I'll give an example. At my previous company there was a program where you basically select a start date, select an end date, select the system and press a button and it reaches out to a database and pulls all the data following that matches those parameters. The horrors of this were 1. The queries were hard coded.

They were stored in a configuration file, in xml format.
The queries were not 1 entry. It was 4, a start, the part between start date and end date, the part between end date and system and then the end part. All of these were then concatenated in the program intermixed with variables.
This was then sent to the server as pure sql, no orm.
Here's my favorite part. You obviously don't want anyone modifying the configuration file so they encrypted it. Now I know what you're thinking at some point you probably will need to modify or add to the configuration so you store an unencrypted version in a secure location. Nope! The program had the ability to encrypt and decrypt but there were no visible buttons to access those functions. The program was written in winforms. You had to open the program in visual studio, manually expand the size of the window(locked size in regular use) and that shows the buttons. Now run the program in debug. Press the decrypt button. DO NOT EXIT THE PROGRAM! Edit the file in a text editor. Save file. Press the encrypt button. Copy the encrypted file to any other location on your computer. Close the program. Manually email the encrypted file to anybody using the file.

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[–] AnarchistArtificer@slrpnk.net 20 points 1 day ago

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.