Freely & Unrepentantly Confessing to Heresy

There is a new post by Keith Robison in which he comments on my Excel/Bioinformatics post from August 28th:

Keith Bradnam reported a huge influx of traffic for a recent post -- not surprising, since he labeled it NSFW (Not Safe For WorK)… Bradnam was, of course, kidding. His short item showered derision on a recent Microsoft announcment about importing sequences into Excel.

The spike in traffic really has been insane. The post has become my most viewed post of anything I have ever written on this blog (by quite a margin). Clearly I have tapped into some anti-Microsoft (or just anti-Excel?) sentiment.

Keith Robison then takes on the 'case for the defense' and makes some fair points about Excel:

But to dismiss Excel as unworthy of any use in bioinformatics is to miss the fact that buried under the residue of years of creeping featurism is a tool useful in specific contexts and with some key advantages. The first advantage is that it is ubiquitous…

He then goes on to include some legitimate examples of how you might want to use Excel in order to work with sequence data.

I will conclude by saying that I bear no ill feelings towards Excel users, even those using it for bioinformatics! I have also used Excel in the past for trying to analyze some bioinformatics data. This was using Excel 2004 for Mac which suffered from a 32,000 row limit which made it unsuitable for incorporating some datasets. It was this limitation that was partly the impetus for me to start learning how to do some things in R.

Fundamentally, I feel that Excel is not a great tool for bioinformatics because: it is not open, it is not obviously workable as part of any standard bioinformatics pipeline, and it is not available on Linux (where a lot of bioinformatics happens). But, as always, you should use the tools that help you get the job done.