Difference between revisions of "2010 GMOD Summer School - Americas"

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| style="background-color: #ddffdd" align="center" |'''[[Galaxy]]'''<br />James Taylor<br />Introduction; Installation and configuration of Galaxy; Defining your own tools; ...
| style="background-color: #ddffdd" align="center" |'''[[Galaxy]]'''<br />[[User:JamesTaylor|James Taylor]]<br />Introduction; Installation and configuration of Galaxy; Defining your own tools; ...
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| [http://berkeley.edu University of California, Berkeley]
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| [http://www.emory.edu Emory University]
| [http://www.emory.edu Emory University]

Revision as of 23:51, 4 February 2010

2010 GMOD Summer School - Americas
6-9 May, 2010
Durham, NC, USA


The 2010 GMOD Summer School - Americas will be held 6-9 May at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina. Like previous GMOD Summer Schools, this course will focus on installing, configuring and integrating popular GMOD Components. Sessions will be taught by GMOD Component developers and GMOD staff. There is space in the course for 25 participants, and admission is competitive.


We are now accepting applications for this course.

Admission to the course is competitive and is based on the strength of the application (especially the statement of interest). Last year there were over 50 applications for the 25 slots. The application deadline is the end of Friday, February 22. Any applications received after February 22 will be automatically put on the waiting list. Applicants will be notified of admission status by March 1.

Tentative 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.

This schedule is subject to change.

Date Time Session
May 6
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
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
Carson Holt
MAKER overview, installation, basic configuration for annotating genomic sequence, re-annotation options, and improving annotation quality
5:30pm JBrowse
Mitch Skinner
JBrowse installation, configuration and administration; converting GFF3 to JSON and loading it into JBrowse.
7:30pm Day ends
May 7
8:45am GBrowse
Scott Cain
1:00pm Lunch
on your own
2:00pm Galaxy
James Taylor
Introduction; Installation and configuration of Galaxy; Defining your own tools; ...
6:00pm Open Discussion and User Presentations
This 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.

7:30pm Day ends
May 8
8:45am Chado I
Scott Cain and Dave Clements
1:00pm Lunch
on your own
2:00pm Chado II
Scott Cain and Dave Clements
3:00pm Apollo
Ed Lee
Overview, basic installation, basic configuration, reading/writing data, and remote analyses. Custom installation (building Apollo from source), advanced configuration, and setting up customized Java Web Start instance.
7:30pm Day ends
May 9
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


The tentative list of instructors includes

Instructor GMOD Affiliation Affiliation
Scott Cain GMOD Project Coordinator; Chado, GBrowse Ontario Institute for Cancer Research
Dave Clements GMOD Help Desk National Evolutionary Synthesis Center (NESCent)
Stephen Ficklin Tripal Clemson University Genomics Institute
Carson Holt MAKER University of Utah
Ed Lee Apollo developer Berkeley Bioinformatics Open-source Projects (BBOP)
Sheldon McKay GBrowse_syn, GBrowse Cold Spring Harbor Laboratory
Mitch Skinner JBrowse University of California, Berkeley
James Taylor Galaxy Emory University


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

  1. Comfortable with the Linux command line interface, and
  2. 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.

System Requirements


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

Windows http://www.microsoft.com/}} Linux}} A free VMware player is available for Microsoft Windows and Linux operating systems from VMware. You will need to register to download it. There are multiple versions. Be sure to download a version that can run on your laptop.

VMware on Mac OS X

Apple http://www.apple.com/macosx/}} 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
Fusion http://www.vmware.com/products/fusion/}}&nbsp; VMware Fusion ($80/corporate, $40/Academic) allows you to run VMware images (as well as 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.
VirtualBox-logo.png VirtualBox is free and open source, and runs on Intel Macs (and Windows, Linux and Solaris too). It claims to be capable of running VMware images, but we have not tested this with our images.


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

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 around $85/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.

A light breakfast will be provided everyday. For other meals, NESCent is adjacent to Durham's 9th Street District, which offers many dining options, and a grocery store.