GMOD
GBrowse PAG 2010 Workshop
 |
The Generic Genome Browser: A Hands on Workshop for
Installing, Configuring and Using Your Own GBrowse January 9-13, 2010 Plant and Animal Genome Conference San Diego, California, USA |
This page provides additional information about the GBrowse workshop at the Plant and Animal Genome XVIII Conference (PAG 2010) held in San Diego on January 9-13, 2009.
Contents
- 1 Overview
- 2 Tutorial Level
- 3 Intended Audience
- 4 Prerequisite Software and Conference PCs
- 5 Outline
- 6 Workshop Instructor
- 7 Other GMOD Presentations and Meetings
Overview
This will 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.
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.
Prerequisite Software and Conference PCs
Prerequisite software for GBrowse will be pre-installed on the conference PCs in the classroom area of the California Room. Participants using these PCs will be able to setup and configure GBrowse during the workshop.
After the workshop, workshop materials and a VMware system image with GBrowse prerequisite software pre-installed will be linked to from this page. You can use VMware image to walk through the material presented at this workshop.
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
Other GMOD Presentations and Meetings
GMOD will have a strong presence at PAG 2010, including
- A workshop on GBrowse_syn, a comparative genomics viewer built on GBrowse
- A workshop on MAKER, a genome annotation pipeline.
- The Gramene Workshop will include a section on the CMap comparative map viewer.
See PAG 2010 for a more complete list of GMOD-related presentations at PAG XVIII.