GMOD
GBrowse PAG 2009 Workshop
 |
The Generic Genome Browser: A Hands on Workshop for
Installing, Configuring and Using Your Own GBrowse January 11, 2009 Plant and Animal Genome Conference San Diego, California, USA |
This page provides additional information about the GBrowse workshop at the Plant and Animal Genome XVII Conference (PAG 2009) held in San Diego on January 10-14, 2009. This workshop was attended by over 60 people.
Contents
- 1 Note on Installation
- 2 Overview
- 3 Tutorial Level
- 4 Intended Audience
- 5 Outline
- 6 Workshop Instructor
- 7 Datasets
- 8 Other GMOD Presentations and Meetings
Note on Installation
An installer package for Microsoft Windows can be downloaded here.
- download the zip file and double-click to unpack
- enter the directory ‘a’ and double-click the executable file ‘install_gbrowse’
- This will install Perl, Apache Web server, and other requirements to run GBrowse on your system
Also, see the Windows installation guide and guides for other operating systems.
Overview
This was be a hands-on tutorial on how to install and use the GBrowse genome browser.
Tutorial Level
Beginner to Intermediate. Students should be comfortable performing simple system administration tasks like stopping and starting services.
Students who wish to use their own computer should preinstall the prerequisites described in the GBrowse installation notes, including Perl, Apache, MySQL and (for Unix) BioPerl.
Intended Audience
GBrowse is sufficiently easy to install that a biologist can easily set up and configure a GBrowse server after the initial hurdles of learning about configuration options and file formats are overcome. This class is intended to help them over those hurdles.
Outline
- The Basics
- The Data File
- Defining Tracks
- Searching for Named Features
- Adding Descriptions to a Feature
- Showing multi-segmented features
- Using Aggregators
- Showing Protein Coding Genes
- Showing the Reading Frame
- Creating Custom Aggregators
- Showing Quantitative Data
- Displaying DNA and 3-frame translations
- Features added in latest release, including draggable and collapsible tracks, and popup balloons
Workshop Instructor
- Scott Cain, GMOD Project Coordinator, Ontario Institute for Cancer Research
Datasets
Example datasets will be posted prior to the conference.
Other GMOD Presentations and Meetings
GMOD will have a strong presence at PAG 2009, including a workshop on GBrowse_syn, a synteny viewer built on GBrowse. See the list of GMOD related PAG 2009 presentations for more. The January 2009 GMOD Meeting was held in San Diego, immediately after PAG 2009.