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 specific interest to the GMOD community. The GMOD Calendar also includes all these events, plus many more. Please see GMOD Promotion if you have an event or presentation you would like to promote within GMOD.
Date
|
Conference / Topic(s)
|
Location
|
Contact
|
|
2 0 1 1
|
October 23-24
|
IEEE Symposium on Biological Data Visualization (BioVis 2011), part of VisWeek
- The Galaxy Track Browser: Transforming the Genome Browser from Visualization Tool to Analysis Tool
|
Providence, Rhode Island, United States
|
Jeremy Goecks
|
October 12-13
|
October 2011 GMOD Meeting
|
Ontario Institute for Cancer Research (OICR), Toronto, Canada
|
Scott Cain
|
September 28-30
|
Genome Annotation Genome annotation using MAKER and Apollo.
|
UC Davis Bioinformatics Core
|
Barry Moore
|
September 19-22
|
Genome Informatics Workshop @ Beyond the Genome 2011
|
Washington, DC, United States
|
Lincoln Stein, James Taylor
|
July 15-19
|
ISMB/ECCB 2011 Included the Bioinformatics Open Source Conference (BOSC) and plenty of GMOD-related content.
|
Vienna, Austria
|
Scott Cain
|
July 10-23
|
Workshop on Comparative Genomics, North America Sessions on BioPerl, Galaxy and GBrowse_syn
|
Fort Collins, Colorado, United States
|
Jason Stajich, Dan Blankenberg, Sheldon McKay
|
June 21-22
|
Pathway Tools Flux Balance Analysis Tutorial
|
SRI, Menlo Park, California, United States
|
Tomer Altman
|
June 9-12
|
Arthropod Genomics Symposium GMOD had a strong presence with a mixture of talks, poster, and these workshops:
- Genome Project 101, June 9, 4:00-6:00 p.m.
- Comparative genomics with the generic synteny browser (GBrowse_syn): Configuration and display of various co-linearity data types, June 11, 10:30-Noon
|
Kansas City, Missouri, United States
|
Scott Cain, Dave Clements, Sheldon McKay
|
May 28-31
|
European Human Genetics Conference 2011 Galaxy Workshop
|
Amsterdam, The Netherlands
|
Dave Clements
|
May 25-26
|
2011 Galaxy Community Conference
- Two full days of presentations and discussion on extending Galaxy to use new tools and data sources, deploying Galaxy at your organization, and best practices for using Galaxy to further your research.
|
Conference Centre De Werelt, Lunteren, The Netherlands
|
Dave Clements
|
April 13-14
|
NBIC Galaxy Hackathon
|
Belgium (near Maastricht, the Netherlands)
|
NBIC
|
April 12-14
|
Dynamically Scalable, Accessible Analysis for High-Throughput Sequence Data (Galaxy)
|
Bio-IT World, Boston, Massachusetts, United States
|
Enis Afgan
|
March 5-12
|
GMOD Americas 2011 This event includes:
- March 2011 GMOD Meeting
- Satellite Meetings - GMOD Americas 2011
- 2011 GMOD Spring Training (application deadline January 7)
|
NESCent, Durham, North Carolina, United States
|
Scott Cain, Dave Clements
|
February 19-22
|
Galaxy Next Generation Sequencing Functionality from Sample Tracking to SNP Calling
|
ABRF 2011, San Antonio, Texas, United States
|
Greg Von Kuster
|
February 2-5
|
Management and Analysis of Second and Third Generation Sequencing Data with Galaxy
|
Advances in Genome Biology and Technology (AGBT 2011), Marco Island, Florida, United States
|
Anton Nekrutenko, James Taylor
|
January 15-19
|
Plant and Animal Genome XIX There was a strong GMOD presence at PAG, including for the first time, a dedicated all-day GMOD Workshop.
|
San Diego, California, United States
|
Scott Cain, Dave Clements
|
January 9-21
|
Workshop on Comparative Genomics, Europe Sessions on Galaxy and GBrowse_syn
|
Český Krumlov, Czech Republic
|
Anton Nekrutenko, Sheldon McKay
|
Date
|
Topic
|
Conference / Location
|
Contact
|
|
2 0 1 0
|
November 15-16
|
InterMine Workshop
|
Department of Genetics, Cambridge, UK
|
Richard Smith
|
November 8-12
|
GMOD Tools For Evolutionary Biology Hackathon
|
NESCent, Durham, North Carolina, United States
|
Dave Clements
|
November 3-9
|
Computational & Comparative Genomics Included material on Galaxy and BioMart.
