2020") - - - - - - \[\[File:GoogleSummer_2016logo.jpg\|272px\|right\|link=GSoC\]\] - ...plication for \[https://summerofcode.withgoogle.com/ Google Summer - of Code (GSoC)\] this year, and we - are soliciting project ideas from people and groups inv - - - - - - 1 KB (215 words) - 06:42, 4 February 2020 - - - -- - - [GSOC Project Ideas - 2021](/wiki/GSOC_Project_Ideas_2021 "GSOC Project Ideas 2021") - - - - - - '''Got an idea for - \[\[GSoC\|GSOC - 2021\]\]?''' - - - - - - 18 KB (2,539 words) - 18:58, 1 April 2021 - - - -- - - [News/Prospecting for Proposals for GSoC - 2021](/wiki/News/Prospecting_for_Proposals_for_GSoC_2021 "News/Prospecting for Proposals for GSoC 2021") - - - - - - \[\[File:GoogleSummer_2016logo.jpg\|272px\|right\|link=GSoC\]\] - ...plication for \[https://summerofcode.withgoogle.com/ Google Summer - of Code (GSoC)\] this year, and we - are soliciting project ideas from people and groups inv - - - - - - 1 KB (208 words) - 20:21, 16 February 2021 - - - -- - - [GSOC Project Ideas - 2022](/wiki/GSOC_Project_Ideas_2022 "GSOC Project Ideas 2022") - - - - - - '''Got an idea for - \[\[GSoC\|GSOC - 2022\]\]?''' - - - - - - 11 KB (1,658 words) - 18:33, 25 March 2022 - - - -- - - [GSOC Project Ideas - 2023](/wiki/GSOC_Project_Ideas_2023 "GSOC Project Ideas 2023") - - - - - - ''Got an idea for - \[\[GSoC\|GSOC - 2023\]\]?''' - - - - - - 9 KB (1,387 words) - 18:23, 16 March 2023 - - - -- - - [GSOC Project Ideas - 2024](/wiki/GSOC_Project_Ideas_2024 "GSOC Project Ideas 2024") - - - - - - ''Got an idea for - \[\[GSoC\|GSOC - 2024\]\]?''' - - - - - - 4 KB (580 words) - 16:41, 12 February 2024 - - - -- - - [News/Prospecting for Proposals for GSoC - 2024](/wiki/News/Prospecting_for_Proposals_for_GSoC_2024 "News/Prospecting for Proposals for GSoC 2024") - - - - - - \[\[File:GoogleSummer_2016logo.jpg\|272px\|right\|link=GSoC\]\] - ...plication for \[https://summerofcode.withgoogle.com/ Google Summer - of Code (GSoC)\] this year, and we - are soliciting project ideas from people and groups inv - - - - - - 1 KB (212 words) - 16:11, 12 February 2024 - - - -## Page text matches - -- - - [News/Google Summer of Code & - OBF](/wiki/News/Google_Summer_of_Code_%26_OBF "News/Google Summer of Code & OBF") - - - - - - ...logo.png\|link=http://open-bio.org/wiki/Google_Summer_of_Code\|right\|OBF - in GSoC\]\] ...For more on - GSoC, see the - \[http://open-bio.org/wiki/Google_Summer_of_Code - GSoC 2010 FAQ\]. - - - - - - 1 KB (216 words) - 23:08, 9 October 2012 - - - -- - - [GSoC](/wiki/GSoC "GSoC") - - - - - - \[\[File:GoogleSummer_2016logo.jpg\|373px\|right\|link=GSoC\]\] - ...GSoC works, please refer to the - \[https://developers.google.com/open-source/gsoc/faq - FAQ\]. - - - - - - 5 KB (719 words) - 16:07, 12 February 2024 - - - -- - - [News/News/Prospecting for Proposals for GSoC - 2015](/wiki/News/News/Prospecting_for_Proposals_for_GSoC_2015 "News/News/Prospecting for Proposals for GSoC 2015") - - - - - - \[\[File:GoogleSummer_2015logo.jpg\|200px\|right\|link=GSoC\]\] - ...tting an application for \[http://google-melange.com Google Summer - of Code (GSoC)\] this year, and we - are soliciting project ideas from people and groups inv - - - - - - 1 KB (208 words) - 21:59, 10 February 2015 - - - -- - - [News/Prospecting for Proposals for GSoC - 2015](/wiki/News/Prospecting_for_Proposals_for_GSoC_2015 "News/Prospecting for Proposals for GSoC 2015") - - - - - - \[\[File:GoogleSummer_2015logo.jpg\|200px\|right\|link=GSoC\]\] - ...tting an application for \[http://google-melange.com Google Summer - of Code (GSoC)\] this year, and we - are soliciting project ideas from people and groups inv - - - - - - 1 KB (206 words) - 17:01, 5 February 2020 - - - -- - - [GSOC Project Ideas - 2015](/wiki/GSOC_Project_Ideas_2015 "GSOC Project Ideas 2015") - - - - - - \[\[Category%253AGSoC\]\] - \[\[Category%253AGSOC\]\] - - - - - - 16 KB (2,455 words) - 09:10, 23 February 2015 - - - -- - - [GSOC Mentoring - Guide](/wiki/GSOC_Mentoring_Guide "GSOC Mentoring Guide") - - - - - - \*\[https://developers.google.com/open-source/gsoc/resources/manual - GSoC Mentoring Guide\] - \*\[https://developers.google.com/open-source/gsoc/help/responsibilities#student_responsibilities - Mentor Responsibilities\] - - - - - - 3 KB (457 words) - 03:07, 25 January 2023 - - - -- - - [GSOC Applications - Guide](/wiki/GSOC_Applications_Guide "GSOC Applications Guide") - - - - - - ...\] are described in the - \[https://developers.google.com/open-source/gsoc/faq - GSoC FAQ\]: \*You have not been - accepted as a GSoC - Contributor/Student in GSoC more than - once. - - - - - - 2 KB (294 words) - 15:31, 12 February 2024 - - - -- - - [GSOC Groups](/wiki/GSOC_Groups "GSOC Groups") - - - - - - \[\[Category%253AGSOC\]\] - - - - - - 4 KB (561 words) - 18:02, 19 February 2016 - - - -- - - [Google summer of - code](/wiki/Google_summer_of_code "Google summer of code") - - - - - - \#REDIRECT \[\[GSoC\]\] - - - - - - 18 B (2 words) - 15:04, 5 March 2011 - - - -- - - [GSoC/IDEA 10](/wiki/GSoC/IDEA_10 "GSoC/IDEA 10") - - - - - - \\<-- ''Back to \[\[GSoC - 2011\]\]''\ - - - - - - 8 KB (1,297 words) - 21:55, 27 February 2014 - - - -- - - [GSoC/IDEA 9](/wiki/GSoC/IDEA_9 "GSoC/IDEA 9") - - - - - - \\<-- Back to - \[\[GSoC\]\]\ \* - irc://irc.freenode.net/#gsoc - - - - - - 12 KB (1,905 words) - 20:08, 5 April 2011 - - - -- - - [News/Apply For GSoC 2013 - Now!](/wiki/News/Apply_For_GSoC_2013_Now! "News/Apply For GSoC 2013 Now!") - - - - - - \[\[Image:soc-logo-google-blue.jpg\|right\|250px\|link=GSoC\]\] - ...tics group is now accepting applications from students to - participate in \[\[GSoC\|Google - Summer of Code 2013\]\]. - - - - - - 1 KB (144 words) - 21:19, 24 April 2013 - - - -- - - [GSoC 2011](/wiki/GSoC_2011 "GSoC 2011") - - - - - - ==Welcome to the Genome Informatics - GSoC== ''“Google Summer of Code - (GSoC) is a global program that - offers student developers stipends to write code - - - - - - 20 KB (2,895 words) - 23:51, 25 July 2012 - - - -- - - [News/GMOD's GSoC Going Great - Guns!](/wiki/News/GMOD%27s_GSoC_Going_Great_Guns! "News/GMOD's GSoC Going Great Guns!") - - - - - - If you have any thoughts or suggestions on the - GSoC project, please send them along - to \[mailto:help@gmod.org the GMOD helpdesk\] - \[\[Category%253AGSoC\]\] - - - - - - 1,017 B (164 words) - 21:31, 9 July 2013 - - - -- - - [Jan 2014 GMOD - Meeting](/wiki/Jan_2014_GMOD_Meeting "Jan 2014 GMOD Meeting") - - - - - - \| - \[\[GSoC\|GSoC - and the Genome Informatics group\]\] - - - - - - 5 KB (666 words) - 07:49, 8 May 2014 - - - -- - - [News/GSoC 2013 Mentors - Wanted!](/wiki/News/GSoC_2013_Mentors_Wanted! "News/GSoC 2013 Mentors Wanted!") - - - - - - ...-melange.com/gsoc/org/google/gsoc2013/genomeinformatics - Genome Informatics GSoC page\]. ...ou - have one, or you are interested in being a mentor, please post on the - \[\[GSoC\|Google Summer of Code - page\]\]. - - - - - - 1 KB (180 words) - 13:26, 15 April 2013 - - - -- - - [GSOC Project Ideas - 2016](/wiki/GSOC_Project_Ideas_2016 "GSOC Project Ideas 2016") - - - - - - ..., JBrowse track, and visualisations implemented in GeneValidator (a - former GSoC project - - http://wurmlab.github.io/tools/genevalidator/) and potentially ot - ...nteractively explore analyse these SNVs in human genomes. The goal - of this GSoC project is to develop an - interactive visualisation platform to better under - - - - - - 28 KB (4,153 words) - 14:34, 8 March 2016 - - - -- - - [News/Prospecting for Proposals for GSoC - 2016](/wiki/News/Prospecting_for_Proposals_for_GSoC_2016 "News/Prospecting for Proposals for GSoC 2016") - - - - - - \[\[File:GoogleSummer_2016logo.jpg\|272px\|right\|link=GSoC\]\] - ...or - \[https://developers.google.com/open-source/gsoc/ - Google Summer of Code (GSoC)\] this - year, and we are soliciting project ideas from people and groups inv - - - - - - 1 KB (209 words) - 16:38, 5 February 2020 - - - -- - - [GSoC 2013](/wiki/GSoC_2013 "GSoC 2013") - - - - - - ...ge:soc-logo-google-blue.jpg\|right\|480px\|link=http://www.google-melange.com/gsoc/homepage/google/gsoc2013\]\] - GSoC has several goals: - - - - - - 17 KB (2,555 words) - 19:59, 12 February 2014 - - - -- - - [News/Prospecting for Proposals for GSoC - 2014](/wiki/News/Prospecting_for_Proposals_for_GSoC_2014 "News/Prospecting for Proposals for GSoC 2014") - - - - - - \[\[File:Landing-page-gsoc2014.png\|200px\|right\|link=GSoC\]\] - GMOD is participating in \[http://google-melange.com Google Summer of - Code (GSoC)\] this year, and we are - soliciting project ideas from people and groups inv - - - - - - 1 KB (180 words) - 03:56, 23 January 2014 - - - -- - - [News/Prospecting for Proposals for GSoC - 2017](/wiki/News/Prospecting_for_Proposals_for_GSoC_2017 "News/Prospecting for Proposals for GSoC 2017") - - - - - - \[\[Image:GoogleSummer_2016logo.jpg\|272px\|right\|link=GSoC\]\] - ...or - \[https://developers.google.com/open-source/gsoc/ - Google Summer of Code (GSoC)\] this - year, and we are soliciting project ideas from people and groups inv - - - - - - 1 KB (209 words) - 16:38, 5 February 2020 - - - -- - - [GSOC Project Ideas - 2017](/wiki/GSOC_Project_Ideas_2017 "GSOC Project Ideas 2017") - - - - - - ...using JBrowse and WebApollo, is completely browser based. The goal - of this GSoC project is to a) migrate - to latest JBrowse for improved performance (and la ...l pull-requests, - that will be merged and deployed throughout the course of - GSoC. - - - - - - 18 KB (2,646 words) - 05:18, 16 March 2017 - - - -- - - [GSOC Project Ideas - 2018](/wiki/GSOC_Project_Ideas_2018 "GSOC Project Ideas 2018") - - - - - - \[\[Category%253AGSOC\]\] - \[\[Category%253AGSoC\]\] - - - - - - 12 KB (1,846 words) - 18:55, 29 January 2018 - - - -- - - [GSOC Project Ideas - 2019](/wiki/GSOC_Project_Ideas_2019 "GSOC Project Ideas 2019") - - - - - - '''Got an idea for - \[\[GSoC\|GSOC - 2019\]\]?''' \# Describe it in the - '''\[http://bit.ly/gsoc-2019-ogi-propose - online form\]''' and ''we'll'' post it here. - - - - - - 7 KB (1,064 words) - 15:52, 19 February 2019 - - - -- - - [GSOC Project Ideas - 2020](/wiki/GSOC_Project_Ideas_2020 "GSOC Project Ideas 2020") - - - - - - '''Got an idea for - \[\[GSoC\|GSOC - 2020\]\]?''' - - - - - - 20 KB (3,057 words) - 02:14, 19 March 2020 - - - -- - - [News/Prospecting for Proposals for GSoC - 2020](/wiki/News/Prospecting_for_Proposals_for_GSoC_2020 "News/Prospecting for Proposals for GSoC 2020") - - - - - - \[\[File:GoogleSummer_2016logo.jpg\|272px\|right\|link=GSoC\]\] - ...plication for \[https://summerofcode.withgoogle.com/ Google Summer - of Code (GSoC)\] this year, and we - are soliciting project ideas from people and groups inv - - - - - - 1 KB (215 words) - 06:42, 4 February 2020 - - - -- - - [GSoD](/wiki/GSoD "GSoD") - - - - - - ....ca\] '''and''' \[mailto:help@gmod.org help@gmod.org\] -- find out - more about GSoC, a specific project, - or your potential mentor(s). - - - - - - 4 KB (632 words) - 02:38, 7 May 2020 - - - -- - - [GSOC Project Ideas - 2021](/wiki/GSOC_Project_Ideas_2021 "GSOC Project Ideas 2021") - - - - - - '''Got an idea for - \[\[GSoC\|GSOC - 2021\]\]?''' - - - - - - 18 KB (2,539 words) - 18:58, 1 April 2021 - - - -- - - [News/Prospecting for Proposals for GSoC - 2021](/wiki/News/Prospecting_for_Proposals_for_GSoC_2021 "News/Prospecting for Proposals for GSoC 2021") - - - - - - \[\[File:GoogleSummer_2016logo.jpg\|272px\|right\|link=GSoC\]\] - ...plication for \[https://summerofcode.withgoogle.com/ Google Summer - of Code (GSoC)\] this year, and we - are soliciting project ideas from people and groups inv - - - - - - 1 KB (208 words) - 20:21, 16 February 2021 - - - -- - - [GSOC Project Ideas - 2022](/wiki/GSOC_Project_Ideas_2022 "GSOC Project Ideas 2022") - - - - - - '''Got an idea for - \[\[GSoC\|GSOC - 2022\]\]?''' - - - - - - 11 KB (1,658 words) - 18:33, 25 March 2022 - - - -- - - [GSOC Project Ideas - 2023](/wiki/GSOC_Project_Ideas_2023 "GSOC Project Ideas 2023") - - - - - - ''Got an idea for - \[\[GSoC\|GSOC - 2023\]\]?''' - - - - - - 9 KB (1,387 words) - 18:23, 16 March 2023 - - - -- - - [GSOC Project Ideas - 2024](/wiki/GSOC_Project_Ideas_2024 "GSOC Project Ideas 2024") - - - - - - ''Got an idea for - \[\[GSoC\|GSOC - 2024\]\]?''' - - - - - - 4 KB (580 words) - 16:41, 12 February 2024 - - - -- - - [News/Prospecting for Proposals for GSoC - 2024](/wiki/News/Prospecting_for_Proposals_for_GSoC_2024 "News/Prospecting for Proposals for GSoC 2024") - - - - - - \[\[File:GoogleSummer_2016logo.jpg\|272px\|right\|link=GSoC\]\] - ...plication for \[https://summerofcode.withgoogle.com/ Google Summer - of Code (GSoC)\] this year, and we - are soliciting project ideas from people and groups inv - - - - - - 1 KB (212 words) - 16:11, 12 February 2024 - - - - - -View (previous 50 \| next 50) (20 \| 50 \| 100 \| 250 \| 500) - - - - - - - - -## Navigation menu - - - -### Namespaces - -- [Special - page](/wiki/Special%253ASearch/GSOC "This is a special page, you cannot edit the page itself") - - - - - - -### Navigation - - - -- [GMOD Home](/wiki/Main_Page) -- [Software](/wiki/GMOD_Components) -- [Categories / - Tags](/wiki/Categories) -- [View all - pages](/wiki/Special:AllPages) - - - - -### Documentation - - - -- [Overview](/wiki/Overview) -- [FAQs](/wiki/Category%253AFAQ) -- [HOWTOs](/wiki/Category%253AHOWTO) -- [Glossary](/wiki/Glossary) - - - - -### Community - - - -- [GMOD News](/wiki/GMOD_News) -- [Training / - Outreach](/wiki/Training_and_Outreach) -- [Support](/wiki/Support) -- [GMOD - 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- -- Showing below **49** results starting with \#**1**. - - - -**Create the page "Generic -Gene Pages" on this wiki!** See also the search results found. - -- - - [NIH 2002 Workshop on Model Organism - Databases](/wiki/NIH_2002_Workshop_on_Model_Organism_Databases "NIH 2002 Workshop on Model Organism Databases") - - - - - - ...operating procedures and data models that would form the basis of a - set of generic components for MOD - building. ...tic constructs and clones; and lastly to provide a common - nomenclature for gene symbols, - anatomic terms and other elements of the scientific vocabulary. By - - - - - - 26 KB (3,975 words) - 05:03, 28 January 2008 - - - -- - - [Overview](/wiki/Overview "Overview") - - - - - - ....mbl.edu/cgi-bin/site/emiliania04 ''Emiliania huxleyi'' Serial - Analysis of Gene Expression\] - database. We even find GMOD databases dedicated to collections What - the user will see is one or more applications. These may be a set of - web pages or a Java application. The - choice of applications is dictated by the nature - - - - - - 34 KB (5,526 words) - 19:56, 7 October 2013 - - - -- - - [Introduction to - Chado](/wiki/Introduction_to_Chado "Introduction to Chado") - - - - - - \* A database that is generic enough - to use for any organism ...currently the best source of documentation - for Chado. Here are more useful pages - in the Wiki: - - - - - - 14 KB (2,071 words) - 22:45, 11 January 2019 - - - -- - - [Chado Tutorial 2010](/wiki/Chado_Tutorial_2010 "Chado Tutorial 2010") - - - - - - ...eloped completely different modules for community, literature, - anatomy and gene expression. If there - is a PATO compatible Chado Phenotype solution we'd pr \* - gene predictions - - - - - - 54 KB (8,190 words) - 23:34, 8 October 2012 - - - -- - - [Chado Tutorial 2012](/wiki/Chado_Tutorial_2012 "Chado Tutorial 2012") - - - - - - ...eloped completely different modules for community, literature, - anatomy and gene expression. If there - is a PATO compatible Chado Phenotype solution we'd pr \* - gene predictions - - - - - - 50 KB (7,599 words) - 16:26, 2 September 2018 - - - -- - - [NBrowse](/wiki/NBrowse "NBrowse") - - - - - - ...ultaneously. Although created for applications in biology, N-Browse - uses a generic database schema that - can be adapted to network representations in any knowl ...e. Links to - the N-Browse GUI at WormBase are available on the - Gene Summary - pages. TAIR's N-Browse search page - can be accessed via the Tools menu on the TAI - - - - - - 6 KB (920 words) - 16:57, 30 September 2010 - - - -- - - [Glossary](/wiki/Glossary "Glossary") - - - - - - ...llowing styles to defined in a single place and then referred to - from many pages. === - Gene Finder Format === - - - - - - 14 KB (2,081 words) - 02:50, 14 March 2014 - - - -- - - [Site Guidelines](/wiki/Site_Guidelines "Site Guidelines") - - - - - - This means that if a user types - "\[\[Generic Genome Browser\]\]" in - the "Go/Search" box and you have a redirect defined fo ...the "create - this page" link. In our example, you would enter/search for - "Generic Genome Browser". - - - - - - 16 KB (2,420 words) - 23:18, 8 November 2013 - - - -- - - [GBrowse 1 Configuration - HOWTO](/wiki/GBrowse_1_Configuration_HOWTO "GBrowse 1 Configuration HOWTO") - - - - - - This document provides information on configuring version 1 of the - \[\[GBrowse\|Generic Genome Browser - (GBrowse)\]\], part of the \[\[Main Page\|GMOD Project\]\]. For ver - ....gb file. I would copy & paste specific sections (i.e. section for - CDS or gene, etc. - any type can be - altered) and then change the type to some key word - - - - - - 79 KB (12,563 words) - 16:45, 15 August 2011 - - - -- - - [August 2009 GMOD - Meeting](/wiki/August_2009_GMOD_Meeting "August 2009 GMOD Meeting") - - - - - - ...neric, lightweight pipeline framework which was initially built to - produce gene predictions. DIYA is - becoming part of GMOD. \*\* Good enough for real time user - interaction, e.g., \<1s for single - gene search, 1-4s for multigene - search (unions) - - - - - - 59 KB (8,741 words) - 19:37, 4 September 2013 - - - -- - - [Common Gene Page](/wiki/Common_Gene_Page "Common Gene Page") - - - - - - =Common Gene Page Rationale= Model - organism/genome databases (MODs) produce - gene - pages of similar - - - - - - 7 KB (1,051 words) - 19:24, 4 September 2013 - - - -- - - [Bio GMOD - GenericGenePage](/wiki/Bio_GMOD_GenericGenePage "Bio GMOD GenericGenePage") - - - - - - ...sary#Perl\|Perl\]\] class that provides a render_xml method to - crete \[\[Common Gene Page\]\] - \[\[Glossary#XML\|XML\]\], but does not fetch the data. In order to - effe ...be seen by clicking on the "Download GMOD XML" link on any of - there locus pages; for example, this - one: - - - - - - 6 KB (755 words) - 01:16, 19 August 2009 - - - -- - - [GBrowse 2.0 HOWTO](/wiki/GBrowse_2.0_HOWTO "GBrowse 2.0 HOWTO") - - - - - - ...the \[http://packages.debian.org/source/sid/gbrowse GBrowse Debian - package pages.\] ...e - \[http://packages.debian.org/source/wheezy/gbrowse GBrowse Debian - package pages.\] - - - - - - 101 KB (15,507 words) - 04:44, 9 January 2014 - - - -- - - [January 2009 GMOD - Meeting](/wiki/January_2009_GMOD_Meeting "January 2009 GMOD Meeting") - - - - - - \|\[\[Bio GMOD - GenericGenePage\|Generic - Gene Page XML\]\] - ...icGenePage.ppt\|PPT\]\], - \[\[Media:Jan2009GenreicGenePage.pdf\|PDF\]\], - \[\[#Generic - Gene Page XML\|Summary\]\], \[\[#Data - Sharing\|Discussion\]\] - - - - - - 50 KB (7,612 words) - 18:53, 8 October 2012 - - - -- - - [Running a GBrowse2 render - farm](/wiki/Running_a_GBrowse2_render_farm "Running a GBrowse2 render farm") - - - - - - ...s one or more computers, you can spread out the work of generating - GBrowse pages, thereby achieving - improved performance. A slave can be attached to a parti % cd - Generic-Genome-Browser - - - - - - 16 KB (2,473 words) - 12:08, 12 October 2011 - - - -- - - [GMOD RPC API](/wiki/GMOD_RPC_API "GMOD RPC API") - - - - - - At present, this API only covers querying and retrieving information - for the gene data class. == Language - Implementation Pages == - - - - - - 25 KB (3,166 words) - 23:02, 15 August 2013 - - - -- - - [GFF](/wiki/GFF "GFF") - - - - - - ...file format for storing genomic features in a text file. GFF stands - for ''Generic Feature Format''. GFF - files are plain text, 9 column, tab-delimited files. ...mmonly CDS - coding segments and UTRs. This example shows how to represent a - gene named "EDEN" which has three - alternatively-spliced mRNA transcripts: - - - - - - 16 KB (2,336 words) - 19:49, 10 September 2012 - - - -- - - [GFF3 2011 tutorial](/wiki/GFF3_2011_tutorial "GFF3 2011 tutorial") - - - - - - ...file format for storing genomic features in a text file. GFF stands - for ''Generic Feature Format''. GFF - files are plain text, 9 column, tab-delimited files. ...mmonly CDS - coding segments and UTRs. This example shows how to represent a - gene named "EDEN" which has three - alternatively-spliced mRNA transcripts: - - - - - - 16 KB (2,387 words) - 22:13, 11 February 2014 - - - -- - - [GBrowse syn PAG - tutorial](/wiki/GBrowse_syn_PAG_tutorial "GBrowse syn PAG tutorial") - - - - - - =The Generic Synteny Browser= ...w to - install, configure and use GBrowse_syn. To get started, browse these - pages: - - - - - - 19 KB (2,507 words) - 18:53, 8 October 2012 - - - -- - - [GBrowse - Configuration/Glyphs](/wiki/GBrowse_Configuration/Glyphs "GBrowse Configuration/Glyphs") - - - - - - \| - \[\[:bp:Module:Bio::Graphics::Glyph::generic\|generic\]\] - \| a gene model - - - - - - 6 KB (919 words) - 18:49, 4 September 2013 - - - -- - - [September 2010 GMOD - Meeting](/wiki/September_2010_GMOD_Meeting "September 2010 GMOD Meeting") - - - - - - ...re.lifesci.dundee.ac.uk/staff/jason_swedlow.html Wellcome Trust - Centre for Gene Regulation and - Expression\], \[http://www.dundee.ac.uk/ University of Dundee\] ...r - value to the GMOD community as many GMOD members expand into - phenotypes, gene expression, fate - mapping, natural diversity, and other image-intensive ques - - - - - - 100 KB (14,725 words) - 17:31, 30 November 2012 - - - -- - - [GBrowse syn Tutorial - new](/wiki/GBrowse_syn_Tutorial_new "GBrowse syn Tutorial new") - - - - - - ...https://gmod.svn.sourceforge.net/svnroot/gmod/Generic-Genome-Browser/trunk - Generic-Genome-Browser\ \$ - \cd - Generic-Genome-Browser\ - - - - - - 21 KB (2,890 words) - 22:24, 3 October 2012 - - - -- - - [GBrowse syn AGS - Tutorial](/wiki/GBrowse_syn_AGS_Tutorial "GBrowse syn AGS Tutorial") - - - - - - feature = gene:ensembl glyph = - gene - - - - - - 23 KB (3,325 words) - 20:52, 3 October 2012 - - - -- - - [GFF3](/wiki/GFF3 "GFF3") - - - - - - ...file format for storing genomic features in a text file. GFF stands - for ''Generic Feature Format''. GFF - files are plain text, 9 column, tab-delimited files. ...mmonly CDS - coding segments and UTRs. This example shows how to represent a - gene named "EDEN" which has three - alternatively-spliced mRNA transcripts: - - - - - - 16 KB (2,350 words) - 20:25, 12 July 2016 - - - -- - - [JBrowse Configuration - Guide](/wiki/JBrowse_Configuration_Guide "JBrowse Configuration Guide") - - - - - - ...acks can be used to visualize localized annotations on a sequence, - such as gene models, transcript - alignments, SNPs and so forth. ...nsidered "top-level" for this track. - For example, if you have a track with - gene-\>mRNA-\>CDS features, but for - some reason want to only display the mRNA feat - - - - - - 185 KB (26,536 words) - 02:48, 30 September 2020 - - - -- - - [Tripal Tutorial - v1.1](/wiki/Tripal_Tutorial_v1.1 "Tripal Tutorial v1.1") - - - - - - ...ook for both \index.php\ and \index.html\ - files when serving pages. ...lt with - Drupal: Page and Story. Here is where a user can add simple new - pages to the website without - knowledge of HTML or CSS. Click the '''Page''' cont - - - - - - 131 KB (21,091 words) - 21:53, 2 January 2014 - - - -- - - [Tripal Developer's - Handbook](/wiki/Tripal_Developer%27s_Handbook "Tripal Developer's Handbook") - - - - - - ...details''' that gives this details box the styling seen on all - Tripal node pages. \\pages/582206" - target="\_blank"\>Encylopeida of Life\\ - - - - - - 70 KB (10,442 words) - 16:45, 14 October 2013 - - - -- - - [GFF Tutorial 2012](/wiki/GFF_Tutorial_2012 "GFF Tutorial 2012") - - - - - - ...file format for storing genomic features in a text file. GFF stands - for ''Generic Feature Format''. GFF - files are plain text, 9 column, tab-delimited files. ...mmonly CDS - coding segments and UTRs. This example shows how to represent a - gene named "EDEN" which has three - alternatively-spliced mRNA transcripts: - - - - - - 16 KB (2,352 words) - 21:54, 11 September 2012 - - - -- - - [Galaxy Tutorial - 2010](/wiki/Galaxy_Tutorial_2010 "Galaxy Tutorial 2010") - - - - - - The dataset we uploaded is a generic - tabular data file (dumped out of the UCSC browser, not in any - particular fe ==== 4. Get Gene - Annotations from UCSC ==== - - - - - - 32 KB (4,846 words) - 21:16, 9 October 2012 - - - -- - - [Chado Tutorial 2011](/wiki/Chado_Tutorial_2011 "Chado Tutorial 2011") - - - - - - ...eloped completely different modules for community, literature, - anatomy and gene expression. If there - is a PATO compatible Chado Phenotype solution we'd pr \* - gene predictions - - - - - - 53 KB (8,083 words) - 20:52, 27 August 2013 - - - -- - - [GBrowse syn Tutorial - 2011](/wiki/GBrowse_syn_Tutorial_2011 "GBrowse syn Tutorial 2011") - - - - - - ...https://gmod.svn.sourceforge.net/svnroot/gmod/Generic-Genome-Browser/trunk - Generic-Genome-Browser\ \$ - \cd - Generic-Genome-Browser\ - - - - - - 20 KB (2,712 words) - 22:39, 13 February 2013 - - - -- - - [Galaxy Tutorial - 2011](/wiki/Galaxy_Tutorial_2011 "Galaxy Tutorial 2011") - - - - - - The dataset we uploaded is a generic - tabular data file (dumped out of the UCSC browser, not in any - particular fe === 4. Get Gene - Annotations from UCSC === - - - - - - 38 KB (5,631 words) - 23:56, 13 February 2013 - - - -- - - [GFF3 Tutorial 2011](/wiki/GFF3_Tutorial_2011 "GFF3 Tutorial 2011") - - - - - - ...file format for storing genomic features in a text file. GFF stands - for ''Generic Feature Format''. GFF - files are plain text, 9 column, tab-delimited files. ...mmonly CDS - coding segments and UTRs. This example shows how to represent a - gene named "EDEN" which has three - alternatively-spliced mRNA transcripts: - - - - - - 16 KB (2,345 words) - 00:23, 14 February 2013 - - - -- - - [Chado Tutorial 2013](/wiki/Chado_Tutorial_2013 "Chado Tutorial 2013") - - - - - - ...eloped completely different modules for community, literature, - anatomy and gene expression. If there - is a PATO compatible Chado Phenotype solution we'd pr \* - gene predictions - - - - - - 50 KB (7,599 words) - 12:36, 20 May 2014 - - - -- - - [GMOD Online Training 2014/Chado - Tutorial](/wiki/GMOD_Online_Training_2014/Chado_Tutorial "GMOD Online Training 2014/Chado Tutorial") - - - - - - ...eloped completely different modules for community, literature, - anatomy and gene expression. If there - is a PATO compatible Chado Phenotype solution we'd pr \* - gene predictions - - - - - - 50 KB (7,595 words) - 12:53, 20 May 2014 - - - -- - - [GBrowse syn Tutorial - 2013](/wiki/GBrowse_syn_Tutorial_2013 "GBrowse syn Tutorial 2013") - - - - - - feature = gene:ensembl glyph = - gene - - - - - - 20 KB (2,714 words) - 10:44, 22 May 2014 - - - -- - - [JBrowse Tutorial Programming for Biology - 2015](/wiki/JBrowse_Tutorial_Programming_for_Biology_2015 "JBrowse Tutorial Programming for Biology 2015") - - - - - - \[\[GFF\]\] (Generic Feature Format) - is a very commonly used text format for describing features ...es a - URL pattern that you can use to link genomic features to specific web - pages. - - - - - - 18 KB (2,519 words) - 23:33, 19 October 2015 - - - -- - - [GSoC 2013](/wiki/GSoC_2013 "GSoC 2013") - - - - - - ;'''\[http://www.gmod.org Generic - Model Organism Database (GMOD)\]''' : An open source project to - develop a co ;'''\[http://gmod.org/wiki/GBrowse GBrowse\]''': The - Generic Genome Browser (GBrowse) is a - web application for searching and displaying - - - - - - 17 KB (2,555 words) - 19:59, 12 February 2014 - - - -- - - [GMOD Malaysia 2014/Tripal - Tutorial](/wiki/GMOD_Malaysia_2014/Tripal_Tutorial "GMOD Malaysia 2014/Tripal Tutorial") - - - - - - ...ook for both \index.php\ and \index.html\ - files when serving pages. ...lt with - Drupal: Page and Story. Here is