GBrowse syn PAG 2009 Workshop

This page provides additional information about the GBrowse_syn workshop at the Plant and Animal Genome XVII Conference (PAG 2009) being held in San Diego on January 10-14, 2009.

Overview

GBrowse_syn is a tool for visualizing synteny in up 5 different genomes. This will be a hands-on tutorial on how to install, configure and use GBrowse_syn.

GBrowse_syn is a part of the GMOD Project and is included in the latest release (1.69) of the popular GBrowse genome browser. (GBrowse is the topic of a separate workshop at PAG.

Workshop Instructors

• Sheldon McKay, iPlant Collaborative (and author of GBrowse_syn), Cold Spring Harbor Laboratory
• Scott Cain, GMOD Project Coordinator, Cold Spring Harbor Laboratory
• Dave Clements, GMOD_Help_Desk, NESCent

Tutorial Level

Beginner to Intermediate. Students should be comfortable performing simple system Linux administration tasks like stopping and starting services, and installing software. No prior knowledge of GBrowse or GBrowse_syn is required.

The tutorial is aimed at computer-savvy biologists and computer scientists working with syntenic data.

Syllabus

The session will include

• Architecture
• Installation
• Loading data
• Configuration

The course will briefly touch on generating syntenic data, but it will not go into detail on different analysis options.

Laptops

This will be a hands-on tutorial and attendees are strongly encouraged to bring their own laptop. We will provide a VMware virtual system image that will have most prerequesites pre-installed. Another option is for students to pre-install all prerequisites and datasets on their own system prior to class.