International PAG - GBrowse Workshop

The Generic Genome Browser: A Hands on Workshop for Installing, Configuring and Using Your Own GBrowse

Sunday Afternoon, January 10, 2010 -- 1:30 pm - 3:40 pm

California Room

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.

Workshop Instructor

Scott Cain, GMOD Project Coordinator, Ontario Institute for Cancer Research

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, a VMware system image with GBrowse prerequisite software pre-installed will be made available on this workshop's page at GMOD.org. You can use this 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

GBrowse and GMOD at PAG

GBrowse is a part of the GMOD Project, a collection of open source software components for visualizing, annotating, and managing biological data. Several other GMOD components are also being presented at PAG XVIII:

CMap - a comparative map viewer; demonstrated during the Gramene Workshop on Tuesday.
GBrowse_syn - a comparative genomics viewer built on top of GBrowse<; featured in the GBrowse_syn Workshop on Wednesday.
MAKER - an easy to run genome annotation pipeline; featured in the MAKER Workshop on Saturday.

See the GMOD web site for a more complete list of GMOD-related presentations at PAG XVIII.

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