where a user can add simple new - pages to the website without - knowledge of HTML or CSS. Click the '''Page''' cont - - - - - - 131 KB (21,099 words) - 00:18, 20 February 2014 - - - -- - - [GMOD Malaysia 2014/Chado - Tutorial](/wiki/GMOD_Malaysia_2014/Chado_Tutorial "GMOD Malaysia 2014/Chado Tutorial") - - - - - - ...eloped completely different modules for community, literature, - anatomy and gene expression. If there - is a PATO compatible Chado Phenotype solution we'd pr \* - gene predictions - - - - - - 51 KB (7,657 words) - 00:19, 20 February 2014 - - - -- - - [GMOD Online Training 2014/GFF3 - Tutorial](/wiki/GMOD_Online_Training_2014/GFF3_Tutorial "GMOD Online Training 2014/GFF3 Tutorial") - - - - - - ...file format for storing genomic features in a text file. GFF stands - for ''Generic Feature Format''. GFF - files are plain text, 9 column, tab-delimited files. ...mmonly CDS - coding segments and UTRs. This example shows how to represent a - gene named "EDEN" which has three - alternatively-spliced mRNA transcripts: - - - - - - 16 KB (2,318 words) - 04:56, 19 May 2014 - - - -- - - [JBrowse Tutorial PAG - 2016](/wiki/JBrowse_Tutorial_PAG_2016 "JBrowse Tutorial PAG 2016") - - - - - - \[\[GFF\]\] (Generic Feature Format) - is a very commonly used text format for describing features ...es a - URL pattern that you can use to link genomic features to specific web - pages. - - - - - - 19 KB (2,697 words) - 06:25, 13 January 2016 - - - -- - - [GMOD Online Training 2014/GBrowse syn - Tutorial](/wiki/GMOD_Online_Training_2014/GBrowse_syn_Tutorial "GMOD Online Training 2014/GBrowse syn Tutorial") - - - - - - feature = gene:ensembl glyph = - gene - - - - - - 20 KB (2,751 words) - 19:05, 22 May 2014 - - - -- - - [JBrowse Tutorial Programming for Biology - 2016](/wiki/JBrowse_Tutorial_Programming_for_Biology_2016 "JBrowse Tutorial Programming for Biology 2016") - - - - - - \[\[GFF\]\] (Generic Feature Format) - is a very commonly used text format for describing features ...es a - URL pattern that you can use to link genomic features to specific web - pages. - - - - - - 20 KB (2,903 words) - 19:59, 16 October 2016 - - - -- - - [JBrowse Tutorial PAG - 2017](/wiki/JBrowse_Tutorial_PAG_2017 "JBrowse Tutorial PAG 2017") - - - - - - \[\[GFF\]\] (Generic Feature Format) - is a very commonly used text format for describing features ...es a - URL pattern that you can use to link genomic features to specific web - pages. - - - - - - 20 KB (2,867 words) - 19:38, 15 January 2017 - - - -- - - [JBrowse Tutorial PAG - 2018](/wiki/JBrowse_Tutorial_PAG_2018 "JBrowse Tutorial PAG 2018") - - - - - - \[\[GFF\]\] (Generic Feature Format) - is a very commonly used text format for describing features ...es a - URL pattern that you can use to link genomic features to specific web - pages. - - - - - - 21 KB (2,962 words) - 05:00, 14 January 2018 - - - -- - - [JBrowse Tutorial PAG - 2019](/wiki/JBrowse_Tutorial_PAG_2019 "JBrowse Tutorial PAG 2019") - - - - - - \[\[GFF\]\] (Generic Feature Format) - is a very commonly used text format for describing features ...es a - URL pattern that you can use to link genomic features to specific web - pages. - - - - - - 22 KB (3,098 words) - 21:05, 13 January 2019 - - - -- - - [JBrowse Tutorial PAG - 2020](/wiki/JBrowse_Tutorial_PAG_2020 "JBrowse Tutorial PAG 2020") - - - - - - \[\[GFF\]\] (Generic Feature Format) - is a very commonly used text format for describing features ...es a - URL pattern that you can use to link genomic features to specific web - pages. - - - - - - 22 KB (3,210 words) - 20:11, 12 January 2020 - - - -- - - [GSOC Project Ideas - 2020](/wiki/GSOC_Project_Ideas_2020 "GSOC Project Ideas 2020") - - - - - - ...fgan et al., ''Nucleic Acids Research'', Volume 46, Issue W1, 2 - July 2018, Pages W537–W544, - https://doi.org/10.1093/nar/gky379 ...may include pathways and - reactions which contain certain genes, proteins, - Gene Ontology terms or - cross-references to other external databases as well as o - - - - - - 20 KB (3,057 words) - 02:14, 19 March 2020 - - - - - -View (previous 50 \| next 50) (20 \| 50 \| 100 \| 250 \| 500) - - - - - - - - -## Navigation menu - - - -### Namespaces - -- [Special - page](/wiki/Special%253ASearch/Generic_Gene_Pages "This is a special page, you cannot edit the page itself") - - - - - - -### Navigation - - - -- [GMOD Home](/wiki/Main_Page) -- [Software](/wiki/GMOD_Components) -- [Categories / - Tags](/wiki/Categories) -- [View all - pages](/wiki/Special:AllPages) - - - - -### Documentation - - - -- [Overview](/wiki/Overview) -- [FAQs](/wiki/Category%253AFAQ) -- [HOWTOs](/wiki/Category%253AHOWTO) -- [Glossary](/wiki/Glossary) - - - - -### Community - - - -- [GMOD News](/wiki/GMOD_News) -- [Training / - Outreach](/wiki/Training_and_Outreach) -- [Support](/wiki/Support) -- [GMOD - Promotion](/wiki/GMOD_Promotion) -- [Meetings](/wiki/Meetings) -- [Calendar](/wiki/Calendar) - - - - -### Tools - - - - - - - - - - - - - - - - - diff --git a/wiki/Special%3ASearch/Install.md b/wiki/Special%3ASearch/Install.md deleted file mode 100644 index f831b5d830..0000000000 --- a/wiki/Special%3ASearch/Install.md +++ /dev/null @@ -1,1297 +0,0 @@ - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=Install&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=Install&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=Install&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=Install&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=Install&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below up to **50** results starting with \#**1**. - - - - -**Create the page "Install" on this -wiki!** See also the search results found. - -## Page title matches - -- - - [Install document](/wiki/Install_document "Install document") - - - - - - - - - - 50 B (6 words) - 19:25, 12 April 2007 - - - -- - - [GBrowse Install - HOWTO](/wiki/GBrowse_Install_HOWTO "GBrowse Install HOWTO") - - - - - - ...e instructions are specific to GBrowse 1.x versions. See the - \[\[GBrowse 2.0 Install - HOWTO\|installation instructions for GBrowse 2.x\]\]. \* - \[\[GBrowse_MacOSX_HOWTO\|Install on - MacOSX\]\] - - - - - - 35 KB (5,565 words) - 22:39, 8 August 2012 - - - -- - - [GBrowse UCSC Plugin Install - HOWTO](/wiki/GBrowse_UCSC_Plugin_Install_HOWTO "GBrowse UCSC Plugin Install HOWTO") - - - - - - ...g on how many assemblies, alignments and types of tracks you would - like to install. Things to consider: - \# Install and configure plugin(s). - - - - - - 19 KB (3,009 words) - 19:45, 15 January 2014 - - - -- - - [Ggb/INSTALL.html](/wiki/Ggb/INSTALL.html "Ggb/INSTALL.html") - - - - - - - - - - 34 B (3 words) - 18:06, 13 January 2008 - - - -- - - [GBrowse 2.0 Install - HOWTO](/wiki/GBrowse_2.0_Install_HOWTO "GBrowse 2.0 Install HOWTO") - - - - - - ...AN_Shell\|Installing via the CPAN Shell\]\] below for more details. - This will install the newest stable - version of GBrowse. Advanced users can also - install the latest, bleeding-edge, - unstable version of GBrowse manually. You will h - - - - - - 14 KB (2,116 words) - 20:00, 22 February 2012 - - - -- - - [GBrowse 2.0 Install - HOWTO/Advanced](/wiki/GBrowse_2.0_Install_HOWTO/Advanced "GBrowse 2.0 Install HOWTO/Advanced") - - - - - - \* For basic GBrowse 2.0 install - instructions, see \[\[GBrowse 2.0 - Install HOWTO\]\] \* ''See also: - \[\[GBrowse Install HOWTO\]\].'' - - - - - - 23 KB (3,672 words) - 14:44, 10 July 2013 - - - -- - - [GBrowse 2.0 Install - Paths](/wiki/GBrowse_2.0_Install_Paths "GBrowse 2.0 Install Paths") - - - - - - - - - - 991 B (156 words) - 19:37, 31 May 2017 - - - -## Page text matches - -- - - [GMOD Middleware](/wiki/GMOD_Middleware "GMOD Middleware") - - - - - - ...Modware is built on top of GMOD and the coonnection is configured - on GMOD install. - - - - - - 40 KB (5,672 words) - 21:27, 15 August 2013 - - - -- - - [GBrowse (DasI) - Presentation]( "GBrowse (DasI) Presentation") - - - - - - \$ sudo make install - - - - - - 3 KB (415 words) - 20:05, 8 October 2012 - - - -- - - [Modware - Presentation](/wiki/Modware_Presentation "Modware Presentation") - - - - - - \* Easy to install - - - - - - 13 KB (1,574 words) - 21:24, 15 August 2013 - - - -- - - [GMOD Developer's - Guide](/wiki/GMOD_Developer%27s_Guide "GMOD Developer's Guide") - - - - - - \* DOCUMENTATION (README, INSTALL, - CONFIGURATION-HOWTO) \A INSTALL - document - - - - - - 6 KB (985 words) - 05:18, 28 January 2008 - - - -- - - [Chado - Getting - Started](/wiki/Chado_-_Getting_Started "Chado - Getting Started") - - - - - - - - - - 3 KB (469 words) - 18:08, 13 February 2014 - - - -- - - [Chado FAQ](/wiki/Chado_FAQ "Chado FAQ") - - - - - - ...irst option to try is to reinstall it, using the UNINST=1 directive - on the install command, like this: - sudo make install UNINST=1 - - - - - - 6 KB (1,058 words) - 17:50, 5 February 2014 - - - -- - - [BLAST Graphic - Viewer](/wiki/BLAST_Graphic_Viewer "BLAST Graphic Viewer") - - - - - - \|install=See the - INSTALL file in the - \[http://sourceforge.net/projects/gmod/files/blastGraphic/ blast - - - - - - 1 KB (175 words) - 01:59, 4 December 2013 - - - -- - - [CMap](/wiki/CMap "CMap") - - - - - - - - - - 7 KB (996 words) - 23:40, 17 October 2013 - - - -- - - [GBrowse](/wiki/GBrowse "GBrowse") - - - - - - ...e standard Perl module build procedure, or automated using a - network-based install script. In - order to use the net installer, you will need to have Perl 5.8.6 - \|install=\* - \[\[GBrowse_2.0_Install_HOWTO\|GBrowse 2.x installation guide\]\] - - - - - - 11 KB (1,422 words) - 16:47, 10 April 2023 - - - -- - - [GMOD - Getting - Started](/wiki/GMOD_-_Getting_Started "GMOD - Getting Started") - - - - - - ...g Requirements\]\] discusses what sort of computing support you - will need to install and run GMOD - components. - - - - - - 1 KB (240 words) - 20:32, 15 September 2009 - - - -- - - [GO Graphic Viewer](/wiki/GO_Graphic_Viewer "GO Graphic Viewer") - - - - - - \|install= - - - - - - 2 KB (264 words) - 23:44, 3 December 2013 - - - -- - - [BLAST Graphic Viewer/tool - data](/wiki/BLAST_Graphic_Viewer/tool_data "BLAST Graphic Viewer/tool data") - - - - - - \| install = See the - INSTALL file in the - \[http://sourceforge.net/projects/gmod/files/blastGraphic/ blast - - - - - - 1 KB (188 words) - 18:37, 10 September 2013 - - - -- - - [Pathway Tools](/wiki/Pathway_Tools "Pathway Tools") - - - - - - \|install= - - - - - - 5 KB (650 words) - 00:07, 16 October 2013 - - - -- - - [PubSearch](/wiki/PubSearch "PubSearch") - - - - - - \* \[http://pubsearch.org/releases/install_guide.pdf - Install documentation\] - - - - - - 1 KB (178 words) - 00:52, 18 November 2010 - - - -- - - [Argos](/wiki/Argos "Argos") - - - - - - For this, - \argos/install/packages.conf\ - configurations point to source servers for fetching read GMOD - developers can add new package sets to the - \argos/install/packages.conf\ - which point to rsync servers for the packages. - - - - - - 12 KB (1,641 words) - 15:41, 16 July 2012 - - - -- - - [GBrowse FAQ](/wiki/GBrowse_FAQ "GBrowse FAQ") - - - - - - ===How do I install GBrowse?=== ...on - instructions will be found in the top level directory, in the file - INSTALL. - - - - - - 11 KB (1,733 words) - 14:48, 18 May 2013 - - - -- - - [CMap FAQ](/wiki/CMap_FAQ "CMap FAQ") - - - - - - == Install == === How do I - install CMap? === - - - - - - 7 KB (1,071 words) - 13:01, 14 October 2010 - - - -- - - [WebGBrowse/tool - data](/wiki/WebGBrowse/tool_data "WebGBrowse/tool data") - - - - - - ...ration in GBrowse without requiring them to prepare any computer - hardware, install any software or - learn sophisticated GBrowse configuration rules for feature \| - install = - - - - - - 4 KB (540 words) - 18:31, 10 September 2013 - - - -- - - [Wiki linking style - guide](/wiki/Wiki_linking_style_guide "Wiki linking style guide") - - - - - - - - - - 3 KB (399 words) - 20:06, 8 October 2012 - - - -- - - [Perl Testing - by Gavin - Sherlock](/wiki/Perl_Testing_-_by_Gavin_Sherlock "Perl Testing - by Gavin Sherlock") - - - - - - make install ...ert a \make - test\ step between \make\ and \make - install\. You can use this - for your own development purposes, and it also ens - - - - - - 9 KB (1,495 words) - 20:05, 8 October 2012 - - - -- - - [September 2003 GMOD - Meeting](/wiki/September_2003_GMOD_Meeting "September 2003 GMOD Meeting") - - - - - - \* It is now possible to install - Pathway Tools with any of the buttons on the main query page (help, - pathway documentation and the install - experience. All the documentation for - - - - - - 28 KB (4,338 words) - 22:06, 29 October 2010 - - - -- - - [April 2004 GMOD - Meeting](/wiki/April_2004_GMOD_Meeting "April 2004 GMOD Meeting") - - - - - - implemented by the TAIR group and plans are underway to - install this the user has at least - tried to install the software. - However, it - - - - - - 42 KB (6,309 words) - 20:37, 30 November 2010 - - - -- - - [Overview](/wiki/Overview "Overview") - - - - - - ...d as prospective users may not have the resources or expertise - required to install the tool and hook - it up to their data. What is generally lacking is a conce ...ought as - performing routine or mechanical tasks. It's important but you'll - install it and typically pay little - attention to it. - - - - - - 34 KB (5,526 words) - 19:56, 7 October 2013 - - - -- - - [Chaos XML](/wiki/Chaos_XML "Chaos XML") - - - - - - The scripts are in the \chaos-xml/bin/\ directory. You - need to install the perl chaos - library before running these scripts. ...d the chaos-xml library and - follow the instructions in the - \chaos-xml/INSTALL\ - file. - - - - - - 4 KB (647 words) - 21:08, 22 January 2008 - - - -- - - [Chado](/wiki/Chado "Chado") - - - - - - \|install= - - - - - - 2 KB (238 words) - 22:55, 2 December 2013 - - - -- - - [Modware](/wiki/Modware "Modware") - - - - - - \* Install - \[\[Chado\_-_Getting_Started\|Chado\]\] ...ware, and there is an - option to \make install_sample\ that will - install the Dictyostelium Genome - - - - - - 4 KB (543 words) - 23:01, 15 August 2013 - - - -- - - [Chado Tables to - Wiki](/wiki/Chado_Tables_to_Wiki "Chado Tables to Wiki") - - - - - - \* Install postgresql_autodoc - (http://www.rbt.ca/autodoc/) - - - - - - 2 KB (366 words) - 21:27, 10 December 2010 - - - -- - - [FlyBase Chado](/wiki/FlyBase_Chado "FlyBase Chado") - - - - - - ...our PostgreSQL dumps from - ftp://ftp.flybase.net/releases/current/psql/ and - install that on a local PostgreSQL - server. Alternatively, you can directly connect - - - - - - 830 B (116 words) - 14:18, 5 June 2008 - - - -- - - [Jim's installation - notes](/wiki/Jim%27s_installation_notes "Jim's installation notes") - - - - - - \* First do this on my G4 laptop. Then consider whether to - install on the XServe. - ...\[http://gmod.cvs.sourceforge.net/\*checkout\*/gmod/schema/chado/INSTALL - the INSTALL document\] - - - - - - 16 KB (2,472 words) - 23:54, 25 January 2008 - - - -- - - [Zheng's installation - notes](/wiki/Zheng%27s_installation_notes "Zheng's installation notes") - - - - - - There suppose to be an easy way and a hard way to - install Chado database on Fedora: - \*the hard way: install by source. - But \[http://en.wikipedia.org/wiki/Yellow_dog_Updater,\_Modified y - - - - - - 7 KB (1,034 words) - 05:56, 28 January 2008 - - - -- - - [Load GFF Into Chado](/wiki/Load_GFF_Into_Chado "Load GFF Into Chado") - - - - - - - - - - 4 KB (642 words) - 15:43, 20 July 2015 - - - -- - - [GBrowse Windows - HOWTO](/wiki/GBrowse_Windows_HOWTO "GBrowse Windows HOWTO") - - - - - - Before installing on Windows systems, you will need to - install - install a database management system - such as MySQL. - - - - - - 4 KB (707 words) - 15:07, 27 July 2011 - - - -- - - [Load GenBank into - Chado](/wiki/Load_GenBank_into_Chado "Load GenBank into Chado") - - - - - - \* Install prerequisites: latest - versions of \[\[Chado\]\] and \[\[GBrowse\]\] - - - - - - 4 KB (729 words) - 21:49, 30 December 2008 - - - -- - - [BioPerl](/wiki/BioPerl "BioPerl") - - - - - - ...BioPerl is used extensively by several GMOD components. You will - need to install it before you can use - those components. ...f Perl. You should address the external - dependencies before attempting to - install BioPerl. - - - - - - 7 KB (1,121 words) - 17:28, 3 October 2012 - - - -- - - [GBrowse MacOSX - HOWTO](/wiki/GBrowse_MacOSX_HOWTO "GBrowse MacOSX HOWTO") - - - - - - '''NOTE:''' These instructions are quite old and describe how to - install GBrowse 1.X. Since Mac OS X - is very "unix-y", once libgd installed, \[\[GBro instructions describe - how to install GBrowse on these - - - - - - 11 KB (1,849 words) - 22:55, 15 August 2013 - - - -- - - [GBrowse Install - HOWTO](/wiki/GBrowse_Install_HOWTO "GBrowse Install HOWTO") - - - - - - ...e instructions are specific to GBrowse 1.x versions. See the - \[\[GBrowse 2.0 Install - HOWTO\|installation instructions for GBrowse 2.x\]\]. \* - \[\[GBrowse_MacOSX_HOWTO\|Install on - MacOSX\]\] - - - - - - 35 KB (5,565 words) - 22:39, 8 August 2012 - - - -- - - [GBrowse Ubuntu - HOWTO](/wiki/GBrowse_Ubuntu_HOWTO "GBrowse Ubuntu HOWTO") - - - - - - ...using apt-get to get all of the prerequisites for GBrowse but use - cpan to install GBrowse. To - install GBrowse on a recent Ubuntu - distribution, just do this: - - - - - - 8 KB (799 words) - 20:37, 8 August 2018 - - - -- - - [GBrowse RPM HOWTO](/wiki/GBrowse_RPM_HOWTO "GBrowse RPM HOWTO") - - - - - - ...old version of GBrowse (1.54 I think). To - install a newer version, first - install the Apache webserver (httpd) - and libgd with yum: sudo yum install - gd-devel httpd - - - - - - 3 KB (350 words) - 11:32, 28 October 2008 - - - -- - - [Chado Tutorial 2010](/wiki/Chado_Tutorial_2010 "Chado Tutorial 2010") - - - - - - - - - - 54 KB (8,190 words) - 23:34, 8 October 2012 - - - -- - - [Chado Tutorial 2012](/wiki/Chado_Tutorial_2012 "Chado Tutorial 2012") - - - - - - ...switch to the postgres user (it was created during the PostgreSQL - package install): ...ficult to - install by CPAN when using - \sudo cpan\ but is easy to - install "by hand" or using - \cpan\. - - - - - - 50 KB (7,599 words) - 16:26, 2 September 2018 - - - -- - - [Biopackages HOWTO](/wiki/Biopackages_HOWTO "Biopackages HOWTO") - - - - - - ...istributions (Centos4 is the supported & tested platform for GMOD) - and you install biopackages on a - clean system (e.g. no source installed software). We recom - ...packages. To configure yum to be aware of the Biopackages.net - repository, install one of the - following configuration RPMs: - - - - - - 6 KB (783 words) - 20:54, 14 April 2010 - - - -- - - [June 2007 Progress - Report](/wiki/June_2007_Progress_Report "June 2007 Progress Report") - - - - - - been packaged and documented, so users can download the software and - install .... A network - install script was created (modified - from the GBrowse network install - script). This script will download the CMap distribution and any - prerequis - - - - - - 26 KB (4,096 words) - 01:17, 19 August 2009 - - - -- - - [GBrowse Gentoo - HOWTO](/wiki/GBrowse_Gentoo_HOWTO "GBrowse Gentoo HOWTO") - - - - - - ;Install Apache - ;Install Mysql (Optional, But highly - recommended) - - - - - - 5 KB (743 words) - 21:00, 23 September 2009 - - - -- - - [Integrating CMAE](/wiki/Integrating_CMAE "Integrating CMAE") - - - - - - ===Install Pre-Requisites=== A bundle - can be used to install most of these - at once. To use this bundle, run: - - - - - - 6 KB (1,072 words) - 18:53, 23 January 2008 - - - -- - - [DBStag](/wiki/DBStag "DBStag") - - - - - - ...ext of Chado is to load \[\[Chado XML\]\]. No configuration is - necessary, just install and run - - - - - - 800 B (115 words) - 23:10, 15 September 2009 - - - -- - - [November 2007 GMOD - Meeting](/wiki/November_2007_GMOD_Meeting "November 2007 GMOD Meeting") - - - - - - ...ncludes a dot plot, new glyphs, and an - install script based on the GBrowse - install script. ...horsepower to - power version 3, and Lincoln wants to keep it as an easy to - install tool. - - - - - - 28 KB (4,093 words) - 05:54, 5 January 2011 - - - -- - - [Apollo PureJDBCTransactionWriter - HOWTO](/wiki/Apollo_PureJDBCTransactionWriter_HOWTO "Apollo PureJDBCTransactionWriter HOWTO") - - - - - - ...save changes directly to a \[\[chado\]\] database via JDBC, without - having to install any stored - procedures or triggers in the target database. ...oth - JDBCTransactionWriter and PureJDBCTransactionWriter in the same Apollo - install?=== - - - - - - 13 KB (1,912 words) - 21:58, 15 September 2009 - - - -- - - [Popup Balloons](/wiki/Popup_Balloons "Popup Balloons") - - - - - - \*\* Note: if you do not install your - balloon images in the default location 'images/balloons', the you will - - - - - - 39 KB (6,111 words) - 14:22, 29 May 2013 - - - -- - - [LuceGene for Daphnia - genome](/wiki/LuceGene_for_Daphnia_genome "LuceGene for Daphnia genome") - - - - - - \* install from the \[\[Downloads \| - GMOD Lucegene distribution\]\] the web archive (lucege - - - - - - 3 KB (443 words) - 22:29, 15 September 2009 - - - -- - - [NBrowse](/wiki/NBrowse "NBrowse") - - - - - - 1\. Download and install the required - software (\[http://tomcat.apache.org/ Tomcat\], \[http://www.perl 4. - Run the install.pl script located in - the nbrowse_server_client/ directory: - - - - - - 6 KB (920 words) - 16:57, 30 September 2010 - - - - - -View (previous 50 \| next 50) (20 \| 50 \| 100 \| 250 \| 500) - - - - - - - - -## Navigation menu - - - - -### Namespaces - -- [Special - page](/wiki/Special%253ASearch/Install "This is a special page, you cannot edit the page itself") - - - -### Navigation - - - -- [GMOD Home](/wiki/Main_Page) -- [Software](/wiki/GMOD_Components) -- [Categories / - Tags](/wiki/Categories) -- [View all - pages](/wiki/Special:AllPages) - - - - -### Documentation - - - -- [Overview](/wiki/Overview) -- [FAQs](/wiki/Category%253AFAQ) -- [HOWTOs](/wiki/Category%253AHOWTO) -- [Glossary](/wiki/Glossary) - - - - -### Community - - - -- [GMOD News](/wiki/GMOD_News) -- [Training / - Outreach](/wiki/Training_and_Outreach) -- [Support](/wiki/Support) -- [GMOD - Promotion](/wiki/GMOD_Promotion) -- [Meetings](/wiki/Meetings) -- [Calendar](/wiki/Calendar) - - - - -### Tools - - - - - - - - - - - - - - - diff --git a/wiki/Special%3ASearch/Jobs.md b/wiki/Special%3ASearch/Jobs.md deleted file mode 100644 index 38fc884e89..0000000000 --- a/wiki/Special%3ASearch/Jobs.md +++ /dev/null @@ -1,842 +0,0 @@ - - - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=Jobs&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=Jobs&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=Jobs&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=Jobs&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=Jobs&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below **34** results starting with \#**1**. - - - -**Create the page -"Jobs" on this wiki!** -See also the search results found. - -## Page title matches - -- - - [News/SGD and ENCODE DCC - Jobs](/wiki/News/SGD_and_ENCODE_DCC_Jobs "News/SGD and ENCODE DCC Jobs") - - - - - - - - - - 476 B (67 words) - 00:09, 31 March 2013 - - - -- - - [News/FlyBase jobs](/wiki/News/FlyBase_jobs "News/FlyBase jobs") - - - - - - '''FlyBase jobs''' - - - - - - 300 B (35 words) - 19:37, 24 August 2012 - - - -- - - [News/FlyBase jobs August - 2012](/wiki/News/FlyBase_jobs_August_2012 "News/FlyBase jobs August 2012") - - - - - - '''FlyBase jobs''' - - - - - - 300 B (35 words) - 18:13, 28 August 2012 - - - -## Page text matches - -- - - [MOD User Interfaces: Sample of several MOD Top Level - functions](/wiki/MOD_User_Interfaces:_Sample_of_several_MOD_Top_Level_functions "MOD User Interfaces: Sample of several MOD Top Level functions") - - - - - - ...e Conflicts\
About RGD: RGD Schema RGD News Citing RGD Our - Staff Open Jobs and more ...\
- Help: HowDoI Glossary FAQs Contact Us - - - - - - 7 KB (948 words) - 19:51, 23 January 2008 - - - -- - - [Genome grid](/wiki/Genome_grid "Genome grid") - - - - - - ...is parallelizing genome data, not software, to run as many separate - 1-cpu jobs as is suitable to the task - and resources. It focuses on data management, ...des scripts for - genome data partitioning, running parallel genome analysis - jobs and collating partial results. - It is being used successfully on TeraGrid c - - - - - - 7 KB (1,032 words) - 22:42, 15 September 2009 - - - -- - - [News/Hiring @ Dolan - DNALC](/wiki/News/Hiring_@_Dolan_DNALC "News/Hiring @ Dolan DNALC") - - - - - - \[\[File:DolanDNALCLogo.jpg\|link=http://www.cshl.edu/hr/jobs.html\|right\|Opening - @ Dolan DNA Learning Center, job ID 934\]\] There's an - \[http://www.cshl.edu/hr/jobs.html - opening (Job ID 934)\] at the \[http://www.dnalc.org Dolan DNA - Learning - - - - - - 1 KB (157 words) - 23:08, 9 October 2012 - - - -- - - [News/Opening at SGD](/wiki/News/Opening_at_SGD "News/Opening at SGD") - - - - - - See the \[http://jobs.stanford.edu - Stanford jobs site\] (search for - posting \[http://recruit.trovix.com/jobhostmaster/jobhost/ - - - - - - 1 KB (185 words) - 23:09, 9 October 2012 - - - -- - - [MAKER Tutorial 2013](/wiki/MAKER_Tutorial_2013 "MAKER Tutorial 2013") - - - - - - ...se ''ab initio'' gene predictors. At the top of the page select - '''Example Jobs''' → '''D. - melanogaster :Dpp'''' and click ''''Load'''. ...munication protocol - primarily used on computer clusters. This allows MAKER - jobs to be broken up across multiple - nodes/processors for increased performance - - - - - - 80 KB (12,961 words) - 23:47, 29 July 2013 - - - -- - - [MWAS Tutorial](/wiki/MWAS_Tutorial "MWAS Tutorial") - - - - - - ...EST sequence file, and a protein homology sequence file for new - annotation jobs. - - - - - - 34 KB (5,308 words) - 22:03, 3 October 2012 - - - -- - - [Biosoftware bench](/wiki/Biosoftware_bench "Biosoftware bench") - - - - - - ...C) support: Optionally, it can utilise the Condor job management - system so jobs run on a PC-farm - instead of the often meek BLAST server. A perl daemon mana - - - - - - 3 KB (539 words) - 01:55, 16 February 2011 - - - -- - - [News/FlyBase jobs](/wiki/News/FlyBase_jobs "News/FlyBase jobs") - - - - - - '''FlyBase jobs''' - - - - - - 300 B (35 words) - 19:37, 24 August 2012 - - - -- - - [News/Galaxy Hiring - Postdocs](/wiki/News/Galaxy_Hiring_Postdocs "News/Galaxy Hiring Postdocs") - - - - - - Please send your CV and names/e-mail addresses of three references to - jobs@galaxyproject.org. - - - - - - 2 KB (325 words) - 23:11, 9 October 2012 - - - -- - - [Tripal Tutorial (pre version - 0.3b)](/wiki/Tripal_Tutorial_(pre_version_0.3b) "Tripal Tutorial (pre version 0.3b)") - - - - - - \* A jobs management utility ...eping - tasks on a regular interval. Cron is a UNIX facility for scheduling - jobs to run at specific intervals. - - - - - - 80 KB (12,830 words) - 20:41, 2 October 2012 - - - -- - - [Tripal Tutorial - (v0.3.1b)](/wiki/Tripal_Tutorial_(v0.3.1b) "Tripal Tutorial (v0.3.1b)") - - - - - - \* A jobs management utility ...eping - tasks on a regular interval. Cron is a UNIX facility for scheduling - jobs to run at specific intervals. - - - - - - 92 KB (14,708 words) - 23:27, 5 September 2012 - - - -- - - [Tripal Tutorial - v1.1](/wiki/Tripal_Tutorial_v1.1 "Tripal Tutorial v1.1") - - - - - - \* A jobs management utility ...eping - tasks on a regular interval. Cron is a UNIX facility for scheduling - jobs to run at specific intervals. - - - - - - 131 KB (21,091 words) - 21:53, 2 January 2014 - - - -- - - [News/Galaxy is - Hiring](/wiki/News/Galaxy_is_Hiring "News/Galaxy is Hiring") - - - - - - ...hould submit a CV and list of references to - \[mailto:jobs@galaxyproject.org - jobs@galaxyproject.org\]. - - - - - - 3 KB (387 words) - 01:39, 15 September 2012 - - - -- - - [Tripal Developer's - Handbook](/wiki/Tripal_Developer%27s_Handbook "Tripal Developer's Handbook") - - - - - - ...with the Chado database as well as the other Tripal core functions - such as jobs management, materialized - views, in-house vocabularies. An understanding of \* - Jobs Management API - - - - - - 70 KB (10,442 words) - 16:45, 14 October 2013 - - - -- - - [Tripal Tutorial - (v1.0)](/wiki/Tripal_Tutorial_(v1.0) "Tripal Tutorial (v1.0)") - - - - - - \* A jobs management utility ...eping - tasks on a regular interval. Cron is a UNIX facility for scheduling - jobs to run at specific intervals. - - - - - - 99 KB (16,007 words) - 17:43, 12 July 2013 - - - -- - - [Tripal Tutorial - 2010](/wiki/Tripal_Tutorial_2010 "Tripal Tutorial 2010") - - - - - - jobs \* - Jobs -- long running items - - - - - - 58 KB (8,529 words) - 18:12, 9 October 2012 - - - -- - - [News/Openings at - Galaxy](/wiki/News/Openings_at_Galaxy "News/Openings at Galaxy") - - - - - - Please send your CV to - jobs@galaxyproject.org. - - - - - - 3 KB (407 words) - 23:14, 9 October 2012 - - - -- - - [News/FlyBase jobs August - 2012](/wiki/News/FlyBase_jobs_August_2012 "News/FlyBase jobs August 2012") - - - - - - '''FlyBase jobs''' - - - - - - 300 B (35 words) - 18:13, 28 August 2012 - - - -- - - [Galaxy Tutorial - 2010](/wiki/Galaxy_Tutorial_2010 "Galaxy Tutorial 2010") - - - - - - ...org/galaxy/galaxy-central/wiki/Config/Cluster Your Galaxy instance - can run jobs on a cluster \] - - - - - - 32 KB (4,846 words) - 21:16, 9 October 2012 - - - -- - - [MAKER Tutorial 2010](/wiki/MAKER_Tutorial_2010 "MAKER Tutorial 2010") - - - - - - ...are deleted as the program advances, but individual files related - to BLAST jobs can be quite large, so - setting TMP to another location can be useful. ...e ''ab initio'' gene - predictors. At the top of the page select '''Example - Jobs''' → '''D. melanogaster - :Dpp'''' and click ''''Load'''. - - - - - - 62 KB (9,933 words) - 22:41, 14 February 2013 - - - -- - - [MAKER Tutorial 2012](/wiki/MAKER_Tutorial_2012 "MAKER Tutorial 2012") - - - - - - ...se ''ab initio'' gene predictors. At the top of the page select - '''Example Jobs''' → '''D. - melanogaster :Dpp'''' and click ''''Load'''. ...munication protocol - primarily used on computer clusters. This allows MAKER - jobs to be broken up across multiple - nodes/processors for increased performance - - - - - - 80 KB (12,923 words) - 20:52, 27 August 2013 - - - -- - - [Galaxy Tutorial - 2011](/wiki/Galaxy_Tutorial_2011 "Galaxy Tutorial 2011") - - - - - - ...org/galaxy/galaxy-central/wiki/Config/Cluster Your Galaxy instance - can run jobs on a cluster \] - - - - - - 38 KB (5,631 words) - 23:56, 13 February 2013 - - - -- - - [MAKER Tutorial 2011](/wiki/MAKER_Tutorial_2011 "MAKER Tutorial 2011") - - - - - - ...are deleted as the program advances, but individual files related - to BLAST jobs can be quite large, so - setting TMP to another location can be useful. ...e ''ab initio'' gene - predictors. At the top of the page select '''Example - Jobs''' → '''D. melanogaster - :Dpp'''' and click ''''Load'''. - - - - - - 69 KB (11,026 words) - 20:52, 27 August 2013 - - - -- - - [Tripal Tutorial - 2011](/wiki/Tripal_Tutorial_2011 "Tripal Tutorial 2011") - - - - - - \* A jobs management utility ...eping - tasks on a regular interval. Cron is a UNIX facility for scheduling - jobs to run at specific intervals. - - - - - - 80 KB (12,788 words) - 22:37, 14 February 2013 - - - -- - - [News/Open Position At - dictyBase](/wiki/News/Open_Position_At_dictyBase "News/Open Position At dictyBase") - - - - - - \[\[Category%253AJobs\]\] - - - - - - 443 B (57 words) - 21:22, 4 November 2013 - - - -- - - [GSOC Project Ideas - 2016](/wiki/GSOC_Project_Ideas_2016 "GSOC Project Ideas 2016") - - - - - - ...planation:'' Galaxy supports running - jobs in Docker containers for running - jobs on a single node. However, the - size of biological datasets and the complexi ...bility to annotate - Galaxy tools with Kubernetes pods and orchestrate these - jobs via Kubernetes orchestration - either in Galaxy directly or via Pulsar. Deve - - - - - - 28 KB (4,153 words) - 14:34, 8 March 2016 - - - -- - - [GSoC 2013](/wiki/GSoC_2013 "GSoC 2013") - - - - - - ...CloudMan CloudMan\] → \[\[Galaxy\]\] and demonstrating how to - run HTCondor jobs from Galaxy across - multiple CloudMan clusters? \* finish our Oozie workflow engine that - allows jobs to be scheduled on a M/R - cluster - - - - - - 17 KB (2,555 words) - 19:59, 12 February 2014 - - - -- - - [News/Postdoc Position in Computational and Plant Evolutionary - Biology](/wiki/News/Postdoc_Position_in_Computational_and_Plant_Evolutionary_Biology "News/Postdoc Position in Computational and Plant Evolutionary Biology") - - - - - - \[\[Category%253AJobs\]\] - - - - - - 1 KB (166 words) - 19:30, 24 January 2014 - - - -- - - [GMOD Malaysia 2014/MAKER - Tutorial](/wiki/GMOD_Malaysia_2014/MAKER_Tutorial "GMOD Malaysia 2014/MAKER Tutorial") - - - - - - ...munication protocol primarily used on computer clusters. This - allows MAKER jobs to be broken up - across multiple nodes/processors for increased performance - - - - - - 85 KB (13,463 words) - 00:56, 27 February 2014 - - - -- - - [GMOD Malaysia 2014/Tripal - Tutorial](/wiki/GMOD_Malaysia_2014/Tripal_Tutorial "GMOD Malaysia 2014/Tripal Tutorial") - - - - - - \* A jobs management utility ...eping - tasks on a regular interval. Cron is a UNIX facility for scheduling - jobs to run at specific intervals. - - - - - - 131 KB (21,099 words) - 00:18, 20 February 2014 - - - -- - - [GMOD Online Training 2014/MAKER - Tutorial](/wiki/GMOD_Online_Training_2014/MAKER_Tutorial "GMOD Online Training 2014/MAKER Tutorial") - - - - - - ...se ''ab initio'' gene predictors. At the top of the page select - '''Example Jobs''' → '''D. - melanogaster :Dpp'''' and click ''''Load'''. ...munication protocol - primarily used on computer clusters. This allows MAKER - jobs to be broken up across multiple - nodes/processors for increased performance - - - - - - 80 KB (12,952 words) - 03:53, 19 May 2014 - - - - - -View (previous 50 \| next 50) (20 \| 50 \| 100 \| 250 \| 500) - - - - - - - - -## Navigation menu - - - -### Namespaces - -- [Special - page](/wiki/Special%253ASearch/Jobs "This is a special page, you cannot edit the page itself") - - - - - - -### Navigation - - - -- [GMOD Home](/wiki/Main_Page) -- [Software](/wiki/GMOD_Components) -- [Categories / - Tags](/wiki/Categories) -- [View all - pages](/wiki/Special:AllPages) - - - - -### Documentation - - - -- [Overview](/wiki/Overview) -- [FAQs](/wiki/Category%253AFAQ) -- [HOWTOs](/wiki/Category%253AHOWTO) -- [Glossary](/wiki/Glossary) - - - - -### Community - - - -- [GMOD News](/wiki/GMOD_News) -- [Training / - Outreach](/wiki/Training_and_Outreach) -- [Support](/wiki/Support) -- [GMOD - Promotion](/wiki/GMOD_Promotion) -- [Meetings](/wiki/Meetings) -- [Calendar](/wiki/Calendar) - - - - -### Tools - - - - - - - - - - - - - - - - - diff --git a/wiki/Special%3ASearch/Pages_containing_blacklisted_links.md b/wiki/Special%3ASearch/Pages_containing_blacklisted_links.md deleted file mode 100644 index c8478ac6c0..0000000000 --- a/wiki/Special%3ASearch/Pages_containing_blacklisted_links.md +++ /dev/null @@ -1,113 +0,0 @@ - - - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=Pages+containing+blacklisted+links&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=Pages+containing+blacklisted+links&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=Pages+containing+blacklisted+links&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=Pages+containing+blacklisted+links&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=Pages+containing+blacklisted+links&fulltext=Search&profile=advanced "Search in custom namespaces") - - - -There were no results matching the query. - -**Create the page "Pages -containing blacklisted links" on this wiki!** - - - - - - - -## Navigation menu - - - -### Namespaces - -- [Special - page](/wiki/Special%253ASearch/Pages_containing_blacklisted_links "This is a special page, you cannot edit the page itself") - - - - - - -### Navigation - - - -- [GMOD Home](/wiki/Main_Page) -- [Software](/wiki/GMOD_Components) -- [Categories / - Tags](/wiki/Categories) -- [View all - pages](/wiki/Special:AllPages) - - - - -### Documentation - - - -- [Overview](/wiki/Overview) -- [FAQs](/wiki/Category%253AFAQ) -- [HOWTOs](/wiki/Category%253AHOWTO) -- [Glossary](/wiki/Glossary) - - - - -### Community - - - -- [GMOD News](/wiki/GMOD_News) -- [Training / - Outreach](/wiki/Training_and_Outreach) -- [Support](/wiki/Support) -- [GMOD - Promotion](/wiki/GMOD_Promotion) -- [Meetings](/wiki/Meetings) -- [Calendar](/wiki/Calendar) - - - - -### Tools - - - - - - - - - - - - - - - - - diff --git a/wiki/Special%3ASearch/Pages_with_broken_file_links.md b/wiki/Special%3ASearch/Pages_with_broken_file_links.md deleted file mode 100644 index 88b906893a..0000000000 --- a/wiki/Special%3ASearch/Pages_with_broken_file_links.md +++ /dev/null @@ -1,222 +0,0 @@ - - - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=Pages+with+broken+file+links&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=Pages+with+broken+file+links&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=Pages+with+broken+file+links&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=Pages+with+broken+file+links&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=Pages+with+broken+file+links&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below **4** results starting with \#**1**. - - - -**Create the page "Pages with -broken file links" on this wiki!** See also the search results -found. - -- - - [GMOD Developer's - Guide](/wiki/GMOD_Developer%27s_Guide "GMOD Developer's Guide") - - - - - - \*\* With Modperl 1.3, temporarily; - need to migrate to Modperl 2.0 (currently - broken) or CGI soon. Prefix all - executables with 2-3 letter app - prefix - - - - - - 6 KB (985 words) - 05:18, 28 January 2008 - - - -- - - [Flash GViewer - Documentation](/wiki/Flash_GViewer_Documentation "Flash GViewer Documentation") - - - - - - \* Annotations can come from a static XML - file or can be dynamically generated - by a server-side script ...sually highlights the region of the - chromosome that the feature is aligned - with - - - - - - 30 KB (4,819 words) - 21:16, 9 October 2012 - - - -- - - [September 2010 GMOD - Meeting](/wiki/September_2010_GMOD_Meeting "September 2010 GMOD Meeting") - - - - - - \| rowspan="1" \| - \[\[File:Sept2010MtgLogo300.png\|250px\|center\]\] - ...MOD Meeting\\
13-14 September 2010\
Cambridge, UK - \
\
\[\[File:Sept2010Group.jpg\|center\]\] - - - - - - 100 KB (14,725 words) - 17:31, 30 November 2012 - - - -- - - [JBrowse Configuration - Guide](/wiki/JBrowse_Configuration_Guide "JBrowse Configuration Guide") - - - - - - '''This page has been replaced with - this page - (\[https://github.com/GMOD/jbrowse/wiki/JBrowse_Configuration_Guid - ...ult this guide when you need information on specific things you - want to do with your JBrowse. - - - - - - 185 KB (26,536 words) - 02:48, 30 September 2020 - - - - - -View (previous 50 \| next 50) (20 \| 50 \| 100 \| 250 \| 500) - - - - - - - - -## Navigation menu - - - -### Namespaces - -- [Special - page](/wiki/Special%253ASearch/Pages_with_broken_file_links "This is a special page, you cannot edit the page itself") - - - - - - -### Navigation - - - -- [GMOD Home](/wiki/Main_Page) -- [Software](/wiki/GMOD_Components) -- [Categories / - Tags](/wiki/Categories) -- [View all - pages](/wiki/Special:AllPages) - - - - -### Documentation - - - -- [Overview](/wiki/Overview) -- [FAQs](/wiki/Category%253AFAQ) -- [HOWTOs](/wiki/Category%253AHOWTO) -- [Glossary](/wiki/Glossary) - - - - -### Community - - - -- [GMOD News](/wiki/GMOD_News) -- [Training / - Outreach](/wiki/Training_and_Outreach) -- [Support](/wiki/Support) -- [GMOD - Promotion](/wiki/GMOD_Promotion) -- [Meetings](/wiki/Meetings) -- [Calendar](/wiki/Calendar) - - - - -### Tools - - - - - - - - - - - - - - - - - diff --git a/wiki/Special%3ASearch/Performance.md b/wiki/Special%3ASearch/Performance.md deleted file mode 100644 index dfe37edd72..0000000000 --- a/wiki/Special%3ASearch/Performance.md +++ /dev/null @@ -1,1210 +0,0 @@ - - - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=Performance&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=Performance&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=Performance&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=Performance&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=Performance&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below up to **50** results starting with \#**1**. - - - -**Create the page "Performance" -on this wiki!** See also the search results found. - -## Page title matches - -- - - [PostgreSQL Performance - Tips](/wiki/PostgreSQL_Performance_Tips "PostgreSQL Performance Tips") - - - - - - \* \[http://wiki.postgresql.org/wiki/Performance_Optimization - Performance Optimization\] - ...FAQ#How_do_I_tune_the_database_engine_for_better_performance.3F - PostgreSQL performance FAQ\] - - - - - - 5 KB (774 words) - 17:57, 5 February 2014 - - - -## Page text matches - -- - - [GMOD Middleware](/wiki/GMOD_Middleware "GMOD Middleware") - - - - - - ...of writing code and extending the software and less attention was - given to performance. Each presenter - focussed on their middleware and few side-by-side compariso - ...perations but that one should test the tool in question and not - assume its performance is adequate to - the given task. Such a test may show an entirely different a - - - - - - 40 KB (5,672 words) - 21:27, 15 August 2013 - - - -- - - [Hibernate - Presentation](/wiki/Hibernate_Presentation "Hibernate Presentation") - - - - - - \* They say: “A powerful, high - performance object/relational - persistence and query service.” - - - - - - 12 KB (1,477 words) - 21:16, 9 October 2012 - - - -- - - [Chado - Getting - Started](/wiki/Chado_-_Getting_Started "Chado - Getting Started") - - - - - - \* \[\[PostgreSQL Performance - Tips\]\] - - - - - - 3 KB (469 words) - 18:08, 13 February 2014 - - - -- - - [About the GMOD Working - Group](/wiki/About_the_GMOD_Working_Group "About the GMOD Working Group") - - - - - - \* Performance - - - - - - 3 KB (403 words) - 17:09, 5 April 2007 - - - -- - - [Comparison of XORT and Hibernate for Chado - reporting](/wiki/Comparison_of_XORT_and_Hibernate_for_Chado_reporting "Comparison of XORT and Hibernate for Chado reporting") - - - - - - ...but it is thought that a mix of the Hibernate table prefetching and - cache performance caused most of it. - By this point we had to start using a disk based cache f Another - possible cause of performance - problems is the fact that, by default, when an object is fetched you - get al - - - - - - 9 KB (1,641 words) - 15:48, 12 September 2011 - - - -- - - [LuceGene](/wiki/LuceGene "LuceGene") - - - - - - ...top of the Apache Lucene project framework, which is an - Open-source, high-performance, - full-featured text search engine library written entirely in Java. It - uses - - - - - - 6 KB (792 words) - 15:09, 6 September 2010 - - - -- - - [GBrowse FAQ](/wiki/GBrowse_FAQ "GBrowse FAQ") - - - - - - ...fixes to GBrowse2 that allow you to display \> 1000 tracks with - reasonable performance, but I've - never tested in the 10,000 track range. If you combine wiggle data - into subtracks, then performance in - GBrowse2 should be quite good. There is also an interface that lets - you - - - - - - 11 KB (1,733 words) - 14:48, 18 May 2013 - - - -- - - [Chado%253A%253AAutoDBI - Presentation](/wiki/Chado%253A%253AAutoDBI_Presentation "Chado%253A%253AAutoDBI Presentation") - - - - - - \* Performance is not as bad as you - might guess Note that speed is relative: one can find bad - performance using the wrong SQL and - Chado%253A%253AAutoDBI approach will be speedier. - - - - - - 6 KB (795 words) - 23:33, 8 October 2012 - - - -- - - [Perl Testing - by Gavin - Sherlock](/wiki/Perl_Testing_-_by_Gavin_Sherlock "Perl Testing - by Gavin Sherlock") - - - - - - ===Testing Performance=== ...ime - there is a new check-in to your code repository, you can track whether - performance regresses beyond just - noise in the measurements. To profile your code in Pe - - - - - - 9 KB (1,495 words) - 20:05, 8 October 2012 - - - -- - - [XORT Presentation](/wiki/XORT_Presentation "XORT Presentation") - - - - - - \* Performance tweaks for Hibernate - can be quite complicated to setup for bulk operations. ...RT is - currently handling ~6 million features in production with only minor - performance problems. - - - - - - 5 KB (737 words) - 18:54, 9 October 2012 - - - -- - - [InterMine - Presentation](/wiki/InterMine_Presentation "InterMine Presentation") - - - - - - \* Optimised for read-only - performance \* - Performance optimisation - - - - - - 7 KB (796 words) - 21:16, 9 October 2012 - - - -- - - [September 2003 GMOD - Meeting](/wiki/September_2003_GMOD_Meeting "September 2003 GMOD Meeting") - - - - - - samples from Medline, GenBank, and others. - Performance has been good, - - - - - - 28 KB (4,338 words) - 22:06, 29 October 2010 - - - -- - - [April 2004 GMOD - Meeting](/wiki/April_2004_GMOD_Meeting "April 2004 GMOD Meeting") - - - - - - Performance has been improved when - uploading large 3d party annotation - Performance is a concern when viewing - large numbers of uploaded - - - - - - 42 KB (6,309 words) - 20:37, 30 November 2010 - - - -- - - [May 2005 GMOD - Meeting](/wiki/May_2005_GMOD_Meeting "May 2005 GMOD Meeting") - - - - - - \* Performance - - - - - - 7 KB (915 words) - 17:07, 14 March 2008 - - - -- - - [Overview](/wiki/Overview "Overview") - - - - - - ...ySQL\]\] or some other sort of database management system, this - assures good performance even if you - have very large amounts of data in GFF format. This is accompli - - - - - - 34 KB (5,526 words) - 19:56, 7 October 2013 - - - -- - - [Chado Sequence - Module](/wiki/Chado_Sequence_Module "Chado Sequence Module") - - - - - - ...result in poorer performance. This - is one of several areas in Chado where - performance - - - - - - 64 KB (9,963 words) - 22:17, 18 December 2013 - - - -- - - [Chado Audit Module](/wiki/Chado_Audit_Module "Chado Audit Module") - - - - - - transaction performance is also - unknown. FlyBase makes a practice of - - - - - - 4 KB (679 words) - 04:31, 18 February 2015 - - - -- - - [GBrowse Windows - HOWTO](/wiki/GBrowse_Windows_HOWTO "GBrowse Windows HOWTO") - - - - - - ...d with the flat-file based implementation a bit and decide you need - better performance. - - - - - - 4 KB (707 words) - 15:07, 27 July 2011 - - - -- - - [GBrowse Install - HOWTO](/wiki/GBrowse_Install_HOWTO "GBrowse Install HOWTO") - - - - - - ...suitable for use on Linux and other Unix-like platforms. It also - contains performance and maintenance - hints useful for all systems. ...small C subroutine for nucleotide - alignments. This will vastly improve the - performance of the gbrowse_details - script when displaying alignments. To use this featu - - - - - - 35 KB (5,565 words) - 22:39, 8 August 2012 - - - -- - - [June 2007 Progress - Report](/wiki/June_2007_Progress_Report "June 2007 Progress Report") - - - - - - \#\*Performance improvements: - - - - - - 26 KB (4,096 words) - 01:17, 19 August 2009 - - - -- - - [Hackathon 2007 info](/wiki/Hackathon_2007_info "Hackathon 2007 info") - - - - - - ...\[Modware\]\] for the newer Chado schema, and tuning PostgreSQL to - get better performance. - \*performance tuning. - - - - - - 11 KB (1,683 words) - 19:54, 9 June 2010 - - - -- - - [November 2007 GMOD - Meeting](/wiki/November_2007_GMOD_Meeting "November 2007 GMOD Meeting") - - - - - - \*\*Performance Strategies - \*\*Performance - See \[\[PostgreSQL - Performance Tips\]\]. - - - - - - 28 KB (4,093 words) - 05:54, 5 January 2011 - - - -- - - [Apollo PureJDBCTransactionWriter - HOWTO](/wiki/Apollo_PureJDBCTransactionWriter_HOWTO "Apollo PureJDBCTransactionWriter HOWTO") - - - - - - ...ps and therefore the speed of the lookups can have a substantial - impact on performance. If both of - these parameters are set to '''false''' then the chado/JDBC ad - - - - - - 13 KB (1,912 words) - 21:58, 15 September 2009 - - - -- - - [GBrowse UCSC Plugin Install - HOWTO](/wiki/GBrowse_UCSC_Plugin_Install_HOWTO "GBrowse UCSC Plugin Install HOWTO") - - - - - - == Performance tweaks == - - - - - - 19 KB (3,009 words) - 19:45, 15 January 2014 - - - -- - - [News/GBrowse 2.13 - Release](/wiki/News/GBrowse_2.13_Release "News/GBrowse 2.13 Release") - - - - - - \* Uploading a Wig file now generates a BigWig database for improved - performance and scalability. This - requires Bio::DB::BigWig to be installed. \* Improved - performance when working with truly - huge (\>1000 track definition) configuration files. - - - - - - 2 KB (346 words) - 23:10, 9 October 2012 - - - -- - - [News/August 2010 - Calendar](/wiki/News/August_2010_Calendar "News/August 2010 Calendar") - - - - - - \* High Performance Bioinformatics - and Biomedicine (HiBB) - - - - - - 1 KB (163 words) - 18:22, 4 October 2012 - - - -- - - [News/InterMine Java / DB - Developer](/wiki/News/InterMine_Java_/_DB_Developer "News/InterMine Java / DB Developer") - - - - - - ...Mine code, in particular taking responsibility for the database - access and performance of the system. - - - - - - 1 KB (188 words) - 23:12, 9 October 2012 - - - -- - - [News/InterMine 0.94.1 - Release](/wiki/News/InterMine_0.94.1_Release "News/InterMine 0.94.1 Release") - - - - - - \* major data loading and query/export - performance improvements - - - - - - 1 KB (167 words) - 23:12, 9 October 2012 - - - -- - - [GMOD Online Training 2014/WebApollo - Tutorial](/wiki/GMOD_Online_Training_2014/WebApollo_Tutorial "GMOD Online Training 2014/WebApollo Tutorial") - - - - - - ...et to false to use hybrid disk/memory store which provides a little - slower performance ...et to false to - use hybrid disk/memory store which provides a little slower - performance - - - - - - 77 KB (11,812 words) - 00:39, 21 May 2014 - - - -- - - [PostgreSQL Performance - Tips](/wiki/PostgreSQL_Performance_Tips "PostgreSQL Performance Tips") - - - - - - \* \[http://wiki.postgresql.org/wiki/Performance_Optimization - Performance Optimization\] - ...FAQ#How_do_I_tune_the_database_engine_for_better_performance.3F - PostgreSQL performance FAQ\] - - - - - - 5 KB (774 words) - 17:57, 5 February 2014 - - - -- - - [Materialized views](/wiki/Materialized_views "Materialized views") - - - - - - ...ual table) and turning it into a real table that can be indexed for - better performance. While - \[\[PostgreSQL\]\] doesn't support maintenance of materialized views, - w - - - - - - 5 KB (791 words) - 05:23, 28 January 2008 - - - -- - - [PostgreSQL](/wiki/PostgreSQL "PostgreSQL") - - - - - - ...us more features on the other hand. With either platform you will - get good performance, excellent - documentation, and well-supported software. Postgres was picked - - - - - - 2 KB (356 words) - 00:52, 18 November 2010 - - - -- - - [Sybil Chado Comparative Genomics - Data](/wiki/Sybil_Chado_Comparative_Genomics_Data "Sybil Chado Comparative Genomics Data") - - - - - - I propose adding another link to this scheme as I feel it could help - with performance and simplify some - queries. The new relationship would be as follows: - - - - - - 2 KB (302 words) - 20:04, 12 April 2008 - - - -- - - [GBrowse 1 Configuration - HOWTO](/wiki/GBrowse_1_Configuration_HOWTO "GBrowse 1 Configuration HOWTO") - - - - - - The server will cache track images for a period of time in order to - speed up performance. After the time - has expired, the cached version of the image will not be us - - - - - - 79 KB (12,563 words) - 16:45, 15 August 2011 - - - -- - - [2008 GMOD Summer - School](/wiki/2008_GMOD_Summer_School "2008 GMOD Summer School") - - - - - - ...\>GBrowse Configuration: Changing defaults and displays, adding - tracks, and performance tuning - - - - - - 11 KB (1,550 words) - 22:11, 16 April 2014 - - - -- - - [August 2009 GMOD - Meeting](/wiki/August_2009_GMOD_Meeting "August 2009 GMOD Meeting") - - - - - - Some performance numbers: ....net/ - Jena\] / \[http://jena.hpl.hp.com/wiki/TDB TDB\] gives much better - load performance (~15-30K tps), on 64 - bit system with \[http://aws.amazon.com/ebs/ Amazon EBS - - - - - - 59 KB (8,741 words) - 19:37, 4 September 2013 - - - -- - - [July 2008 GMOD - Meeting](/wiki/July_2008_GMOD_Meeting "July 2008 GMOD Meeting") - - - - - - ...out GBrowse 2, the next major release of GBrowse. This release - focuses on performance and stability. - GBrowse 2 will be cluster aware: - - - - - - 28 KB (4,301 words) - 18:53, 8 October 2012 - - - -- - - [Chado Documentation - Reorganization](/wiki/Chado_Documentation_Reorganization "Chado Documentation Reorganization") - - - - - - \*\*\* Include performance tips and - discussion of backups. - - - - - - 7 KB (1,015 words) - 22:30, 29 December 2010 - - - -- - - [GBrowse/Uploading Wiggle - Tracks](/wiki/GBrowse/Uploading_Wiggle_Tracks "GBrowse/Uploading Wiggle Tracks") - - - - - - .... The BED format is essentially the same as GFF3 and does not give - you any performance advantages over - using straight GFF3. However, you are dealing with features \*For the - intial upload to the website, there is more of a - performance hit associated with BED - formatted data. After loading, access and rendered - - - - - - 15 KB (2,251 words) - 21:22, 25 April 2013 - - - -- - - [News/SynBrowse Developers - Needed](/wiki/News/SynBrowse_Developers_Needed "News/SynBrowse Developers Needed") - - - - - - ...parts of \[\[GBrowse\]\]. SynBrowse2 need particular improvements - in run-time performance and its - alignment parsing tools. Ideally, programmers will develop SynBrow - - - - - - 1 KB (154 words) - 23:23, 3 October 2012 - - - -- - - [News/GBrowse 1.69 - Released](/wiki/News/GBrowse_1.69_Released "News/GBrowse 1.69 Released") - - - - - - ...is release of GBrowse comes with a variety of user interface - enhancements, performance - improvements, bug fixes and a security fix. This release come courtesy - of \* Caching of individual tracks for better - performance; use "cache time" option - to control. - - - - - - 2 KB (283 words) - 21:25, 24 January 2011 - - - -- - - [News/InterMine 0.92 - Released](/wiki/News/InterMine_0.92_Released "News/InterMine 0.92 Released") - - - - - - ...gration keys and priorities are configured and validated, a BioPax - parser, performance enhancements and - some webapp fixes. - - - - - - 799 B (111 words) - 23:12, 9 October 2012 - - - -- - - [Chado Django HOWTO](/wiki/Chado_Django_HOWTO "Chado Django HOWTO") - - - - - - === High Performance === - - - - - - 16 KB (2,412 words) - 18:11, 9 October 2012 - - - -- - - [GBrowse 2.0 HOWTO](/wiki/GBrowse_2.0_HOWTO "GBrowse 2.0 HOWTO") - - - - - - ...rce-specific files to be shorter and more concise. This also - increases the performance for sites - that use hundreds of configuration files to display annotations o - ...ses and machines via a series of "slave" renderers. This greatly - increases performance. - - - - - - 101 KB (15,507 words) - 04:44, 9 January 2014 - - - -- - - [Grouping GBrowse - Features](/wiki/Grouping_GBrowse_Features "Grouping GBrowse Features") - - - - - - ...y data in which a feature might extend from one chromosome to - another. For performance reasons, you - may not wish to read the entire chromosome-length feature into - - - - - - 3 KB (463 words) - 06:09, 25 September 2009 - - - -- - - [Running a GBrowse2 render - farm](/wiki/Running_a_GBrowse2_render_farm "Running a GBrowse2 render farm") - - - - - - ...pread out the work of generating GBrowse pages, thereby achieving - improved performance. A slave can be - attached to a particular track, a particular set of tracks, ...rocess; - however it is possible to launch multiple processes for a possible - performance boost. The three - databases are located on a single NFS-mounted volume, so t - - - - - - 16 KB (2,473 words) - 12:08, 12 October 2011 - - - -- - - [GBrowse 2.0 - Prerequisites](/wiki/GBrowse_2.0_Prerequisites "GBrowse 2.0 Prerequisites") - - - - - - Those who want to obtain the best - performance should consider the - mod_perl, or FastCGI Apache modules: - - - - - - 8 KB (1,147 words) - 21:20, 15 January 2017 - - - -- - - [2008 GMOD Community - Survey](/wiki/2008_GMOD_Community_Survey "2008 GMOD Community Survey") - - - - - - \* Please rank the relative - performance of the Help Desk in each - of 5 areas. - - - - - - 14 KB (1,816 words) - 21:33, 5 October 2009 - - - -- - - [GBrowse Backends](/wiki/GBrowse_Backends "GBrowse Backends") - - - - - - ...n a 1000 features or so, GBrowse will begin to slow down. You can - increase performance by using the - BerkeleyDB backend. In exactly the way that you did with the i - ==Performance== - - - - - - 10 KB (1,607 words) - 17:16, 23 April 2013 - - - -- - - [Gbrowse clean.pl](/wiki/Gbrowse_clean.pl "Gbrowse clean.pl") - - - - - - ...ck data is purged from the system. Caching for up to a few hours - increases performance because users - frequently reload the same region. Caching for longer periods - - - - - - 3 KB (513 words) - 14:13, 2 November 2009 - - - - - -View (previous 50 \| next 50) (20 \| 50 \| 100 \| 250 \| 500) - - - - - - - - -## Navigation menu - - - -### Namespaces - -- [Special - page](/wiki/Special%253ASearch/Performance "This is a special page, you cannot edit the page itself") - - - - - - -### Navigation - - - -- [GMOD Home](/wiki/Main_Page) -- [Software](/wiki/GMOD_Components) -- [Categories / - Tags](/wiki/Categories) -- [View all - pages](/wiki/Special:AllPages) - - - - -### Documentation - - - -- [Overview](/wiki/Overview) -- [FAQs](/wiki/Category%253AFAQ) -- [HOWTOs](/wiki/Category%253AHOWTO) -- [Glossary](/wiki/Glossary) - - - - -### Community - - - -- [GMOD News](/wiki/GMOD_News) -- [Training / - Outreach](/wiki/Training_and_Outreach) -- [Support](/wiki/Support) -- [GMOD - Promotion](/wiki/GMOD_Promotion) -- [Meetings](/wiki/Meetings) -- [Calendar](/wiki/Calendar) - - - - -### Tools - - - - - - - - - - - - - - - - - diff --git a/wiki/Special%3ASearch/REST.md b/wiki/Special%3ASearch/REST.md deleted file mode 100644 index cea9cc7d3a..0000000000 --- a/wiki/Special%3ASearch/REST.md +++ /dev/null @@ -1,1219 +0,0 @@ - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=REST&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=REST&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=REST&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=REST&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=REST&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below up to **50** results starting with \#**1**. - - - - -**Create the page -"REST" on this wiki!