GBrowse syn PAG 2009 Workshop

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PAG 2009 http://www.intl-pag.org/}} Comparative Genomics with GBrowse_syn: A hands on workshop for visualizing your syntenic data with GBrowse_syn

January 14, 2009
Plant and Animal Genome Conference
San Diego, California, USA

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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 had out copies of the VMware image and encourage people to experiment with it after the workshop.

Prerequisite Software

VMware

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.

VMware http://www.vmware.com}} The DVD distributed at the workshop contained a VMware system image.

VMware on Windows and Linux

Windows http://www.microsoft.com/}} Linux}} A free VMware player is available for Microsoft Windows and Linux operating systems from VMware. You will need to register to download it.

VMware on Mac OS X

Apple http://www.apple.com/macosx/}} There is no free VMware player that runs directly under Mac OS X. However, there are several options.
NOTE: All options for using VMware on a Mac require an Intel Mac.:
VMware Fusion
Fusion http://www.vmware.com/products/fusion/}} VMware Fusion ($79.99) allows you to run VMware images, Windows and Linux under Mac OS. This is our recommended choice for Mac users. A fully functional, 30 day free trial version of VMware Fusion is available for download.
Mac OS 10.5 (Leopard) and Boot Camp
Boot Camp http://www.apple.com/macosx/features/bootcamp.html}} The Leopard release of Mac OS (10.5) includes Boot Camp, a feature that allows you to boot your Mac into another operating system, including Windows or Linux. From there you can install the VMware player for your OS.*
* Apple tells you that you can partition your disk drive at any time using Boot Camp. In practice, this appears to only work easily when you first get your system.

System Image

  • The virtual disk image can be downloaded here
  • 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.

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