Difference between revisions of "Template:TutorialList"

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{| class="wikitable"
 
{| class="wikitable"
 
! Component
 
! Component
! Title
+
! Title, Description
! Desription
+
 
|-
 
|-
! rowspan="3" | [[Apollo]]
+
! [[Apollo]]
| '''[[Apollo Tutorial]]'''
+
| {{:Apollo/tool_data | template = TutorialLinks }}
| The Apollo session from the [[2010 GMOD Summer School - Americas]].
+
|-
+
| '''[http://apollo.berkeleybop.org/current/userguide.html Apollo Userguide]'''
+
| A comprehensive guide to installing and using Apollo.
+
|-
+
| '''[http://www.dynamicgene.dnalc.org Apollo tutorials at the Dynamic Gene web site]'''
+
| Flash based tutorials on how to use Apollo, using rice as an example.  Sections of particular interest are [http://www.dynamicgene.dnalc.org/annotation/annotation.html annotation tutorial], on how to use Apollo, and [http://www.dynamicgene.dnalc.org/resources/resources.html resources], on how to download sample data and install Apollo on an MS Windows system.
+
 
|-
 
|-
 
! [[BioMart]]
 
! [[BioMart]]
| '''[[BioMart Tutorial]]'''
+
|  
| Based on the BioMart workshop at the [[October 2011 GMOD Meeting]].
+
; [[BioMart Tutorial]]
 +
: Based on the BioMart workshop at the [[October 2011 GMOD Meeting]].
 
|-
 
|-
! rowspan="2" | [[Chado]]
+
! [[Chado]]
| '''[[Chado Tutorial]]'''
+
|
| Based on the Chado session from the [[2012 GMOD Summer School]].
+
; [[Chado Tutorial]]
 +
: Based on the Chado session from the [[2013 GMOD Summer School]].
 +
; [[Artemis-Chado Integration Tutorial]]
 +
: Based on the session of the same title from the [[2009 GMOD Summer School - Europe]].
 
|-
 
|-
| '''[[Artemis-Chado Integration Tutorial]]'''
+
! [[Cloud|GMOD in the Cloud]]
| Based on the session of the same title from the [[2009 GMOD Summer School - Europe]].
+
|
 +
; [[AWS walkthrough]]
 +
: A gentle introduction to getting a machine up and running on the Amazon Cloud
 
|-
 
|-
 
! [[CMap]]
 
! [[CMap]]
| '''[http://www.gramene.org/tutorials/cmap.html Gramene CMap User Tutorial]'''
+
| {{:CMap/tool_data | template = TutorialLinks }}
| Available in both [http://www.gramene.org/tutorials/cmap_tutorial.pdf PDF] and [http://www.gramene.org/tutorials/cmap_tutorial.ppt PowerPoint] formats.  This explains how to use CMap in the context of Gramene.
+
 
|-
 
|-
! rowspan="6" | [[Galaxy]]
+
! [[Galaxy]]
| '''[[Galaxy Tutorial]]'''
+
| {{:Galaxy/tool_data | template = TutorialLinks }}
| How to install Galaxy. Based on [[Galaxy]] session from the [[2012 GMOD Summer School]]
+
 
|-
 
|-
| '''[http://usegalaxy.org/galaxy101 Galaxy 101]'''
+
! [[GBrowse]]
| An introduction to using Galaxy.
+
| {{:GBrowse/tool_data | template = TutorialLinks }}
 
|-
 
|-
| '''[http://wiki.galaxyproject.org/Learn/Screencasts Galaxy Screencasts]'''
+
! [[GBrowse_syn]]
| Short screencasts showing how to do many common tasks using [[Galaxy]].
+
| {{:GBrowse_syn/tool_data | template = TutorialLinks }}
 
