Essential software for biology grad students: Part I Overview

When I started grad school, I had no idea at the time just how much I’d learn doing a PhD. I’m not just talking about the “big picture” stuff: how to do research, design and conduct experiments, analyze data, and synthesize information. I mean all of the day-to-day skills associated with academic writing, data entry, and organization.

Over the next few weeks, I’ll explain a bit about the workflows I use and the various pieces of software that make my life quite a bit easier. After numerous discussions with colleagues over the years, providing various software and workflow recommendations to others, and attending (and running) various software workshops, it turns out I have a lot of suggestions for fellow biology grad students.

I’ll try to keep my recommendations general, because I think they are applicable not just to grad students in biology, but are also likely of interest to undergrads (even post-grads) in the sciences and perhaps elsewhere. I won’t put together detailed How-To’s, and I won’t be able to cover everything, but here’s an overview of what to expect:

• Part II will cover some essential computing basics: automated backups, using online (cloud) storage, and version control;
• Part III will deal with different writing tools including Microsoft Word, Libre Office Writer, Markdown, Pandoc, and LaTeX;
• Part IV will discuss reference management and citation software options;
• Part V will touch on using databases instead of spreadsheets;
• Part VI will delve into statistics software and the majestic use of R for stats, graphics, and (if I have time) get into using Sweave with R and LaTeX;
• Part VII will go into a little bit about programming and shell scripting;
• and finally, Part VIII will wrap things all up.

So stay tuned! I’m still fleshing out my ideas on some of these topics, so as we go along I look forward to comments and suggestions.