Difference between revisions of "GBrowse syn PAG 2009 Workshop"

From GMOD
Jump to: navigation, search
(System Image)
m (reformatting, removing #icon stuff)
 
(6 intermediate revisions by 3 users not shown)
Line 1: Line 1:
<center>
+
{{ TutorialHeader
{| style="font-size: 140%; vertical-align: middle; border: 2px solid #A6A6BC; line-height: 120%" cellpadding="10"
+
| title = Comparative Genomics with GBrowse_syn: A hands on workshop for visualizing your syntenic data with GBrowse_syn
| {{#icon: Paglogo.gif|PAG 2009||http://www.intl-pag.org/}}
+
| what = GBrowse syn
| valign="center" | <b>[http://www.intl-pag.org/17/17-gbrowse2.html Comparative Genomics with GBrowse_syn: A hands on workshop for visualizing your syntenic data with GBrowse_syn]</b><br /><br />January 14, 2009<br />[http://www.intl-pag.org/ Plant and Animal Genome Conference]<br />San Diego, California, USA
+
| when = January 2009
|}
+
| where = [http://www.intl-pag.org/ Plant and Animal Genome Conference]
</center>
+
| who = [[User:Mckays|Sheldon McKay]], [[User:Scott|Scott Cain]], and [[User:Clements|Dave Clements]]
__NOTITLE__
+
| logo = GBrowse_syn_logo.png
 +
}}
  
  
This page provides additional information about the [http://www.intl-pag.org/17/17-gbrowse2.html GBrowse_syn workshop] at the [http://www.intl-pag.org/ Plant and Animal Genome XVII Conference (PAG 2009)] being held in San Diego on January 10-14, 2009.
+
This page provides additional information about the [http://www.intl-pag.org/17/17-gbrowse2.html GBrowse_syn workshop] at the [http://www.intl-pag.org/ 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.
 
+
'''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 mailing list] and read the [[#Prerequisite Software|prerequisites]].'''  We will use the mailing list to notify participants when files are available for download.
+
  
 
== Overview ==
 
== Overview ==
Line 16: Line 15:
 
[[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 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 [http://www.intl-pag.org/17/17-gbrowse.html separate workshop] at PAG.
+
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 [[GBrowse PAG 2009 Workshop|separate workshop]] at [[PAG 2009]].
  
 
== Workshop Instructors ==
 
== Workshop Instructors ==
Line 28: Line 27:
 
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.
 
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.
+
The tutorial was aimed at computer-savvy biologists and computer scientists working with syntenic data.
  
 
== Syllabus ==
 
== Syllabus ==
  
The session will include
+
The session included
  
 
* Architecture
 
* Architecture
Line 39: Line 38:
 
* Configuration
 
* Configuration
  
The course will briefly touch on generating syntenic data, but it will not go into detail on different analysis options.
+
The course briefly touched on generating syntenic data, but it did not go into detail on different analysis options.
 
+
== Mailing List ==
+
 
+
'''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 mailing list].'''  We will use the mailing list to notify participants when files are available for download.
+
  
 
== Laptops ==
 
== 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 of an Ubuntu linux system with GBrowse_syn and prerequisites pre-installed.
+
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 ==
 
== Prerequisite Software ==
  
 
=== VMware ===
 
=== 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.
 
  
{|
+
{{Template:VMwareOptions}}
| {{#icon: VmwareLogoSmall.jpg|VMware||http://www.vmware.com}}
+
|''Participants are required to bring their own laptops, already set up to be capable of running a [http://www.vmware.com VMware] system image.''
+
|}
+
  
==== VMware on Windows and Linux ====
+
'''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 [http://www.vmware.com VMware] system image.''
| {{#icon: WindowsLogoSmall.jpg|Windows||http://www.microsoft.com/}}
+
| {{#icon: LinuxLogoSmall.jpg|Linux}}
+
|A free VMware player is available for [[:Category:Windows|Microsoft Windows]] and [[:Category:Linux|Linux]] [[Glossary#Operating System|operating systems]] from [http://vmware.com/products/player/ VMware].  You will need to register to download it.
+
|}
+
 
+
==== VMware on Mac OS X ====
+
 
+
 
+
{|
+
| {{#icon: AppleSmall.gif|Apple||http://www.apple.com/macosx/}}
+
| There is no free VMware player that runs ''directly'' under [[:Category:Mac OS X|Mac OS X]].  However, there are several options.<br />'''NOTE: All options for using VMware on a Mac require an Intel Mac.''':
+
 
+
|}
+
 
+
; VMware Fusion
+
{|
+
| {{#icon: VMWareFusionsLogo.jpg|Fusion||http://www.vmware.com/products/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
+
{|
+
| {{#icon: AppleBootCampLogo.jpg|Boot Camp||http://www.apple.com/macosx/features/bootcamp.html}}
+
| The [http://www.apple.com/macosx/ Leopard release of Mac OS (10.5)] includes [http://www.apple.com/macosx/features/bootcamp.html 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.*
+
|}
+
 
+
{|
+
| valign="top" | '''*'''
+
| ''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 ===
 
=== System Image ===
* The virtual disk image can be downloaded <span class="pops">[ftp://ftp.wormbase.org/pub/gmod here]</span>
+
* The virtual disk image can be downloaded from [ftp://ftp.wormbase.org/pub/gmod WormBase ftp]
* The disk image is approximately 1 Gbyte.  If it is not possible to download the image, a limited number of copies will be available at the workshop.
+
* The disk image is approximately 1 gigabyte.
  
 
== Datasets ==
 
== Datasets ==
Line 101: Line 62:
 
== Other GMOD Presentations and Meetings ==
 
== Other GMOD Presentations and Meetings ==
  
GMOD will have a [[PAG 2009|strong presence]] at PAG 2009, including a [[GBrowse PAG 2009 Workshop|workshop on GBrowse]] itself.  See the [[PAG 2009|list of GMOD related PAG 2009 presentations]] for more.
+
GMOD had a [[PAG 2009|strong presence]] at PAG 2009, including a [[GBrowse PAG 2009 Workshop|workshop on GBrowse]] itself.  See the [[PAG 2009|list of GMOD related PAG 2009 presentations]] for more. The [[January 2009 GMOD Meeting]] was held in San Diego, immediately after PAG 2009.
 
+
The [[January 2009 GMOD Meeting]] will be held in San Diego, immediately after PAG 2009.  If you want to meet with GMOD users and developers and learn more about GMOD, then [[January 2009 GMOD Meeting|please consider attending]].
+
  
 
[[Category:Education and Outreach]]
 
[[Category:Education and Outreach]]
 +
[[Category:GBrowse syn]]

Latest revision as of 21:29, 3 October 2012


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.