|
Cold Spring Harbor, NY, USA
|
William Pearson
|
November 3-4
|
UCSC Genome Browseer and Galaxy Workshops
|
American Society of Human Genetics (ASHG), Washington DC, United States
|
Robert Kuhn
|
November 2
|
World Tour of Genome Browser and Galaxy of Analysis Tools
|
Pre-ASHG workshop put on by OpenHelix including content on BioMart and Galaxy. Washington DC, United States
|
OpenHelix
|
October 25-29
|
Pathway Tools Workshop
|
SRI International, Menlo Park, CA, USA
|
Tomer Altman
|
October 11-14
|
Biocuration 2010
|
Tokyo International Exchange Center, Odaiba, Tokyo, Japan
|
Biocuration2010@ics-inc.co.jp
|
September 13-16
|
GMOD Europe 2010 This 4 day event included:
|
University of Cambridge, Cambridge, UK
|
Scott Cain, Dave Clements
|
- September 2010 GMOD Meeting
|
Scott Cain
|
- Satellite Meetings
|
Dave Clements
|
- InterMine Workshop
|
Richard Smith
|
- BioMart Workshop
|
Xose Fernandez
|
July 9-13
|
There was a lot of GMOD related content at ISMB 2010 this year. See the ISMB 2010 page and flier for a complete list.
|
ISMB 2010, Boston, MA, USA
|
Scott Cain
|
June 29-30
|
GMOD for Evolutionary Biology
|
iEvoBio 2010, Portland, OR, USA
|
Dave Clements
|
June 10-13
|
MAKER: Genome annotation made easy
|
Arthropod Genomics Symposium, Kansas City, MO, USA
|
Carson Holt
|
May 15-17
|
First Galaxy Developers Conference
|
Cold Spring Harbor, NY, USA
|
|
May 6-9
|
2010 GMOD Summer School - Americas
|
NESCent, Durham, North Carolina, United States
|
Dave Clements
|
March 20-23
|
GMOD Browser Tools and Exercises Workshop
|
ABRF 2010, Sacramento, CA, USA
|
Mitch Skinner
|
March 3-5
|
EMBO Workshop on Visualizing Biological Data (VizBi)
|
EMBL Advanced Training Centre, Heidelberg, Germany.
|
Adela Valceanu
|
February 22-26
|
Programmatic Access To Biological Databases (Perl)
This includes sessions on BioMart and DAS.
|
EMBL-EBI, Hinxton, UK
|
|
January 14-15
|
January 2010 GMOD Meeting
|
San Diego, California, United States
|
Scott Cain
|
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
|
December 8
|
Database Tools for Biologists
|
Texas A&M University, College Station, Texas, US
|
Dave Clements
|
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 (ASHG), Honolulu, Hawaii
|
|
October 12-27
|
Programming for Biology Session on GBrowse.
|
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
|
Scott Cain
|
August 3-7
|
GMOD Europe 2009 This week-long event included:
|
University of Oxford, Oxford, United Kingdom
|
Scott Cain, Dave Clements
|
- 2009 GMOD Summer School - Europe
|
Dave Clements
|
- August 2009 GMOD Meeting
|
Scott Cain
|
July 20-23
|
Biomedical Ontologies Tutorials
|
International Conference of Biomedical Ontologies (ICBO), Buffalo, NY, USA
|
Barry Smith
|
July 16-19
|
2009 GMOD Summer School - Americas
|
NESCent, Durham, North Carolina, United States
|
Dave Clements
|
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 15-16
|
January 2010 GMOD Meeting
|
San Diego, CA, USA
|
Scott Cain
|
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
|
|
July 16-17
|
July 2008 GMOD Meeting
|
University of Toronto, Toronto, ON, Canada
|
Scott Cain
|
July 11-13
|
2008 GMOD Summer School
|
NESCent, Durham, North Carolina, United States
|
Dave Clements
|
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 5-7
|
November 2007 GMOD Meeting
|
Cold Spring Harbor, NY, USA
|
Scott Cain
|
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
|
August 23-24
|
Hackathon 2007
|
Northwestern University, Chicago, Illinois, USA
|
Scott Cain
|
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
|
January 18-19
|
January 2007 GMOD Meeting
|
San Diego, CA, USA
|
Scott Cain
|
|
2006
|
June 29-30
|
June 2006 GMOD Meeting
|
NESCent, Durham, North Carolina, United States
|
Scott Cain
|
May 10-14
|
An Example Comparative Genome Database for Yeasts Using GMOD Tools
|
The Biology of Genomes, Cold Spring Harbor, NY, USA
|
Scott Cain
|
|
2005
|
October 27-28
|
October 2005 GMOD Meeting
|
Cold Spring Harbor, New York, before Genome Informatics
|
Scott Cain
|
May 16-17
|
May 2005 GMOD Meeting
|
Menlo Park, California, at SRI
|
Scott Cain
|
|
2004
|
October 4-5
|
October 2004 GMOD Meeting
|
Cold Spring Harbor, New York
|
Scott Cain
|
April 26-28
|
April 2004 GMOD Meeting
|
Cambridge, Massachusetts
|
Scott Cain
|
|
2003
|
May 6-7
|
May 2003 GMOD Meeting
|
Cold Spring Harbor, New York, before Genome Informatics
|
Scott Cain
|
February 5
|
February 2003 GMOD Meeting
|
San Diego, California, coinciding with the O'Reilly Bioinformatics Technology Conference
|
Scott Cain
|
|
2002
|
April 29-30
|
NIH 2002 Workshop on Model Organism Databases The meeting where GMOD was born.
|
NIH, Bethesda, Maryland
|
|