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) 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

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.

Mailing List

If you are planning on or thinking about attending this workshop, please sign up for the workshop's the mailing list. We will use the mailing list to notify participants when files are available for download.

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 prerequesites pre-installed.

Prerequisite Software

VMware

VMware http://www.vmware.com}} Participants are required to bring their own laptops, already set up to be capable of running 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

Datasets

Other GMOD Presentations at PAG 2009

GMOD will have a strong presence at PAG 2009, including a workshop on GBrowse itself. See the list of GMOD related PAG 2009 presentations for more.