2008 GMOD Summer School

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GMOD Summer School

July 11-13, 2008
National Evolutionary Synthesis
  Center (NESCent)

Durham, North Carolina, USA


The first annual GMOD Summer School is a 2 1/2 day hands-on workshop aimed at teaching new GMOD users how to get up and running with popular GMOD components.

The course is now full. However, you are still encouraged to submit an application. The course has a (short) waiting list and we will pull people from that list if any openings occur.

If you have applied for the GMOD Summer School you should have received an e-mail from the Help Desk informing you of your admission status.


The program features two and half days of hands on training starting with an overview of GMOD and then covering installation and configuration of popular GMOD tools, include Chado, GBrowse, CMap, Apollo, and the Community Annotation System.

Tentative Program

Date Time Session
July 11
9am - 10:30am GMOD 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, course overview, and installing VMware appliances on student computers.
10:30am - Noon Chado: Theory
Dave Clements
Architecture and logical design of the Chado database schema: Chado's modules and extensibility, how IDs and database cross references are handled, the central role of ontologies/controlled vocabularies, and an overview of how sequence data is handled.
Noon - 1pm Lunch Break
Places to eat
NESCent is adjacent to Durham's 9th Street District.
1pm - 3pm Chado: Practice
Scott Cain
Using Chado: Installation, importing and exporting data, and a complete worked example of loading example sequence data.
3pm - 5pm GBrowse 1
Scott Cain
Overview, GBrowse installation and using GBrowse adaptors
5pm - 6pm Social Hour
Get to know your fellow GMOD Summer School participants, the instructors, and NESCent researchers.
6pm - 7:30pm Dinner Break
Places to eat
7:30pm - 9:30pm Open Discussion
Scott, Dave, Ben, Ed, and You!
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. We expect this to be lively.
July 12
9am - 11:30pm GBrowse 2
Scott Cain
GBrowse Configuration: Changing defaults and displays, adding tracks, and performance tuning
11:30pm - 12:30pm Lunch Break
Places to eat
12:30pm - 4pm Apollo
Ed Lee
Overview, installation, configuration, reading/writing data, setting up a Java WebStart instance.
4pm - 5pm CMap 1
Ben Faga
Overview, installation, configuration and data importation.
5pm - 6:30pm Dinner Break
Places to eat
6:30pm - 9pm CMap 2
Ben Faga
Overview, installation, configuration and data importation.
July 13
9am - 12:30pm Community Annotation System
Scott Cain
How to install and configure the GMOD Community Annotation System, an integrated package of GMOD components (including all the ones covered in this course) that reduces much of the installation, integration, and configuration work of doing each component individually.
12:30 - 1pm Wrapup and Resources
Scott Cain and Dave Clements
Describe the resources available to GMOD users and attempt to bring the course to a coherent close.

Last changed 2008/05/12


Sessions will be taught by experienced GMOD personnel, including:

Who Should Attend?

The GMOD Summer School is for both the people who implement GMOD at your organization, and for Principal Investigators who would benefit from having their organizations use GMOD.

The course goes into detail about how to install and configure GMOD components. It is aimed primarily at GMOD System Administrators, the people who actually implement and manage a GMOD installation on a day to day basis. This course is for organizations that are either planning to use GMOD components, or are in the early phases of implementing GMOD.


The course requires a minimal level of Linux systems administration knowledge (see Computing Requirements). Attendees without that minimal level of knowledge will likely be lost for most of the course.

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. This is a non-trivial task for beginning Linux sys admins, but if you can do this successfully then you will likely fully participate in the course. If you can't then the course will be, at best, frustrating for you.

System Requirements

VmwareLogoSmall.jpg Participants are required to bring their own laptops, and those laptops must already be capable of running a VMware system image.

Each session will start with different VMware image that was built specifically for that session. Some VMware images will incorporate work covered in earlier sessions. For example, the image used in the GBrowse session will already have PostgreSQL and Chado installed and Chado will be preloaded with example data.

VMware on Windows and Linux

WindowsLogoSmall.jpg LinuxLogoSmall.jpg 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

AppleSmall.gif 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:
Mac OS 10.5 (Leopard) and Boot Camp
AppleBootCampLogo.jpg The latest release of Mac OS (10.5, Leopard) 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.*
VMware Fusion
VMWareFusionsLogo.jpg VMware's Fusion product ($79.99) allows you to run Windows or Linux under Mac OS. From there you can install the VMware player for your OS. Scott uses Fusion on a regular basis and is pretty happy with it (though he paid half price for it when it came out).
Parallels Desktop for Mac
ParallelsDesktopLogo.gif Another option is Parallels Desktop for Mac ($79.99). Like Fusion, Parallels allows you to run Windows and Linux under Mac OS. And once again, from there you can install the VMware player for your OS. This requires two 'levels' of virtualization: Parallels to get Windows or Linux and then VMware Player to run the course Linux.*
* This is how they are supposed to work anyway! We haven't tested these options all the way through yet. We will update this page as we try them.


There is no tuition cost for the GMOD Summer School. It's free. Participants are responsible for their own travel, lodging and meal expenses. Assistance is available for travel and living expenses to participants from underrepresented groups; please contact the GMOD Help Desk for more information.


The course is now full. However, you are still encouraged to submit an application The course has a (short) waiting list and we will pull people from that list as openings occur.

If you have applied for the GMOD Summer School you should have received an e-mail from the Help Desk informing you of your admission status.


NESCentMainPageIcon.png The GMOD Summer School will be held at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, United States.

Transportation and lodging information will be added here as the course draws nearer.

Transportation, Lodging, and Meals

Raleigh-Durham International Airport (RDU) is 30 minutes from NESCent. Cheaper flights are sometimes available into Piedmont Triad International Airport near Greensboro which is about 90 minutes from Durham. See Directions to NESCent for more.

NESCent visitors usually stay at Millennium Hotel Durham. The Millennium provides a free shuttle to and from NESCent. We are currently negotiating room rates with them and will post a link here once that is done. We are also investigating other less convenient, but probably lower cost housing options.

The Millennium offers a shuttle between the airport and the hotel for $35 each way. If you are taking the Millennium shuttle, the hotel recommends calling them (919 383 8575) as soon as you are on the ground so they can dispatch the shuttle immediately. You can also call them from a courtesy phone in the baggage area. Charlene's Safe Ride is another option, offering rides to the Millennium for $30.

NESCent is adjacent to Durham's 9th Street District which offers many places to eat. The Millennium Hotel also has a restaurant. Meals are not provided as part of the summer school.

Posters and Fliers

Note: Both of these posters are now out of date. The PI Track has now been combined with the Implementation track, and the schedule details shown on the second one have now changed.


A poster (US Letter size) announcing the 2008 GMOD Summer School is available for download.


A flier with the schedule on it also available for download.

Please post these at your organization.


The GMOD Summer School is funded by NIH grant 1R01HG004483-01 under Ian Holmes.