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Training and Outreach

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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.

Training and outreach are done by the GMOD Project Coordinator, the GMOD Help Desk, GMOD component developers, and by GMOD users.

See also GMOD Meetings.


Please contact the GMOD Help Desk if you have a training and outreach question or request.

Online Tutorials

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

This website also has a large collection of HOWTOs on more specific tasks.

GMOD Schools

GMOD Online Training 2014 GMOD Malaysia 2014 2013 GMOD Summer School 2012 GMOD Summer School 2011 GMOD Spring Training 2010 Americas 2009 Europe 2009 Americas

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.

Date School Location
2014 February 26-28 GMOD Malaysia 2014 Kuala Lumpur, Malaysia
May 19-23 GMOD Online Training 2014 Online!
2013 July 19-23 2013 GMOD Summer School NESCent, Durham, NC, United States
2012 August 24-29 2012 GMOD Summer School NESCent, Durham, NC, United States
2011 March 8-12 2011 GMOD Spring Training NESCent, Durham, NC, United States
2010 May 6-9 2010 GMOD Summer School - Americas NESCent, Durham, NC, United States
2009 3-6 August 2009 GMOD Summer School - Europe Oxford, United Kingdom
16-19 July 2009 GMOD Summer School - Americas NESCent, Durham, NC, United States
2008 11-13 July 2008 GMOD Summer School NESCent, Durham, NC, United States


Events: Courses, Meetings, Workshops, Presentations and Posters

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.

See the Posters and Presentations categories for many additional presentations by GMOD staff, developers and users.

See the GMOD meetings page for more on GMOD community meetings and other related rendezvous.


2013 Events

Date Conference / Topic(s) Location Contact

2
0
1
3
July 19-23 2013 GMOD Summer School

Training course on all things GMOD

NESCent, Durham, NC GMOD Help Desk
June 30 - July 2 2013 Galaxy Community Conference (GCC2013)
The Galaxy project's annual meeting.
Oslo, Norway Dave Clements
April 7-10 Biocuration 2013 Cambridge, United Kingdom n/a
April 5-6 2013 GMOD Meeting
Colocated with and immediately before Biocuration 2013
Scott Cain
January PAGXXI (Plant and Animal Genomes)
See PAG 2013 for details of GMOD at PAGXXI
San Diego, CA Scott Cain

2012 Events

Date Conference / Topic(s) Location Contact

2
0
1
2
August 24-29 2012 GMOD Summer School NESCent, Durham, North Carolina, United States Scott Cain
July 25-27 2012 Galaxy Community Conference (GCC2012)
The Galaxy project's annual meeting.
Chicago, Illinois, United States Dave Clements
April 5-6 April 2012 GMOD Meeting
Colocated with and immediately following Biocuration 2012
Washington, DC, United States Scott Cain
April 2-4 Biocuration 2012
January 23-25 GMOD Workshop Český Krumlov, Czech Republic Scott Cain
January 8-21 Workshop on Genomics
Covers a plethora of topics, including Galaxy
James Taylor
January 14-18 Plant and Animal Genome XX (PAG 2012)
There will once again be a strong GMOD presence at PAG, including a dedicated all-day GMOD Workshop.
San Diego, California, United States Scott Cain

2011 Events

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

2002 through 2010 Events

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