About

StatGenLab is a virtual machine for helping researchers better accomplish their genetics data analysis goals.  For those unfamiliar with the concept of virtualization, you can think of this virtual machine, or VM for short, as a custom computer that you can run either on your own desktop or on another, more powerful computer. If you have been struggling with trying to compile, build, and test statistical genetics programs yourself, or have just not found the right platform for carrying out your data analyses, we invite you to explore what StatGenLab has to offer, from providing a ready-to-go computing lab environment if you are teaching a class, to analyzing real data as a scientific investigator on a big grant, to many things in between.

What programs are installed?

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

  • PLINK
  • Bioconductor
  • MACH
  • minimac
  • CpGassoc
  • SKAT
  • PennCNV
  • bowtie
  • MACS
  • IGV
  • bsseq
  • DSS
  • HapSeq

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, not just by the sysadmin, but in tandem with the data analyst, statistical programmer, or other scientific end user.

These challenges make the creation and availability of a carefully and professionally curated collection of statistical genetics programs a worthwhile exercise, so based on pioneering work by programmers, sysadmins, and faculty in the SSG to create ssglabvm, and the lessons learned from teaching statistical genetics from ssglabvm since the mid-2000s, we created StatGenLab.

Starting from scratch allowed us to make a number of technology improvements, including a smaller VM footprint and more modern tools for distributing new software packages to end users. Now, instead of having to install and test dozens of programs yourself, you can benefit from our hard work and download and install just one program, the VM loader, to perform your statistical genetics data analyses.

We invite you to explore StatGenLab and look forward to your feedback!