2009 GMOD Summer School - Americas

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2009 GMOD Summer School - Americas
16-19 July, 2009
NESCent
Durham, NC, USA

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The 2009 GMOD Summer School - Americas will be held 16-19 July at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina. Like the 2008 GMOD Summer School, this course will focus on installing, configuring and integrating popular GMOD Components.

Another GMOD Summer School is being offered in Oxford, UK in August, as part of the GMOD Europe 2009 week.

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Draft Program

The program will feature 4 full 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
Thursday
July 16
8:45am 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
10:25am VMware and BioPerl Setup
Everyone
Get the GMOD Summer School VMware image up and running on your laptop, and then finish installation of BioPerl.
12:15pm Lunch
on your own
1:15pm MAKER I
Carson Holt
Maker overview, installation, and basic configuration for annotating genomic sequence
4:30pm Social Hour w/ NESCent Staff
and then Dinner on your own
6:30pm MAKER II
Carson Holt
Advanced Maker configuration, re-annotation options, and improving annotation quality
7:30pm JBrowse
Scott Cain or Dave Clements
JBrowse installation, configuration and administration; converting GFF3 to JSON and loading it into JBrowse.
9:00pm Day ends
Friday
July 17
8:45am Chado I
Scott Cain, Joshua Orvis, and Dave Clements
12:30pm Lunch
on your own
1:30pm Chado II
Scott Cain, Joshua Orvis, and Dave Clements
3:00pm Apollo I
Ed Lee
Overview, basic installation, basic configuration, reading/writing data, and remote analyses.
5:30pm Dinner
on your own
7:00pm Apollo II
Ed Lee
Custom installation (building Apollo from source), advanced configuration, and setting up customized Java Web Start instance.
9:00pm Day ends
Saturday
July 18
8:45am GBrowse I
Scott Cain and Sheldon McKay
12:30pm Lunch
on your own
1:30pm GBrowse II
Scott Cain and Sheldon McKay
2:30pm BioMart
Junjun Zhang
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.
6:00pm Dinner
on your own
7:30pm Open Discussion and User Presentations
Everyone
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. Students will also have the opportunity to share work from their projects with the rest of the group.

We expect this session to be lively.

9:00pm Day ends
Sunday
July 19
8:45am GBrowse_syn
Sheldon McKay
12:30pm Lunch
on your own
1:30pm Tripal
Stephen Ficklin
Tripal is a web front end to Chado databases built on Drupal. This class will introduce Drupal and Tripal architecture, and then cover Tripal installation, configuration and administration.
6:00pm Wrapup and Resources
Dave Clements and Scott Cain
6:30pm Summer School Ends

Instructors

Instructor GMOD Affiliation Affiliation
Scott Cain GMOD Project Coordinator Ontario Institute for Cancer Research
Dave Clements GMOD Help Desk National Evolutionary Synthesis Center (NESCent)
Stephen Ficklin Lead Tripal developer Clemson University Genomics Institute
Carson Holt MAKER developer University of Utah
Ed Lee Lead Apollo developer Berkeley Bioinformatics Open-source Projects (BBOP)
Sheldon McKay Lead GBrowse_syn developer, GBrowse developer Cold Spring Harbor Laboratory
Joshua Orvis Lead Ergatis developer and power Chado user Institute for Genome Sciences
Junjun Zhang BioMart developer Ontario Institute for Cancer Research

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

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
Windoze
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.

Apple
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
VMWareFusionsLogo.jpg
VMware Fusion ({{{1}}}) 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.

Applications

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Cost

This course will be free thanks to NIH grant 1R01HG004483-01 under Ian Holmes, and to the grants of the individual instructors.

Participants are responsible for their own travel, lodging, and living expenses. Some travel scholarships are available for participants from underrepresented groups. Please indicate on your application if you would like to be considered for this option.

Travel, Lodging and Food

The course will be held at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, United States. The closest airport is Raleigh-Durham International Airport (RDU), a 30 minute drive from NESCent.

Participants will be responsible for their own travel, lodging and some meal costs. We will offer a block of rooms in a local hotel at a discounted rate of $79/night (including tax). Participants can share a room to further reduce their costs. The hotel is within walking distance and also will have a free shuttle service to NESCent.

Some meals are included in the summer school. For meals that aren't, NESCent is adjacent to Durham's 9th Street District, which offers many dining options.

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.”