From what I've seen, amid all the research, failed experiments, constant fight for funding (in some cases) and "life" in general, people have much less time to learn these critical things like programming / tools so useful to them. They will do it at some point, but probably not till their life depended on it. On the other hand, if life depended on me recognizing those amino acids, we'd all be :-)
Compounded by the fact that in science once you have the result the code is probably just an artifact so there's no real reason to refactor it
Could you explain what you mean by this?
It's easier to break the mould if you're not bound by other people's software, but starts to look awfully sciency if you explore too far : D So it's useful to keep wiping the slate to not be bogged down by previous experiments
pd, processing, chuck, cm/clm, or just old-school mod-tracking are some good ways to get going
I wonder if the problem is twofold: 1) a lack of education compounded by 2) the rapid evolution of computer systems.
Unix is a rare beast in that not just its philosophy but even its components survive to this day and remain relevant[1]. People in unrelated fields rebuild tools that could just as well be assembled using Unix's basic components, but they're just not aware of them. And why would they look for these antiquated tools? They've been trained to reasonably expect old tools to have been replaced by newer, better, more featureful ones.
[1] AWK was created before I was born, and I'm among the more senior engineers in my 20+ team.