GBrowse syn PAG 2009 Workshop

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GBrowse syn

This Comparative Genomics with GBrowse_syn: A hands on workshop for visualizing your syntenic data with GBrowse_syn tutorial was presented by Sheldon McKay, Scott Cain, and Dave Clements at the Plant and Animal Genome Conference, January 2009. The most recent GBrowse syn tutorial can be found at the GBrowse syn Tutorial page.


This page provides additional information about the GBrowse_syn 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 almost 70 people.

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 2009.

Workshop Instructors

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 was aimed at computer-savvy biologists and computer scientists working with syntenic data.

Syllabus

The session included

  • Architecture
  • Installation
  • Loading data
  • Configuration

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

Laptops

Our intention was to have this be a hands-on tutorial running GBrowse_syn under VMware. However, we chose instead to hand out copies of the VMware image and encourage people to experiment with it after the workshop.

Prerequisite Software

VMware

Which software to use to run VMware images depends on the operating system you will run the image under. (It does not depend on the operating system inside the VMware image.)

VMware on Windows and Linux
Windoze
Linux

A free VMware player is available for Microsoft Windows and Linux operating systems from VMware. You will need to register to download it. There are multiple versions. Be sure to download a version that can run on your laptop.


VMware on Mac OS X
Apple

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
Fusion

VMware Fusion ($80/corporate, $40/Academic) allows you to run VMware images (as well as 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.


VirtualBox
VirtualBox

VirtualBox is free and open source, and runs on Intel Macs (and Windows, Linux and Solaris too). It claims to be capable of running VMware images, but we have not tested this with our images.

Note:. VMWare and Linux are used to standardize GBrowse_syn installation and configuration for the workshop. They are not mandatory for installation and use of GBrowse or GBrowse_syn.

The DVD distributed at the workshop contained a VMware system image.

System Image

  • The virtual disk image can be downloaded from WormBase ftp
  • The disk image is approximately 1 gigabyte.

Datasets

Other GMOD Presentations and Meetings

GMOD had a strong presence at PAG 2009, including a workshop on GBrowse itself. 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.