GMOD
2009 GMOD Summer School - Americas
|
2009 GMOD
Summer School - Americas 16-19 July, 2009 NESCent Durham, NC, USA |
The 2009 GMOD Summer School - Americas was held 16-19 July at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina. Like the 2008 GMOD Summer School, this course focused on installing, configuring and integrating popular GMOD Components.
The course wiki is here (login required).
Another GMOD Summer School was offered in Oxford, UK in August, 2009, as part of GMOD Europe 2009.
Contents
Program
The program featured 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 summer school GMOD component sessions are available as online tutorials. To access the tutorials, follow the links for MAKER, JBrowse, Chado, Apollo, GBrowse, BioMart, GBrowse_syn, and Tripal
| 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 Mitch Skinner 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; Chado develoepr | <a href=”http://www.oicr.on.ca/” class=”external text” |
| rel=”nofollow”>Ontario Institute for Cancer Research</a> | ||
| Dave Clements | GMOD Help Desk | <a href=”http://nescent.org/” class=”external text” |
| rel=”nofollow”>National Evolutionary Synthesis Center (NESCent)</a> | ||
| Stephen Ficklin | Tripal developer | <a href=”http://www.genome.clemson.edu/” class=”external text” |
| rel=”nofollow”>Clemson University Genomics Institute</a> | ||
| Carson Holt | MAKER developer | <a href=”http://www.utah.edu” class=”external text” |
| rel=”nofollow”>University of Utah</a> | ||
| Ed Lee | Apollo developer | <a href=”http://www.berkeleybop.org/” class=”external text” |
| rel=”nofollow”>Berkeley Bioinformatics Open-source Projects (BBOP)</a> | ||
| Sheldon McKay | GBrowse_syn developer, GBrowse developer | Cold |
| Spring Harbor Laboratory</a> | ||
| Joshua Orvis | Ergatis developer and power Chado user | <a href=”http://www.igs.umaryland.edu/” class=”external text” |
| rel=”nofollow”>Institute for Genome Sciences</a> | ||
| Mitch Skinner | JBrowse developer | <a href=”http://berkeley.edu” class=”external text” |
| rel=”nofollow”>University of California, Berkeley</a> | ||
| Junjun Zhang | BioMart developer | <a href=”http://www.oicr.on.ca/” class=”external text” |
| rel=”nofollow”>Ontario Institute for Cancer Research</a> |
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
| | |
|—-|—-|
| 
| 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
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.
Cost
This course was free thanks to NIH grant 1R01HG004483-01 under Ian Holmes, and to the grants of the individual instructors.
Feedback
17 of 25 students provided feedback on the course.
Q: Would you recommend GMOD Summer School to others?
| No | Yes, with reservations | Yes | No opinion |
|---|---|---|---|
| 0% | 12% | 88% | 0% |
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 1 |
(Poor) 2 |
Average 3 |
(Good) 4 |
Very Good 5 |
N.A. |
|---|---|---|---|---|---|
| 0% | 0% | 12% | 59% | 23% | 6% |