Biology Magazine

The MATLAB Handcuff

Posted on the 26 June 2014 by Ccc1685 @ccc1685

The first computer language I learned was BASIC back in the stone age, which led directly to Fortran. These are procedural languages that allow the infamous GOTO statement, now shunned by the computer literati. Programming with the GOTO gives you an appreciation for why the Halting problem is undecidable.  Much of what I did in those days was to track down infinite loops. I was introduced to structured programming in university, where I learned Pascal. I didn’t really know what structured programming meant except that I no longer could use GOTO and there were data structures like records. I was forced to use APL at a summer job. I have little recollection of the language except that it was extremely terse and symbolic. It was fun to try to construct the shortest program possible to do the task. The ultimate program was the so-called “APL one liner”. APL gave me first hand experience of the noncomputability of Kolmogorov complexity. In graduate school I went back to Fortran, which was the default language to do scientific computing at that time. I also used the computer algebra system called Macsyma, which was much better than Mathematica. I used it to do Taylor expansions and perturbation theory. I was introduced to C and C++ in my first postdoc. That was an eye-opening experience as I never really understood how a computer worked until I programmed in C. Pointer arithmetic was a revelation. I now had such control and power. C++ was the opposite of C for me. Object oriented programming takes you very far away from the workings of a computer. I basically programmed exclusively in C for a decade – just C and XPP, which was a real game changer. I had no need for anything else until I got to NIH. It was only then that I finally sat down and programmed in MATLAB. I had resisted up to that point and still feel like it is cheating but I now almost do all of my programming in MATLAB, with a smattering of R and XPP of course. I’m also biased against MATLAB because it gave a wrong answer in a previous version. At first, I programmed in MATLAB as I would in C or Fortran but when it came down to writing the codes to estimate heritability directly from GWAS (see here), the matrix manipulating capabilities of MATLAB really became useful. I also learned that statistics is basically applied linear algebra. Now, when I code I think instinctively in matrix terms and it is very hard for me to go back to programming in C. (Although I did learn Objective C recently to write an iPhone App to predict body weight. But that was mostly point-and-click and programming by trial and error.The App does work though (download it here). I did that because I wanted to get a sense of what real programmers actually do.) My goal is to switch from MATLAB to Python and not rely on proprietary software. I encourage my fellows to use Python instead of MATLAB because it will be a cinch to learn MATLAB later if they already know Python. The really big barrier for me for all languages is to learn the ancillary stuff like what do you actually type to you run programs, how does Python know where programs are, how do you read in data, how do you plot graphs, etc? In MATLAB, I just click on an icon and everything is there. I keep saying that I will uncuff myself from MATLAB one day and maybe this is the year that I actually do.


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