2009 GMOD Summer School - Americas

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2009 GMOD Summer School - Americas
16-19 July, 2009
Durham, NC, USA

The 2009 GMOD Summer School - Americas was held 16-19 July at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina. Like the 2008 GMOD Summer School, this course focused on installing, configuring and integrating popular GMOD Components.

The course wiki is here (login required).

Another GMOD Summer School was offered in Oxford, UK in August, 2009, as part of GMOD Europe 2009.


The program featured 4 full days of hands-on training starting with an overview of GMOD, and then covering the installation, configuration, and administration of several popular GMOD Components.

The summer school GMOD component sessions are available as online tutorials. To access the tutorials, follow the links for MAKER, JBrowse, Chado, Apollo, GBrowse, BioMart, GBrowse_syn, and Tripal

Time Session
July 16
8:45am Introduction and Overview
Scott Cain and Dave Clements
Participant and instructor introductions, how the GMOD project works, what software tools are available in GMOD, how they interoperate, what resources are needed to get a GMOD installation up and running, and course overview
10:25am VMware and BioPerl Setup
Get the GMOD Summer School VMware image up and running on your laptop, and then finish installation of BioPerl.
12:15pm Lunch
on your own
1:15pm MAKER I
Carson Holt
MAKER overview, installation, and basic configuration for annotating genomic sequence
4:30pm Social Hour w/ NESCent Staff
and then Dinner on your own
6:30pm MAKER II
Carson Holt
Advanced MAKER configuration, re-annotation options, and improving annotation quality
7:30pm JBrowse
Mitch Skinner
JBrowse installation, configuration and administration; converting GFF3 to JSON and loading it into JBrowse.
9:00pm Day ends
July 17
8:45am Chado I
Scott Cain, Joshua Orvis, and Dave Clements
12:30pm Lunch
on your own
1:30pm Chado II
Scott Cain, Joshua Orvis, and Dave Clements
3:00pm Apollo I
Ed Lee
Overview, basic installation, basic configuration, reading/writing data, and remote analyses.
5:30pm Dinner
on your own
7:00pm Apollo II
Ed Lee
Custom installation (building Apollo from source), advanced configuration, and setting up customized Java Web Start instance.
9:00pm Day ends
July 18
8:45am GBrowse I
Scott Cain and Sheldon McKay
12:30pm Lunch
on your own
1:30pm GBrowse II
Scott Cain and Sheldon McKay
2:30pm BioMart
Junjun Zhang
Introduction; exploring over 20 public databases through BioMart central portal; system installation; accessing BioMart server via API, webservice and DAS; configuration of BioMart server including federation; demonstration of creating data mart.
6:00pm Dinner
on your own
7:30pm Open Discussion and User Presentations
This optional session is open to any and all questions you have on the GMOD Project, GMOD Components, and GMOD users. The instructors will come with their knowledge of GMOD and their opinions on the project's strengths, weaknesses, and future directions. Students will also have the opportunity to share work from their projects with the rest of the group.

We expect this session to be lively.

9:00pm Day ends
July 19
8:45am GBrowse_syn
Sheldon McKay
12:30pm Lunch
on your own
1:30pm Tripal
Stephen Ficklin
Tripal is a web front end to Chado databases built on Drupal. This class will introduce Drupal and Tripal architecture, and then cover Tripal installation, configuration and administration.
6:00pm Wrapup and Resources
Dave Clements and Scott Cain
6:30pm Summer School Ends


Instructor GMOD Affiliation Affiliation
Scott Cain GMOD Project Coordinator; Chado develoepr Ontario Institute for Cancer Research
Dave Clements GMOD Help Desk National Evolutionary Synthesis Center (NESCent)
Stephen Ficklin Tripal developer Clemson University Genomics Institute
Carson Holt MAKER developer University of Utah
Ed Lee Apollo developer Berkeley Bioinformatics Open-source Projects (BBOP)
Sheldon McKay GBrowse_syn developer, GBrowse developer Cold Spring Harbor Laboratory
Joshua Orvis Ergatis developer and power Chado user Institute for Genome Sciences
Mitch Skinner JBrowse developer University of California, Berkeley
Junjun Zhang BioMart developer Ontario Institute for Cancer Research


The course requires a minimal level of Linux systems administration knowledge (see Computing Requirements). By "a minimal level of Linux systems administration knowledge" we mean that participants should be comfortable installing packages under Linux. A good benchmark for this level of knowledge is that you should be able to get a basic GBrowse installation (that is, GBrowse without MySQL) up and running with the example GBrowse data. This also requires installing Apache, and BioPerl and all its dependencies.

Getting a basic GBrowse up and running on your system will be assigned as homework to be done prior to the course's start.

System Requirements

VMware Participants are required to bring their own laptops, already capable of running a VMware system image.

The course started with getting a VMware image built specifically for the course up and running on your machine. We then built upon that image in each succeeding session.

VMware on Windows and Linux
A free VMware player is available for Microsoft Windows and Linux operating systems from VMware. You will need to register to download it.

VMware on Mac OS X

Participants can also bring newer Macs with Intel processors. The Intel processor is a requirement for all the packages discussed below.

There is no free VMware player that runs directly under Mac OS X. However, there are several other options, all of which require an Intel Mac:

VMware Fusion
VMware Fusion ($80) allows you to run VMware images, Windows and Linux under Mac OS. We recommend this option for Mac users. There is a fully functional, 30 day free trial version of VMware Fusion available for download.

Mac OS 10.5 (Leopard) and Boot Camp
Boot Camp

The Leopard release of Mac OS (10.5) includes Boot Camp, a feature that allows you to boot your Mac into another operating system, including Windows or Linux. From there you can install the VMware player for your OS.*

* Apple tells you that you can partition your disk drive at any time using Boot Camp. In practice, this appears to only work easily when you first get your system.


This course was free thanks to NIH grant 1R01HG004483-01 under Ian Holmes, and to the grants of the individual instructors.


17 of 25 students provided feedback on the course.

Q: Would you recommend GMOD Summer School to others?

No Yes, with reservations Yes No opinion
0% 12% 88% 0%

Q: Please rate the quality of the sessions overall, from 1 (very poor) to 3 (average) to 5 (very good), or N.A. if you have no opinion.

Very Poor
Very Good
0% 0% 12% 59% 23% 6%