|-
 
|-
| '''[http://wiki.galaxyproject.org/Learn#Other_Tutorials Community Tutorials List]'''
+
! [[GFF3]]
| List of online tutorials written by the Galaxy Community.
+
|
|-
+
; [[GFF3]]  
| '''[http://bit.ly/gxyRNASEX RNA-Seq Example]'''
+
: Introduction to and documentation of the GFF3 format
| An introduction to NGS processing (specifically RNA-Seq) with [[Galaxy]].
+
|-
+
| '''[http://www.openhelix.com/cgi/tutorialInfo.cgi?id=82 OpenHelix Galaxy User Tutorial]'''
+
| A Flash based tutorial on using Galaxy.  Provided by [http://www.openhelix.com OpenHelix].  Tutorial includes slides, handouts and exercises.  Requires subscription.
+
|-
+
! rowspan="4" | [[GBrowse]]
+
| '''[http://www.openhelix.com/gbrowse GBrowse User Tutorial]'''
+
| A Flash based tutorial on using GBrowse.  Provided by [http://www.openhelix.com OpenHelix].  Tutorial includes slides, handouts and exercises.
+
|-
+
| '''{{GBrowseAdminTutorialLink|GBrowse Administration Tutorial}}'''
+
| Detailed explanation of how to install and configure [[GBrowse]].  An administration tutorial is also available for {{GBrowse1AdminTutorialLink|GBrowse 1.x}}
+
|-
+
| '''[[GBrowse NGS Tutorial]]'''
+
| Instructions on how to visualize [[next generation sequencing]] data in GBrowse using [http://samtools.sourceforge.net SAMtools].  The tutorial  includes a starting [[VMware]] image, and uses the example data that comes with SAMtools.
+
|-
+
| '''[[GBrowse Tutorial]]'''
+
| Based on the GBrowse session from the [[2012 GMOD Summer School]].  This relies heavily on the {{GBrowseAdminTutorialLink| GBrowse Administration Tutorial}}.
+
|-
+
! [[GBrowse_syn]]
+
| '''[[GBrowse_syn Tutorial]]'''
+
| Based on the GBrowse_syn session from the [[2012 GMOD Summer School]].
+
 
|-
 
|-
 
! [[JBrowse]]
 
! [[JBrowse]]
| '''[[JBrowse Tutorial]]'''
+
| {{:JBrowse/tool_data | template = TutorialLinks }}
| Based on the JBrowse session from the [[2012 GMOD Summer School]].
+
 
|-
 
|-
 
! [[MAKER]]
 
! [[MAKER]]
| '''[[MAKER Tutorial]]'''
+
| {{:MAKER/tool_data | template = TutorialLinks }}
| Based on the MAKER session from the [[2012 GMOD Summer School]].
+
|-
 +
! [[Pathway Tools]]
 +
| {{:Pathway Tools/tool_data | template = TutorialLinks }}
 
|-
 
|-
 
! [[SOBA]]
 
! [[SOBA]]
| '''[[SOBA Tutorial]]'''
+
| {{:SOBA/tool_data | template = TutorialLinks }}
| Based on the SOBA session from the [[2012 GMOD Summer School]].
+
 
|-
 
|-
 
! [[Tripal]]
 
! [[Tripal]]
| '''[[Tripal Tutorial]]'''
+
| {{:Tripal/tool_data | template = TutorialLinks }}
| Based on the Tripal session from the [[2012 GMOD Summer School]].
+
 
|-
 
|-
 
! [[WebApollo]]
 
