GMOD
2009 GMOD Summer School - Europe
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2009 GMOD
Summer School - Europe 3-6 August, 2009 Oxford UK
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The 2009 GMOD Summer School - Europe was held 3-6 August in Oxford, UK. Like the 2008 GMOD Summer School, this course focused on installing, configuring and integrating popular GMOD Components.
The summer school was a part of GMOD Europe 2009 a week long event that also included the August 2009 GMOD Meeting. Another GMOD Summer School was offered in Durham, North Carolina in July 2009.
Contents
- 1 Program
- 2 Instructors
- 3 Prerequisites
- 4 Cost
- 5 Location
- 6 Transportation, Lodging, Meals
- 7 Sponsors
- 8 Feedback
Program
The program featured 3 ½ 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 Chado, GBrowse, GBrowse_syn, BioMart, Apollo, Artemis-Chado Integration, and JBrowse.
| Time | Session | |
|---|---|---|
| Monday 3 August | ||
| 8:30 | 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. |
|
| 10:10 | VMware
and BioPerl Setup Everyone Get the GMOD Summer School VMware image up and running on your laptop, and then finish installation of BioPerl. |
|
| 12:00 | Catered Lunch | |
| 13:00 | Chado Scott Cain and Dave Clements |
|
| 18:00 | Day ends | |
| Tuesday 4 August | ||
| 8:30 | GBrowse Scott Cain and Sheldon McKay |
|
| 12:30 | Catered Lunch | |
| 13:30 | GBrowse_syn Sheldon McKay |
|
| 18:00 | Day ends | |
| Wednesday 5 August | ||
| 8:30 | BioMart Junjun Zhang and Syed Haider 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. |
|
| 12:30 | Lunch on your own | |
| 13:45 | Apollo Ed Lee Overview, installation (from installers and from source), configuration, reading/writing data, remote analyses, and setting up a customized Java Web Start instance. |
|
| 18:00 | Day ends | |
| Thursday 6 August | ||
| 8:30 | Artemis-Chado
Integration Robin Houston, Tim Carver and Giles Velarde Artemis and ACT: Overview, installation, configuration, reading & writing data to Chado. |
|
| 10:10 | JBrowse Ian Holmes |
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| 11:30 | Wrapup
and Resources Dave Clements and Scott Cain |
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| 12:00 | Summer School Ends | |
| 13:30- 18:00 |
August 2009 GMOD Meeting | |
| Friday 7 August | ||
| 8:30- 18:00 |
August 2009 GMOD Meeting | |
Instructors
| Instructor | GMOD Contribution | Affiliation |
|---|---|---|
| Scott Cain | GMOD Project Coordinator | <a href=”http://www.oicr.on.ca/” class=”external text” |
| rel=”nofollow”>Ontario Institute for Cancer Research (OICR)</a> | ||
| Tim Carver | Artemis lead developer | <a href=”http://www.sanger.ac.uk/” class=”external text” |
| rel=”nofollow”>Wellcome Trust Sanger Institute</a> | ||
| Dave Clements | GMOD Help Desk | <a href=”http://nescent.org/” class=”external text” |
| rel=”nofollow”>National Evolutionary Synthesis Center (NESCent)</a> | ||
| Syed Haider | BioMart developer | <a href=”http://www.ebi.ac.uk/” class=”external text” |
| rel=”nofollow”>European Bioinformatics Institute</a> | ||
| Ian Holmes | JBrowse PI | <a href=”http://berkeley.edu” class=”external text” |
| rel=”nofollow”>University of California, Berkeley</a> | ||
| Robin Houston | Artemis manager | <a href=”http://www.sanger.ac.uk/” class=”external text” |
| rel=”nofollow”>Wellcome Trust Sanger Institute</a> | ||
| Ed Lee | Lead Apollo developer | <a href=”http://www.berkeleybop.org/” class=”external text” |
| rel=”nofollow”>Berkeley Bioinformatics Open-source Projects (BBOP)</a> | ||
| Sheldon McKay | Lead GBrowse_syn developer, GBrowse developer | Cold |
| Spring Harbor Laboratory</a> | ||
| Giles Velarde | Developer | <a href=”http://www.sanger.ac.uk/” class=”external text” |
| rel=”nofollow”>Wellcome Trust Sanger Institute</a> | ||
| Junjun Zhang | BioMart developer | <a href=”http://www.oicr.on.ca/” class=”external text” |
| rel=”nofollow”>OICR</a> |
Prerequisites
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
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 (~ £62 / €67) 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
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.
Cost
Tuition for the course was £95. Participants were responsible for their own travel and living expenses.
Tuition for this course did not include registration for the August 2009 GMOD Meeting. The meeting had a separate registration cost from the summer school.
Location
The course was held at the Medical Science Teaching Centre (MSTC) at the University of Oxford, in Oxford, United Kingdom.
Transportation, Lodging, Meals
See the Transportation and Lodging sections of the GMOD Europe 2009 page for information on transport and lodging for both the summer school and August 2009 GMOD Meeting.
Sponsors
We would like to thank the Computational Biology Research Group (CBRG) at the University of Oxford for hosting and financially supporting the week’s events.
Feedback
19 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% | 16% | 84% | 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 1 |
(Poor) 2 |
Average 3 |
(Good) 4 |
Very Good 5 |
N.A. |
|---|---|---|---|---|---|
| 0% | 0% | 21% | 47% | 32% | 0% |