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Joined 2 years ago
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Cake day: June 9th, 2023

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  • I don’t have any specific examples, but the standard of code is really bad in science. I don’t mean this in an overly judgemental way — I am not surprised that scientists who have minimal code specific education end up with the kind of “eh, close enough” stuff that you see in personal projects. It is unfortunate how it leads to code being even less intelligible on average, which makes collaboration harder, even if the code is released open source.

    I see a lot of teams basically reinventing the wheel. For example, 3D protein structures in the Protein Database (pdb) don’t have hydrogens on them. This is partly because that’ll depend a heckton on the pH of the environment that the protein is. Aspartic acid, for example, is an amino acid where its variable side chain (different for each amino acid) is CH2COOH in acidic conditions, but CH2COO- in basic conditions. Because it’s so relative to both the protein and the protein’s environment, you tend to get research groups just bashing together some simple code to add hydrogens back on depending on what they’re studying. This can lead to silly mistakes and shabby code in general though.

    I can’t be too mad about it though. After all, wanting to learn how to be better at this stuff and to understand what was best practice caused me to go out and learn this stuff properly (or attempt to). Amongst programmers, I’m still more biochemist than programmer, but amongst my fellow scientists, I’m more programmer than biochemist. It’s a weird, liminal existence, but I sort of dig it.