** -See also the search results found. - -## Page title matches - -- - - [GMOD REST Hackathon](/wiki/GMOD_REST_Hackathon "GMOD REST Hackathon") - - - - - - The goal of this hackathon is to produce a working prototype of the - \[\[GMOD REST API\]\]. It will be a - very low key event with no official reserved location \* Produce a - working version of the - \[\[GMOD_REST_API\|REST API\]\] - - - - - - 1 KB (191 words) - 19:54, 9 June 2010 - - - -- - - [GMOD REST API](/wiki/GMOD_REST_API "GMOD REST API") - - - - - - - - - - 26 B (4 words) - 19:53, 13 January 2010 - - - -- - - [GBrowse2 REST API](/wiki/GBrowse2_REST_API "GBrowse2 REST API") - - - - - - This article describes the '''GBrowse2 - REST API'''. =The GBrowse2 - REST API= - - - - - - 6 KB (982 words) - 15:29, 27 August 2012 - - - -## Page text matches - -- - - [Summary of Fall 2005 CHSL - Meeting](/wiki/Summary_of_Fall_2005_CHSL_Meeting "Summary of Fall 2005 CHSL Meeting") - - - - - - ...these two volunteers can agree on some common use cases and - implement, the rest of the group can - then evaluate the technologies better. - - - - - - 2 KB (257 words) - 15:02, 13 February 2007 - - - -- - - [Pathway Tools](/wiki/Pathway_Tools "Pathway Tools") - - - - - - ...annotated genome in the form of a Genbank file; Pathway Tools will - do the rest. - - - - - - 5 KB (650 words) - 00:07, 16 October 2013 - - - -- - - [BioMart](/wiki/BioMart "BioMart") - - - - - - \|output=APIs: REST/SOAP, JAVA, - SPARQL - - - - - - 2 KB (228 words) - 22:26, 15 October 2013 - - - -- - - [Chado Manual](/wiki/Chado_Manual "Chado Manual") - - - - - - ...bility and schema evolution within specific modules without - disrupting the rest of the schema. - Finally, it allows for a mix and match approach - it is the - - - - - - 17 KB (2,655 words) - 13:43, 14 March 2014 - - - -- - - [MOD User Interfaces: outline of - topics](/wiki/MOD_User_Interfaces%253A_outline_of_topics "MOD User Interfaces: outline of topics") - - - - - - ...arches/filters be combined with any outputs\
-- SQL, - WebServices, Web-REST, related - programmed query support - - - - - - 4 KB (644 words) - 01:37, 29 March 2007 - - - -- - - [April 2004 GMOD - Meeting](/wiki/April_2004_GMOD_Meeting "April 2004 GMOD Meeting") - - - - - - UTRs are now shown in a different (configurable) color from the - rest of - - - - - - 42 KB (6,309 words) - 20:37, 30 November 2010 - - - -- - - [Overview](/wiki/Overview "Overview") - - - - - - \*Supports GFF3, BED, FASTA, Wiggle, BigWig, BAM, VCF (with tabix), - REST, and more. BAM, BigWig, and VCF - data are displayed directly from the compr - - - - - - 34 KB (5,526 words) - 19:56, 7 October 2013 - - - -- - - [Chado XML](/wiki/Chado_XML "Chado XML") - - - - - - The rest of this document concerns - syntactic issues related to the XML representatii - - - - - - 10 KB (1,539 words) - 21:16, 9 October 2012 - - - -- - - [Chado Tutorial 2010](/wiki/Chado_Tutorial_2010 "Chado Tutorial 2010") - - - - - - \*\* Use only what you need, ignore the - rest - - - - - - 54 KB (8,190 words) - 23:34, 8 October 2012 - - - -- - - [Chado Tutorial 2012](/wiki/Chado_Tutorial_2012 "Chado Tutorial 2012") - - - - - - \*\* Use only what you need, ignore the - rest - - - - - - 50 KB (7,599 words) - 16:26, 2 September 2018 - - - -- - - [November 2007 GMOD - Meeting](/wiki/November_2007_GMOD_Meeting "November 2007 GMOD Meeting") - - - - - - \*\* REST-like style. - - - - - - 28 KB (4,093 words) - 05:54, 5 January 2011 - - - -- - - [GMOD Online Training 2014/WebApollo - Tutorial](/wiki/GMOD_Online_Training_2014/WebApollo_Tutorial "GMOD Online Training 2014/WebApollo Tutorial") - - - - - - ...s display \Name\, \Symbol\, and - \Description\ but the rest - is optional. This allows you to make the editor more compact if you're - not ...tt\>maker.gff\. We need to handle that file a bit - differently than the rest of the - files since the GFF represents the features as gene, transcript, exo - - - - - - 77 KB (11,812 words) - 00:39, 21 May 2014 - - - -- - - [Distributed Annotation - System](/wiki/Distributed_Annotation_System "Distributed Annotation System") - - - - - - \*\* REST-like style. - - - - - - 2 KB (224 words) - 18:47, 17 September 2012 - - - -- - - [GBrowse 1 Configuration - HOWTO](/wiki/GBrowse_1_Configuration_HOWTO "GBrowse 1 Configuration HOWTO") - - - - - - ...n example that draws the first and last parts of a feature in blue - and the rest in red: - - - - - - 79 KB (12,563 words) - 16:45, 15 August 2011 - - - -- - - [August 2009 GMOD - Meeting](/wiki/August_2009_GMOD_Meeting "August 2009 GMOD Meeting") - - - - - - Josh talked about the progress of the \[\[GMOD - REST API\]\] group that was started - at the \[\[January 2009 GMOD Meeting\]\]. \* \[\[GMOD - REST API\]\] - Presentation of the - current draft spec and a feedback/discussion pe - - - - - - 59 KB (8,741 words) - 19:37, 4 September 2013 - - - -- - - [2009 GMOD Summer School - - Americas](/wiki/2009_GMOD_Summer_School_-_Americas "2009 GMOD Summer School - Americas") - - - - - - ...will also have the opportunity to share work from their projects - with the rest of the group. - - - - - - 11 KB (1,433 words) - 22:13, 16 April 2014 - - - -- - - [2018 PAG Hackathon](/wiki/2018_PAG_Hackathon "2018 PAG Hackathon") - - - - - - Registration is \$50 which covers part of the fee for the room (where - the rest is made up from the kind - JBrowse folks) and lunch on the first day. Please - - - - - - 5 KB (692 words) - 18:48, 17 January 2018 - - - -- - - [News/gmod (Chado) 1.1 - Released]( "News/gmod (Chado) 1.1 Released") - - - - - - ...\[\[User%253ARobertBuels\|Rob Buels\]\] and \[\[User%253ANaamaMenda\|Naama - Menda\]\] and the rest of the people - at the \[http://solgenomics.net/ Sol Genomics Network (SGN)\] f - - - - - - 2 KB (316 words) - 23:00, 24 January 2011 - - - -- - - [JBrowse](/wiki/JBrowse "JBrowse") - - - - - - \*Supports GFF3, BED, FASTA, Wiggle, BigWig, BAM, VCF (with tabix), - REST, and more. BAM, BigWig, and VCF - data are displayed directly from the compr - - - - - - 8 KB (1,157 words) - 19:18, 15 April 2016 - - - -- - - [Bio GMOD - GenericGenePage](/wiki/Bio_GMOD_GenericGenePage "Bio GMOD GenericGenePage") - - - - - - The EcoliWiki implementation is written as a - REST-like service in PHP. - http://ecoliwiki.net/rest/gmod_gene.php/gene_symbol/pfkA - - - - - - 6 KB (755 words) - 01:16, 19 August 2009 - - - -- - - [GBrowse 2.0 HOWTO](/wiki/GBrowse_2.0_HOWTO "GBrowse 2.0 HOWTO") - - - - - - ...n example that draws the first and last parts of a feature in blue - and the rest in red: =The GBrowse2 - REST API= - - - - - - 101 KB (15,507 words) - 04:44, 9 January 2014 - - - -- - - [January 2009 GMOD - Meeting](/wiki/January_2009_GMOD_Meeting "January 2009 GMOD Meeting") - - - - - - ...lyBase\]\] project proposed that GMOD support a - \[http://tomayko.com/writings/rest-to-my-wife - RESTful interface\] for biological data. Josh started by listing Why - go with REST? - - - - - - 50 KB (7,612 words) - 18:53, 8 October 2012 - - - -- - - [Running a GBrowse2 render - farm](/wiki/Running_a_GBrowse2_render_farm "Running a GBrowse2 render farm") - - - - - - ...der slave running on port 8101 on the host - ''slavehost1.example.org''. The rest - of the stanza is as usual, and contains options for selecting the - glyph, co - - - - - - 16 KB (2,473 words) - 12:08, 12 October 2011 - - - -- - - [Web services working - group](/wiki/Web_services_working_group "Web services working group") - - - - - - The \[\[GMOD REST API\]\] is being - developed in order to provide a useful and easy to use inter - ...ridging the semantic Web and Web 2.0 with Representational State - Transfer (REST)\] - - - - - - 2 KB (278 words) - 01:17, 19 August 2009 - - - -- - - [GMOD RPC API](/wiki/GMOD_RPC_API "GMOD RPC API") - - - - - - ...PI all web calls should be versioned according to what version of - the GMOD REST API they are using. The - version number included in the URLs corresponds to '''Current GMOD - REST API Version:''' 1.1 - - - - - - 25 KB (3,166 words) - 23:02, 15 August 2013 - - - -- - - [CVS to Subversion - Conversion](/wiki/CVS_to_Subversion_Conversion "CVS to Subversion Conversion") - - - - - - ...S. See \[\[Subversion\]\] for how to access the new repository. We - spent the rest of the day locking - down CVS access (it is still there, but is read-only), a - - - - - - 10 KB (1,550 words) - 18:12, 3 October 2012 - - - -- - - [January 2010 GMOD - Meeting](/wiki/January_2010_GMOD_Meeting "January 2010 GMOD Meeting") - - - - - - : \[\[GMOD REST Hackathon\]\] ! - \[\[GMOD REST Hackathon\]\] - - - - - - 26 KB (3,722 words) - 19:17, 4 September 2013 - - - -- - - [GBrowse NGS - Tutorial](/wiki/GBrowse_NGS_Tutorial "GBrowse NGS Tutorial") - - - - - - And the rest are optional prereqs. - library installed, you can still compile the - rest of SAMtools by - - - - - - 38 KB (5,742 words) - 18:11, 9 October 2012 - - - -- - - [GMOD REST Hackathon](/wiki/GMOD_REST_Hackathon "GMOD REST Hackathon") - - - - - - The goal of this hackathon is to produce a working prototype of the - \[\[GMOD REST API\]\]. It will be a - very low key event with no official reserved location \* Produce a - working version of the - \[\[GMOD_REST_API\|REST API\]\] - - - - - - 1 KB (191 words) - 19:54, 9 June 2010 - - - -- - - [2010 GMOD Summer School - - Americas](/wiki/2010_GMOD_Summer_School_-_Americas "2010 GMOD Summer School - Americas") - - - - - - ...will also have the opportunity to share work from their projects - with the rest of the group. - - - - - - 13 KB (1,782 words) - 22:14, 16 April 2014 - - - -- - - [GBrowse2 REST API](/wiki/GBrowse2_REST_API "GBrowse2 REST API") - - - - - - This article describes the '''GBrowse2 - REST API'''. =The GBrowse2 - REST API= - - - - - - 6 KB (982 words) - 15:29, 27 August 2012 - - - -- - - [Notes on simplified nd schema and Use - Cases](/wiki/Notes_on_simplified_nd_schema_and_Use_Cases "Notes on simplified nd schema and Use Cases") - - - - - - ...either way? If we check 1000 flies and 500 of them had white eyes - and the rest of them had red eyes, we - can only have two rows in phenotype table - red or - - - - - - 15 KB (2,389 words) - 00:18, 5 January 2011 - - - -- - - [GMOD Evo Hackathon Proposal Supplemental - Information](/wiki/GMOD_Evo_Hackathon_Proposal_Supplemental_Information "GMOD Evo Hackathon Proposal Supplemental Information") - - - - - - This is a great example of how evolutionary biology can help lead the - rest of the GMOD community. - - - - - - 9 KB (1,301 words) - 20:44, 7 July 2010 - - - -- - - [MolGenIS](/wiki/MolGenIS "MolGenIS") - - - - - - ...erfaces to RDF, SPARQL and ontologies, processing interfaces to R - and SOAP/REST web services, a - text-file exchange format and full documentation. There is - - - - - - 2 KB (351 words) - 01:36, 3 October 2012 - - - -- - - [September 2010 GMOD - Meeting](/wiki/September_2010_GMOD_Meeting "September 2010 GMOD Meeting") - - - - - - ; SOAP and REST \* Via - REST - - - - - - 100 KB (14,725 words) - 17:31, 30 November 2012 - - - -- - - [InterMine Workshop - GMOD Europe - 2010](/wiki/InterMine_Workshop_-_GMOD_Europe_2010 "InterMine Workshop - GMOD Europe 2010") - - - - - - ...d used it to run some example queries. We will also ran queries - using the REST web service - - - - - - 2 KB (338 words) - 18:53, 8 October 2012 - - - -- - - [Chado Schema Documentation - HOWTO](/wiki/Chado_Schema_Documentation_HOWTO "Chado Schema Documentation HOWTO") - - - - - - ...f a table was dropped or added. The Table Templates will take care - of the rest. - - - - - - 13 KB (1,916 words) - 20:28, 29 January 2013 - - - -- - - [March 2011 GMOD - Meeting](/wiki/March_2011_GMOD_Meeting "March 2011 GMOD Meeting") - - - - - - ...he intro to GMOD session tremendously, as it was a very nice setup - for the rest of the meeting. I found - the 'showcasing' of different GMOD modules very use - - - - - - 18 KB (2,659 words) - 19:19, 4 September 2013 - - - -- - - [Satellite Meetings - GMOD Americas - 2011](/wiki/Satellite_Meetings_-_GMOD_Americas_2011 "Satellite Meetings - GMOD Americas 2011") - - - - - - \* ''\[\[GMOD REST Hackathon\]\]'' at - the \[\[January 2010 GMOD Meeting\]\] - - - - - - 4 KB (576 words) - 18:55, 8 October 2012 - - - -- - - [October 2011 GMOD - Meeting](/wiki/October_2011_GMOD_Meeting "October 2011 GMOD Meeting") - - - - - - ...er to provide data access, and how to query BioMart server via web - GUI and REST API. Junjun Zhang of the - \[http://biomart.org/ BioMart Project\] will lead th - - - - - - 13 KB (1,892 words) - 18:54, 8 October 2012 - - - -- - - [Chado Natural Diversity Module/natdiv schema changes - call](/wiki/Chado_Natural_Diversity_Module/natdiv_schema_changes_call "Chado Natural Diversity Module/natdiv schema changes call") - - - - - - \*\*\* I also think prop tables for linking tables are not consistent - with the rest of chado tables and - make chado schema too complicated (Sook). \* nd_geolocationprop.value - is varchar(250) while others in NatDiv are 255. - Rest of chado is type 'text'. Propose - change to text. - - - - - - 11 KB (1,777 words) - 15:05, 4 February 2012 - - - -- - - [WebApollo Tutorial - 2012](/wiki/WebApollo_Tutorial_2012 "WebApollo Tutorial 2012") - - - - - - ...tt\>maker.gff\. We need to handle that file a bit differently - than the rest of the files since the - GFF represents the features as gene, transcript, exo - - - - - - 43 KB (6,301 words) - 20:52, 27 August 2013 - - - -- - - [News/JBrowse 1.9.0 - released](/wiki/News/JBrowse_1.9.0_released "News/JBrowse 1.9.0 released") - - - - - - \JBrowse now ships with a - \REST datastore - backend\ that lets developers serve data to JBrowse from - - - - - - 2 KB (263 words) - 14:09, 17 April 2013 - - - -- - - [JBrowse Configuration - Guide](/wiki/JBrowse_Configuration_Guide "JBrowse Configuration Guide") - - - - - - // one. for example, the default REST - ...se it, a developer can implement server-side web services that - satisfy the REST API it expects. - - - - - - 185 KB (26,536 words) - 02:48, 30 September 2020 - - - -- - - [Tripal Tutorial - v1.1](/wiki/Tripal_Tutorial_v1.1 "Tripal Tutorial v1.1") - - - - - - ...ing the production instance. The production instance serves content - to the rest of the world. Once you - are certain that customizations and new functionali - - - - - - 131 KB (21,091 words) - 21:53, 2 January 2014 - - - -- - - [Tripal Tutorial - 2010](/wiki/Tripal_Tutorial_2010 "Tripal Tutorial 2010") - - - - - - \# Drupal API provide the rest - - - - - - 58 KB (8,529 words) - 18:12, 9 October 2012 - - - -- - - [GSoC 2011](/wiki/GSoC_2011 "GSoC 2011") - - - - - - ...t to make science faster and more open make your heart race? Do you - speak REST, CSS, Javascript, Perl and - related technologies? If so, please consider jo - - - - - - 20 KB (2,895 words) - 23:51, 25 July 2012 - - - -- - - [WebApollo v2013-05-16 - Installation](/wiki/WebApollo_v2013-05-16_Installation "WebApollo v2013-05-16 Installation") - - - - - - ...tt\>maker.gff\. We need to handle that file a bit differently - than the rest of the files since the - GFF represents the features as gene, transcript, exo - - - - - - 55 KB (8,533 words) - 19:02, 24 August 2013 - - - -- - - [Pathway Tools/tool - data](/wiki/Pathway_Tools/tool_data "Pathway Tools/tool data") - - - - - - ...annotated genome in the form of a Genbank file; Pathway Tools will - do the rest. - - - - - - 5 KB (661 words) - 18:32, 10 September 2013 - - - -- - - [WebApollo - Installation](/wiki/WebApollo_Installation "WebApollo Installation") - - - - - - ...s display \Name\, \Symbol\, and - \Description\ but the rest - is optional. This allows you to make the editor more compact if you're - not ...tt\>maker.gff\. We need to handle that file a bit - differently than the rest of the - files since the GFF represents the features as gene, transcript, exo - - - - - - 88 KB (13,531 words) - 19:06, 20 March 2017 - - - - - -View (previous 50 \| next 50) (20 \| 50 \| 100 \| 250 \| 500) - - - - - - - - -## Navigation menu - - - - -### Namespaces - -- [Special - page](/wiki/Special%253ASearch/REST "This is a special page, you cannot edit the page itself") - - - -### Navigation - - - -- [GMOD Home](/wiki/Main_Page) -- [Software](/wiki/GMOD_Components) -- [Categories / - Tags](/wiki/Categories) -- [View all - pages](/wiki/Special:AllPages) - - - - -### Documentation - - - -- [Overview](/wiki/Overview) -- [FAQs](/wiki/Category%253AFAQ) -- [HOWTOs](/wiki/Category%253AHOWTO) -- [Glossary](/wiki/Glossary) - - - - -### Community - - - -- [GMOD News](/wiki/GMOD_News) -- [Training / - Outreach](/wiki/Training_and_Outreach) -- [Support](/wiki/Support) -- [GMOD - Promotion](/wiki/GMOD_Promotion) -- [Meetings](/wiki/Meetings) -- [Calendar](/wiki/Calendar) - - - - -### Tools - - - - - - - - - - - - - - - diff --git a/wiki/Special%3ASearch/RPC.md b/wiki/Special%3ASearch/RPC.md deleted file mode 100644 index 8a7eab7c7d..0000000000 --- a/wiki/Special%3ASearch/RPC.md +++ /dev/null @@ -1,297 +0,0 @@ - - - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=RPC&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=RPC&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=RPC&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=RPC&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=RPC&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below **8** results starting with \#**1**. - - - -**Create the page -"RPC" on this wiki!** -See also the search results found. - -## Page title matches - -- - - [GMOD RPC API](/wiki/GMOD_RPC_API "GMOD RPC API") - - - - - - \* \[\[GMOD RPC API Use Cases\]\] - \[\[Category%253ARPC\]\] - - - - - - 25 KB (3,166 words) - 23:02, 15 August 2013 - - - -- - - [GMOD RPC API/PHP](/wiki/GMOD_RPC_API/PHP "GMOD RPC API/PHP") - - - - - - Plans/Architecture for the PHP tools for implementing - gmod-rpc - gmod-rpc/index.php - - - - - - 1 KB (197 words) - 18:12, 9 October 2012 - - - -## Page text matches - -- - - [News/GMOD Europe 2010 - Report](/wiki/News/GMOD_Europe_2010_Report "News/GMOD Europe 2010 Report") - - - - - - ...September 2010 GMOD Meeting#GMOD - RPC API: The almost RESTful GMOD - API\|GMOD RPC API: The almost RESTful - GMOD API\]\] - - - - - - 3 KB (444 words) - 23:36, 3 October 2012 - - - -- - - [GMOD RPC API](/wiki/GMOD_RPC_API "GMOD RPC API") - - - - - - \* \[\[GMOD RPC API Use Cases\]\] - \[\[Category%253ARPC\]\] - - - - - - 25 KB (3,166 words) - 23:02, 15 August 2013 - - - -- - - [January 2010 GMOD - Meeting](/wiki/January_2010_GMOD_Meeting "January 2010 GMOD Meeting") - - - - - - \| \[\[GMOD RPC API\]\] - - - - - - 26 KB (3,722 words) - 19:17, 4 September 2013 - - - -- - - [GMOD RPC API/PHP](/wiki/GMOD_RPC_API/PHP "GMOD RPC API/PHP") - - - - - - Plans/Architecture for the PHP tools for implementing - gmod-rpc - gmod-rpc/index.php - - - - - - 1 KB (197 words) - 18:12, 9 October 2012 - - - -- - - [September 2010 GMOD - Meeting](/wiki/September_2010_GMOD_Meeting "September 2010 GMOD Meeting") - - - - - - \| \[\[GMOD RPC API\]\]: The almost - RESTful GMOD API \| \[\[Media:GMOD_RPC_Sept_2010.pdf\|PDF\]\], - \[\[#GMOD RPC API: The almost RESTful - GMOD API\|Summary\]\] - - - - - - 100 KB (14,725 words) - 17:31, 30 November 2012 - - - -- - - [Satellite Meetings - GMOD Americas - 2011](/wiki/Satellite_Meetings_-_GMOD_Americas_2011 "Satellite Meetings - GMOD Americas 2011") - - - - - - ! \[\[GMOD RPC API\|GMOD Web services - toolkit\]\] \| \Come to work on or discuss the \[\[GMOD - RPC API\|GMOD Web services API and - the toolkit\]\].\ - - - - - - 4 KB (576 words) - 18:55, 8 October 2012 - - - - - -View (previous 50 \| next 50) (20 \| 50 \| 100 \| 250 \| 500) - - - - - - - - -## Navigation menu - - - -### Namespaces - -- [Special - page](/wiki/Special%253ASearch/RPC "This is a special page, you cannot edit the page itself") - - - - - - -### Navigation - - - -- [GMOD Home](/wiki/Main_Page) -- [Software](/wiki/GMOD_Components) -- [Categories / - Tags](/wiki/Categories) -- [View all - pages](/wiki/Special:AllPages) - - - - -### Documentation - - - -- [Overview](/wiki/Overview) -- [FAQs](/wiki/Category%253AFAQ) -- [HOWTOs](/wiki/Category%253AHOWTO) -- [Glossary](/wiki/Glossary) - - - - -### Community - - - -- [GMOD News](/wiki/GMOD_News) -- [Training / - Outreach](/wiki/Training_and_Outreach) -- [Support](/wiki/Support) -- [GMOD - Promotion](/wiki/GMOD_Promotion) -- [Meetings](/wiki/Meetings) -- [Calendar](/wiki/Calendar) - - - - -### Tools - - - - - - - - - - - - - - - - - diff --git a/wiki/Special%3ASearch/Rails.md b/wiki/Special%3ASearch/Rails.md deleted file mode 100644 index 804d89a06b..0000000000 --- a/wiki/Special%3ASearch/Rails.md +++ /dev/null @@ -1,286 +0,0 @@ - - - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=Rails&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=Rails&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=Rails&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=Rails&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=Rails&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below **7** results starting with \#**1**. - - - -**Create the page -"Rails" on this -wiki!** See also the search results found. - -## Page title matches - -- - - [Chado on Rails](/wiki/Chado_on_Rails "Chado on Rails") - - - - - - ...d is used in the Bovine Genome Database, BeeBase and NasoniaBase. - Chado on Rails is free as in - beer/speech. got a non-standard Chado schema? CoR can \[automatically - create Rails objects and unit tests - for your schema using magic chado, a component of Co - - - - - - 7 KB (1,041 words) - 22:20, 28 March 2014 - - - -## Page text matches - -- - - [News/GMOD Evo Hackathon - Report](/wiki/News/GMOD_Evo_Hackathon_Report "News/GMOD Evo Hackathon Report") - - - - - - ...rsity}} module in Chado. This was built on top of the emerging - \[\[Chado on Rails\]\] project. The - second was a better understanding, slight refactoring, and - - - - - - 4 KB (504 words) - 23:11, 9 October 2012 - - - -- - - [Chado Django HOWTO](/wiki/Chado_Django_HOWTO "Chado Django HOWTO") - - - - - - ...www.hibernate.org/ Hibernate\] (Java), - \[http://www.rubyonrails.org/ Ruby on - Rails\] and - \[http://www.catalystframework.org/ Catalyst\] (Perl). Choose what you - l - - - - - - 16 KB (2,412 words) - 18:11, 9 October 2012 - - - -- - - [January 2009 GMOD - Meeting](/wiki/January_2009_GMOD_Meeting "January 2009 GMOD Meeting") - - - - - - ...hey have a submission and publishing pipeline that is written with - Ruby on Rails. It also uses the - GoogleGraph API. - - - - - - 50 KB (7,612 words) - 18:53, 8 October 2012 - - - -- - - [GMOD Evo Hackathon](/wiki/GMOD_Evo_Hackathon "GMOD Evo Hackathon") - - - - - - ...rsity}} module in Chado. This was built on top of the emerging - \[\[Chado on Rails\]\] project. The - second was a better understanding, slight refactoring, and - - - - - - 17 KB (2,407 words) - 13:22, 13 November 2015 - - - -- - - [January 2010 GMOD - Meeting](/wiki/January_2010_GMOD_Meeting "January 2010 GMOD Meeting") - - - - - - \| Chado on Rails - (\[http://rubyonrails.org/ Ruby on - Rails\] and \[\[Chado\]\]) - ...do.ppt\|PPT\]\], - \[\[Media:Jan2010RubyOnRailsAndChado.pdf\|PDF\]\]\ - - - - diff --git a/wiki/Special%3ASearch/Reactome.md b/wiki/Special%3ASearch/Reactome.md deleted file mode 100644 index b45e9f8969..0000000000 --- a/wiki/Special%3ASearch/Reactome.md +++ /dev/null @@ -1,776 +0,0 @@ - - - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=Reactome&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=Reactome&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=Reactome&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=Reactome&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=Reactome&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below **29** results starting with \#**1**. - - - -**Create the page "Reactome" on this -wiki!** See also the search results found. - -## Page title matches - -- - - [News/Reactome User - Survey](/wiki/News/Reactome_User_Survey "News/Reactome User Survey") - - - - - - ...r background and research interests so that we can continue to - improve the Reactome site and tools. - Manager of Reactome Outreach - - - - - - 726 B (115 words) - 22:11, 24 January 2011 - - - -## Page text matches - -- - - [IGS Data - Representation](/wiki/IGS_Data_Representation "IGS Data Representation") - - - - - - xref_analog: Reactome:83524 - - - - - - 17 KB (2,330 words) - 23:34, 8 October 2012 - - - -- - - [News/Reactome User - Survey](/wiki/News/Reactome_User_Survey "News/Reactome User Survey") - - - - - - ...r background and research interests so that we can continue to - improve the Reactome site and tools. - Manager of Reactome Outreach - - - - - - 726 B (115 words) - 22:11, 24 January 2011 - - - -- - - [January 2010 GMOD - Meeting](/wiki/January_2010_GMOD_Meeting "January 2010 GMOD Meeting") - - - - - - \| Reactome \| - http://www.reactome.org - - - - - - 26 KB (3,722 words) - 19:17, 4 September 2013 - - - -- - - [Tripal Working - Group](/wiki/Tripal_Working_Group "Tripal Working Group") - - - - - - \| \[http://www.reactome.org - Reactome\] - - - - - - 1 KB (221 words) - 00:43, 3 October 2012 - - - -- - - [GMOD Evo Hackathon Proposal Supplemental - Information](/wiki/GMOD_Evo_Hackathon_Proposal_Supplemental_Information "GMOD Evo Hackathon Proposal Supplemental Information") - - - - - - ...ons in the past about integrating NBrowse into GMOD. Key personnel - on the Reactome project are also key - personnel on GMOD. Adding genetic network support to - - - - - - 9 KB (1,301 words) - 20:44, 7 July 2010 - - - -- - - [September 2010 GMOD - Meeting](/wiki/September_2010_GMOD_Meeting "September 2010 GMOD Meeting") - - - - - - ...ent resources (\[http://www.ebi.ac.uk/intact/ IntAct\], - \[http://reactome.org - Reactome\], - \[http://www.ebi.ac.uk/chembldb/ ChEMBL\], ...) available using - PSICQUIC. - - - - - - 100 KB (14,725 words) - 17:31, 30 November 2012 - - - -- - - [GSoC](/wiki/GSoC "GSoC") - - - - - - ...