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| In addition to in person training, there are in depth online tutorials on several [[GMOD Components]]: | | In addition to in person training, there are in depth online tutorials on several [[GMOD Components]]: |
| | | |
− | {| class="wikitable" | + | {{TutorialList}} |
− | ! Component
| + | |
− | ! Title
| + | |
− | ! Desription
| + | |
− | |-
| + | |
− | ! rowspan="3" | [[Apollo]]
| + | |
− | | '''[[Apollo Tutorial]]'''
| + | |
− | | The Apollo session from the [[GMOD Summer School|2009 GMOD Summer Schools]].
| + | |
− | |-
| + | |
− | | '''[http://apollo.berkeleybop.org/current/userguide.html Apollo Userguide]'''
| + | |
− | | A comprehensive guide to installing and using Apollo.
| + | |
− | |-
| + | |
− | | '''[http://www.dynamicgene.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.org/annotation/annotation.html Annotation] - how to use Apollo, and [http://www.dynamicgene.org/resources/resources.html Resources] - how to download sample data and install Apollo on an MS Windows system.
| + | |
− | |-
| + | |
− | ! [[BioMart]]
| + | |
− | | '''[[BioMart Tutorial]]'''
| + | |
− | | Based on the BioMart session from the [[GMOD Summer School|2009 GMOD Summer Schools]].
| + | |
− | |-
| + | |
− | ! rowspan="2" | [[Chado]]
| + | |
− | | '''[[Chado Tutorial]]'''
| + | |
− | | Based on the Chado session from the [[GMOD Summer School|2009 GMOD Summer Schools]].
| + | |
− | |-
| + | |
− | | '''[[Artemis-Chado Integration Tutorial]]'''
| + | |
− | | Based on the session of the same title from the [[2009 GMOD Summer School - Europe]].
| + | |
− | |-
| + | |
− | ! [[CMap]]
| + | |
− | | '''[http://www.gramene.org/tutorials/cmap.html Gramene CMap User Tutorial]'''
| + | |
− | | 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="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.
| + | |
− | |-
| + | |
− | | '''[[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 [[GMOD Summer School|2009 GMOD Summer Schools]]. This relies heavily on the {{GBrowseAdminTutorialLink| GBrowse Administration Tutorial}}.
| + | |
− | |-
| + | |
− | ! [[GBrowse_syn]]
| + | |
− | | '''[[GBrowse_syn Tutorial]]'''
| + | |
− | | Based on the GBrowse_syn session from the [[GMOD Summer School|2009 GMOD Summer Schools]].
| + | |
− | |-
| + | |
− | ! [[JBrowse]]
| + | |
− | | '''[[JBrowse Tutorial]]'''
| + | |
− | | Based on the JBrowse session from the [[GMOD Summer School|2009 GMOD Summer Schools]].
| + | |
− | |-
| + | |
− | ! [[MAKER]]
| + | |
− | | '''[[MAKER Tutorial]]'''
| + | |
− | | Based on the MAKER session from the [[2009 GMOD Summer School - Americas]].
| + | |
− | |-
| + | |
− | ! [[Tripal]]
| + | |
− | | '''[[Tripal Tutorial]]'''
| + | |
− | | Based on the Tripal session from the [[GMOD Summer School|2009 GMOD Summer Schools]].
| + | |
− | |-
| + | |
− | |}
| + | |
| | | |
| This website also has a large collection of [[:Category:HOWTO|HOWTOs]] on more specific tasks. | | This website also has a large collection of [[:Category:HOWTO|HOWTOs]] on more specific tasks. |
Training and outreach is about several things. GMOD training teaches new and existing GMOD users how to use GMOD Components to help meet the goals of their organizations. GMOD outreach activities aim to inform biologists and bioinformaticists about what GMOD can do. This page describes GMOD training and outreach activities. See Support for other support options in GMOD.
In addition to in person training, there are in depth online tutorials on several GMOD Components:
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
|
GMOD Schools are hands-on multi-day courses aimed at teaching new GMOD users how to get up and running with GMOD. Schools introduce participants to GMOD and focus on installation, configuration and integration of popular GMOD Components.
The items listed here are either about GMOD and its components, or are of general interest to the GMOD community.
Date
|
Topic
|
Conference / Location
|
Contact
|
|
2 0 1 0
|
May 15-17
|
First Galaxy Developers Conference
|
Penn State, State College, PA, USA
|
|
March 3-5
|
EMBO Workshop on Visualizing Biological Data (VizBi)
|
EMBL Advanced Training Centre, Heidelberg, Germany.
|
Adela Valceanu
|
January 9-13
|
The Generic Genome Browser: A Hands on Workshop for Installing, Configuring and Using Your Own GBrowse
|
Plant and Animal Genome XVII Conference (PAG 2010), San Diego, CA, USA See PAG 2010 for links to many talks and presentations.
