Software tools

Collated here is a series of blog posts which provide recommended software for biological scientists, which I compiled mostly for my Masters-level module in Research Presentation Skills. It may be of help to other post-graduates and researchers. Note that all recommendations are personal and based on my own experience. I will be very glad to receive further suggestions and comments and will keep these posts updated.

  1. Writing tools
  2. Data management and analysis
  3. Preparing figures
  4. Writing presentations
  5. Choosing a new operating system

I’ve emphasised Free Open-Source Software (FOSS) for two reasons. Firstly, everyone likes free stuff, right? There’s a more important point though, which is that no-one should be prevented from contributing to scientific research because they can’t afford the software to do it properly. As with the open access movement, which argues that the findings of research should be freely available to all, I believe that the tools to conduct, validate and apply research should be free too. Secondly, the advantage of open-source software is that it’s free to obtain and modify the original code. This means that someone has almost certainly created a specific tool to meet your needs as a scientist. Proprietary commercial software is aimed at the market and the average user, whereas open-source software can be tweaked and modified.

But my computer works fine!

Many people assume, when they buy a new computer and first boot it up, that it will come pre-installed with all the programs they need for their work. On reflection this is a rather strange attitude. If you wanted to play video games, you wouldn’t rely on the ones that were shipped with the console, at least unless your imagination didn’t stretch beyond Minesweeper. Why would Microsoft (or Apple) have benevolently supplied you with the best available software for scientific research?

The simple truth is that the reason Microsoft Windows and Office have become the international standards (Word, Excel, Powerpoint etc.) is not because they’re the best, but because most users don’t know any better. If you believe that Excel is easiest way to handle scientific data then you’ve never tried to produce a bar chart with error bars (and if you think it’s easy then you’re probably doing it wrong).

Perhaps you can already do everything you need to just fine with your existing resources. If so then carry on. Why learn to walk when you already know how to crawl? If, however, you would like to find ways to make yourself more productive and have a happier computing experience then here are some suggestions. All require some time investment to get up and running, but will eventually both save you time and improve the quality of your research, writing and presentation. There’s no excuse for making do when you can find something better with only a few clicks. If it’s something you’ll only use occasionally then the time investment may not be worthwhile. Even so, the distributed benefits can be substantial, and once you have a new set of tools in your repertoire they will open new opportunities.

The best news is that all of the tools recommended here are completely free. You can download them directly from their websites. They also tend, like all open-source software, to have user groups and forums where you can easily find help if you get stuck. A quick internet search will resolve most problems.

If you’re going to be spending the majority of your working life in front of a computer, then why not make sure you’re working in the most efficient, effective and enjoyable environment?