\]; \[https://oicr.on.ca/research-portfolio/ OICR\]; - \[http://www.reactome.org - Reactome\]; \[http://www.wormbase.org - WormBase\]; and \[https://bioconda.github.io/ Bioc - \[\[Category%253AReactome\]\] - - - - - - 5 KB (719 words) - 16:07, 12 February 2024 - - - -- - - [GSOC Project Ideas - 2015](/wiki/GSOC_Project_Ideas_2015 "GSOC Project Ideas 2015") - - - - - - \*'''Project Idea 7: Use Galaxy to run - Reactome analysis and processes on - genomic data''' \*\*''Brief explanation:'' - Reactome is a free, open-source, - curated and peer reviewed pathway database. Our goa - - - - - - 16 KB (2,455 words) - 09:10, 23 February 2015 - - - -- - - [GSOC Groups](/wiki/GSOC_Groups "GSOC Groups") - - - - - - ...ormatics Institute. Links: - \[http://www.reactome.org Website\], - \[http://wiki.reactome.org - ReactomeWiki \]. - - - - - - 4 KB (561 words) - 18:02, 19 February 2016 - - - -- - - [SettingUpReactome](/wiki/SettingUpReactome "SettingUpReactome") - - - - - - =Reactome Installation Instructions= - ...site to work, such as Apache and MySQL. The second involves - installing the Reactome data, modules - and web site code. - - - - - - 24 KB (3,874 words) - 14:55, 28 March 2011 - - - -- - - [SupplementaryInformation](/wiki/SupplementaryInformation "SupplementaryInformation") - - - - - - =Supplementary information for - Reactome= ==Installing your own - Reactome== - - - - - - 1 KB (198 words) - 10:50, 12 April 2011 - - - -- - - [PathwaySummaryVisualizationSpec](/wiki/PathwaySummaryVisualizationSpec "PathwaySummaryVisualizationSpec") - - - - - - ...the little arrows. You can see what the old "Sky" looked like - \[http://www.reactome.org/cgi-bin/frontpage?CLASSIC=1 - here\]. A special version of the "Sky", cal ...way. We would like to - provide a more visual overview of the entire set of - Reactome pathways, using visual cues - to tell the user about average expression level - - - - - - 3 KB (448 words) - 13:49, 14 February 2012 - - - -- - - [April 2012 GMOD - Meeting](/wiki/April_2012_GMOD_Meeting "April 2012 GMOD Meeting") - - - - - - \| \[http://www.reactome.org - Reactome\] \* - \[http://reactome.org/ - Reactome\] -- Robin Haw - - - - - - 10 KB (1,319 words) - 18:52, 8 October 2012 - - - -- - - [GSoC 2011](/wiki/GSoC_2011 "GSoC 2011") - - - - - - The Genome Infomatics group is organizing the joint efforts of - WormBase, Reactome, and GBrowse (see - below). This is a great opportunity for students to contr ...ormatics - Institute. Links: - \[http://www.reactome.org Website\], - \[http://wiki.reactome.org - ReactomeWiki \]. - - - - - - 20 KB (2,895 words) - 23:51, 25 July 2012 - - - -- - - [GMOD Online Training - 2014/Schedule](/wiki/GMOD_Online_Training_2014/Schedule "GMOD Online Training 2014/Schedule") - - - - - - ...cr.on.ca/ Ontario Institute for Cancer Research\], - \[http://www.reactome.org - Reactome\]\\[\[GBrowse_syn\]\], - \[\[GBrowse\]\] - - - - - - 3 KB (382 words) - 07:42, 22 May 2014 - - - -- - - [News/GSoC 2013 Mentors - Wanted!](/wiki/News/GSoC_2013_Mentors_Wanted! "News/GSoC 2013 Mentors Wanted!") - - - - - - ...ts: \[\[Galaxy\]\], \[\[GBrowse\]\], '''GMOD''', \[\[JBrowse\]\], - \[http://reactome.org - Reactome\], and \[http://wormbase.org - Wormbase\]. See the \[\[GSoC\|GSoC wiki page\]\] for m - - - - - - 1 KB (180 words) - 13:26, 15 April 2013 - - - -- - - [InterMine Tutorial - 2011](/wiki/InterMine_Tutorial_2011 "InterMine Tutorial 2011") - - - - - - longDescription="For a specified KEGG, - REACTOME or FlyReactome pathway, list - all the genes that are involved for a particul \# template - description - For a specified KEGG, - REACTOME or FlyReactome pathway, list - all the genes that are involved for a particul - - - - - - 43 KB (6,258 words) - 17:56, 14 February 2013 - - - -- - - [GSOC Project Ideas - 2016](/wiki/GSOC_Project_Ideas_2016 "GSOC Project Ideas 2016") - - - - - - \*'''Project Idea 10: Use Galaxy to run - Reactome analysis and processes on - genomic data''' \*\*''Brief explanation:'' - Reactome is a free, open-source, - curated and peer reviewed pathway database. Our goa - - - - - - 28 KB (4,153 words) - 14:34, 8 March 2016 - - - -- - - [GSoC 2013](/wiki/GSoC_2013 "GSoC 2013") - - - - - - ...s group is organizing the joint efforts of Galaxy, GBrowse, GMOD, - JBrowse, Reactome, SeqWare, and - Wormbase (see below). This is a great opportunity for student - ...ormatics Institute. Links: - \[http://www.reactome.org Website\], - \[http://wiki.reactome.org - ReactomeWiki \]. - - - - - - 17 KB (2,555 words) - 19:59, 12 February 2014 - - - -- - - [GSOC Project Ideas - 2017](/wiki/GSOC_Project_Ideas_2017 "GSOC Project Ideas 2017") - - - - - - \*'''1. Project Publication Reference Tracking - (Galaxy/Reactome)''' ...Project, - Johns Hopkins University, clements@galaxyproject.org, Robin Haw, - Reactome, Ontario Institute for - Cancer Research. - - - - - - 18 KB (2,646 words) - 05:18, 16 March 2017 - - - -- - - [GSOC Project Ideas - 2018](/wiki/GSOC_Project_Ideas_2018 "GSOC Project Ideas 2018") - - - - - - \*'''Project Idea 2: Reactome - Javascript Widget for Pathway Browser''' ...ay knowledge. The Pathway - Browser - (https://reactome.org/PathwayBrowser) - is Reactome’s primary means of - viewing and interacting with specific pathways. (a sho - - - - - - 12 KB (1,846 words) - 18:55, 29 January 2018 - - - -- - - [GSOC Project Ideas - 2019](/wiki/GSOC_Project_Ideas_2019 "GSOC Project Ideas 2019") - - - - - - == Use Galaxy to run Reactome - analysis and processes on genomic data - (Reactome) == \*\*''Brief - explanation:'' Reactome is a free, - open-source, curated and peer-reviewed pathway database. Our goa - - - - - - 7 KB (1,064 words) - 15:52, 19 February 2019 - - - -- - - [GSOC Project Ideas - 2020](/wiki/GSOC_Project_Ideas_2020 "GSOC Project Ideas 2020") - - - - - - == Use Galaxy to run Reactome - analysis and processes on genomic data - (Reactome) == \*\*''Brief - explanation:'' Reactome is a free, - open-source, curated and peer-reviewed pathway database. Our goa - - - - - - 20 KB (3,057 words) - 02:14, 19 March 2020 - - - -- - - [GSoD](/wiki/GSoD "GSoD") - - - - - - ...\]; \[https://oicr.on.ca/research-portfolio/ OICR\]; - \[http://www.reactome.org - Reactome\]; \[http://www.wormbase.org - WormBase\]; and \[https://bioconda.github.io/ Bioc Project Name: - Reactome - - - - - - 4 KB (632 words) - 02:38, 7 May 2020 - - - -- - - [GSOC Project Ideas - 2021](/wiki/GSOC_Project_Ideas_2021 "GSOC Project Ideas 2021") - - - - - - \*\*''Project Home Page URL:'' - Reactome.org \*\*''Project Home Page - URL:'' Reactome.org - - - - - - 18 KB (2,539 words) - 18:58, 1 April 2021 - - - -- - - [GSOC Project Ideas - 2022](/wiki/GSOC_Project_Ideas_2022 "GSOC Project Ideas 2022") - - - - - - == Use Galaxy to run Reactome - analysis and processes on proteomics data - (Reactome) == \*''Brief - explanation:'' Reactome is a free, - open-source, curated and peer-reviewed pathway database. Our goa - - - - - - 11 KB (1,658 words) - 18:33, 25 March 2022 - - - -- - - [GSOC Project Ideas - 2023](/wiki/GSOC_Project_Ideas_2023 "GSOC Project Ideas 2023") - - - - - - \* Project Home Page URL: - https://reactome.org, - https://reactome.org/ContentService/ - == Improved Continuous Integration for - Reactome== - - - - - - 9 KB (1,387 words) - 18:23, 16 March 2023 - - - -- - - [GSOC Project Ideas - 2024](/wiki/GSOC_Project_Ideas_2024 "GSOC Project Ideas 2024") - - - - - - ...to predict the effects of perturbations on biological pathways. - Utilizing Reactome's pathway models, - MP-BioPath employs an optimization model. Our objective i \*''Project - Home Page URL:'' - \[https://reactome.org - Reactome\] - \[https://github.com/OICR/mp-biopath MP-BioPath\] - - - - - - 4 KB (580 words) - 16:41, 12 February 2024 - - - - - -View (previous 50 \| next 50) (20 \| 50 \| 100 \| 250 \| 500) - - - - - - - - -## Navigation menu - - - -### Namespaces - -- [Special - page](/wiki/Special%253ASearch/Reactome "This is a special page, you cannot edit the page itself") - - - - - - -### Navigation - - - -- [GMOD Home](/wiki/Main_Page) -- [Software](/wiki/GMOD_Components) -- [Categories / - Tags](/wiki/Categories) -- [View all - pages](/wiki/Special:AllPages) - - - - -### Documentation - - - -- [Overview](/wiki/Overview) -- [FAQs](/wiki/Category%253AFAQ) -- [HOWTOs](/wiki/Category%253AHOWTO) -- [Glossary](/wiki/Glossary) - - - - -### Community - - - -- [GMOD News](/wiki/GMOD_News) -- [Training / - Outreach](/wiki/Training_and_Outreach) -- [Support](/wiki/Support) -- [GMOD - Promotion](/wiki/GMOD_Promotion) -- [Meetings](/wiki/Meetings) -- [Calendar](/wiki/Calendar) - - - - -### Tools - - - - - - - - - - - - - - - - - diff --git a/wiki/Special%3ASearch/SAMtools.md b/wiki/Special%3ASearch/SAMtools.md deleted file mode 100644 index 5acd467ed1..0000000000 --- a/wiki/Special%3ASearch/SAMtools.md +++ /dev/null @@ -1,792 +0,0 @@ - - - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=SAMtools&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=SAMtools&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=SAMtools&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=SAMtools&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=SAMtools&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below **31** results starting with \#**1**. - - - -**Create the page "SAMtools" on this -wiki!** See also the search results found. - -- - - [GBrowse](/wiki/GBrowse "GBrowse") - - - - - - ...ncludes a starting VMware image, and uses the example data that - comes with SAMtools. - - - - - - 11 KB (1,422 words) - 16:47, 10 April 2023 - - - -- - - [GBrowse Ubuntu - HOWTO](/wiki/GBrowse_Ubuntu_HOWTO "GBrowse Ubuntu HOWTO") - - - - - - sudo apt-get install gbrowse gbrowse-calign gbrowse-data - libbio-samtools-perl apache2 - libapache2-mod-fcgid libxml-sax-writer-perl libxml-xpathengine-perl - libyaml-syck-perl samtools - - - - - - 8 KB (799 words) - 20:37, 8 August 2018 - - - -- - - [Glossary](/wiki/Glossary "Glossary") - - - - - - ...e Alignment/Map (SAM)\]\]'' format. BAM and SAM are both part of - \[\[#SAMtools\|SAMtools\]\]. - BAM is compressed, binary, indexed format for \[\[Next Generation - Sequenc ...rmat for \[\[Next Generation Sequencing\]\] data. It is a - part of - \[\[#SAMtools\|SAMtools\]\]. - \[\[GBrowse\]\] 2 has an adaptor that can read SAM data. - - - - - - 14 KB (2,081 words) - 02:50, 14 March 2014 - - - -- - - [GBrowse Adaptors](/wiki/GBrowse_Adaptors "GBrowse Adaptors") - - - - - - \| \[http://samtools.sourceforge.net/ - SAMtools\] - - - - - - 3 KB (443 words) - 16:22, 7 August 2012 - - - -- - - [August 2009 GMOD - Meeting](/wiki/August_2009_GMOD_Meeting "August 2009 GMOD Meeting") - - - - - - ...on next generation sequencing, including - \[http://samtools.sourceforge.net - SAMtools\], BWA, and - \[http://maq.sourceforge.net MAQ\].\ ...: Sequence - alignment/map format (SAM) and - \[http://samtools.sourceforge.net - SAMtools\] - - - - - - 59 KB (8,741 words) - 19:37, 4 September 2013 - - - -- - - [GBrowse Tutorial](/wiki/GBrowse_Tutorial "GBrowse Tutorial") - - - - - - ...des a starting \[\[VMware\]\] image, and uses the example data that - comes with SAMtools. - - - - - - 2 KB (236 words) - 17:10, 18 December 2013 - - - -- - - [News/Aug 2009 GMOD Meeting - Report](/wiki/News/Aug_2009_GMOD_Meeting_Report "News/Aug 2009 GMOD Meeting Report") - - - - - - ...on \[\[August 2009 GMOD Meeting#Visualising NGS Data in GBrowse - 2\|using SAM/SAMtools in GBrowse\]\]. - - - - - - 2 KB (301 words) - 19:37, 4 September 2013 - - - -- - - [News/GMOD Tutorials! GMOD - Training!](/wiki/News/GMOD_Tutorials!_GMOD_Training! "News/GMOD Tutorials! GMOD Training!") - - - - - - ...tion Sequence\]\] Data with \[\[GBrowse\]\] and - \[http://samtools.sourceforge.net - SAMtools\]''' (poster) - - - - - - 4 KB (542 words) - 23:11, 9 October 2012 - - - -- - - [News/GBrowse NGS Tutorial & - Poster](/wiki/News/GBrowse_NGS_Tutorial_%26_Poster "News/GBrowse NGS Tutorial & Poster") - - - - - - ...ep instructions for visualizing the example human data that comes - with the SAMtools package. - - - - - - 1 KB (156 words) - 23:10, 9 October 2012 - - - -- - - [News/NGS Analyses in - Galaxy](/wiki/News/NGS_Analyses_in_Galaxy "News/NGS Analyses in Galaxy") - - - - - - ...ncludes a variety of utilities for SAM/BAM manipulation. Some are - based on SAMtools library, some are - written by \[\[Galaxy\]\] team. - - - - - - 2 KB (239 words) - 23:09, 9 October 2012 - - - -- - - [Next Generation - Sequencing](/wiki/Next_Generation_Sequencing "Next Generation Sequencing") - - - - - - ...rowse\]\] 2 to visualize NGS data using the - \[http://samtools.sourceforge.net - SAMtools\] GBrowse adaptor, - Bio::DB::Sam. This includes a \[\[VMware\]\] image to work w ...) and - SAMtools\|Quest for Standard: - Sequence alignment/map format (SAM) and - SAMtools\]\] - - - - - - 3 KB (450 words) - 00:52, 18 November 2010 - - - -- - - [JBrowse Tutorial - 2010](/wiki/JBrowse_Tutorial_2010 "JBrowse Tutorial 2010") - - - - - - \* samtools, and its dependency - libncurses5-dev \$ wget - http://sourceforge.net/projects/samtools/files/samtools/0.1.7/samtools-0.1.7a.tar.bz2/download - - - - - - 9 KB (1,327 words) - 22:46, 3 October 2012 - - - -- - - [GBrowse NGS - Tutorial](/wiki/GBrowse_NGS_Tutorial "GBrowse NGS Tutorial") - - - - - - ...eration Sequencing\]\] (NGS) data using the - \[http://samtools.sourceforge.net - SAMtools\] GBrowse adaptor, - Bio::DB::Sam. ...urceforge.net - SAMtools\]. We'll use the example - human data that comes with SAMtools - to do that. First we'll load the reference sequence and some gene - models. - - - - - - 38 KB (5,742 words) - 18:11, 9 October 2012 - - - -- - - [ABRF2010 Workshop](/wiki/ABRF2010_Workshop "ABRF2010 Workshop") - - - - - - \*\[http://samtools.sourceforge.net/ - BAM or SAM\] (for sequence alignment data) ...ompact, fast to read - way, as part of the - \[http://samtools.sourceforge.net/ - SAMtools\] project. - - - - - - 17 KB (2,763 words) - 18:52, 8 October 2012 - - - -- - - [September 2010 GMOD - Meeting](/wiki/September_2010_GMOD_Meeting "September 2010 GMOD Meeting") - - - - - - \*\* SQLite, SAMtools (NGS) adaptors - - - - - - 100 KB (14,725 words) - 17:31, 30 November 2012 - - - -- - - [GBrowse 2.0 Install - HOWTO/Advanced](/wiki/GBrowse_2.0_Install_HOWTO/Advanced "GBrowse 2.0 Install HOWTO/Advanced") - - - - - - ...equires the C Samtools library. - See - http://cpansearch.perl.org/src/LDS/Bio-SamTools-1.35/README - for details. - - - - - - 23 KB (3,672 words) - 14:44, 10 July 2013 - - - -- - - [Arthropod Genomics 2011/Genome Project 101 - Workshop](/wiki/Arthropod_Genomics_2011/Genome_Project_101_Workshop "Arthropod Genomics 2011/Genome Project 101 Workshop") - - - - - - Install Samtools ....16.tar.bz2 - http://sourceforge.net/projects/samtools/files/samtools/0.1.16/samtools-0.1.16.tar.bz2/download - - - - - - 15 KB (2,338 words) - 18:52, 8 October 2012 - - - -- - - [News/GMOD in the Cloud 2.0 - Released](/wiki/News/GMOD_in_the_Cloud_2.0_Released "News/GMOD in the Cloud 2.0 Released") - - - - - - \* \[\[GBrowse\]\] 2.54 (with - samtools, BigWig and fastCGI support) - - - - - - 982 B (152 words) - 19:14, 14 June 2013 - - - -- - - [JBrowse Configuration - Guide](/wiki/JBrowse_Configuration_Guide "JBrowse Configuration Guide") - - - - - - Syntax used to import a indexed fasta(i.e. a fasta file where you run - \`samtools faidx yourfile.fa\` which - outputs yourfile.fa.fai) .... Exactly one of these three options must - be used. With indexed_fasta, the - samtools faidx yourfile.fa must be - run before hand. With twobit, the twobit file wil - - - - - - 185 KB (26,536 words) - 02:48, 30 September 2020 - - - -- - - [GBrowse Volvox SAM - Tutorial](/wiki/GBrowse_Volvox_SAM_Tutorial "GBrowse Volvox SAM Tutorial") - - - - - - ...xy\]\] to run Bowtie and produce a SAM file. In order to use this - tutorial, SAMtools and Bio::DB::Sam - must be installed. This is based on the \[\[GBrowse_NGS_Tut - samtools faidx volvox.fa - - - - - - 5 KB (853 words) - 00:19, 23 October 2012 - - - -- - - [JBrowse Tutorial - 2013](/wiki/JBrowse_Tutorial_2013 "JBrowse Tutorial 2013") - - - - - - \* samtools, and its dependency - libncurses5-dev - - - - - - 14 KB (1,948 words) - 20:48, 27 August 2013 - - - -- - - [GBrowse/tool data](/wiki/GBrowse/tool_data "GBrowse/tool data") - - - - - - ...ncludes a starting VMware image, and uses the example data that - comes with SAMtools. - - - - - - 8 KB (1,065 words) - 18:35, 10 September 2013 - - - -- - - [GBrowse Tutorial - 2011](/wiki/GBrowse_Tutorial_2011 "GBrowse Tutorial 2011") - - - - - - ===Updating SAMtools=== The version - of SAMtools may need to be updated. - Get the samtools release: - - - - - - 7 KB (932 words) - 22:50, 13 February 2013 - - - -- - - [JBrowse Tutorial - 2011](/wiki/JBrowse_Tutorial_2011 "JBrowse Tutorial 2011") - - - - - - \* samtools, and its dependency - libncurses5-dev \$ wget - http://sourceforge.net/projects/samtools/files/samtools/0.1.7/samtools-0.1.7a.tar.bz2 - - - - - - 9 KB (1,328 words) - 17:58, 14 February 2013 - - - -- - - [JBrowse FAQ](/wiki/JBrowse_FAQ "JBrowse FAQ") - - - - - - ...ve run prepare-refseqs.pl on a FASTA file. Instead you can simply - use the "samtools faidx" program to - index your fasta file in a data directory, and set trackL To create an - Indexed FASTA, install samtools and - run - - - - - - 65 KB (10,432 words) - 15:23, 16 September 2020 - - - -- - - [GMOD Malaysia 2014/JBrowse - Tutorial](/wiki/GMOD_Malaysia_2014/JBrowse_Tutorial "GMOD Malaysia 2014/JBrowse Tutorial") - - - - - - \* samtools, and its dependency - libncurses5-dev - - - - - - 14 KB (1,931 words) - 00:01, 20 February 2014 - - - -- - - [GMOD Online Training 2014/JBrowse - Tutorial](/wiki/GMOD_Online_Training_2014/JBrowse_Tutorial "GMOD Online Training 2014/JBrowse Tutorial") - - - - - - \* samtools, and its dependency - libncurses5-dev - - - - - - 13 KB (1,905 words) - 14:21, 21 May 2014 - - - -- - - [JBrowse Desktop](/wiki/JBrowse_Desktop "JBrowse Desktop") - - - - - - ...to use Indexed FASTA (selecting both a fasta and a fai file - generated by \`samtools faidx - file.fasta\`) or 2bit. Even small genomes with normal FASTA will be mu - - - - - - 3 KB (528 words) - 22:30, 19 July 2018 - - - -- - - [JBrowse 2 Tutorial PAG - 2022](/wiki/JBrowse_2_Tutorial_PAG_2022 "JBrowse 2 Tutorial PAG 2022") - - - - - - .../doc/bgzip.html \bgzip\\] from the - \\[http://www.htslib.org/ - Samtools\]\ package. The - commands to create these files are: - samtools faidx yourfile.fa.gz - - - - - - 24 KB (4,099 words) - 19:23, 29 January 2022 - - - -- - - [JBrowse2 Tutorial PAG - 2023](/wiki/JBrowse2_Tutorial_PAG_2023 "JBrowse2 Tutorial PAG 2023") - - - - - - ...ed bgzip, tabix, samtools and - minimap2 via apt: \sudo apt-get install - samtools tabix minimap2\. \* - Created a bgzipped and samtools - faidx'ed FASTAs file for ''C. elegans'' and ''C. brenneri''. - - - - - - 34 KB (5,728 words) - 18:21, 23 January 2023 - - - -- - - [JBrowse2 Tutorial PAG - 2024](/wiki/JBrowse2_Tutorial_PAG_2024 "JBrowse2 Tutorial PAG 2024") - - - - - - ...ed bgzip, tabix, samtools and - minimap2 via apt: \sudo apt-get install - samtools tabix minimap2\. \* - Created a bgzipped and samtools - faidx'ed FASTAs file for ''C. elegans'' and ''C. brenneri''. - - - - - - 39 KB (6,446 words) - 03:36, 18 January 2024 - - - - - -View (previous 50 \| next 50) (20 \| 50 \| 100 \| 250 \| 500) - - - - - - - - -## Navigation menu - - - -### Namespaces - -- [Special - page](/wiki/Special%253ASearch/SAMtools "This is a special page, you cannot edit the page itself") - - - - - - -### Navigation - - - -- [GMOD Home](/wiki/Main_Page) -- [Software](/wiki/GMOD_Components) -- [Categories / - Tags](/wiki/Categories) -- [View all - pages](/wiki/Special:AllPages) - - - - -### Documentation - - - -- [Overview](/wiki/Overview) -- [FAQs](/wiki/Category%253AFAQ) -- [HOWTOs](/wiki/Category%253AHOWTO) -- [Glossary](/wiki/Glossary) - - - - -### Community - - - -- [GMOD News](/wiki/GMOD_News) -- [Training / - Outreach](/wiki/Training_and_Outreach) -- [Support](/wiki/Support) -- [GMOD - Promotion](/wiki/GMOD_Promotion) -- [Meetings](/wiki/Meetings) -- [Calendar](/wiki/Calendar) - - - - -### Tools - - - - - - - - - - - - - - - - - diff --git a/wiki/Special%3ASearch/SemanticLink.md b/wiki/Special%3ASearch/SemanticLink.md deleted file mode 100644 index 9c6e6b451d..0000000000 --- a/wiki/Special%3ASearch/SemanticLink.md +++ /dev/null @@ -1,477 +0,0 @@ - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=SemanticLink&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=SemanticLink&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=SemanticLink&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=SemanticLink&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=SemanticLink&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below **22** results starting with \#**1**. - - - - -**Create the page "SemanticLink" -on this wiki!** See also the search results found. - -- - - [BLAST Graphic - Viewer](/wiki/BLAST_Graphic_Viewer "BLAST Graphic Viewer") - - - - - - - - - - 1 KB (175 words) - 01:59, 4 December 2013 - - - -- - - [CMap](/wiki/CMap "CMap") - - - - - - - - - - 7 KB (996 words) - 23:40, 17 October 2013 - - - -- - - [GBrowse](/wiki/GBrowse "GBrowse") - - - - - - - - - - 11 KB (1,422 words) - 16:47, 10 April 2023 - - - -- - - [GO Graphic Viewer](/wiki/GO_Graphic_Viewer "GO Graphic Viewer") - - - - - - - - - - 2 KB (264 words) - 23:44, 3 December 2013 - - - -- - - [Pathway Tools](/wiki/Pathway_Tools "Pathway Tools") - - - - - - - - - - 5 KB (650 words) - 00:07, 16 October 2013 - - - -- - - [BioMart](/wiki/BioMart "BioMart") - - - - - - - - - - 2 KB (228 words) - 22:26, 15 October 2013 - - - -- - - [Textpresso](/wiki/Textpresso "Textpresso") - - - - - - - - - - 5 KB (697 words) - 17:56, 17 October 2013 - - - -- - - [XORT](/wiki/XORT "XORT") - - - - - - - - - - 1 KB (221 words) - 21:22, 16 October 2013 - - - -- - - [Chado](/wiki/Chado "Chado") - - - - - - - - - - 2 KB (238 words) - 22:55, 2 December 2013 - - - -- - - [Galaxy](/wiki/Galaxy "Galaxy") - - - - - - - - - - 6 KB (748 words) - 19:43, 13 December 2018 - - - -- - - [GBrowse syn](/wiki/GBrowse_syn "GBrowse syn") - - - - - - - - - - 6 KB (800 words) - 21:39, 15 October 2013 - - - -- - - [MAKER](/wiki/MAKER "MAKER") - - - - - - - - - - 9 KB (1,211 words) - 21:53, 2 February 2014 - - - -- - - [InterMine](/wiki/InterMine "InterMine") - - - - - - - - - - 4 KB (623 words) - 16:36, 6 November 2014 - - - -- - - [WebApollo2](/wiki/WebApollo2 "WebApollo2") - - - - - - - - - - 3 KB (445 words) - 23:04, 4 January 2016 - - - -- - - [DIYA](/wiki/DIYA "DIYA") - - - - - - - - - - 2 KB (218 words) - 14:58, 17 October 2013 - - - -- - - [JBrowse](/wiki/JBrowse "JBrowse") - - - - - - - - - - 8 KB (1,157 words) - 19:18, 15 April 2016 - - - -- - - [Tripal](/wiki/Tripal "Tripal") - - - - - - - - - - 3 KB (420 words) - 16:33, 29 June 2016 - - - -- - - [WebGBrowse](/wiki/WebGBrowse "WebGBrowse") - - - - - - - - - - 4 KB (530 words) - 21:26, 16 October 2013 - - - -- - - [WebApollo](/wiki/WebApollo "WebApollo") - - - - - - - - - - 4 KB (536 words) - 20:37, 6 April 2015 - - - -- - - [Canto](/wiki/Canto "Canto") - - - - - - - - - - 3 KB (358 words) - 23:11, 18 April 2014 - - - -- - - [GO::TermFinder](/wiki/GO::TermFinder "GO::TermFinder") - - - - - - - - - - 2 KB (267 words) - 02:20, 4 December 2013 - - - -- - - [JBrowse2](/wiki/JBrowse2 "JBrowse2") - - - - - - - - - - 2 KB (268 words) - 22:46, 30 March 2021 - - - - - -View (previous 50 \| next 50) (20 \| 50 \| 100 \| 250 \| 500) - - - - - - - - -## Navigation menu - - - - -### Namespaces - -- [Special - page](/wiki/Special%253ASearch/SemanticLink "This is a special page, you cannot edit the page itself") - - - -### Navigation - - - -- [GMOD Home](/wiki/Main_Page) -- [Software](/wiki/GMOD_Components) -- [Categories / - Tags](/wiki/Categories) -- [View all - pages](/wiki/Special:AllPages) - - - - -### Documentation - - - -- [Overview](/wiki/Overview) -- [FAQs](/wiki/Category%253AFAQ) -- [HOWTOs](/wiki/Category%253AHOWTO) -- [Glossary](/wiki/Glossary) - - - - -### Community - - - -- [GMOD News](/wiki/GMOD_News) -- [Training / - Outreach](/wiki/Training_and_Outreach) -- [Support](/wiki/Support) -- [GMOD - Promotion](/wiki/GMOD_Promotion) -- [Meetings](/wiki/Meetings) -- [Calendar](/wiki/Calendar) - - - - -### Tools - - - - - - - - - - - - - - - diff --git a/wiki/Special%3ASearch/Session.md b/wiki/Special%3ASearch/Session.md deleted file mode 100644 index 2f170e72d8..0000000000 --- a/wiki/Special%3ASearch/Session.md +++ /dev/null @@ -1,1181 +0,0 @@ - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=Session&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=Session&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=Session&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=Session&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=Session&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below up to **50** results starting with \#**1**. - - - - -**Create the page "Session" on this -wiki!** See also the search results found. - -- - - [Hibernate - Presentation](/wiki/Hibernate_Presentation "Hibernate Presentation") - - - - - - \* Create a new Hibernate Session - based on the configuration import - org.hibernate.Session; - - - - - - 12 KB (1,477 words) - 21:16, 9 October 2012 - - - -- - - [News/GCC2013: Register! - Present!](/wiki/News/GCC2013%253A_Register!_Present! "News/GCC2013: Register! Present!") - - - - - - ...ot in the Training Day workshops you want to attend.  Once a - Training Day session becomes full, it - will be closed to new registrations.  Early registration - - - - - - 3 KB (361 words) - 03:37, 25 February 2013 - - - -- - - [Comparison of XORT and Hibernate for Chado - reporting](/wiki/Comparison_of_XORT_and_Hibernate_for_Chado_reporting "Comparison of XORT and Hibernate for Chado reporting") - - - - - - ...le. To get around this we had to explicitly cast the pub object out - of the session cache after we were - done processing it. - - - - - - 9 KB (1,641 words) - 15:48, 12 September 2011 - - - -- - - [Face Caucus UCSC: User Interface - Issues](/wiki/Face_Caucus_UCSC%253A_User_Interface_Issues "Face Caucus UCSC: User Interface Issues") - - - - - - \#\* Session management - - - - - - 893 B (114 words) - 01:37, 29 March 2007 - - - -- - - [January 2007 GMOD meeting - agenda](/wiki/January_2007_GMOD_meeting_agenda "January 2007 GMOD meeting agenda") - - - - - - \| end session/dinner \| tentative - Chado database discussion/tutorial - session - - - - - - 2 KB (295 words) - 15:02, 13 February 2007 - - - -- - - [NIH 2002 Workshop on Model Organism - Databases](/wiki/NIH_2002_Workshop_on_Model_Organism_Databases "NIH 2002 Workshop on Model Organism Databases") - - - - - - After an introductory session, - attendees joined break out working groups, and later reassembled in a - gene - - - - - - 26 KB (3,975 words) - 05:03, 28 January 2008 - - - -- - - [Interface test](/wiki/Interface_test "Interface test") - - - - - - The MOD user interface session - brought to light some very useful - - - - - - 18 KB (2,786 words) - 17:34, 31 January 2008 - - - -- - - [September 2003 GMOD - Meeting](/wiki/September_2003_GMOD_Meeting "September 2003 GMOD Meeting") - - - - - - into a fresh Apollo session or layer - them on top of the currently - - - - - - 28 KB (4,338 words) - 22:06, 29 October 2010 - - - -- - - [April 2004 GMOD - Meeting](/wiki/April_2004_GMOD_Meeting "April 2004 GMOD Meeting") - - - - - - Breakout session for Apollo - developers\ \Q&A session - with curators & Apollo developers\ - - - - - - 42 KB (6,309 words) - 20:37, 30 November 2010 - - - -- - - [MOD Face Talks](/wiki/MOD_Face_Talks "MOD Face Talks") - - - - - - \| end session/dinner \| Chado - database discussion/tutorial session - - - - - - 2 KB (244 words) - 01:35, 29 March 2007 - - - -- - - [Jim's installation - notes](/wiki/Jim%27s_installation_notes "Jim's installation notes") - - - - - - Try installing the CPAN Graphviz again. Need to export in that - session, but then it installs, - following dependencies. Do make images again. Takes - - - - - - 16 KB (2,472 words) - 23:54, 25 January 2008 - - - -- - - [GBrowse Install - HOWTO](/wiki/GBrowse_Install_HOWTO "GBrowse Install HOWTO") - - - - - - :\*CGI::Session (4.03 or higher) - - - - - - 35 KB (5,565 words) - 22:39, 8 August 2012 - - - -- - - [GBrowse Ubuntu - HOWTO](/wiki/GBrowse_Ubuntu_HOWTO "GBrowse Ubuntu HOWTO") - - - - - - libcarp-clan-perl libcgi-session-perl - libclass-c3-perl libclass-c3-xs-perl ...