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ASPB 2012 GBrowse Tutorial

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Registration for the GBrowse tutorial at ASPB is now closed, with 97 registered attendees.

Other Items of Interest

  • GMOD Summer School - Applications are officially closed, but if you indicate you were at this workshop, you might get in on "stand by".
  • GMOD in the Cloud - An Amazon Web Services (AWS), aka "the Cloud", instance with lots of GMOD software preinstalled and configured.

VirtualBox Appliance

For this workshop, we will be using a VirtualBox appliance (or virtual machine) that is running Ubuntu 12.04. VirtualBox is a free, open source application available for Windows, MacOS X and Linux that is similar to Parellels or VMware. Please download and install the version appropriate for your laptop.

The appliance should also be downloaded from the GMOD ftp site before the start of the workshop. The appliance is 1.3 GB as a compressed tar file (which can be uncompressed by 7zip on Windows or built in compression tools on Linux or MacOS X systems) and is 3.5 GB when uncompressed. After downloading and unpacking, you should have a folder called GBrowse Tutorial. In that folder is a file called "GBrowse tutorial.vbox". Double clicking on that file will start up the Ubuntu virtual machine. If that doesn't work, you can also start VirtualBox and select "Add..." from the Machine menu, and find the GBrowse tutorial.vbox file in the open dialog. The Ubuntu appliance will start up and automatically log you in as a user named "gmod"; the password for that user is also gmod, which we may need during the tutorial.

Tutorial Flow

GBrowse 2.49 and all of its prerequisites are already installed on the appliance. For the bulk of the tutorial, we will be following the tutorial that comes with GBrowse and can be found via this URL when you launch Firefox inside the virtual machine: http://localhost/gbrowse2/tutorial/tutorial.html (note that if you click this link from somewhere other than inside the virtual machine, Firefox will try to contact a web server on your own machine, whether there is one there or not).

Next Gen Sequence

While we cover as much as we can in the standard tutorial, I will skip around some and we will certainly not finish the tutorial. For the last 30 minutes, I'll switch to another tutorial to cover working with Next Generation sequence data presented on a separate wiki page.

Thoughts after the workshop

If we go to ASPB again, there are a few things I'd do differently:

  • Try to figure out some way to get "compliance" on having VirtualBox and the tutorial appliance installed before we start--debugging problems with these during the class is a real "drag".
  • Present a poster too to have a place to discuss with passers by.
  • Rope somebody (CSHL people?) into being TAs to help the course move more smoothly.
  • Charge a small fee to encourage registered attendees to attended (The workshop started at 7:30pm on Saturday night in Austin--which would you choose: GBrowse workshop or Austin night life?)