I am a technician in a relatively small molecular biology lab at a large university in the Northeast. We are beginning to get involved in more computationally intense work -- lots of ChIP(-seq, -chip) and next gen sequencing -- and are looking at expanding our computational capacity. We currently rely on a few 32-bit iMacs to do the bulk of our computing. The way we see it currently, we have the following options:
- Do our big stuff using a cloud service like Amazon's EC2.
- Purchase time on our university's cluster.
- Build a local computing grid. The first two of these options do not appear to be cost-effective for us at this time, and the third appears to be too costly in terms of construction and maintenance. We are more interested in the following options:
- Purchase a MacPro and use it as a dedicated computer for alignment and analysis.
- Purchase an IBM x-series server and use it for the same purpose (using a Linux distro).
- Construct a small in-lab cluster. Most of our current computers are Apple, and everyone in the lab is comfortable with Mac OS and are a little reluctant to switch to Linux.
Personally, I think that going the IBM route would be best for us. The servers appear to be pretty good and I think it would be relatively painless for the lab to transition to Linux, especially since most of the analysis we do is based on Python scripts. So, I'd just like to know: How do other molecular biology or biochemistry labs do their bioinformatics? If we were to purchase our own hardware, what would people recommend? It seems like every bioinformatics book recommends the LAMP toolkit, but will we have any issues finding software or applications for Linux that my lab-mates are used to using on Mac OS?
Edit: Removed Reddit reference.