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| ; [[Chado Tutorial]] | | ; [[Chado Tutorial]] |
− | : Based on the Chado session from the [[2012 GMOD Summer School]]. | + | : Based on the Chado session from the [[2013 GMOD Summer School]]. |
| ; [[Artemis-Chado Integration Tutorial]] | | ; [[Artemis-Chado Integration Tutorial]] |
| : Based on the session of the same title from the [[2009 GMOD Summer School - Europe]]. | | : Based on the session of the same title from the [[2009 GMOD Summer School - Europe]]. |
| + | |- |
| + | ! [[Cloud|GMOD in the Cloud]] |
| + | | |
| + | ; [[AWS walkthrough]] |
| + | : A gentle introduction to getting a machine up and running on the Amazon Cloud |
| |- | | |- |
| ! [[CMap]] | | ! [[CMap]] |
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| |- | | |- |
| ! [[Galaxy]] | | ! [[Galaxy]] |
− | | | + | | {{:Galaxy/tool_data | template = TutorialLinks }} |
− | ; [[Galaxy Tutorial]]
| + | |
− | : How to install Galaxy. Based on [[Galaxy]] session from the [[2012 GMOD Summer School]] | + | |
− | ; [http://usegalaxy.org/galaxy101 Galaxy 101]
| + | |
− | : An introduction to using Galaxy.
| + | |
− | ; [http://wiki.galaxyproject.org/Learn/Screencasts Galaxy Screencasts]
| + | |
− | : Short screencasts showing how to do many common tasks using [[Galaxy]].
| + | |
− | ; [http://wiki.galaxyproject.org/Learn#Other_Tutorials Community Tutorials List]
| + | |
− | : List of online tutorials written by the Galaxy Community.
| + | |
− | ; [http://bit.ly/gxyRNASEX RNA-Seq Example]
| + | |
− | : 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.
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| |- | | |- |
| ! [[GBrowse]] | | ! [[GBrowse]] |
− | | | + | | {{:GBrowse/tool_data | template = TutorialLinks }} |
− | ; [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]] |
| + | | {{:GBrowse_syn/tool_data | template = TutorialLinks }} |
| + | |- |
| + | ! [[GFF3]] |
| | | | | |
− | ; [[GBrowse_syn Tutorial]] | + | ; [[GFF3]] |
− | : Based on the GBrowse_syn session from the [[2012 GMOD Summer School]]. | + | : Introduction to and documentation of the GFF3 format |
| |- | | |- |
| ! [[JBrowse]] | | ! [[JBrowse]] |
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
|