! [[WebApollo]]
| '''[[WebApollo Tutorial]]'''
+
| {{:WebApollo/tool_data | template = TutorialLinks }}
| Based on the WebApollo session from the [[2012 GMOD Summer School]].
+
 
|}
 
|}

Latest revision as of 23:26, 2 August 2013

Component Title, Description
Apollo
Apollo Tutorial 2011
The Apollo session from the 2011 GMOD Spring Training
Apollo Tutorial 2010
The Apollo session from the 2010 GMOD Summer School - Americas.
Apollo tutorials at the Dynamic Gene web site.
Flash based tutorials on how to use Apollo, using rice as an example. Sections of particular interest are
  • Annotation - how to use Apollo
  • Resources - how to download sample data and install Apollo on an MS Windows system.
Apollo user guide
The current user guide, which has comprehensive instructions for installation and usage of Apollo.
BioMart
BioMart Tutorial
Based on the BioMart workshop at the October 2011 GMOD Meeting.
Chado
Chado Tutorial
Based on the Chado session from the 2013 GMOD Summer School.
Artemis-Chado Integration Tutorial
Based on the session of the same title from the 2009 GMOD Summer School - Europe.
GMOD in the Cloud
AWS walkthrough
A gentle introduction to getting a machine up and running on the Amazon Cloud
CMap
Tutorial @ Gramene
Galaxy
Galaxy Tutorial
As taught at the 2013 GMOD Summer School
Galaxy Learning Hub
A wealth of training materials, including:
RNA-Seq Example
An introduction to NGS processing (specifically RNA-Seq) with Galaxy.
OpenHelix Galaxy User Tutorial
A Flash based tutorial on using Galaxy. Provided by OpenHelix. Tutorial includes slides, handouts and exercises. Requires subscription.
GBrowse
GBrowse tutorial from 2012 GMOD Summer School. This relies heavily on the GBrowse2 Admin Tutorial.
Demonstrates setting up, configuring and using GBrowse with some sample data. GBrowse is provided on an Amazon Machine Image; see GMOD in the Cloud for more information on getting a GMOD AMI.
GBrowse tutorial from 2010 GMOD Summer School
Set up and run GBrowse with sample data. It provides a VMware image to work on, and relies heavily on the GBrowse2 Admin Tutorial.
GBrowse2 Admin Tutorial
Step by step guide on how to configure and load data into GBrowse. Administration tutorials are available for both the GBrowse2 Admin Tutorial, and the earlier 1.x versions.
Usage tutorial
GBrowse usage tutorial
GBrowse NGS Tutorial
Instructions on how to visualize next generation sequencing data in GBrowse using SAMtools. The tutorial includes a starting VMware image, and uses the example data that comes with SAMtools.
GBrowse video tutorial
Produced by EuPathDB; please direct praise and thanks to them!
GBrowse User Tutorial at OpenHelix
A Flash based tutorial on using GBrowse. Provided by OpenHelix. Tutorial includes slides, handouts and exercises. NB: this tutorial is for GBrowse 1.x
GBrowse_syn
GBrowse syn Tutorial
Installing and configuring GBrowse_syn; from the 2013 GMOD Summer School
GFF3
GFF3
Introduction to and documentation of the GFF3 format
JBrowse
JBrowse Tutorial covering installation and configuration
part of the 2013 GMOD Summer School
Getting Started with JBrowse Tutorial
part of the JBrowse documentation
Exploration of structural variation in the tomato clade using JBrowse
Tutorial explaining how to browse structural variants from the 150+ tomato genome resequencing project (http://www.tomatogenome.net) using JBrowse
MAKER
MAKER Tutorial
taught as part of the 2013 GMOD Summer School
Pathway Tools


Pathway Tools slides
General information about Pathway Tools, including slides from tutorials and user guides
Upcoming Events
Pathway Tools tutorials and workshops
SOBA
SOBA Tutorial
taught as part of the 2013 GMOD Summer School
Tripal


Tripal Tutorial v1.1
used during the 2013 GMOD Summer School
Tripal Tutorial (v1.0)
used during the 2012 GMOD Summer School
Tripal Tutorial (v0.3.1b)
The full v0.3.1b tutorial
Tripal Tutorial (v0.3.1b VM)
for use with the Tripal virtual machine
Tripal Tutorial (pre version 0.3b)
from the 2010 GMOD Spring School
WebApollo
WebApollo Tutorial
taught as part of the 2013 GMOD Summer School