-scf-perl libbit-vector-perl - libbsd-resource-perl libcarp-clan-perl - libcgi-session-perl libclass-c3-perl - libclass-c3-xs-perl libclass-load-perl libclass-load- - - - - - - 8 KB (799 words) - 20:37, 8 August 2018 - - - -- - - [Chado Tutorial 2010](/wiki/Chado_Tutorial_2010 "Chado Tutorial 2010") - - - - - - ...eing the database schema of the GMOD - project. This session introduces - database concepts, provides an overview of Chado's design and ar - ...'ll be working with genome annotation data from the \[\[MAKER - Tutorial\|MAKER session\]\]. We'll - simplify this and start by considering that we have annotation on - - - - - - 54 KB (8,190 words) - 23:34, 8 October 2012 - - - -- - - [Chado Tutorial 2012](/wiki/Chado_Tutorial_2012 "Chado Tutorial 2012") - - - - - - Chado is the database schema of the GMOD project. This - session introduces database concepts, - and then provides an overview of Chado's desi - - - - - - 50 KB (7,599 words) - 16:26, 2 September 2018 - - - -- - - [Apollo PureJDBCTransactionWriter - HOWTO](/wiki/Apollo_PureJDBCTransactionWriter_HOWTO "Apollo PureJDBCTransactionWriter HOWTO") - - - - - - ...timestamped log files in the specified directory for each and every - Apollo session. These log files will - contain a record of all the SQL statements executed ...rs that assign - "temp" ids (which are unique only within the current Apollo - session) that are later replaced by - "permanent" ids (which are unique within the ta - - - - - - 13 KB (1,912 words) - 21:58, 15 September 2009 - - - -- - - [News/GMOD @ ISMB - 2010](/wiki/News/GMOD_@_ISMB_2010 "News/GMOD @ ISMB 2010") - - - - - - ...for a full listing of GMOD related content, including a \[\[ISMB - 2010#Flier\|session listing\]\] you - can print in advance. See the \[http://www.iscb.org/ismb2010 - - - - - - 705 B (100 words) - 23:10, 9 October 2012 - - - -- - - [News/Comparative Genomics - Workshop](/wiki/News/Comparative_Genomics_Workshop "News/Comparative Genomics Workshop") - - - - - - ...eading a session on \[\[Galaxy\]\] - and \[\[User%253AMckays\|Sheldon McKay\]\] leading a - session on \[\[GBrowse_syn\]\]. - - - - - - 1 KB (181 words) - 23:07, 9 October 2012 - - - -- - - [News/GMOD Americas: March - 2011](/wiki/News/GMOD_Americas%253A_March_2011 "News/GMOD Americas: March 2011") - - - - - - ...to GMOD\|Introduction to GMOD\]\]'' - session on the evening of March 4. - This session will be targeted at GMOD - newcomers. - - - - - - 2 KB (229 words) - 23:10, 9 October 2012 - - - -- - - [GBrowse 1 Configuration - HOWTO](/wiki/GBrowse_1_Configuration_HOWTO "GBrowse 1 Configuration HOWTO") - - - - - - ...is higher than the saved version, then GBrowse will reset the - user's page session to its default - values. Use this if you want to reset all users sessions to ; - session driver, - session args - - - - - - 79 KB (12,563 words) - 16:45, 15 August 2011 - - - -- - - [GBrowse Configuration/URL - schema](/wiki/GBrowse_Configuration/URL_schema "GBrowse Configuration/URL schema") - - - - - - The id is a unique session ID that - will store persistent configuration information. You do not typical - The "id" argument is used to associated the upload with a - session. Pick some long, hard to - guess number. This will be associated stably with - - - - - - 8 KB (1,385 words) - 15:45, 6 June 2011 - - - -- - - [GBrowse - Configuration/BioMOBY](/wiki/GBrowse_Configuration/BioMOBY "GBrowse Configuration/BioMOBY") - - - - - - ...k on a configured DETAILS GFF attribute type, and initiate a MOBY - browsing session with information - from that link. Most information is discarded. The only us - - - - - - 9 KB (1,441 words) - 10:45, 9 July 2010 - - - -- - - [GBrowse syn - Configuration](/wiki/GBrowse_syn_Configuration "GBrowse syn Configuration") - - - - - - \| The URL for cached image and - session data - - - - - - 6 KB (815 words) - 19:51, 18 October 2011 - - - -- - - [WebApollo2](/wiki/WebApollo2 "WebApollo2") - - - - - - \*Per-session track configuration to - set annotation colors, height, and other properties - - - - - - 3 KB (445 words) - 23:04, 4 January 2016 - - - -- - - [2008 GMOD Summer - School](/wiki/2008_GMOD_Summer_School "2008 GMOD Summer School") - - - - - - ! style="background-color: \#d6eee4" \| - Session ...s\|Dave\]\], - \[\[User%253AFaga\|Ben\]\], Ed, and '''''You!'''''\
This - ''optional'' session is open to any - and all questions you have on the GMOD Project, GMOD compone - - - - - - 11 KB (1,550 words) - 22:11, 16 April 2014 - - - -- - - [GBrowse syn PAG 2009 - Workshop](/wiki/GBrowse_syn_PAG_2009_Workshop "GBrowse syn PAG 2009 Workshop") - - - - - - The session included - - - - - - 3 KB (454 words) - 21:29, 3 October 2012 - - - -- - - [2009 GMOD Summer School - - Europe](/wiki/2009_GMOD_Summer_School_-_Europe "2009 GMOD Summer School - Europe") - - - - - - ! width="75%" style="background-color: \#99ccff" \| - Session ...running on your machine. - We then built upon that image in each succeeding - session. - - - - - - 10 KB (1,210 words) - 22:13, 16 April 2014 - - - -- - - [August 2009 GMOD - Meeting](/wiki/August_2009_GMOD_Meeting "August 2009 GMOD Meeting") - - - - - - ! width="70%" \| Session - - - - - - 59 KB (8,741 words) - 19:37, 4 September 2013 - - - -- - - [2009 GMOD Summer School - - Americas](/wiki/2009_GMOD_Summer_School_-_Americas "2009 GMOD Summer School - Americas") - - - - - - ! width="93%" style="background-color: \#99ccff" \| - Session ...ssion''' and '''User - Presentations'''\
Everyone\
This ''optional'' - session is open to any and all - questions you have on the \[\[Main Page\|GMOD Project\]\] - - - - - - 11 KB (1,433 words) - 22:13, 16 April 2014 - - - -- - - [ISMB 2008](/wiki/ISMB_2008 "ISMB 2008") - - - - - - \| rowspan="3" \| Poster Session \| - rowspan="3"\|Poster Session - - - - - - 4 KB (534 words) - 01:21, 3 October 2012 - - - -- - - [News/Pathway Tools - Workshop](/wiki/News/Pathway_Tools_Workshop "News/Pathway Tools Workshop") - - - - - - A session at the Cambridge Healthtech - \[http://www.tri-conference.com/08_gdd.asp Pathw - - - - - - 588 B (73 words) - 20:58, 24 January 2011 - - - -- - - [News/GMOD Summer - School](/wiki/News/GMOD_Summer_School "News/GMOD Summer School") - - - - - - ...unning with popular GMOD components. There will also be a - concurrent 1 day session aimed at - principal investigators that will give decision makers an overview - - - - - - 1 KB (163 words) - 23:45, 3 October 2012 - - - -- - - [News/Upcoming Pathway Tools - Tutorial](/wiki/News/Upcoming_Pathway_Tools_Tutorial "News/Upcoming Pathway Tools Tutorial") - - - - - - ...\[http://bioinformatics.ai.sri.com/ptools/tutorial/ Pathway Tools - tutorial session\] from September - 2-5, 2008, at SRI International in Menlo Park, CA. Each da - - - - - - 828 B (116 words) - 21:22, 24 January 2011 - - - -- - - [News/Lepidoptera - Bioinformatics](/wiki/News/Lepidoptera_Bioinformatics "News/Lepidoptera Bioinformatics") - - - - - - A session on data analysis, mining, - general bioinformatics support, and related topic ...g in your own - work. We will then produce a list to be discussed during the - session and focus on soliciting ideas - on how to organize collaborative and centrali - - - - - - 2 KB (258 words) - 23:09, 9 October 2012 - - - -- - - [News/GMOD Tutorials! GMOD - Training!](/wiki/News/GMOD_Tutorials!_GMOD_Training! "News/GMOD Tutorials! GMOD Training!") - - - - - - ...du/courses/c-info09.shtml Programming for Biology\]'''\
This - includes a session on - \[\[GBrowse\]\]. - - - - - - 4 KB (542 words) - 23:11, 9 October 2012 - - - -- - - [GBrowse 2.0 HOWTO](/wiki/GBrowse_2.0_HOWTO "GBrowse 2.0 HOWTO") - - - - - - \# session settings - session lock type = default - - - - - - 101 KB (15,507 words) - 04:44, 9 January 2014 - - - -- - - [January 2009 GMOD - Meeting](/wiki/January_2009_GMOD_Meeting "January 2009 GMOD Meeting") - - - - - - ...ng biology within \[\[Chado\]\] in the same way across - organizations. In this session we - proposed converging on common representations by having organizations - po ...itional discussion during \[\[User%253ASivam\|Dhileep Sivam\]\] and - Isabelle Phan's session on \[\[#Chado - and GUS at SBRI\|Chado and GUS at SBRI\]\]. \[http://dev.isb-sib.c - - - - - - 50 KB (7,612 words) - 18:53, 8 October 2012 - - - -- - - [PAG 2009](/wiki/PAG_2009 "PAG 2009") - - - - - - ! EVEN Numbered Poster Session ! ODD - Numbered Poster Session - - - - - - 10 KB (1,390 words) - 18:16, 2 October 2012 - - - -- - - [Migrating from GBrowse 1.X to - 2.X](/wiki/Migrating_from_GBrowse_1.X_to_2.X "Migrating from GBrowse 1.X to 2.X") - - - - - - ...ific configuration files, static HTML, Javascript and CSS files, - timeouts, session settings and global - appearance settings. It also contains one or more data- - - - - - - 6 KB (983 words) - 06:14, 26 August 2010 - - - -- - - [Running a GBrowse2 render - farm](/wiki/Running_a_GBrowse2_render_farm "Running a GBrowse2 render farm") - - - - - - ...the same prerequisites as the master server, including Bio::Perl, - GD, CGI::Session, JSON, etc. However, - an Apache server is '''not''' needed to run a slave. - - - - - - 16 KB (2,473 words) - 12:08, 12 October 2011 - - - -- - - [GBrowse 2.0 - Prerequisites](/wiki/GBrowse_2.0_Prerequisites "GBrowse 2.0 Prerequisites") - - - - - - libcapture-tiny-perl - libcgi-session-perl libwww-perl - libstatistics-descriptive-perl \\ ...l-GD perl-Module-Build perl-CPAN - perl-IO-String perl-Capture-Tiny - perl-CGI-Session \\ - - - - - - 8 KB (1,147 words) - 21:20, 15 January 2017 - - - -- - - [GBrowse Persistent - Variables](/wiki/GBrowse_Persistent_Variables "GBrowse Persistent Variables") - - - - - - =Session= - ...owser2::Session object containing - information regarding the current user's - session. It contains the following - key-\>value pairs: - - - - - - 7 KB (988 words) - 20:06, 8 October 2012 - - - -- - - [Gbrowse clean.pl](/wiki/Gbrowse_clean.pl "Gbrowse clean.pl") - - - - - - '''-verbose''': Report actions verbosely, printing out each - session, file and directory deleted. - ...tes a number of temporary files during its operations. These files - include session data, data cache - files, and temporary image files, as well as user upload d - - - - - - 3 KB (513 words) - 14:13, 2 November 2009 - - - -- - - [JBrowse Tutorial - 2010](/wiki/JBrowse_Tutorial_2010 "JBrowse Tutorial 2010") - - - - - - === If you didn't follow along in the chado - session === We'll be using the chado - database from the chado session; if - you didn't follow along exactly, re-load the database like so: - - - - - - 9 KB (1,327 words) - 22:46, 3 October 2012 - - - -- - - [MAKER Tutorial 2013](/wiki/MAKER_Tutorial_2013 "MAKER Tutorial 2013") - - - - - - ...he web interface. Web Start will be described in more detail in the - Apollo session. This must be done as - root or using \sudo\. - - - - - - 80 KB (12,961 words) - 23:47, 29 July 2013 - - - -- - - [Artemis-Chado Integration - Tutorial](/wiki/Artemis-Chado_Integration_Tutorial "Artemis-Chado Integration Tutorial") - - - - - - ...d for completeness only and you should refer to the \[\[Chado - Tutorial\|Chado session\]\] for more - details on this. - - - - - - 17 KB (2,626 words) - 23:33, 8 October 2012 - - - -- - - [GBrowse syn PAG 2010 - Workshop](/wiki/GBrowse_syn_PAG_2010_Workshop "GBrowse syn PAG 2010 Workshop") - - - - - - The session will include - - - - - - 2 KB (362 words) - 18:52, 8 October 2012 - - - -- - - [PAG 2010](/wiki/PAG_2010 "PAG 2010") - - - - - - ! rowspan="8" valign="top" \| EVEN Numbered Poster - Session\
Monday\
Jan 11 ! - rowspan="15" valign="top" \| ODD Numbered Poster - Session\Monday\
Jan 11 - - - - - - 13 KB (1,711 words) - 18:17, 2 October 2012 - - - -- - - [January 2010 GMOD - Meeting](/wiki/January_2010_GMOD_Meeting "January 2010 GMOD Meeting") - - - - - - \* REST Hackathon, Strategies SDK, Open Mic - session, Chado on Rails, \* JBrowse, - NoSQL ...ted talk was also excellent and very impressive and I thought - the open mic session was also a great - idea. - - - - - - 26 KB (3,722 words) - 19:17, 4 September 2013 - - - -- - - [2010 GMOD Summer School - - Americas](/wiki/2010_GMOD_Summer_School_-_Americas "2010 GMOD Summer School - Americas") - - - - - - ! width="93%" style="background-color: \#99ccff" \| - Session ...'''Open Discussion''' and - '''User Presentations'''\
Everyone\
This - session is open to any and all - questions you have on the \[\[Main Page\|GMOD Project\]\] - - - - - - 13 KB (1,782 words) - 22:14, 16 April 2014 - - - - - -View (previous 50 \| next 50) (20 \| 50 \| 100 \| 250 \| 500) - - - - - - - - -## Navigation menu - - - - -### Namespaces - -- [Special - page](/wiki/Special%253ASearch/Session "This is a special page, you cannot edit the page itself") - - - -### Navigation - - - -- [GMOD Home](/wiki/Main_Page) -- [Software](/wiki/GMOD_Components) -- [Categories / - Tags](/wiki/Categories) -- [View all - pages](/wiki/Special:AllPages) - - - - -### Documentation - - - -- [Overview](/wiki/Overview) -- [FAQs](/wiki/Category%253AFAQ) -- [HOWTOs](/wiki/Category%253AHOWTO) -- [Glossary](/wiki/Glossary) - - - - -### Community - - - -- [GMOD News](/wiki/GMOD_News) -- [Training / - Outreach](/wiki/Training_and_Outreach) -- [Support](/wiki/Support) -- [GMOD - Promotion](/wiki/GMOD_Promotion) -- [Meetings](/wiki/Meetings) -- [Calendar](/wiki/Calendar) - - - - -### Tools - - - - - - - - - - - - - - - diff --git a/wiki/Special%3ASearch/Social_Media.md b/wiki/Special%3ASearch/Social_Media.md deleted file mode 100644 index 1809aaa802..0000000000 --- a/wiki/Special%3ASearch/Social_Media.md +++ /dev/null @@ -1,479 +0,0 @@ - - - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=Social+Media&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=Social+Media&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=Social+Media&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=Social+Media&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=Social+Media&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below **16** results starting with \#**1**. - - - -**Create the page "Social Media" -on this wiki!** See also the search results found. - -- - - [Galaxy](/wiki/Galaxy "Galaxy") - - - - - - \|linktype=social - media - - - - - - 6 KB (748 words) - 19:43, 13 December 2018 - - - -- - - [2008 GMOD Summer - School](/wiki/2008_GMOD_Summer_School "2008 GMOD Summer School") - - - - - - \| style="background-color: \#d6fff5" align="center" \| - '''Social Hour'''\
Get to know - your fellow GMOD Summer School participants, the i - ...hoolPoster2008Thumb.png\|Media:SummerSchoolPoster2008.pdf\|Poster - 1\]\]\
\[\[Media:SummerSchoolPoster2008.pdf\|Download\]\]\
A poster (US Letter size) announ - - - - - - 11 KB (1,550 words) - 22:11, 16 April 2014 - - - -- - - [JBrowse](/wiki/JBrowse "JBrowse") - - - - - - \|presentations=\* April 2013 - Bio-IT World, Robert Buels: - \[\[Media:JBrowse_bioit_world_apr2013.pdf\|PDF\]\] - ...st 2012 - presentation given as part of the \[\[2012 GMOD Summer - School\]\]: - \[\[Media:JBrowse_gmod_aug2012.pdf\|PDF\]\] - - - - - - 8 KB (1,157 words) - 19:18, 15 April 2016 - - - -- - - [January 2009 GMOD - Meeting](/wiki/January_2009_GMOD_Meeting "January 2009 GMOD Meeting") - - - - - - \|\[\[Media:Jan2009StateOfGMOD.ppt\|PPT\]\], - \[\[#The State of GMOD\|Summary\]\] - \|\[\[Media:Jan2009HelpDesk.pdf\|PDF\]\], - \[\[#GMOD Help Desk\|Summary\]\] - - - - - - 50 KB (7,612 words) - 18:53, 8 October 2012 - - - -- - - [September 2010 GMOD - Meeting](/wiki/September_2010_GMOD_Meeting "September 2010 GMOD Meeting") - - - - - - \| - \[\[Media:TheStateofGMODSept2010.pdf\|PDF\]\], - \[\[#The State of GMOD\|Summary\]\] \| - \[\[Media:HelpDeskSept2010.pdf\|PDF\]\], - \[ftp://ftp.gmod.org/pub/gmod/Meetings/2010/GMOD - - - - - - 100 KB (14,725 words) - 17:31, 30 November 2012 - - - -- - - [Tripal Tutorial (pre version - 0.3b)](/wiki/Tripal_Tutorial_(pre_version_0.3b) "Tripal Tutorial (pre version 0.3b)") - - - - - - \*\*Social Networking \# You need CMS - capabilities (distributed content editing, user management, - social networking... i.e. Drupal) - - - - - - 80 KB (12,830 words) - 20:41, 2 October 2012 - - - -- - - [Tripal Tutorial - (v0.3.1b)](/wiki/Tripal_Tutorial_(v0.3.1b) "Tripal Tutorial (v0.3.1b)") - - - - - - \*\*Social Networking \# You need CMS - capabilities (distributed content editing, user management, - social networking... i.e. Drupal) - - - - - - 92 KB (14,708 words) - 23:27, 5 September 2012 - - - -- - - [News/WormBase Is - Hiring](/wiki/News/WormBase_Is_Hiring "News/WormBase Is Hiring") - - - - - - ...ms, and platforms. You are passionate about trending technology and - social - media and how they might enhance the - scientific process. You can work within the ...nd be receptive to - exchanging ideas via IM, Google Hangouts, Skype, - social - media outlets, conference calls, and - email threads. In short, excellent communica - - - - - - 3 KB (471 words) - 23:49, 9 July 2012 - - - -- - - [Tripal Tutorial - v1.1](/wiki/Tripal_Tutorial_v1.1 "Tripal Tutorial v1.1") - - - - - - \*\*Social Networking - ...ent-management capabilities (distributed content editing, user - management, social networking... i.e. - Drupal) - - - - - - 131 KB (21,091 words) - 21:53, 2 January 2014 - - - -- - - [Tripal Tutorial - (v1.0)](/wiki/Tripal_Tutorial_(v1.0) "Tripal Tutorial (v1.0)") - - - - - - \*\*Social Networking \# You need CMS - capabilities (distributed content editing, user management, - social networking... i.e. Drupal) - - - - - - 99 KB (16,007 words) - 17:43, 12 July 2013 - - - -- - - [GSoC 2011](/wiki/GSoC_2011 "GSoC 2011") - - - - - - Are you passionate about social - media? Do you dream in Pantone? Are - you interested in exploring the clearest wa ...h other members of the - research community. This facility would incorporate - social networking features such as - Facebook's "like" mechanism. - - - - - - 20 KB (2,895 words) - 23:51, 25 July 2012 - - - -- - - [News/GMOD is - tweeting](/wiki/News/GMOD_is_tweeting "News/GMOD is tweeting") - - - - - - \[\[Category%253ASocial - Media\]\] - - - - - - 712 B (116 words) - 21:25, 16 November 2012 - - - -- - - [Tripal Tutorial - 2011](/wiki/Tripal_Tutorial_2011 "Tripal Tutorial 2011") - - - - - - \*\*Social Networking \# You need CMS - capabilities (distributed content editing, user management, - social networking... i.e. Drupal) - - - - - - 80 KB (12,788 words) - 22:37, 14 February 2013 - - - -- - - [GMOD Malaysia 2014/Tripal - Tutorial](/wiki/GMOD_Malaysia_2014/Tripal_Tutorial "GMOD Malaysia 2014/Tripal Tutorial") - - - - - - \*\*Social Networking - ...ent-management capabilities (distributed content editing, user - management, social networking... i.e. - Drupal) - - - - - - 131 KB (21,099 words) - 00:18, 20 February 2014 - - - -- - - [News/Now Hiring JBrowse Lead - Developer](/wiki/News/Now_Hiring_JBrowse_Lead_Developer "News/Now Hiring JBrowse Lead Developer") - - - - - - ...ting offshoots planned, from synthetic biology design aids to - genome-based social networking tools. - These will demand the visualization of more bioinformatic - \*\*Experience with CSS and CSS3 (e.g. responsive layout, - media queries) - - - - - - 4 KB (619 words) - 19:51, 16 February 2021 - - - -- - - [JBrowse2](/wiki/JBrowse2 "JBrowse2") - - - - - - \|linktype=social - media - - - - - - 2 KB (268 words) - 22:46, 30 March 2021 - - - - - -View (previous 50 \| next 50) (20 \| 50 \| 100 \| 250 \| 500) - - - - - - - - -## Navigation menu - - - -### Namespaces - -- [Special - page](/wiki/Special%253ASearch/Social_Media "This is a special page, you cannot edit the page itself") - - - - - - -### Navigation - - - -- [GMOD Home](/wiki/Main_Page) -- [Software](/wiki/GMOD_Components) -- [Categories / - Tags](/wiki/Categories) -- [View all - pages](/wiki/Special:AllPages) - - - - -### Documentation - - - -- [Overview](/wiki/Overview) -- [FAQs](/wiki/Category%253AFAQ) -- [HOWTOs](/wiki/Category%253AHOWTO) -- [Glossary](/wiki/Glossary) - - - - -### Community - - - -- [GMOD News](/wiki/GMOD_News) -- [Training / - Outreach](/wiki/Training_and_Outreach) -- [Support](/wiki/Support) -- [GMOD - Promotion](/wiki/GMOD_Promotion) -- [Meetings](/wiki/Meetings) -- [Calendar](/wiki/Calendar) - - - - -### Tools - - - - - - - - - - - - - - - - - diff --git a/wiki/Special%3ASearch/Software_Engineer.md b/wiki/Special%3ASearch/Software_Engineer.md deleted file mode 100644 index 7997a8e333..0000000000 --- a/wiki/Special%3ASearch/Software_Engineer.md +++ /dev/null @@ -1,429 +0,0 @@ - - - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=Software+Engineer&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=Software+Engineer&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=Software+Engineer&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=Software+Engineer&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=Software+Engineer&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below **13** results starting with \#**1**. - - - -**Create the page "Software -Engineer" on this wiki!** See also the search results found. - -- - - [GMOD Middleware](/wiki/GMOD_Middleware "GMOD Middleware") - - - - - - ...his applies to applications, database schemas, as well as to - middleware, a software ''layer'' that - mediates the exchange of data between the applications and t ...the - development of more effective - software as well as the best use of - the software in practice. Finally, - this study should generate a central reference docume - - - - - - 40 KB (5,672 words) - 21:27, 15 August 2013 - - - -- - - [News/InterMine/BioMart Job @ - FlyBase](/wiki/News/InterMine/BioMart_Job_@_FlyBase "News/InterMine/BioMart Job @ FlyBase") - - - - - - ...forums/forum.php?forum_id=8313 FlyBase is looking for a qualified - software - engineer\] to undertake a project to - deploy the \[\[InterMine\]\] and \[\[BioMart\]\] data ma - - - - - - 1 KB (198 words) - 23:29, 3 October 2012 - - - -- - - [News/Positions @ - JCVI](/wiki/News/Positions_@_JCVI "News/Positions @ JCVI") - - - - - - ...aM309CBtHV%2b%2bLtKWW0PRb6H39%2fWK4hiwgS3QLR6dvwqIVTrFzs%3d - Bioinformatics/Software Engineers - positions\] at the \[http://www.jcvi.org/ J.Craig Venter Institute - Besides working with Galaxy, these positions involve quite a broad - range of software development - opportunities (languages ranging from Perl to Java), while at t - - - - - - 2 KB (238 words) - 23:09, 9 October 2012 - - - -- - - [News/Job Openings at - Georgetown](/wiki/News/Job_Openings_at_Georgetown "News/Job Openings at Georgetown") - - - - - - '''Bioinformatics Engineer''' - ...n.edu/nasonia/ NasoniaBase\] (wasp genome). This person will - implement GMOD software and develop - new query interfaces; develop scripts for automated data retrie - - - - - - 1 KB (159 words) - 21:36, 24 January 2011 - - - -- - - [News/FlyBase Bioinformatics - Engineer](/wiki/News/FlyBase_Bioinformatics_Engineer "News/FlyBase Bioinformatics Engineer") - - - - - - ...ndiana Bloomington, Indiana\] is currently looking for a qualified - software - engineer to help with deploying the - \[http://intermine.org InterMine\] and \[http://bio - - - - - - 1 KB (171 words) - 23:26, 9 October 2012 - - - -- - - [News/Galaxy Project - Hiring](/wiki/News/Galaxy_Project_Hiring "News/Galaxy Project Hiring") - - - - - - ...ral open \[http://bitbucket.org/galaxy/galaxy-central/wiki/job_rc2 - software - engineer and postdoc positions\] with - the \[\[Galaxy\]\] project. Galaxy is looking for - - - - - - 988 B (130 words) - 23:08, 9 October 2012 - - - -- - - [News/SGD and ENCODE DCC - Jobs](/wiki/News/SGD_and_ENCODE_DCC_Jobs "News/SGD and ENCODE DCC Jobs") - - - - - - ...ior Biocurator, Data Wrangler (Bioinformatic Analyst), and Python - Software - Engineer for UI construction. Please - see \[http://goo.gl/m90gf the job advertisement - - - - - - 476 B (67 words) - 00:09, 31 March 2013 - - - -- - - [News/Entagen Bioinformatican - Wanted](/wiki/News/Entagen_Bioinformatican_Wanted "News/Entagen Bioinformatican Wanted") - - - - - - '''Genomics Computational - Biologist/Software - Engineer''' ...en.com) is a leading - provider of specialized software - platforms and custom software - development services to biomedical research and development (R&D) - organizat - - - - - - 2 KB (247 words) - 13:54, 3 May 2011 - - - -- - - [News/WormBase Is - Hiring](/wiki/News/WormBase_Is_Hiring "News/WormBase Is Hiring") - - - - - - ...tario Institute for Cancer Research\] seeks an agile and adaptable - software - engineer with a broad skill set and - an interest in applying it to scientific problem ...rowse. Those from - other non-biological science backgrounds but with strong - software engineering skills will also - be considered. - - - - - - 3 KB (471 words) - 23:49, 9 July 2012 - - - -- - - [News/dictyBase is - Hiring](/wiki/News/dictyBase_is_Hiring "News/dictyBase is Hiring") - - - - - - ...ybase.org/dictybase_jobs.html open position\] for a Bioinformatics - Software - Engineer at \[http://dictybase.org - dictyBase\]. The job involves developing web applic - - - - - - 558 B (77 words) - 23:09, 9 October 2012 - - - -- - - [News/Software Developer - - Phytozome](/wiki/News/Software_Developer_-_Phytozome "News/Software Developer - Phytozome") - - - - - - '''Software Developer 3/4 - - Phytozome - 74226'''\
...an exciting opportunity available for - an experienced Software Developer / - Engineer to support the Phytozome - group. The Phytozome group in the JGI Plant Genom - - - - - - 6 KB (822 words) - 19:16, 16 May 2012 - - - -- - - [News/Open Position At - dictyBase](/wiki/News/Open_Position_At_dictyBase "News/Open Position At dictyBase") - - - - - - ...ybase.org/dictybase_jobs.html open position\] for a Bioinformatics - Software - Engineer at \[http://dictybase.org - dictyBase\].\
