2009 GMOD Summer School - Europe
| 2009 GMOD Summer School - Europe|
3-6 August, 2009
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.
|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|
Get the GMOD Summer School VMware image up and running on your laptop, and then finish installation of BioPerl.
Scott Cain and Dave Clements
Scott Cain and Sheldon McKay
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|
Overview, installation (from installers and from source), configuration, reading/writing data, remote analyses, and setting up a customized Java Web Start instance.
Robin Houston, Tim Carver and Giles Velarde
Artemis and ACT: Overview, installation, configuration, reading & writing data to Chado.
|11:30||Wrapup and Resources|
Dave Clements and Scott Cain
|12:00||Summer School Ends|
|August 2009 GMOD Meeting|
|Scott Cain||GMOD Project Coordinator||Ontario Institute for Cancer Research (OICR)|
|Tim Carver||Artemis lead developer||Wellcome Trust Sanger Institute|
|Dave Clements||GMOD Help Desk||National Evolutionary Synthesis Center (NESCent)|
|Syed Haider||BioMart developer||European Bioinformatics Institute|
|Ian Holmes||JBrowse PI||University of California, Berkeley|
|Robin Houston||Artemis manager||Wellcome Trust Sanger Institute|
|Ed Lee||Lead Apollo developer||Berkeley Bioinformatics Open-source Projects (BBOP)|
|Sheldon McKay||Lead GBrowse_syn developer, GBrowse developer||Cold Spring Harbor Laboratory|
|Giles Velarde||Developer||Wellcome Trust Sanger Institute|
|Junjun Zhang||BioMart developer||OICR|
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.
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
- 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.Mac OS X. However, there are several other options, all of which require an Intel Mac:
- VMware Fusion
- 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.
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.
Transportation, Lodging, Meals
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.
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|
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