|
Scott Cain
|
Comparative Genomics with GBrowse_syn: A hands on workshop for visualizing your comparative genomics data with GBrowse_syn
|
Sheldon McKay
|
MAKER: An easy to use genome annotation pipeline
|
Carson Holt
|
|
2 0 0 9
|
November 16-17
|
InterMine Data Warehouse Workshop
|
Cambridge, UK
|
Richard Smith
|
GMOD for Comparative Genomics
|
Information Systems for Insect Pests, Rennes, France
|
Dave Clements
|
October 28-30
|
Database Tools for Biologists: A Half-Day GMOD Workshop
|
Bioinformatics Australia 2009 (BA2009), Melbourne, Australia
|
Dave Clements
|
Visualizing Next Generation Sequence Data with GBrowse and SAMtools (poster)
|
October 27-30
|
GBrowse and Next Generation Sequencing Data
|
Genome Informatics, Cold Spring Harbor, New York, USA
|
Scott Cain
|
Genome Visualization and Comparison using CMap and Circos
|
Ken Youens-Clark
|
October 21-22
|
Interactive Workshops on the UCSC Genome Browser and Galaxy Framework
|
The American Society of Human Genetics (AHSG), Honolulu, Hawaii
|
|
October 12-27
|
Programming for Biology This includes a session on GBrowse.
|
Cold Spring Harbor Laboratory, Cold Spring Harobr, NY, USA
|
Scott Cain
|
July 20-23
|
Biomedical Ontologies Tutorials
|
International Conference of Biomedical Ontologies (ICBO), Buffalo, NY, USA
|
Barry Smith
|
June 11
|
Chado Databases and Integration with GMOD Tools
|
2009 Arthropod Genomics Symposium, Kansas City, MO, USA
|
Scott Cain
|
June 11-13
|
Seeing the forest and the trees: visualizing next generation sequence data
|
Next Generation Genome Analysis in Non-Model Organisms, Storrs, CT, USA
|
Dave Clements
|
June 6
|
Database Tools for Evolutionary Genomics: An introduction to GMOD software for managing, annotating and visualizing genomic data See below for links to individual talks.
|
SMBE 2009, Iowa City, IA, USA
|
Dave Clements
|
- Using GMOD for evolutionary genomics and next generation sequence data
|
Dave Clements
|
- The CMap Comparative Map Browser and Displaying Population distributions with GBrowse and PhyloGeoViz
|
Ben Faga
|
- Comparative genomics with GBrowse_syn
|
Sheldon McKay
|
- Simplifying genome annotation and functional genomics with MAKER—the easy-to-use genome annotation pipeline
|
Mark Yandell
|
April 2
|
Visualizing and Integrating Next Generation Sequence Data using GMOD
|
Evolutionary Genetics - the impact of next generation sequencing technologies, Lutherstadt-Wittenberg, Germany
|
Dave Clements
|
January 10-14
|
See PAG 2009 for links to many talks and presentations.
|
Plant and Animal Genome XVII Conference (PAG 2009), San Diego, CA, USA
|
|
Comparative Genomics with GBrowse_syn: A hands on workshop for visualizing your syntenic data with GBrowse_syn
|
Sheldon McKay
|
The Generic Genome Browser: A Hands on Workshop for Installing, Configuring and Using Your Own GBrowse
|
Scott Cain
|
|
2 0 0 8
|
October 30-31
|
InterMine Data Warehouse Workshop
|
Cambridge, UK
|
Richard Smith
|
September 22-23
|
BioCyc / Pathway Tools Tutorial
|
London, UK
|
Peter Karp
|
September 2-5
|
Pathway Tools Tutorial
|
Menlo Park, CA, USA
|
Peter Karp
|
July 20-24
|
See ISMB 2008 for a full list of GMOD related posters and presentations.
|
ISMB 2008, Toronto, ON, Canada
|
|
June 4-7
|
GMOD: Genomics Resources for Emerging Model Organisms
|
American Genetic Association Annual Symposium, Raleigh, NC, USA
|
Dave Clements
|
April 10-13
|
Community Contributions to Genome Annotation (Apollo)
|
Arthropod Genomics Symposium, Kansas City, MO, USA See GMOD at Arthropod Genomics for a complete list.
|
Christine Elsik
|
Chado - A Database Schema for Integrating Biological Data
|
Scott Cain
|
GMOD: Database Resources for Emerging Model Organisms
|
Dave Clements
|
April 4-6
|
GMOD: Informatics Resources for Evolutionary Research
|
IGERT Symposium on Evolution, Development, and Genomics, Eugene, OR, USA
|
Dave Clements
|
GMOD Tools for Comparative Genomics
|
January 15
|
The Generic Genome Browser: A Hands on Workshop for Installing, Configuring and Using Your Own GBrowse
|
Plant and Animal Genome XVII Conference (PAG 2008)
|
Scott Cain
|
|
2 0 0 7
|
November 1-5
|
Digesting the Genome Glut: Promoting the Use and Extension of GMOD To Emerging Model Organisms
|
Genome Informatics 2007, Cold Spring Harbor, NY, USA
|
Dave Clements
|
July 9
|
The GMOD Project: Creating Reusable Software Components for Genome Data
|
Ohio Collaborative Conference on Bioinformatics at Miami University, Oxford, OH, USA
|
Scott Cain
|
|
2006
|
May 10-14
|
An Example Comparative Genome Database for Yeasts Using GMOD Tools
|
The Biology of Genomes, Cold Spring Harbor, NY, USA
|
Scott Cain
|