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.

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 Desription
Apollo Apollo Tutorial The Apollo session from the 2009 GMOD Summer Schools.
Apollo Userguide A comprehensive guide to installing and using Apollo.
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, and Resources - how to download sample data and install Apollo on an MS Windows system.
Chado Chado Tutorial Based on the Chado session from the 2009 GMOD Summer Schools.
Artemis-Chado Integration Tutorial Based on the session of the same title from the 2009 GMOD Summer School - Europe.
CMap Gramene CMap User Tutorial Available in both PDF and PowerPoint formats. This explains how to use CMap in the context of Gramene.
GBrowse GBrowse User Tutorial A Flash based tutorial on using GBrowse. Provided by OpenHelix. Tutorial includes slides, handouts and exercises.
GBrowse2 Admin Tutorial Detailed explanation of how to install and configure GBrowse.
GBrowse Tutorial Based on the GBrowse session from the 2009 GMOD Summer Schools. This relies heavily on the GBrowse2 Admin Tutorial.
GBrowse_syn GBrowse_syn Tutorial Based on the GBrowse_syn session from the 2009 GMOD Summer Schools.
JBrowse JBrowse Tutorial Based on the JBrowse session from the 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 2009 GMOD Summer Schools.

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

GMOD Summer 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

Workshops, Presentations and Posters

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
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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
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November 16-17 InterMine Data Warehouse Workshop Cambridge, UK Richard Smith
Comparative Genomics with GMOD Information Systems for Insect Pests, Rennes, France Dave Clements
Oct 28 Database Tools for Biologists: A Half-Day GMOD Workshop Bioinformatics Australia 2009 (BA2009), Melbourne, Australia Dave Clements
Oct 21-22 Interactive Workshops on the UCSC Genome Browser and Galaxy Framework The American Society of Human Genetics (AHSG), Honolulu, Hawaii
Oct 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
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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
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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

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

GMOD Community Meetings

August 2009 GMOD Meeting

Finally, once or twice a year the GMOD community gathers to discuss GMOD Components, best practices, and project direction. These meetings usually occur immediately before or after a major conference that is likely to be of interest to members of the community. Meetings are open to everyone: developers, users, and potential users. Registration is often free. GMOD also sponsors a few other types of meetings such as hackathons. See Meetings for more.