- \[\[Category%253ASoftware - Engineer\]\] - - - - - - 443 B (57 words) - 21:22, 4 November 2013 - - - -- - - [News/BBOP Job - Openings](/wiki/News/BBOP_Job_Openings "News/BBOP Job Openings") - - - - - - ==Project Lead- Software Developer - (Berkeley Bioinformatics Open-Source Projects-79548)== ...challenges - of biology, and use these insights to produce robust, flexible - software that empowers researchers in - the biological sciences. This experience will - - - - - - 10 KB (1,399 words) - 19:51, 16 February 2021 - - - - - -View (previous 50 \| next 50) (20 \| 50 \| 100 \| 250 \| 500) - - - - - - - - -## Navigation menu - - - -### Namespaces - -- [Special - page](/wiki/Special%253ASearch/Software_Engineer "This is a special page, you cannot edit the page itself") - - - - - - -### Navigation - - - -- [GMOD Home](/wiki/Main_Page) -- [Software](/wiki/GMOD_Components) -- [Categories / - Tags](/wiki/Categories) -- [View all - pages](/wiki/Special:AllPages) - - - - -### Documentation - - - -- [Overview](/wiki/Overview) -- [FAQs](/wiki/Category%253AFAQ) -- [HOWTOs](/wiki/Category%253AHOWTO) -- [Glossary](/wiki/Glossary) - - - - -### Community - - - -- [GMOD News](/wiki/GMOD_News) -- [Training / - Outreach](/wiki/Training_and_Outreach) -- [Support](/wiki/Support) -- [GMOD - Promotion](/wiki/GMOD_Promotion) -- [Meetings](/wiki/Meetings) -- [Calendar](/wiki/Calendar) - - - - -### Tools - - - - - - - - - - - - - - - - - diff --git a/wiki/Special%3ASearch/Template.md b/wiki/Special%3ASearch/Template.md deleted file mode 100644 index c76fa8ae71..0000000000 --- a/wiki/Special%3ASearch/Template.md +++ /dev/null @@ -1,1079 +0,0 @@ - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=Template&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=Template&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=Template&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=Template&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=Template&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below up to **50** results starting with \#**1**. - - - - -**Create the page "Template" on this -wiki!** See also the search results found. - -- - - [GMOD Middleware](/wiki/GMOD_Middleware "GMOD Middleware") - - - - - - ...utoDBI\]\] interface is autogenerated directly from the Chado - schema using a template adapted from - the \[http://turnkey.sf.net Turnkey\] project. This greatly redu - - - - - - 40 KB (5,672 words) - 21:27, 15 August 2013 - - - -- - - [Main Page](/wiki/Main_Page "Main Page") - - - - - - - - - - 5 KB (651 words) - 18:39, 1 June 2024 - - - -- - - [Apollo-Chado](/wiki/Apollo-Chado "Apollo-Chado") - - - - - - all tables using sqlt and the perl - Template::Toolkit - template, sqlt -f PostgreSQL -t - TTSchema --template - bin/privileges.tmpl modules/nofuncs.sql \| psql - - - - - - 4 KB (635 words) - 18:06, 28 December 2007 - - - -- - - [BLAST Graphic - Viewer](/wiki/BLAST_Graphic_Viewer "BLAST Graphic Viewer") - - - - - - \|use template=yes - - - - - - 1 KB (175 words) - 01:59, 4 December 2013 - - - -- - - [CMap](/wiki/CMap "CMap") - - - - - - \|use template=yes - - - - - - 7 KB (996 words) - 23:40, 17 October 2013 - - - -- - - [GBrowse](/wiki/GBrowse "GBrowse") - - - - - - \|use template=Yes - - - - - - 11 KB (1,422 words) - 16:47, 10 April 2023 - - - -- - - [GMODTools](/wiki/GMODTools "GMODTools") - - - - - - \* \bulkfiles_template.xml\ : documented - template for creating your - project/organism configuration - - - - - - 10 KB (1,496 words) - 23:00, 15 August 2013 - - - -- - - [GO Graphic Viewer](/wiki/GO_Graphic_Viewer "GO Graphic Viewer") - - - - - - \|use template=yes - - - - - - 2 KB (264 words) - 23:44, 3 December 2013 - - - -- - - [BLAST Graphic Viewer/tool - data](/wiki/BLAST_Graphic_Viewer/tool_data "BLAST Graphic Viewer/tool data") - - - - - - - - - - 1 KB (188 words) - 18:37, 10 September 2013 - - - -- - - [Pathway Tools](/wiki/Pathway_Tools "Pathway Tools") - - - - - - - - - - 5 KB (650 words) - 00:07, 16 October 2013 - - - -- - - [Argos](/wiki/Argos "Argos") - - - - - - template/ -- - template information system structure - myorg/ -- template information system - structure - - - - - - 12 KB (1,641 words) - 15:41, 16 July 2012 - - - -- - - [Textpresso](/wiki/Textpresso "Textpresso") - - - - - - \|use template=yes - - - - - - 5 KB (697 words) - 17:56, 17 October 2013 - - - -- - - [XORT](/wiki/XORT "XORT") - - - - - - - - - - 1 KB (221 words) - 21:22, 16 October 2013 - - - -- - - [WebGBrowse/tool - data](/wiki/WebGBrowse/tool_data "WebGBrowse/tool data") - - - - - - - - - - 4 KB (540 words) - 18:31, 10 September 2013 - - - -- - - [Downloads](/wiki/Downloads "Downloads") - - - - - - - - - - 2 KB (236 words) - 08:57, 9 April 2013 - - - -- - - [InterMine - Presentation](/wiki/InterMine_Presentation "InterMine Presentation") - - - - - - \* Template queries pre-computed \*\* - ~40 template queries run per gene - details page - renders in seconds - - - - - - 7 KB (796 words) - 21:16, 9 October 2012 - - - -- - - [SynView](/wiki/SynView "SynView") - - - - - - ...tten to be reasonably generic, and so it may be possible to use - this as a template for creating an - adaptor for any database. - - - - - - 3 KB (374 words) - 18:55, 8 October 2012 - - - -- - - [April 2004 GMOD - Meeting](/wiki/April_2004_GMOD_Meeting "April 2004 GMOD Meeting") - - - - - - Apollo, to be used with chado. Addtionally, - template based web front end for - - - - - - 42 KB (6,309 words) - 20:37, 30 November 2010 - - - -- - - [Chado Library - Module](/wiki/Chado_Library_Module "Chado Library Module") - - - - - - \* cDNA: DNA synthesized by reverse transcriptase using RNA as a - template. - - - - - - 11 KB (1,556 words) - 04:36, 18 February 2015 - - - -- - - [Chado Tables](/wiki/Chado_Tables "Chado Tables") - - - - - - General properties about an array. An array is a - template used to generate physical - slides, etc. It contains layout information, as w - - - - - - 121 KB (17,433 words) - 21:13, 2 November 2012 - - - -- - - [Chado Mage Module](/wiki/Chado_Mage_Module "Chado Mage Module") - - - - - - General properties about an array. An array is a - template used to generate physical - slides, etc. It contains layout information, as w - - - - - - 31 KB (4,363 words) - 23:33, 8 October 2012 - - - -- - - [Chado Tables to - Wiki](/wiki/Chado_Tables_to_Wiki "Chado Tables to Wiki") - - - - - - ...Chado Tables page\]\], where all links are internal to the page) - and another template to create table - documentation for a module (e.g. \[\[Chado_Organism_Module\|Ch - - - - - - 2 KB (366 words) - 21:27, 10 December 2010 - - - -- - - [Chado Best - Practices](/wiki/Chado_Best_Practices "Chado Best Practices") - - - - - - ...tes when the insertion is absent, 1 if present, and -1 (?) to link - to the "template" -- generic - representation of the transposon? - - - - - - 30 KB (4,629 words) - 08:47, 16 April 2013 - - - -- - - [Jim's installation - notes](/wiki/Jim%27s_installation_notes "Jim's installation notes") - - - - - - ABW/Template-Toolkit-2.18.tar.gz : - install NO - - - - - - 16 KB (2,472 words) - 23:54, 25 January 2008 - - - -- - - [Zheng's installation - notes](/wiki/Zheng%27s_installation_notes "Zheng's installation notes") - - - - - - \*create PL language, template, - several roles - \[http://search.cpan.org/~abw/Template-Toolkit-2.18/lib/Template.pm - Template\] (chado) - - - - - - 7 KB (1,034 words) - 05:56, 28 January 2008 - - - -- - - [Databases and GMOD](/wiki/Databases_and_GMOD "Databases and GMOD") - - - - - - ...ustom data. A web application allows creation of custom queries, - includes template queries (web forms - to run 'canned' queries) and can upload and operate on l - - - - - - 9 KB (1,355 words) - 22:31, 25 March 2014 - - - -- - - [Chado Tutorial 2012](/wiki/Chado_Tutorial_2012 "Chado Tutorial 2012") - - - - - - - - - - 50 KB (7,599 words) - 16:26, 2 September 2018 - - - -- - - [Galaxy](/wiki/Galaxy "Galaxy") - - - - - - \|use template=Yes - - - - - - 6 KB (748 words) - 19:43, 13 December 2018 - - - -- - - [TableEdit](/wiki/TableEdit "TableEdit") - - - - - - \$template = "Gene_allele_table"; - echo "\$page_name\t \$template\n"; - - - - - - 8 KB (1,315 words) - 18:12, 9 October 2012 - - - -- - - [Hackathon wikidb](/wiki/Hackathon_wikidb "Hackathon wikidb") - - - - - - \*\*\* wikiloader to add to create gene page, select gene page/table - template, add gene wiki-string; Jim - ...adata (not displayed) that middleware can use to format data for - each wiki template. Example templates - are found from a wiki via Special,All Pages, category - - - - - - 4 KB (660 words) - 01:23, 10 December 2009 - - - -- - - [GMOD News](/wiki/GMOD_News "GMOD News") - - - - - - \# '''Once you have added the NewsItem - template and saved the page, try to - avoid editing the page after that.''' - - - - - - 4 KB (627 words) - 19:40, 13 December 2018 - - - -- - - [News/InterMine Workshop 15-16 - Nov](/wiki/News/InterMine_Workshop_15-16_Nov "News/InterMine Workshop 15-16 Nov") - - - - - - ...rying any data is easily customisable. It provides a custom query - builder, template queries for - creating simple 'canned queries', upload and operations on list - - - - - - 2 KB (283 words) - 23:12, 9 October 2012 - - - -- - - [News/InterMine 0.94.1 - Release](/wiki/News/InterMine_0.94.1_Release "News/InterMine 0.94.1 Release") - - - - - - \* template queries with optional - constraints \* selection of multiple values in - template query constraints - - - - - - 1 KB (167 words) - 23:12, 9 October 2012 - - - -- - - [GMOD Online Training 2014/WebApollo - Tutorial](/wiki/GMOD_Online_Training_2014/WebApollo_Tutorial "GMOD Online Training 2014/WebApollo Tutorial") - - - - - - - - - - 77 KB (11,812 words) - 00:39, 21 May 2014 - - - -- - - [Installing Chado on Ubuntu - HOWTO](/wiki/Installing_Chado_on_Ubuntu_HOWTO "Installing Chado on Ubuntu HOWTO") - - - - - - \*libtemplate-perl -- Template - toolkit - - - - - - 3 KB (494 words) - 16:37, 12 July 2013 - - - -- - - [Site Guidelines](/wiki/Site_Guidelines "Site Guidelines") - - - - - - ...erated by feeding the information on the \tool_data\ - page through a template. To edit what - appears on the component page, you need to edit the correspon The - value can be formatted wiki text or a wiki - template, and may span numerous - lines. For example: - - - - - - 16 KB (2,420 words) - 23:18, 8 November 2013 - - - -- - - [GBrowse syn](/wiki/GBrowse_syn "GBrowse syn") - - - - - - - - - - 6 KB (800 words) - 21:39, 15 October 2013 - - - -- - - [MAKER](/wiki/MAKER "MAKER") - - - - - - \|use template=yes - - - - - - 9 KB (1,211 words) - 21:53, 2 February 2014 - - - -- - - [GMODTools TestCase](/wiki/GMODTools_TestCase "GMODTools TestCase") - - - - - - This is an abbreviated example, current as of May 2008. It uses a - Chado-db template in Postgres, and - assumes you have installed/tested GMOD components availabl \# create - GMOD Bulkfiles conf/bulkfiles/anogam.xml from - template.xml : dbname, etc. edits - - - - - - 2 KB (338 words) - 17:03, 20 June 2008 - - - -- - - [GBrowse 1 Configuration - HOWTO](/wiki/GBrowse_1_Configuration_HOWTO "GBrowse 1 Configuration HOWTO") - - - - - - ...se page at strategic places. Eventually this will be replaced with - an HTML template system, but for now, - this is the best we have. - - - - - - 79 KB (12,563 words) - 16:45, 15 August 2011 - - - -- - - [InterMine](/wiki/InterMine "InterMine") - - - - - - ...lists with graphs and enrichment statistics. An admin user can - publish new template queries, change - report pages and create public lists at any time without an \|use - template=No - - - - - - 4 KB (623 words) - 16:36, 6 November 2014 - - - -- - - [WebApollo2](/wiki/WebApollo2 "WebApollo2") - - - - - - \|use template=Yes - - - - - - 3 KB (445 words) - 23:04, 4 January 2016 - - - -- - - [2008 GMOD Summer - School](/wiki/2008_GMOD_Summer_School "2008 GMOD Summer School") - - - - - - - - - - 11 KB (1,550 words) - 22:11, 16 April 2014 - - - -- - - [GBrowse syn PAG 2009 - Workshop](/wiki/GBrowse_syn_PAG_2009_Workshop "GBrowse syn PAG 2009 Workshop") - - - - - - - - - - 3 KB (454 words) - 21:29, 3 October 2012 - - - -- - - [BioDIG/tool data](/wiki/BioDIG/tool_data "BioDIG/tool data") - - - - - - - - - - 2 KB (278 words) - 19:05, 10 September 2013 - - - -- - - [DIYA](/wiki/DIYA "DIYA") - - - - - - \|use template=yes - - - - - - 2 KB (218 words) - 14:58, 17 October 2013 - - - -- - - [Chado Documentation - Reorganization](/wiki/Chado_Documentation_Reorganization "Chado Documentation Reorganization") - - - - - - ...ction of user installation/experience logs would be darn useful. - Create a template for this that - encourages users to list things like versions used. This red \| - \[\[Template:ChadoModules\]\] - - - - - - 7 KB (1,015 words) - 22:30, 29 December 2010 - - - -- - - [Debian Stable Installation - Notes](/wiki/Debian_Stable_Installation_Notes "Debian Stable Installation Notes") - - - - - - Template - - - - - - 8 KB (1,270 words) - 06:14, 25 September 2009 - - - -- - - [GMOD Schools](/wiki/GMOD_Schools "GMOD Schools") - - - - - - - - - - 2 KB (250 words) - 22:22, 16 April 2014 - - - -- - - [JBrowse](/wiki/JBrowse "JBrowse") - - - - - - \|use template=Yes - - - - - - 8 KB (1,157 words) - 19:18, 15 April 2016 - - - - - -View (previous 50 \| next 50) (20 \| 50 \| 100 \| 250 \| 500) - - - - - - - - -## Navigation menu - - - - -### Namespaces - -- [Special - page](/wiki/Special%253ASearch/Template "This is a special page, you cannot edit the page itself") - - - -### Navigation - - - -- [GMOD Home](/wiki/Main_Page) -- [Software](/wiki/GMOD_Components) -- [Categories / - Tags](/wiki/Categories) -- [View all - pages](/wiki/Special:AllPages) - - - - -### Documentation - - - -- [Overview](/wiki/Overview) -- [FAQs](/wiki/Category%253AFAQ) -- [HOWTOs](/wiki/Category%253AHOWTO) -- [Glossary](/wiki/Glossary) - - - - -### Community - - - -- [GMOD News](/wiki/GMOD_News) -- [Training / - Outreach](/wiki/Training_and_Outreach) -- [Support](/wiki/Support) -- [GMOD - Promotion](/wiki/GMOD_Promotion) -- [Meetings](/wiki/Meetings) -- [Calendar](/wiki/Calendar) - - - - -### Tools - - - - - - - - - - - - - - - diff --git a/wiki/Special%3ASearch/Tools_using_GMOD.md b/wiki/Special%3ASearch/Tools_using_GMOD.md deleted file mode 100644 index 408d1f09d8..0000000000 --- a/wiki/Special%3ASearch/Tools_using_GMOD.md +++ /dev/null @@ -1,1230 +0,0 @@ - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=Tools+using+GMOD&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=Tools+using+GMOD&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=Tools+using+GMOD&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=Tools+using+GMOD&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=Tools+using+GMOD&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below up to **50** results starting with \#**1**. - - - - -**Create the page "Tools using -GMOD" on this wiki!** See also the search results found. - -- - - [GMOD Middleware](/wiki/GMOD_Middleware "GMOD Middleware") - - - - - - ...ed notes from the ''Chado Middleware Bake Off'' held at the - \[\[January 2007 GMOD Meeting\]\]. - Although GMOD uses the \[\[Chado\]\] - \[\[Glossary#Schema\|schema\]\] for its underlying database, - - - - - - 40 KB (5,672 words) - 21:27, 15 August 2013 - - - -- - - [Hibernate - Presentation](/wiki/Hibernate_Presentation "Hibernate Presentation") - - - - - - \* GMOD Demo \*\* Search Engine and - Indexer using Lucene - - - - - - 12 KB (1,477 words) - 21:16, 9 October 2012 - - - -- - - [Main Page](/wiki/Main_Page "Main Page") - - - - - - \GMOD - is Social\ ...ht\|link=http://twitter.com/gmodproject\|It's a - bird! It's a plane! It's the GMOD - project on Twitter!\]\] - - - - - - 5 KB (651 words) - 18:39, 1 June 2024 - - - -- - - [GMOD Developer's - Guide](/wiki/GMOD_Developer%27s_Guide "GMOD Developer's Guide") - - - - - - This is the GMOD Developer's Guide. \* - \$GMOD_HOME=\/usr/local/gmod/\ - (default -- set before installing) - - - - - - 6 KB (985 words) - 05:18, 28 January 2008 - - - -- - - [Chado - Getting - Started](/wiki/Chado_-_Getting_Started "Chado - Getting Started") - - - - - - ...abase Schema\|relational database schema\]\] that underlies - \[\[GMOD_Users\|many GMOD - installations\]\]. It is capable of representing many of the general - classes ...u'll probably get the best support by choosing Unix. (See - \[\[Databases and GMOD\]\] for more - discussion.) Once you've installed your RDBMS you can install C - - - - - - 3 KB (469 words) - 18:08, 13 February 2014 - - - -- - - [CMap](/wiki/CMap "CMap") - - - - - - ...genetic, etc.) from any number of species. The CMap package also - includes tools for curating map data. - ...\* \[\[File:CMapGenomeInformatics2009.pdf\|Genome Visualization and - Comparison using CMap and Circos\]\], - poster from \[http://meetings.cshl.edu/meetings/info09.sh - - - - - - 7 KB (996 words) - 23:40, 17 October 2013 - - - -- - - [GMODTools](/wiki/GMODTools "GMODTools") - - - - - - ...ta releases on a regular basis. It produces all the contents needed - for a GMOD \[\[Standard URL\]\] - genome data download folder. Why use this package rather than - using other - \[\[:Category%253AMiddleware\|middleware layers\]\] to Chado db - - \[\[Chado XML\] - - - - - - 10 KB (1,496 words) - 23:00, 15 August 2013 - - - -- - - [Software Testing - Recommendations](/wiki/Software_Testing_Recommendations "Software Testing Recommendations") - - - - - - ...eone new to GMOD development will - have a good idea of a recommended set of - tools and practices that one should - employ to develop reliable software. - \[\[Category%253AGMOD Developers\]\] - - - - - - 819 B (126 words) - 17:14, 5 April 2007 - - - -- - - [Summary of Fall 2005 CHSL - Meeting](/wiki/Summary_of_Fall_2005_CHSL_Meeting "Summary of Fall 2005 CHSL Meeting") - - - - - - ==GMOD Architecture Work Group - Discussion (Fall 2005 meeting)== Brain O'Connor agreed on trying out - some tools for interfaces testing. - Http::Unit, Apache::Test were suggested at the meet - - - - - - 2 KB (257 words) - 15:02, 13 February 2007 - - - -- - - [GenoGrid](/wiki/GenoGrid "GenoGrid") - - - - - - ...infrastructure. One emphasis here is on simplified use of grids and - genome tools, to make it feasible for - new genome projects to take advantage of these rea - http://gmod.cvs.sourceforge.net/gmod/genogrid/ - - - - - - 784 B (98 words) - 05:02, 5 September 2007 - - - -- - - [Pathway Tools](/wiki/Pathway_Tools "Pathway Tools") - - - - - - \ - - diff --git a/wiki/Special%3ASearch/Tutorial.md b/wiki/Special%3ASearch/Tutorial.md deleted file mode 100644 index 165515a1df..0000000000 --- a/wiki/Special%3ASearch/Tutorial.md +++ /dev/null @@ -1,2227 +0,0 @@ - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=Tutorial&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=Tutorial&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=Tutorial&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=Tutorial&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=Tutorial&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below up to **50** results starting with \#**1**. - - - - -**Create the page "Tutorial" on this -wiki!** See also the search results found. - -## Page title matches - -- - - [Tripal Tutorial](/wiki/Tripal_Tutorial "Tripal Tutorial") - - - - - - \#REDIRECT \[\[Tripal Tutorial - v1.1\]\] - - - - - - 97 B (10 words) - 17:44, 12 July 2013 - - - -- - - [Chado Tutorial 2010](/wiki/Chado_Tutorial_2010 "Chado Tutorial 2010") - - - - - - This - \[\[:Category%253ATutorials\|tutorial\]\] - walks you through how to install and configure a \[\[Chado\]\] - database, Chad ...this course you'll be working with genome annotation - data from the \[\[MAKER - Tutorial\|MAKER session\]\]. We'll - simplify this and start by considering that we have - - - - - - 54 KB (8,190 words) - 23:34, 8 October 2012 - - - -- - - [Chado Tutorial 2012](/wiki/Chado_Tutorial_2012 "Chado Tutorial 2012") - - - - - - This \[\[Has topic::Chado\]\] - tutorial was presented by - \[\[User%253AScott\|Scott Cain\]\] as part of the \[\[2012 GMOD Summe - - - - - - 50 KB (7,599 words) - 16:26, 2 September 2018 - - - -- - - [GMOD Online Training 2014/WebApollo - Tutorial](/wiki/GMOD_Online_Training_2014/WebApollo_Tutorial "GMOD Online Training 2014/WebApollo Tutorial") - - - - - - - - - - 77 KB (11,812 words) - 00:39, 21 May 2014 - - - -- - - [GBrowse syn - Tutorial](/wiki/GBrowse_syn_Tutorial "GBrowse syn Tutorial") - - - - - - \#redirect \[\[GBrowse syn Tutorial - 2013\]\] - - - - - - 117 B (12 words) - 16:02, 22 July 2013 - - - -- - - [GBrowse Tutorial](/wiki/GBrowse_Tutorial "GBrowse Tutorial") - - - - - - ; \[\[GBrowse Tutorial 2012\|GBrowse - tutorial from 2013 GMOD Summer - School\]\] : This tutorial was taught - by \[\[User%253AScott\|Scott Cain\]\] at the \[\[2013 GMOD Summer - School\]\] - - - - - - 2 KB (236 words) - 17:10, 18 December 2013 - - - -- - - [News/GBrowse Tutorial at PAG - XVI](/wiki/News/GBrowse_Tutorial_at_PAG_XVI "News/GBrowse Tutorial at PAG XVI") - - - - - - ...ce (PAG-XVI)\], January 12-16, 2008, in San Diego. This will be a - hands-on tutorial on how to install - and use the \[\[GBrowse\]\] genome browser. If you are atten See the - \[http://www.intl-pag.org/16/16-gbrowse.html PAG - tutorial page\] for additional - information. - - - - - - 515 B (77 words) - 20:55, 24 January 2011 - - - -- - - [News/Upcoming Pathway Tools - Tutorial](/wiki/News/Upcoming_Pathway_Tools_Tutorial "News/Upcoming Pathway Tools Tutorial") - - - - - - ...ll hold a - \[http://bioinformatics.ai.sri.com/ptools/tutorial/ - Pathway Tools tutorial session\] from - September 2-5, 2008, at SRI International in Menlo Park, CA. ...e see - the - \[http://bioinformatics.ai.sri.com/ptools/tutorial/ - Pathway Tools Tutorial page\] for a - detailed schedule, registration information, and other details. - - - - - - 828 B (116 words) - 21:22, 24 January 2011 - - - -- - - [News/Pathway Tools Tutorial in - London](/wiki/News/Pathway_Tools_Tutorial_in_London "News/Pathway Tools Tutorial in London") - - - - - - ...tutorial\] well be held September - 22-23, 2008 at Kings College London. This - tutorial is kindly hosted by the - \[http://www.kcl.ac.uk/schools/pse/bioinform/ Centre The - tutorial is free of charge. - - - - - - 1 KB (194 words) - 21:26, 24 January 2011 - - - -- - - [News/GBrowse User - Tutorial](/wiki/News/GBrowse_User_Tutorial "News/GBrowse User Tutorial") - - - - - - ...released by \[http://www.openhelix.com OpenHelix\] this week. The - narrated tutorial covers: The - tutorial also includes - \[http://www.openhelix.com/downloads/gbrowse/gbrowseslidesDL.s - - - - - - 2 KB (268 words) - 23:07, 9 October 2012 - - - -- - - [News/GBrowse NGS Tutorial & - Poster](/wiki/News/GBrowse_NGS_Tutorial_%26_Poster "News/GBrowse NGS Tutorial & Poster") - - - - - - \[\[File:BA2009Logo.png\|link=GBrowse NGS - Tutorial\|100px\|right\|GBrowse NGS - Tutorial\]\] ...the - \[\[BA2009\|Bioinformatics Australia 2009 (BA2009) GMOD Workshop\]\]. - The tutorial includes a - \[\[VMware\]\] image to work with and step-by-step instructions for - - - - - - 1 KB (156 words) - 23:10, 9 October 2012 - - - -- - - [GFF3 2011 tutorial](/wiki/GFF3_2011_tutorial "GFF3 2011 tutorial") - - - - - - ...tutorial/tutorial.html?content-type=text%2Fhtml - The GBrowse Administration Tutorial\] - for more information. - ...-Browser/docs/tutorial/tutorial.html?pathrev=stable - GBrowse Administration Tutorial\]. - - - - - - 16 KB (2,387 words) - 22:13, 11 February 2014 - - - -- - - [MAKER Tutorial](/wiki/MAKER_Tutorial "MAKER Tutorial") - - - - - - \#REDIRECT \[\[MAKER Tutorial - 2013\]\] - - - - - - 76 B (7 words) - 23:34, 29 July 2013 - - - -- - - [WebApollo Tutorial](/wiki/WebApollo_Tutorial "WebApollo Tutorial") - - - - - - \#REDIRECT \[\[WebApollo Tutorial - 2013\]\] - - - - - - 84 B (7 words) - 23:35, 29 July 2013 - - - -- - - [JBrowse Tutorial - 2010](/wiki/JBrowse_Tutorial_2010 "JBrowse Tutorial 2010") - - - - - - This - \[\[:Category%253ATutorials\|tutorial\]\] - walks you through setting up and running a \[\[JBrowse\]\] server. - ...latfile-to-json.pl\. We'll use some more of the data from the - \[\[MAKER Tutorial\|MAKER - session\]\]: - - - - - - 9 KB (1,327 words) - 22:46, 3 October 2012 - - - -- - - [JBrowse Tutorial - 2012](/wiki/JBrowse_Tutorial_2012 "JBrowse Tutorial 2012") - - - - - - \#REDIRECT \[\[JBrowse Tutorial - 2013\]\] - - - - - - 112 B (10 words) - 16:02, 22 July 2013 - - - -- - - [MAKER Tutorial 2013](/wiki/MAKER_Tutorial_2013 "MAKER Tutorial 2013") - - - - - - If you're following this tutorial - outside of the course you can copy the example files to the - \example1_dm ...discuss these options in more detail later on. if - you are following this tutorial - outside of class adjust the following values in a text editor. - - - - - - 80 KB (12,961 words) - 23:47, 29 July 2013 - - - -- - - [Artemis-Chado Integration - Tutorial](/wiki/Artemis-Chado_Integration_Tutorial "Artemis-Chado Integration Tutorial") - - - - - - This - \[\[:Category%253ATutorials\|tutorial\]\] - walks you through how to use the Artemis annotation editor with a - \[\[Chado ...this is included for completeness only and you should - refer to the \[\[Chado - Tutorial\|Chado session\]\] for more - details on this. - - - - - - 17 KB (2,626 words) - 23:33, 8 October 2012 - - - -- - - [Galaxy Tutorial](/wiki/Galaxy_Tutorial "Galaxy Tutorial") - - - - - - \#REDIRECT \[\[Galaxy Tutorial - 2013\]\] - - - - - - 78 B (7 words) - 23:35, 29 July 2013 - - - -- - - [Apollo Tutorial](/wiki/Apollo_Tutorial "Apollo Tutorial") - - - - - - \#REDIRECT \[\[Apollo Tutorial - 2011\]\] - - - - - - 78 B (7 words) - 22:30, 12 February 2013 - - - -- - - [Chado Tutorial](/wiki/Chado_Tutorial "Chado Tutorial") - - - - - - \#REDIRECT \[\[Chado Tutorial - 2013\]\] - - - - - - 76 B (7 words) - 15:52, 17 July 2013 - - - -- - - [BioMart Tutorial](/wiki/BioMart_Tutorial "BioMart Tutorial") - - - - - - - - - - 199 B (27 words) - 21:41, 2 October 2012 - - - -- - - [JBrowse Tutorial](/wiki/JBrowse_Tutorial "JBrowse Tutorial") - - - - - - \#REDIRECT \[\[JBrowse Tutorial - 2013\]\] - - - - - - 80 B (7 words) - 23:35, 29 July 2013 - - - -- - - [GBrowse NGS - Tutorial](/wiki/GBrowse_NGS_Tutorial "GBrowse NGS Tutorial") - - - - - - This - \[\[:Category%253ATutorials\|tutorial\]\] - walks you through how to configure the \[\[GBrowse\]\] genome browser - to disp This tutorial was taught - using a \[\[VMware\]\] system image as a starting point. If you wan - - - - - - 38 KB (5,742 words) - 18:11, 9 October 2012 - - - -- - - [Gbrowse tutorial](/wiki/Gbrowse_tutorial "Gbrowse tutorial") - - - - - - \#REDIRECT \[\[GBrowse Tutorial\]\] - - - - - - 30 B (3 words) - 19:49, 22 October 2009 - - - -- - - [MWAS Tutorial](/wiki/MWAS_Tutorial "MWAS Tutorial") - - - - - - - - - - 34 KB (5,308 words) - 22:03, 3 October 2012 - - - -- - - [GBrowse syn PAG - tutorial](/wiki/GBrowse_syn_PAG_tutorial "GBrowse syn PAG tutorial") - - - - - - ...stall and configure the \[\[GBrowse_syn\]\] comparative genomics - viewer. This tutorial was originally - taught by \[\[User%253AMckays\|Sheldon McKay\]\] at the 2009 \[\[GMOD S \| - valign="top" \|This tutorial was - taught using a \[\[VMware\]\] system image as a starting point. If you - wan - - - - - - 19 KB (2,507 words) - 18:53, 8 October 2012 - - - -- - - [News/Pathway Tools Flux Balance - Tutorial](/wiki/News/Pathway_Tools_Flux_Balance_Tutorial "News/Pathway Tools Flux Balance Tutorial") - - - - - - A remote online attendance option for the - tutorial is available. - - - - - - 1,011 B (149 words) - 05:24, 5 May 2011 - - - -- - - [Apollo Tutorial - 2011](/wiki/Apollo_Tutorial_2011 "Apollo Tutorial 2011") - - - - - - There's a roughly written tutorial on - how to create your own data adapter. It covers some information on the - - - - - - 34 KB (5,242 words) - 00:21, 14 February 2013 - - - -- - - [Tripal Tutorial (pre version - 0.3b)]( "Tripal Tutorial (pre version 0.3b)") - - - - - - '''The most recent version of this - tutorial is available at the - \[\[Tripal Tutorial\]\] page.''' - ...ent in the screen shots but will appear in the live version. - However, the tutorial is still quite - useful for learning to use Tripal v0.3b. - - - - - - 80 KB (12,830 words) - 20:41, 2 October 2012 - - - -- - - [SOBA Tutorial](/wiki/SOBA_Tutorial "SOBA Tutorial") - - - - - - \#REDIRECT \[\[SOBA Tutorial 2012\]\] - - - - - - 74 B (7 words) - 23:37, 29 July 2013 - - - -- - - [GBrowse syn Tutorial - new](/wiki/GBrowse_syn_Tutorial_new "GBrowse syn Tutorial new") - - - - - - - - - - 21 KB (2,890 words) - 22:24, 3 October 2012 - - - -- - - [GBrowse syn AGS - Tutorial](/wiki/GBrowse_syn_AGS_Tutorial "GBrowse syn AGS Tutorial") - - - - - - - - - - 23 KB (3,325 words) - 20:52, 3 October 2012 - - - -- - - [Tripal Tutorial - (v0.3.1b)]( "Tripal Tutorial (v0.3.1b)") - - - - - - ...for your server you will need to manually convert the paths shown - in this tutorial to wherever your - Apache document root may reside. ...When possible, alternative - command-line statements have been added to this - tutorial as users of other Linux - version have provided feedback. Unless specificall - - - - - - 92 KB (14,708 words) - 23:27, 5 September 2012 - - - -- - - [WebApollo Tutorial - 2012](/wiki/WebApollo_Tutorial_2012 "WebApollo Tutorial 2012") - - - - - - This \[\[Has topic::WebApollo\]\] - tutorial was presented by - \[\[User%253AElee\|Ed Lee\]\] at the \[\[2012 GMOD Summer School\]\]. - ...bApollo was not officially released when this session was taught, - and this tutorial was run using a - beta version of the tool.''' - - - - - - 43 KB (6,301 