Difference between revisions of "Training and Outreach"

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== Workshops, Presentations and Posters ==
 
== Workshops, Presentations and Posters ==
  
The items listed here are either about GMOD and its components, or are of general interest to the GMOD community.
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The items listed here are either about GMOD and its components, or are of general interest to the GMOD community.
  
 
'''The GMOD [[Calendar]] also includes all these events, plus many more.'''
 
'''The GMOD [[Calendar]] also includes all these events, plus many more.'''
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! May 15-17
 
! May 15-17
| '''First [[Galaxy]] Developers Conference'''
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| '''[http://galaxy.psu.edu/dev2010/ First Galaxy Developers Conference]'''
 
| Penn State, State College, PA, USA
 
| Penn State, State College, PA, USA
 
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|
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|-
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! March 20-23
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| '''[[ABRF2010_Workshop|GMOD Browser Tools and Exercises Workshop]]'''
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| [http://www.abrf2010.org/ ABRF 2010], Sacramento, CA, USA
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| [[User:MitchSkinner|Mitch Skinner]]
 
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|-
 
! March 3-5
 
! March 3-5

Revision as of 00:24, 27 February 2010

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, 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 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

GMOD Community Meetings

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. The most recent meeting was in January 2010 in San Diego, immediately after PAG 2010. See Meetings for more.
January 2010 GMOD Meeting

Workshops, Presentations and Posters

The items listed here are either about GMOD and its components, or are of general interest to the GMOD community.

The GMOD Calendar also includes all these events, plus many more.

Date Topic Conference / Location Contact
2
0
1
0
May 15-17 First Galaxy Developers Conference Penn State, State College, PA, USA
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 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
PAG 2010 will be immediately followed by the January 2010 GMOD Meeting. If you are attending PAG, you are encourage to also attend the the GMOD meeting.
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 (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

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