We use mostly open source software, including R, R Commander, and R Studio plus a suite of sequence manipulation and phylogeny software for these courses (e.g., R package ape, CLUSTAL, MEGA, PHYLIP, R package Rphylip, R package seqinr, TreeGraph, UGENE). While we do have a computer lab in which the macbooks come installed with all of the software for the students, I encourage (but not require) them to install the software on their own computers.

I’ve found that many students are hesitant to load software, with fears based on lack of knowledge about how to install software right up to the very sensible concern about the safety and integrity of software downloaded from websites they have never heard about. I’ll post at a later time on how I instruct students about checksum and other aspects of verifying software. A quick Google search finds all kind of advice on such things. Instead, in this post I wanted to address another interesting aspect of student’s knowledge about their own computers — how to manage the software bloat that comes with new computers and the pre-installed applications.

After installing one or more of these recommended applications I often get complaints from students about how slow their computers have become. Naturally they connect the two — my software slowed their computer. A reasonable conclusion, but not true. While some statistical or bioinformatics routines will tax your personal computer, most of what we will run do not — we run statistics on projects with sample size in the 100s and variables in the range of dozens. Even when we run nonlinear estimation routines or matrix manipulations, these procedures are completed in seconds. Similarly, while sequence alignment and other manipulations potentially can tax a computer, the kinds of work we do in these classes rarely will hang a computer for more than a minute or two.

With this as a backdrop, here’s the advise and help I give students.

Assuming you downloaded the software from the appropriate source and checked it against your anti-virus software, the problem of a computer is probably not due to the software you just installed. Poor computer performance is more likely because of the number of processes running on your computer.

On Macs you can check for active processes with Activity Monitor (Applications ? Utilities folder); on Windows machines use the Task Manager and select Services. Activity Monitor provides an extensive look at your computer, Task Manager less so, but both can be used to stop processes and thus free up system CPU and memory — and make your computer run faster! Some caution here — do a little Google work to look up process names and confirm that you can indeed stop the process without harming your computer.