Time for me to get more serious about Linux

My group started into bioinformatics thanks to former students Hai Zhu and Leonardo Marino-Ramirez, who set up the first LAMP webserver in the lab, a box they made that we called tofu.tamu.edu. Being Mac users, we thought that the Unix roots of OSX would be useful in the transition to doing informatics and web-based resources, so I purchased a G5 XServe  which started a series of machines we named based on protein quaternary structure. It was called dimer.tamu.edu. As the EcoliHub/PortEco/EcoliWiki projects got funded and we got some stimulus money to work on B. subtilis, we gradually added to our collection of machines. trimer and tetramer were intel XServes. hexamer was the last version of the Apple Intel Xserve shipped by Apple. Meanwhile pentamer and heptamer were linux boxes running Ubuntu. For the most part the heavy work was done on the Macs, and we even moved GONUTS to run on a mac mini after one of the Intel Xserves died.

One of the things I liked about the XServe setup when we first got dimer was the way we could do server administration via the Server Admin and Workgroup Manager apps. But as the machines aged, and the older ones were not supported on newer OSX versions, Apple did something annoying: they made Server Admin incompatible with older OSX releases, even though it was pretty obvious that it was just a pretty front end to send unix commands and show the outputs in the GUI. So I gradually started learning how to do various system admin tasks via the terminal; there are some I’ve never figured out how to do completely without the GUI, though.

The rack mountable blade servers stopped supporting updates with Snow Leopard. We’ve kept the TAMU IT security people at bay by running MacPorts to replace obsolete packages, but it’s gotten to the point where time to give up on the Mac servers and migrate everything to Linux. My department prefers Ubuntu, so that’s the way I’m going to go.

In the long run I expect we will move from our own hardware to A&M server virtualization or maybe something like Amazon. But for now, I’m not comfortable with the capability and price for our own hosting, and there are issues with URLs and domains for moving some of our sites off campus.