Serious bioinformatics tools are generally designed for Unix (Linux and Mac) systems. Some of you will obviously be on Windows computers, and some on Mac, and maybe even a few of you will be using Linux. The thing is, we really all need to be in a similar computing environment. If you’re a Mac or Linux user, you could work through this whole class without issue (the book is written by a Mac user). If you’re using Windows, there is a lot of bioinformatics that will be practically impossible to accomplish.
So, rather than force everyone to convert to a Unix system, we will be quickly getting you set up to remotely use a Unix supercomputer. This allows everyone to work in a Linux system, which puts us all on the same page.
As we start out (and through the whole semester) we will be using our “Terminal” a lot. Mac users have this built in already. Windows users will want to install a program called GitBash which emulates a Unix terminal. We will walk you through that on day one of class.
Current Windows users: No need to rush out and buy a new computer for this class, but if scientific computing is going to be a part of your future education/career, my own opinion is that you will want to consider switching a Mac (expensive) or Linux (free) computer for your next laptop. The benefits of Linux include:
Pretty much any laptop will do the job for this course. Having more RAM and more cores will greatly speed things up for you once the data sets get larger. Once you learn how to efficiently push jobs onto remote computing clusters, you can even get the job done with a cell phone app (as long as you have infinite patience and love suffering).
If you have 4 Gb of RAM and a working WiFi card and keyboard, you’ll be just fine in this class.
My personal computer setup:
Pros:
Cons:
For everyday professional bioinformatics use, this computer has proven very capable. For big heavy tasks, I either leave it to run overnight or push the job to a remote cluster.