words) - 20:52, 27 August 2013 - - - -- - - [Tripal Tutorial - v1.1](/wiki/Tripal_Tutorial_v1.1 "Tripal Tutorial v1.1") - - - - - - ...allation, usage and administration of a Tripal-based genome - website. This tutorial guides the - user through the process of installation, setup and data loading - ...When possible, alternative command-line statements have been added - to this tutorial as users of other - Linux version have provided feedback. Unless specificall - - - - - - 131 KB (21,091 words) - 21:53, 2 January 2014 - - - -- - - [Tripal Tutorial (v0.3.1b - VM)]( "Tripal Tutorial (v0.3.1b VM)") - - - - - - This tutorial is intended to be used - with the Virtual Machine Image that comes pre-instal ...t we can skip - large sections as the VM has already been prepared. For this - tutorial, follow these steps: - - - - - - 2 KB (375 words) - 23:28, 5 September 2012 - - - -- - - [BioMart Tutorial - 2011](/wiki/BioMart_Tutorial_2011 "BioMart Tutorial 2011") - - - - - - \#REDIRECT \[\[BioMart Tutorial\]\] - - - - - - 52 B (5 words) - 05:08, 11 November 2011 - - - -- - - [Tripal Tutorial - (v1.0)]( "Tripal Tutorial (v1.0)") - - - - - - Welcome to the \[\[Tripal\]\] v1.0 - Tutorial. Here you will find - instructions for installation, usage and administratio \'''Note:''' An updated - tutorial for Tripal v1.1 can be found - \[http://www.gmod.org/wiki/Tripal_Tutorial_v1.1 - - - - - - 99 KB (16,007 words) - 17:43, 12 July 2013 - - - -- - - [ASPB 2012 GBrowse - Tutorial](/wiki/ASPB_2012_GBrowse_Tutorial "ASPB 2012 GBrowse Tutorial") - - - - - - Registration for the GBrowse tutorial - at ASPB is now closed, with 97 registered attendees. ...od"; the - password for that user is also gmod, which we may need during the - tutorial. - - - - - - 3 KB (527 words) - 00:06, 12 September 2012 - - - -- - - [GBrowse Volvox SAM - Tutorial](/wiki/GBrowse_Volvox_SAM_Tutorial "GBrowse Volvox SAM Tutorial") - - - - - - ...B::Sam must be installed. This is based on the - \[\[GBrowse_NGS_Tutorial\|NGS - tutorial\]\] that Dave Clements - wrote. ...am.gz\|SAM file\]\] and save in the GBrowse database - directory for the volvox tutorial. - Also make sure that the volvox fasta file, volvox.fa, is in the - directory - - - - - - 5 KB (853 words) - 00:19, 23 October 2012 - - - -- - - [Tripal Tutorial - 2010](/wiki/Tripal_Tutorial_2010 "Tripal Tutorial 2010") - - - - - - ...g and configuring \[\[Tripal\]\], a web front end to \[\[Chado\]\] - databases. This tutorial references - (and complements) the \[\[Media:TripalUsersGuideJan2010.pdf\|Tripal - - - - - - 58 KB (8,529 words) - 18:12, 9 October 2012 - - - -- - - [JBrowse Tutorial - 2013](/wiki/JBrowse_Tutorial_2013 "JBrowse Tutorial 2013") - - - - - - This \[\[Has topic::JBrowse\]\] - tutorial was presented by - \[\[User%253ARobertBuels\|Robert Buels\]\] at the \[\[2013 GMOD Summe This - tutorial uses the AWS AMI - '''ami-d2c8b1bb''' named '''2013 GMOD start day 3''' in th - - - - - - 14 KB (1,948 words) - 20:48, 27 August 2013 - - - -- - - [GMOD Cloud Tutorial](/wiki/GMOD_Cloud_Tutorial "GMOD Cloud Tutorial") - - - - - - For the moment, - \[http://tomotvos.ca/cloud/how-to-resize-an-aws-volume/ this - tutorial\] is a good guide to - resizing EBS partitions on EC2 machines. - - - - - - 8 KB (1,350 words) - 01:26, 13 September 2012 - - - -- - - [SOBA 2011 Tutorial](/wiki/SOBA_2011_Tutorial "SOBA 2011 Tutorial") - - - - - - The following tutorial was presented - as part of the \[\[2011 GMOD Spring Training\]\]. - - - - - - 15 KB (1,843 words) - 23:03, 20 August 2012 - - - -- - - [GFF Tutorial 2012](/wiki/GFF_Tutorial_2012 "GFF Tutorial 2012") - - - - - - This tutorial on \[\[GFF\]\] was - given by \[\[User%253AScott\|Scott Cain\]\] at the \[\[2012 GMOD Summer - ...tutorial/tutorial.html?content-type=text%2Fhtml - The GBrowse Administration Tutorial\] - for more information. - - - - - - 16 KB (2,352 words) - 21:54, 11 September 2012 - - - -- - - [Galaxy Tutorial - 2010](/wiki/Galaxy_Tutorial_2010 "Galaxy Tutorial 2010") - - - - - - This - \[\[:Category%253ATutorials\|tutorial\]\] - walks you through setting up and running a \[\[Galaxy\]\] server. - ...ttp://bitbucket.org/galaxy/galaxy-central/wiki/ExternalDisplayApplications/Tutorial - You can customize what external applications are available for - displaying d - - - - - - 32 KB (4,846 words) - 21:16, 9 October 2012 - - - -- - - [GBrowse Tutorial - 2010](/wiki/GBrowse_Tutorial_2010 "GBrowse Tutorial 2010") - - - - - - ==Tutorial== - - - - - - 3 KB (525 words) - 21:38, 2 October 2012 - - - -- - - [GBrowse Tutorial - 2012](/wiki/GBrowse_Tutorial_2012 "GBrowse Tutorial 2012") - - - - - - This \[\[Has topic::GBrowse\]\] - tutorial was taught at the \[\[2012 - GMOD Summer School\]\] by \[\[User%253AScott\|Scott Cain\]\]. - ==Tutorial== - - - - - - 8 KB (1,132 words) - 20:52, 27 August 2013 - - - -- - - [MAKER Tutorial 2010](/wiki/MAKER_Tutorial_2010 "MAKER Tutorial 2010") - - - - - - This - \[\[:Category%253ATutorials\|tutorial\]\] - walks you through setting up and running the \[\[MAKER\]\] genome - annotation - - - - - - 62 KB (9,933 words) - 22:41, 14 February 2013 - - - -## Page text matches - -- - - [GMOD Middleware](/wiki/GMOD_Middleware "GMOD Middleware") - - - - - - ...his eventually became what is described in the \[\[Artemis-Chado - Integration Tutorial\]\]. - \[\[User%253AClements\|Dave C.\]\]'' - - - - - - 40 KB (5,672 words) - 21:27, 15 August 2013 - - - -- - - [GMOD Developer's - Guide](/wiki/GMOD_Developer%27s_Guide "GMOD Developer's Guide") - - - - - - \Including a tutorial for - guiding the user on the application's use is a very good idea. - - - - - - 6 KB (985 words) - 05:18, 28 January 2008 - - - -- - - [Chado - Getting - Started](/wiki/Chado_-_Getting_Started "Chado - Getting Started") - - - - - - \* \[\[Chado Tutorial\]\] - - - - - - 3 KB (469 words) - 18:08, 13 February 2014 - - - -- - - [Bioperl Pipeline](/wiki/Bioperl_Pipeline "Bioperl Pipeline") - - - - - - ...last pipeline and a protein analysis pipeline.It is hope that - through this tutorial, two objectives - are achieved: - - - - - - 2 KB (272 words) - 12:53, 29 December 2010 - - - -- - - [CMap](/wiki/CMap "CMap") - - - - - - \|tutorials=;\[http://www.gramene.org/tutorials/cmap.html - Tutorial @ Gramene\] \|doc=\* - \[http://www.gramene.org/tutorials/cmap.html Gramene CMap User - Tutorial\], - - - - - - 7 KB (996 words) - 23:40, 17 October 2013 - - - -- - - [GBrowse](/wiki/GBrowse "GBrowse") - - - - - - - - - - 11 KB (1,422 words) - 16:47, 10 April 2023 - - - -- - - [Comparison of XORT and Hibernate for Chado - reporting](/wiki/Comparison_of_XORT_and_Hibernate_for_Chado_reporting "Comparison of XORT and Hibernate for Chado reporting") - - - - - - ...d for those who may not be familiar with Chado and how it is - structured. A tutorial with a few use - case scenarious that describe what each line does would be i - - - - - - 9 KB (1,641 words) - 15:48, 12 September 2011 - - - -- - - [GBrowse FAQ](/wiki/GBrowse_FAQ "GBrowse FAQ") - - - - - - ...ff/tutorial.html?content-type=text%2Fhtml - Using GBrowse with Bio::DB::GFF\] - tutorial, is the older version of the - \[\[GFF\]\] feature annotation format. Its main li - - - - - - 11 KB (1,733 words) - 14:48, 18 May 2013 - - - -- - - [WebGBrowse/tool - data](/wiki/WebGBrowse/tool_data "WebGBrowse/tool data") - - - - - - \* - \[http://webgbrowse.cgb.indiana.edu/tutorial.html - User Tutorial\] - this is an - extensive user guide for WebGBrowse - ;\[http://webgbrowse.cgb.indiana.edu/webgbrowse/tutorial.html - WebGBrowse Tutorial\] - - - - - - 4 KB (540 words) - 18:31, 10 September 2013 - - - -- - - [January 2007 GMOD meeting - agenda](/wiki/January_2007_GMOD_meeting_agenda "January 2007 GMOD meeting agenda") - - - - - - \| tentative Chado database - discussion/tutorial session - - - - - - 2 KB (295 words) - 15:02, 13 February 2007 - - - -- - - [MOD User Interface - Caucus](/wiki/MOD_User_Interface_Caucus "MOD User Interface Caucus") - - - - - - ...arrive at how your MOD\[\[can best answer scientists questions, - more than a tutorial on how to use - your MOD, is of interest. We are expecting a varied audience - - - - - - 4 KB (599 words) - 01:32, 29 March 2007 - - - -- - - [MOD User Interfaces: Sample of several MOD Top Level - functions](/wiki/MOD_User_Interfaces:_Sample_of_several_MOD_Top_Level_functions "MOD User Interfaces: Sample of several MOD Top Level functions") - - - - - - ...tion, Pathways, Expression Connection, and more.\
Gene - Ontology: GO Tutorial, What is GO?, - GO Slim Mapper, GO Term Finder, and more.\
C - - - - - - 7 KB (948 words) - 19:51, 23 January 2008 - - - -- - - [Perl Testing - by Gavin - Sherlock](/wiki/Perl_Testing_-_by_Gavin_Sherlock "Perl Testing - by Gavin Sherlock") - - - - - - ...tutorial on testing, see - http://search.cpan.org/dist/Test-Simple/lib/Test/Tutorial.pod - - - - - - 9 KB (1,495 words) - 20:05, 8 October 2012 - - - -- - - [April 2004 GMOD - Meeting](/wiki/April_2004_GMOD_Meeting "April 2004 GMOD Meeting") - - - - - - \* User tutorial added - Tutorial on March 15-18, 2004 - - - - - - 42 KB (6,309 words) - 20:37, 30 November 2010 - - - -- - - [MOD Face Talks](/wiki/MOD_Face_Talks "MOD Face Talks") - - - - - - \| Chado database discussion/tutorial - session - - - - - - 2 KB (244 words) - 01:35, 29 March 2007 - - - -- - - [GMOD virtual machine - project](/wiki/GMOD_virtual_machine_project "GMOD virtual machine project") - - - - - - give a tutorial), and for creating - virtual machines that could be used - - - - - - 3 KB (412 words) - 17:21, 24 September 2009 - - - -- - - [GBrowse Install - HOWTO](/wiki/GBrowse_Install_HOWTO "GBrowse Install HOWTO") - - - - - - More configuration information and a short - tutorial are located at: - - - - - - 35 KB (5,565 words) - 22:39, 8 August 2012 - - - -- - - [VMware HOWTO](/wiki/VMware_HOWTO "VMware HOWTO") - - - - - - - - - - 3 KB (543 words) - 18:43, 17 September 2012 - - - -- - - [Tripal Tutorial](/wiki/Tripal_Tutorial "Tripal Tutorial") - - - - - - \#REDIRECT \[\[Tripal Tutorial - v1.1\]\] - - - - - - 97 B (10 words) - 17:44, 12 July 2013 - - - -- - - [Chado Tutorial 2010](/wiki/Chado_Tutorial_2010 "Chado Tutorial 2010") - - - - - - This - \[\[:Category%253ATutorials\|tutorial\]\] - walks you through how to install and configure a \[\[Chado\]\] - database, Chad ...this course you'll be working with genome annotation - data from the \[\[MAKER - Tutorial\|MAKER session\]\]. We'll - simplify this and start by considering that we have - - - - - - 54 KB (8,190 words) - 23:34, 8 October 2012 - - - -- - - [Chado Tutorial 2012](/wiki/Chado_Tutorial_2012 "Chado Tutorial 2012") - - - - - - This \[\[Has topic::Chado\]\] - tutorial was presented by - \[\[User%253AScott\|Scott Cain\]\] as part of the \[\[2012 GMOD Summe - - - - - - 50 KB (7,599 words) - 16:26, 2 September 2018 - - - -- - - [Galaxy](/wiki/Galaxy "Galaxy") - - - - - - ...ly accessible websites\]. Galaxy servers make analysis tools, - genomic data, tutorial - demonstrations, persistent workspaces, and publication services - available t - - - - - - 6 KB (748 words) - 19:43, 13 December 2018 - - - -- - - [November 2007 GMOD - Meeting](/wiki/November_2007_GMOD_Meeting "November 2007 GMOD Meeting") - - - - - - ...ter is not yet released. (''But it is now: see \[\[Artemis-Chado - Integration Tutorial\]\].'') - - - - - - 28 KB (4,093 words) - 05:54, 5 January 2011 - - - -- - - [News/GMOD @ ISMB - 2010](/wiki/News/GMOD_@_ISMB_2010 "News/GMOD @ ISMB 2010") - - - - - - \* a tutorial on \[\[Galaxy\]\], - - - - - - 705 B (100 words) - 23:10, 9 October 2012 - - - -- - - [News/Virtual Issue in Journal - Database](/wiki/News/Virtual_Issue_in_Journal_Database "News/Virtual Issue in Journal Database") - - - - - - ...tiple papers with different emphases (for example, \[\[Chado\]\] - theory, Chado tutorial, and Chado - community papers). Please \[mailto:scott@scottcain.net contact m - - - - - - 2 KB (282 words) - 23:08, 9 October 2012 - - - -- - - [News/WebGBrowse Joins - GMOD](/wiki/News/WebGBrowse_Joins_GMOD "News/WebGBrowse Joins GMOD") - - - - - - ...WebGBrowse comes with - \[http://webgbrowse.cgb.indiana.edu/tutorial.html - a tutorial\], - \[http://webgbrowse.cgb.indiana.edu/faq.html FAQ\], and a - \[\[WebGBrowse#Mail - - - - - - 2 KB (245 words) - 23:14, 9 October 2012 - - - -- - - [JBrowse PSB 2020](/wiki/JBrowse_PSB_2020 "JBrowse PSB 2020") - - - - - - \[\[Category%253ATutorial\]\] - - - - - - 2 KB (301 words) - 19:41, 18 October 2019 - - - -- - - [Site Guidelines](/wiki/Site_Guidelines "Site Guidelines") - - - - - - ...ere these were used to format the - \[\[Training_and_Outreach#Online_Tutorials\|Tutorial - pages\]\]. - - - - - - 16 KB (2,420 words) - 23:18, 8 November 2013 - - - -- - - [GBrowse syn](/wiki/GBrowse_syn "GBrowse syn") - - - - - - \|tutorials=;\[\[GBrowse syn - Tutorial\]\] - - - - - - 6 KB (800 words) - 21:39, 15 October 2013 - - - -- - - [IGS Data - Representation](/wiki/IGS_Data_Representation "IGS Data Representation") - - - - - - ...f storing the same biological information. This page is not meant - to be a tutorial of how YOU should - model your biological information in Chado. Rather, it i - - - - - - 17 KB (2,330 words) - 23:34, 8 October 2012 - - - -- - - [MAKER](/wiki/MAKER "MAKER") - - - - - - \|tutorials=;\[\[MAKER Tutorial\]\] - - - - - - 9 KB (1,211 words) - 21:53, 2 February 2014 - - - -- - - [GBrowse 1 Configuration - HOWTO](/wiki/GBrowse_1_Configuration_HOWTO "GBrowse 1 Configuration HOWTO") - - - - - - - - - - 79 KB (12,563 words) - 16:45, 15 August 2011 - - - -- - - [GBrowse - Configuration/Balloons](/wiki/GBrowse_Configuration/Balloons "GBrowse Configuration/Balloons") - - - - - - .../Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html - Administrators Tutorial\]. - - - - - - 7 KB (1,138 words) - 13:06, 29 September 2010 - - - -- - - [GBrowse syn PAG 2009 - Workshop](/wiki/GBrowse_syn_PAG_2009_Workshop "GBrowse syn PAG 2009 Workshop") - - - - - - ...visualizing \[\[synteny\]\] in up 5 different genomes. This will be - a hands-on tutorial on how to - install, configure and use GBrowse_syn. == - Tutorial Level == - - - - - - 3 KB (454 words) - 21:29, 3 October 2012 - - - -- - - [2009 GMOD Summer School - - Europe](/wiki/2009_GMOD_Summer_School_-_Europe "2009 GMOD Summer School - Europe") - - - - - - ...emis-Chado Integration - Tutorial\|Artemis-Chado - Integration\]\], and \[\[JBrowse - Tutorial\|JBrowse\]\]. \| - style="background-color: \#ddffff" align="center" \| '''\[\[Chado - Tutorial\|Chado\]\]'''\
\[\[User%253AScott\|Scott Cain\]\] and \[\[User%253AClements\|Dave Clements - - - - - - 10 KB (1,210 words) - 22:13, 16 April 2014 - - - -- - - [2009 GMOD Summer School - - Americas](/wiki/2009_GMOD_Summer_School_-_Americas "2009 GMOD Summer School - Americas") - - - - - - ...art Tutorial\|BioMart\]\], - \[\[GBrowse_syn - Tutorial\|GBrowse_syn\]\], and - \[\[Tripal Tutorial\|Tripal\]\] \| - style="background-color: \#ddffff" align="center" \| '''\[\[MAKER - Tutorial\|MAKER I\]\]'''\
\[\[User%253ACarsonholt\|Carson Holt\]\]\
\[\[MAKER\]\] overview, - - - - - - 11 KB (1,433 words) - 22:13, 16 April 2014 - - - -- - - [GBrowse syn - Tutorial](/wiki/GBrowse_syn_Tutorial "GBrowse syn Tutorial") - - - - - - \#redirect \[\[GBrowse syn Tutorial - 2013\]\] - - - - - - 117 B (12 words) - 16:02, 22 July 2013 - - - -- - - [GBrowse Tutorial](/wiki/GBrowse_Tutorial "GBrowse Tutorial") - - - - - - ; \[\[GBrowse Tutorial 2012\|GBrowse - tutorial from 2013 GMOD Summer - School\]\] : This tutorial was taught - by \[\[User%253AScott\|Scott Cain\]\] at the \[\[2013 GMOD Summer - School\]\] - - - - - - 2 KB (236 words) - 17:10, 18 December 2013 - - - -- - - [Gbgff](/wiki/Gbgff "Gbgff") - - - - - - - - - - 2 KB (386 words) - 15:52, 25 September 2009 - - - -- - - [News/GBrowse Tutorial at PAG - XVI](/wiki/News/GBrowse_Tutorial_at_PAG_XVI "News/GBrowse Tutorial at PAG XVI") - - - - - - ...ce (PAG-XVI)\], January 12-16, 2008, in San Diego. This will be a - hands-on tutorial on how to install - and use the \[\[GBrowse\]\] genome browser. If you are atten See the - \[http://www.intl-pag.org/16/16-gbrowse.html PAG - tutorial page\] for additional - information. - - - - - - 515 B (77 words) - 20:55, 24 January 2011 - - - -- - - [News/Upcoming Pathway Tools - Tutorial](/wiki/News/Upcoming_Pathway_Tools_Tutorial "News/Upcoming Pathway Tools Tutorial") - - - - - - ...ll hold a - \[http://bioinformatics.ai.sri.com/ptools/tutorial/ - Pathway Tools tutorial session\] from - September 2-5, 2008, at SRI International in Menlo Park, CA. ...e see - the - \[http://bioinformatics.ai.sri.com/ptools/tutorial/ - Pathway Tools Tutorial page\] for a - detailed schedule, registration information, and other details. - - - - - - 828 B (116 words) - 21:22, 24 January 2011 - - - -- - - [News/Pathway Tools Tutorial in - London](/wiki/News/Pathway_Tools_Tutorial_in_London "News/Pathway Tools Tutorial in London") - - - - - - ...tutorial\] well be held September - 22-23, 2008 at Kings College London. This - tutorial is kindly hosted by the - \[http://www.kcl.ac.uk/schools/pse/bioinform/ Centre The - tutorial is free of charge. - - - - - - 1 KB (194 words) - 21:26, 24 January 2011 - - - -- - - [News/New Ergatis - Release](/wiki/News/New_Ergatis_Release "News/New Ergatis Release") - - - - - - ...yotic Annotation Pipeline is also included, as well as a pipeline - creation tutorial. For a full list of - the changes, see the \[http://ergatis.svn.sourceforge.n - - - - - - 1 KB (164 words) - 21:37, 24 January 2011 - - - -- - - [News/GBrowse User - Tutorial](/wiki/News/GBrowse_User_Tutorial "News/GBrowse User Tutorial") - - - - - - ...released by \[http://www.openhelix.com OpenHelix\] this week. The - narrated tutorial covers: The - tutorial also includes - \[http://www.openhelix.com/downloads/gbrowse/gbrowseslidesDL.s - - - - - - 2 KB (268 words) - 23:07, 9 October 2012 - - - -- - - [News/Pathway Tools Workshop, - August](/wiki/News/Pathway_Tools_Workshop,_August "News/Pathway Tools Workshop, August") - - - - - - '''Part 1: Tutorial, August 19-21''' - This introductory tutorial will - educate the new user on aspects of \[\[Pathway Tools\]\] including - basic u - - - - - - 2 KB (297 words) - 23:09, 9 October 2012 - - - -- - - [News/WebGBrowse Has - Arrived](/wiki/News/WebGBrowse_Has_Arrived "News/WebGBrowse Has Arrived") - - - - - - ...s an extensive - \[http://webgbrowse.cgb.indiana.edu/webgbrowse/tutorial.html - tutorial\] and - \[http://webgbrowse.cgb.indiana.edu/webgbrowse/faq.html FAQ\], and was - j - - - - - - 2 KB (292 words) - 23:22, 3 October 2012 - - - -- - - [News/GBrowse 1.70 - Released](/wiki/News/GBrowse_1.70_Released "News/GBrowse 1.70 Released") - - - - - - ...oved along with \[\[GBrowse_syn\|documentation\]\] and a - \[\[GBrowse_syn - Tutorial\|tutorial\]\]. - - - - - - 2 KB (333 words) - 21:56, 24 January 2011 - - - -- - - [News/Tripal: A Web Front End for - Chado](/wiki/News/Tripal%253A_A_Web_Front_End_for_Chado "News/Tripal: A Web Front End for Chado") - - - - - - ...\[Media:TripalUsersGuideJune2009.pdf\|User's Guide\]\] and a - \[\[Tripal - Tutorial\|tutorial\]\] - to help users install, configure and extend Tripal. - - - - - - 1 KB (150 words) - 23:14, 9 October 2012 - - - -- - - [News/GMOD Tutorials! GMOD - Training!](/wiki/News/GMOD_Tutorials!_GMOD_Training! "News/GMOD Tutorials! GMOD Training!") - - - - - - ...were covered at the \[\[GMOD Summer School\|2009 GMOD Summer - Schools\]\]. Each tutorial includes a - \[\[VMware\]\] system image to work with, and detailed instructions \* - '''\[\[Apollo Tutorial\]\]''' - by - \[\[User%253AElee\|Ed Lee\]\] - - - - - - 4 KB (542 words) - 23:11, 9 October 2012 - - - -- - - [News/GBrowse NGS Tutorial & - Poster](/wiki/News/GBrowse_NGS_Tutorial_%26_Poster "News/GBrowse NGS Tutorial & Poster") - - - - - - \[\[File:BA2009Logo.png\|link=GBrowse NGS - Tutorial\|100px\|right\|GBrowse NGS - Tutorial\]\] ...the - \[\[BA2009\|Bioinformatics Australia 2009 (BA2009) GMOD Workshop\]\]. - The tutorial includes a - \[\[VMware\]\] image to work with and step-by-step instructions for - - - - - - 1 KB (156 words) - 23:10, 9 October 2012 - - - - - -View (previous 50 \| next 50) (20 \| 50 \| 100 \| 250 \| 500) - - - - - - - - -## Navigation menu - - - - -### Namespaces - -- [Special - page](/wiki/Special%253ASearch/Tutorial "This is a special page, you cannot edit the page itself") - - - -### Navigation - - - -- [GMOD Home](/wiki/Main_Page) -- [Software](/wiki/GMOD_Components) -- [Categories / - Tags](/wiki/Categories) -- [View all - pages](/wiki/Special:AllPages) - - - - -### Documentation - - - -- [Overview](/wiki/Overview) -- [FAQs](/wiki/Category%253AFAQ) -- [HOWTOs](/wiki/Category%253AHOWTO) -- [Glossary](/wiki/Glossary) - - - - -### Community - - - -- [GMOD News](/wiki/GMOD_News) -- [Training / - Outreach](/wiki/Training_and_Outreach) -- [Support](/wiki/Support) -- [GMOD - Promotion](/wiki/GMOD_Promotion) -- [Meetings](/wiki/Meetings) -- [Calendar](/wiki/Calendar) - - - - -### Tools - - - - - - - - - - - - - - - diff --git a/wiki/Special%3ASearch/Users.md b/wiki/Special%3ASearch/Users.md deleted file mode 100644 index 41bdc0ebdd..0000000000 --- a/wiki/Special%3ASearch/Users.md +++ /dev/null @@ -1,1227 +0,0 @@ - - - - - - - -# Search results - - - - - - - - -- [Content - pages](/mediawiki/index.php?title=Special:Search&search=Users&fulltext=Search&profile=default "Search in (Main)") -- [Multimedia](/mediawiki/index.php?title=Special:Search&search=Users&fulltext=Search&profile=images "Search for files") -- [Help and Project - pages](/mediawiki/index.php?title=Special:Search&search=Users&fulltext=Search&profile=help "Search in GMOD, Help") -- [Everything](/mediawiki/index.php?title=Special:Search&search=Users&fulltext=Search&profile=all "Search all of content (including talk pages)") -- [Advanced](/mediawiki/index.php?title=Special:Search&search=Users&fulltext=Search&profile=advanced "Search in custom namespaces") - - -- Showing below up to **50** results starting with \#**1**. - - - - -**Create the page -"Users" on this -wiki!** See also the search results found. - -## Page title matches - -- - - [GMOD Users](/wiki/GMOD_Users "GMOD Users") - - - - - - \ - - diff --git a/wiki/Textpresso.md b/wiki/Textpresso.md index f9085b5c8d..66a244ac71 100644 --- a/wiki/Textpresso.md +++ b/wiki/Textpresso.md @@ -70,9 +70,7 @@ class="external free" rel="nofollow">http://textpresso.yeastgenome.org/textpresso/ [+](Special%253ASearchByProperty/Has-20URL/http%253A-2F-2Ftextpresso.yeastgenome.org-2Ftextpresso-2F "Special%253ASearchByProperty/Has-20URL/http%253A-2F-2Ftextpresso.yeastgenome.org-2Ftextpresso-2F") and http://www.textpresso.org/celegans/ [+](Special%253ASearchByProperty/Has-20URL/http%253A-2F-2Fwww.textpresso.org-2Fcelegans-2F "Special%253ASearchByProperty/Has-20URL/http%253A-2F-2Fwww.textpresso.org-2Fcelegans-2F") | | [Has description](Property%253AHas_description "Property:Has description") | Textpresso is an information extracting an … Textpresso is an information extracting and processing (text mining) package for biological literature whose capabilities go far beyond that of a simple keyword search engine. The two key elements are the collection of the full text of scientific articles split into individual sentences, and the implementation of semantic categories, for which a database of articles and individual sentences can be searched. The source of the full text articles are PDFs, and additional bibliographical information that is obtained from other citation databases can be processed as well. Alere is a package of scripts that can be used to construct a corpus (retrieve articles) for use with **Textpresso**. Textpresso is supported by a grant from the National Human Genome Research Institute at the US National Institutes of Health \# HG004090. National Institutes of Health \# HG004090. + | +rel="nofollow">Alere is a package of scripts that can be used to construct a corpus (retrieve articles) for use with **Textpresso**. Textpresso is supported by a grant from the National Human Genome Research Institute at the US National Institutes of Health \# HG004090. National Institutes of Health \# HG004090. | | [Has development status](Property%253AHas_development_status "Property:Has development status") | active [+](Special%253ASearchByProperty/Has-20development-20status/active "Special%253ASearchByProperty/Has-20development-20status/active") | | [Has input format](Property%253AHas_input_format "Property:Has input format") | Plain text [+](Special%253ASearchByProperty/Has-20input-20format/Plain-20text "Special%253ASearchByProperty/Has-20input-20format/Plain-20text"), PDF [+](Special%253ASearchByProperty/Has-20input-20format/PDF "Special%253ASearchByProperty/Has-20input-20format/PDF") and html [+](Special%253ASearchByProperty/Has-20input-20format/html "Special%253ASearchByProperty/Has-20input-20format/html") | | [Has licence](Property%253AHas_licence "Property:Has licence") | Modified GPL [+](Special%253ASearchByProperty/Has-20licence/Modified-20GPL "Special%253ASearchByProperty/Has-20licence/Modified-20GPL") | diff --git a/wiki/XORT.1.md b/wiki/XORT.1.md index f665322388..fd067ca09e 100644 --- a/wiki/XORT.1.md +++ b/wiki/XORT.1.md @@ -49,9 +49,7 @@ Resources | [Has URL](Property%253AHas_URL "Property:Has URL") | http://sourceforge.net/projects/gmod/files/OldFiles/ [+](Special%253ASearchByProperty/Has-20URL/http%253A-2F-2Fsourceforge.net-2Fprojects-2Fgmod-2Ffiles-2FOldFiles-2F "Special%253ASearchByProperty/Has-20URL/http%253A-2F-2Fsourceforge.net-2Fprojects-2Fgmod-2Ffiles-2FOldFiles-2F") | -| [Has description](Property%253AHas_description "Property:Has description") | XORT is a utility written in Perl that can … XORT is a utility written in Perl that can be used to read to and write from a [relational](Glossary#Relational "Glossary") [schema](Glossary#Schema "Glossary") using [XML](Glossary#XML "Glossary") as an interchange format. In GMOD XORT is frequently used to transfer data to and from Chado. XORT’s three major elements are an XML-database schema mapping specification, an XORT language for both data retrieval and data construction, and a collection of tools that are based on the specification to facilitate the mapping and data exchange. The mapping specification specifies the schema requirement, mapping, operation, and object reference mechanism; the XORT language is used to construct the dump specification; the tool collections comprise the data validation, data input, data output and data debug system. Because it originates from the Chado database, we denote the corresponding XML "Chado XML." denote the corresponding XML "Chado XML." + | +| [Has description](Property%253AHas_description "Property:Has description") | XORT is a utility written in Perl that can … XORT is a utility written in Perl that can be used to read to and write from a [relational](Glossary#Relational "Glossary") [schema](Glossary#Schema "Glossary") using [XML](Glossary#XML "Glossary") as an interchange format. In GMOD XORT is frequently used to transfer data to and from Chado. XORT’s three major elements are an XML-database schema mapping specification, an XORT language for both data retrieval and data construction, and a collection of tools that are based on the specification to facilitate the mapping and data exchange. The mapping specification specifies the schema requirement, mapping, operation, and object reference mechanism; the XORT language is used to construct the dump specification; the tool collections comprise the data validation, data input, data output and data debug system. Because it originates from the Chado database, we denote the corresponding XML "Chado XML." denote the corresponding XML "Chado XML." | | [Has development status](Property%253AHas_development_status "Property:Has development status") | maintenance [+](Special%253ASearchByProperty/Has-20development-20status/maintenance "Special%253ASearchByProperty/Has-20development-20status/maintenance") | | [Has download URL](Property%253AHas_download_URL "Property:Has download URL") |