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

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| [[GBrowse_syn]] developer, [[GBrowse]] developer
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| [http://cshl.edu Cold Spring Harbor Laboratory]
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| [[User:MitchSkinner|Mitch Skinner]]
| [[User:MitchSkinner|Mitch Skinner]]
| [[JBrowse]] developer
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| [http://berkeley.edu University of California, Berkeley]
| [http://berkeley.edu University of California, Berkeley]

Revision as of 18:35, 26 January 2010

Under Construction

This page or section is under construction.

We expect this page to be done, and to start taking applications on January 29, 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 focused on installing, configuring and integrating popular GMOD Components.

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.

The 2010 program will be very similar to what was offered in 2009. A few things will change, but the core will stay the same.

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 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
JBrowse installation, configuration and administration; converting GFF3 to JSON and loading it into JBrowse.
9:00pm Day ends
May 7
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 8
8:45am GBrowse
Scott Cain
1:00pm Lunch
on your own
2:00pm Galaxy
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 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 develoepr Ontario Institute for Cancer Research
Dave Clements GMOD Help Desk National Evolutionary Synthesis Center (NESCent)
Stephen Ficklin Tripal developer Clemson University Genomics Institute
Carson Holt MAKER developer University of Utah
Ed Lee Apollo developer Berkeley Bioinformatics Open-source Projects (BBOP)
Sheldon McKay GBrowse_syn developer, GBrowse developer Cold Spring Harbor Laboratory


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

VMware http://www.vmware.com}} 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 ($80) 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.


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 (probably 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.


Registrations for the course will be competitive. Last year there were over 50 applications for the 25 slots. We will start taking applications for the summer school in late January 2010. Watch this page, the GMOD News, or the GMOD Mailing Lists for the announcements.