VirtualBox Installation

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Install VirtualBox

If your machine doesn't already have VirtualBox on it, you must download and install it. If you run Ubuntu linux you can do this with the following command:

 sudo apt-get install virtualbox

Download ExpressionPlot Virtual Hard Disks

Next download the ExpressionPlot virtual hard disk (12 GB).

You can optionally also download virtual hard disks containing the human (hg18) (6.7 GB) and/or mouse (mm9) (3.6 GB) bowtie indexes. These include pre-computed bowtie indexes for the whole genome (as found on the bowtie website) as well as bowtie indexes for the splice junctions. The whole genome indexes are the same ones found on the bowtie website, but the splice junction indexes are specially designed for use with ExpressionPlot. If you just want to try out the system without doing any new alignments there is a pre-computed data set on the basic virtual hard disk, so you won't need these.

Create your new Virtual Machine

Finally you have to set up your new virtual machine. The main decision to make here is how much memory to allocate. If you just want to run the pre-computed data set you should be fine with only 2 GB or even less (I have gone down as low as 1792 MB with no problems), but if you want to run new datasets you will need minimally 3 GB of memory, preferably 4 GB, because the bowtie indexes alone are almost 3GB. If you are going to work with a smaller bowtie index or if you aren't going to do alignments then you can get away with less. In any case, remember that you can't allocate all your memory to the guest machine; you probably have to save at least 500 MB for your host machine.

To create the virtual machine follow these steps

  1. Open VirtualBox. Under Ubuntu it can be found in Applications->System Tools->Oracle VM VirtualBox
  2. Click New to open the Create New Virtual Machine wizard
    • Name your virtual machine, then choose Linux as the OS and Ubuntu as the Version.
    • Set your base memory size. At least 1.5 GB to try out ExpressionPlot, at least 4 GB if you want to run the pipeline with new alignments.
    • On the next screen you'll choose your virtual boot hard disk. Make sure "Boot Hard Disk" is checked, then choose Use Existing Hard Disk. You want to choose ExpressionPlot.vdi (the 12GB file you downloaded). If it's not in the drop-down menu, click the little folder icon to the right of the drop-down menu to open the Virtual Media Manager. A new window will pop up. Click the "Add" icon within that window, then navigate to the location of the Expression.vdi file. Select the file and return to the wizard.
    • Click "Next" then, on the final window of the wizard, click "Finish".
  3. If you want to use the bowtie indices, first make the virtual media manager aware of them.
    • Open File->Virtual Media Manager...
    • Click Add and add one or both virtual hard disks. Click "OK" to save them and close the manager.
    • Now attach them to your new virtual machine. Click on the "Settings" for your virtual machine.
    • Click "Storage".
    • Click on the first green "+" icon (the "+" in front of a cylinder, not the one in front of a diamond) to "Add Attachment".
    • Add your hard drives.
    • Click "OK" to save the configuration.

Start up the machine

If you didn't attach one or the other bowtie index volumes then on startup just type "S" when prompted during startup to skip trying to mount them. Login using

 username: expressionplot
 password: highthroughput

This is also the username and password for the mysql database and for the website.

After the login process is complete you can open the ExpressionPlot website by clicking the link on the desktop. A subset of the Human Tissue Panel data set from the Burge lab comes preloaded.


Next: Preparing Raw Data with The EP Backend or Using the EP Web Interface