Difference between revisions of "2009 GMOD Summer School - Europe"

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| [[User:Buggy|Giles Velarde]]
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| [http://www.sanger.ac.uk/ Wellcome Trust Sanger Institute]

Revision as of 13:33, 5 August 2009

Follow this link to the GMOD Summer School Europe wiki (login required).

GMOD Europe 2009 GMOD Europe 2009}} 2009 GMOD Summer School - Europe
3-6 August, 2009
Oxford UK

Part of GMOD Europe 2009, five days of GMOD including a Community Meeting


The 2009 GMOD Summer School - Europe is being held 3-6 August in Oxford, UK. Like the 2008 GMOD Summer School, this course will focus on installing, configuring and integrating popular GMOD Components.

The summer school is a part of GMOD Europe 2009 a week long event that also includes the August 2009 GMOD Meeting. Another GMOD Summer School is being offered in Durham, North Carolina in July 2009.



The program features 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.

Date Time Session
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
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
4 August
8:30 GBrowse
Scott Cain and Sheldon McKay
12:30 Catered Lunch
13:30 GBrowse_syn
Sheldon McKay
18:00 Day ends
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
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
11:30 Wrapup and Resources
Dave Clements and Scott Cain
12:00 Summer School Ends
August 2009 GMOD Meeting
7 August


Instructor GMOD Contribution Affiliation
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.

System Requirements

VMware http://www.vmware.com}} Participants are required to bring their own laptops, already capable of running a VMware system image.

The course starts with getting a VMware image built specifically for the course up and running on your machine. We then build 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
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.



Submit an application to get on the waiting list.


Tuition for the course will be £95. In addition, participants will be responsible for their own travel and living expenses.

Tuition for this course does not include registration for the August 2009 GMOD Meeting. The meeting will have a separate registration cost from the summer school.


The course is being 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 tranport and lodging for both the summer school and August 2009 GMOD Meeting.

Breakfast is provided by the recommended lodging option(s). Lunch will be provided for the first two days of the course. Dinner is on your own every night.



We would like to thank the Computational Biology Research Group (CBRG) at the University of Oxford for hosting and sponsoring the week's events.

We would also welcome additional sponsors to help reduce the cost of registration. Please contact the GMOD Help Desk if you are interested.

Comments on the 2008 GMOD Summer School
“This was a very smooth course. All of the programs were focused, and well prepared. The instructions on the wiki were clear and the support from the instructors was very lively.” “Great job everybody!”

“Overall an exceptional experience!”
“Well done!”

“Great job all around.”

“I was very impressed by everyone involved in putting on the school. It was very apparent that they had gone the extra mile and really cared about the quality of the classes.”
“Thank you very much for this first GMOD Summer School.” “The course was what I was expecting and more.”