Difference between revisions of "GBrowse syn PAG 2009 Workshop"
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'''If you are planning on or thinking about attending this workshop, please [https://lists.nescent.org/mailman/listinfo/gbrowse-syn-workshop-pag2009 sign up for the workshop's the mailing list].''' We will use the mailing list to notify participants when files are available for download. | '''If you are planning on or thinking about attending this workshop, please [https://lists.nescent.org/mailman/listinfo/gbrowse-syn-workshop-pag2009 sign up for the workshop's the mailing list].''' We will use the mailing list to notify participants when files are available for download. | ||
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== Laptops == | == Laptops == |
Revision as of 21:42, 22 August 2008
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:
Contents
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.
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. |