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2008 GMOD Summer School
GMOD Summer School July 11-13, 2008 National Evolutionary Synthesis Center (NESCent) Durham, North Carolina, USA |
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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.
Contents
Program
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 |
---|---|---|
Friday 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. | |
Saturday 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. | |
Sunday 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
Instructors
Sessions will be taught by experienced GMOD personnel, including:
- Scott Cain - GMOD Project Coordinator
- Dave Clements - GMOD Help Desk
- Ben Faga - CMap (and other GMOD components) developer
- Ed Lee - Apollo developer
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.
Prerequisites
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
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
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
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
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
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. A fully functional, 30 day trial version, of VMware Fusion is available for download. |
- Parallels Desktop for Mac
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. A fully functional, 15 day trial version of Parallels Desktop for Mac is available for download. |
* | 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. |
Cost
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.
Registration
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.
Location
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 the Millennium Hotel Durham. The Millennium provides a free shuttle to and from NESCent. We have negotiated a special room rate of $114 per night, including tax. To get that rate click here, or you call the Millennium directly at 1 800 633 5379. Finally you can book through the general hotel website. Our group code is 7243.
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 around $30. Taxi fare is around $42.
We are currently also negotiating room rates and shuttles with other lower cost, but also less convenient, housing options.
NESCent is adjacent to Durham's 9th Street District which offers many places to eat, including breakfast options. 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.
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Please post these at your organization.
Acknowledgements
The GMOD Summer School is funded by NIH grant 1R01HG004483-01 under Ian Holmes.