Is your research software correct?

July 23rd, 2015 | Categories: RSE, Scientific Software | Tags:

You’ve written a computer program in your favourite language as part of your research and are getting some great-looking results. The results could change everything! Perhaps they’ll influence world-economics, increase understanding of multidrug resistanceimprove health and well-being for the population of entire countries or help with the analysis of brain MRI scans.

Thanks to you and your research, the world will be a better place. Life is wonderful; this is why you went into research.

It’s just a shame that you’re completely wrong but don’t yet know it.

What went wrong?

If you click on any of the studies linked to above, you’ll find a common theme – problems with software. These days it’s close to impossible to do science without either using or developing specialist software. Using research software can be difficult, complex and extremely time consuming. Developing it is orders of magnitude more difficult.

What can be done?

When I’m writing code, my first and main assumption is always ‘I can be an idiot and will make mistakes.’ Some people I’ve worked with assume that I’m either being self-deprecating or have a self-confidence problem when I talk like this. The reality is that it’s simply true. I’m fallible: my knowledge of everything is incomplete and if I haven’t had at least two cups of coffee in the morning, I’m essentially good for nothing.

Rather than lament my weaknesses, I try to develop methods of working that mitigate my inevitable stupidity. These methods are actually very simple.

  • Write tests. Every programming language worth its salt provides testing frameworks (e.g. Python, MATLAB, R). Learn how to use them and use them whenever you can. Whenever you make a change to your code or install it somewhere new, run your tests to see if anything has broken.
  • Get a code buddy. Find yourself another programmer and hand them your code with the remit ‘Tell me where you think I could do better’. This will be a painful experience. Suck it up because your code will almost certainly be better as a result. There is only one true measure of code quality!
  • Use version control. It doesn’t matter if its git, SVN, Mercurial or whatever the particular flavour of the month is. Choose a system, learn it and use it (for the record, I use git and have a twitter account called @git_tricks that posts tips on how to use it). When you use your code to get results, refer back to the actual commit that you used to get those results. This greatly assists the reproducibility of your research. If you cannot reproduce your own results with your own code and data, neither can anyone else.
  • Share code as openly as possible. Ideally, ‘openly’ should mean on the public internet. GitHub, blog posts, personal websites etc. Whenever I’ve posted code here on WalkingRandomly, mistakes usually get caught very quickly. Geeks love telling other geeks that they’ve made a mistake. Sure, your pride takes a hit but you quickly become immune to such things. The code is better, you learn something useful and the geeks that point out your errors feel good about themselves. Everyone’s a winner.

Sadly, the great majority of scientists I work with really don’t want to share their code openly for numerous reasons and so much of the stuff I’ve worked on is in the dark. Sometimes, collaborators don’t even want to share code with me.I’m about to start work on one optimisation case where the researcher tells me that they are not allowed to email me their code. So, he’s bringing his laptop to me and will sit next to me for a few hours while I try to figure out if I can help or not. Such is the lot of a working research software engineer.

Along with organisations such as the Sheffield Open Data Science Initiative and The Software Sustainability Institute, I am trying to improve this state of affairs but have to admit that progress is slower than I’d like.

These steps won’t guarantee that your code is correct but they are great steps in the right direction. For more in-depth advice, I refer you to Greg Wilson’s paper Best Practices for Scientific Computing.

  1. Bob Alvarez
    July 29th, 2015 at 17:34
    Reply | Quote | #1

    This post really hit home for me since most of my research is based on computer simulations. I particularly like the Wilson et al. paper. Reading it is like listening to a good sermon with suggestions for how to improve my ways. One thing I am particularly guilty of–I confess I confess :-) is coding by copying and pasting instead of writing functions. This is particularly a problem for me since I use Matlab and my code is developed by writing and testing pieces of it using scripts. It is easy to stop there and copy and paste instead of putting the code into functions and re-using them.