Overview

This is the home page of the Section on Statistical Genetics (SSG) Mobile Lab Virtual Machine we call ssglabvm. If you are unfamiliar with the concept of virtualization, you can think of this "virtual" machine as a custom computer for statistical genetics research, analysis, and demonstration that you can run on your own computer.

What programs are installed?

Here is a short, representative, but non-exhaustive list:

Why a virtual machine?

While it is true that anyone can download and install these freely available programs themselves on their own computers, doing so takes time and in some cases, specialized system administration or programming expertise. Though many software come with pre-compiled binaries for different operating systems, some statistical genetics programs may require non-trivial effort to compile and install. Furthermore, after the initial installation, the software should ideally be rigorously tested, by both the system administrator and by the data analyst or statistical programmer. These challenges make the creation and availability of an installed, tested, and reliable collection of statistical genetics programs a worthwhile exercise for us.


The programmers, system administrators, and faculty in the SSG have put together and tested such a collection of statistical genetics programs as a virtual machine that can be run on your own desktop or notebook computer. In other words, instead of having to install and test dozens of programs yourself, you download and install one program (the virtual machine loader) to run a virtual machine for statistical genetics instruction and data analysis.

How to download, install, and run ssglabvm?

The virtualization software that we currently use is called VMware. While this is not the only virtualization software you can use, we describe instructions for downloading and installing VMware Player to run ssglabvm.

Installing VMware Player

  1. Download the latest installer, version 5.0, from the VMware web site. [screenshot]
  2. Make sure the md5sum matches. [wikipedia] [vmware] [screenshot]
  3. Run the installer.
  4. Need help? Watch this video. [SWF] (3.0 MB)
    • Note this video is for an older version of VMware Player, but the mechanics of each step are the same.

Downloading ssglabvm

  1. Download the compressed 7z archive of the virtual machine.
    • file size: 4.0 GB
    • approx. download time for the average broadband connection: 3.8 hours
    • md5sum: ce8df3289839d8a00e494b9f0c03c9ff.
    • Note this is a large file, if your internet connection is unstable, please consider using one of the many download managers available that allow the resumption of incomplete downloads.
  2. Uncompress the 7z archive to the target installation directory.
    • On Windows, you can uncompress 7z archives using the freely available 7-zip program. On Mac and Linux, you can use p7zip.
    • On Windows, the installation directory is typically C:\Virtual Machines.
  3. Need help? Watch this video. [SWF] (3.2 MB)
    • Note this video is for an older version of ssglabvm with different file name, size, and md5sum, but the mechanics of each step are the same.

Running ssglabvm in VMware Player

  1. Run VMware Player.
  2. Click Open.
  3. Browse to the location of the installation directory.
    • On Windows, this is typically C:\Virtual Machines\ssglabvm.
  4. Select the ssglabvm.vmx file and click open.
  5. The ssglabvm should "boot up".
  6. Need help? Watch this video. [SWF] (2.1 MB)
    • Note this video is for an older version of ssglabvm and VMWare Player, but the mechanics of each step are the same.
  7. Don't forget to read the FAQ, including "How do I turn off the virtual machine?".

System Requirements

Recommended

  1. 2 GHz CPU
  2. 4 GB of memory
  3. 20 GB of available disk space

Minimum

  1. Meets VMware Player requirements
  2. 2 GB of memory
  3. 15 GB of available disk space

FAQ

Where do I find the example files used by the lab instructors?

See ~ssglabuser/downloads/<program name> for example files that were included with the software distributions or ~ssglabuser/lab-examples for data, source code, and other material from instructors.

Help! My mouse pointer is stuck inside the VM!

If you click within the guest window, then you will need to type CTRL-ALT to release the mouse pointer and keyboard control back to the host operating system.

How do I run a program?

Right-click on the desktop, this will open a menu of options. Need help? Watch this video. [SWF] (1.9 MB)

How do I turn off the virtual machine?

To gracefully shut down the virtual machine, right-click on the desktop and click "Shutdown virtual lab". [screenshot]

What text editors are installed?

vim, nano, emacs, joe, jed, jove.

I am not familiar with Linux or the shell.

Many statistical genetics programs are command-line and designed to be run from a shell so this is a great opportunity to learn. While there are many good resources on the internet, here is a nice intro to basic Linux commands by Corey Shum from the School of Engineering at UAB. Also see the videotaped Linux primers from past HPC bootcamps at http://www.soph.uab.edu/ssg/courses/hpcbootcamp.

How do I enter and exit full-screen mode in the guest VM?

Use CTRL-ALT-ENTER.

What is your prototype USB stick procedure?

We will have something better soon, but here it is. You'll need the root password (see below).

How do I copy & paste?

Copy and paste in the ssglabvm works similarly to (if not exactly the same as) the way it works on any other physical computer installed with Linux and X.

For computers with two buttons, a middle button click can be simulated by pressing both the left and right mouse buttons simultaneously. NOTE: It is important that the correct mouse driver (especially on notebook computers) on the host physical computer is installed, up-to-date, and configured to simulate middle button clicks. Otherwise, copy and paste may not work in ssglabvm.

How to increase (or decrease) the font size in rxvt?

Try Shift-KP_Add and Shift-KP_Subtract. In other words, press the "Shift" key at the same time as the "+" or "-" key on the keypad.

What is the root password?

If you would like to tinker around, the root password is "ssglabvm".

How to run on a Mac?

Currently, the majority of our target audience is using Windows computers, so our examples and demo videos are created with this in mind. However, the general steps should translate fairly well to other operating systems, like Mac OS. Our focus is, of course, on developing the virtual machine (ssglabvm), whereas it is largely the responsibility of the virtual machine loader (e.g. VMware) to make sure it can run a virtual machine in a reasonable way on different operating systems. Here are a few pointers that may be helpful:

Please send us feedback on how ssglabvm is working for you on the Mac and if you'd like to be a tester, get in touch!

Who else is using virtualization in this way?

  1. Scientific Linux Distro
  2. VMware Virtual Appliance Marketplace

Future work

The current version of ssglabvm is still in alpha testing, meaning more programs will be installed and more features will be added, so please send us your feedback. Here are some of the improvements we are considering: