GMOD

Training and Outreach

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.

Contents

• 1 Online Tutorials
• 2 GMOD Schools
• 3 Events: Courses, Meetings, Workshops, Presentations and Posters
  • 3.1 2013 Events
  • 3.2 2012 Events
  • 3.3 2011 Events
  • 3.4 2002 through 2010 Events

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: Galaxy 101 Screencasts Shared Pages, Histories & Workflows Other Tutorials Working With Datasets and more! 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 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	<a href=”http://www.nescent.org” class=”external text”
rel=”nofollow”>NESCent</a>, Durham, NC, United States
2012	August 24-29	2012 GMOD Summer School	<a href=”http://www.nescent.org” class=”external text”
rel=”nofollow”>NESCent</a>, Durham, NC, United States
2011	March 8-12	2011 GMOD Spring Training	<a href=”http://www.nescent.org” class=”external text”
rel=”nofollow”>NESCent</a>, Durham, NC, United States
2010	May 6-9	2010 GMOD Summer School - Americas	<a href=”http://www.nescent.org” class=”external text”
rel=”nofollow”>NESCent</a>, Durham, NC, United States
2009	3-6 August	2009 GMOD Summer School - Europe	Oxford, United Kingdom
	16-19 July	2009 GMOD Summer School - Americas	<a href=”http://www.nescent.org” class=”external text”
rel=”nofollow”>NESCent</a>, Durham, NC, United States
2008	11-13 July	2008 GMOD Summer School	<a href=”http://www.nescent.org” class=”external text”
rel=”nofollow”>NESCent</a>, 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

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• GBrowse syn
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• Last updated at 21:09 on 6 August 2013.
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