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The coder spectrum, scientists on one end, software engineers on the other. Only balance can save us. I have read code used in research papers. The theoretical

The coder spectrum, scientists on one end, software engineers on the other. Only balance can save us. I have read code used in research papers. The theoretical math usually goes beyond my comprehension, so I always dive into the code to better understand the logic, only to find... it's way worse... unintelligible. At the end of the day we are used to what we do, and anything different will be foreign to us.

dlisboa 2y ago
A lot of the code written in math, physics or data analysis settings is really written for the authors alone to understand. They benefit from tens of pages of documentation (papers) plus decades of previous experience from the readers. None of which commercial software systems have.
_yb2s 2y ago
I agree- I'd like to think I'm somewhere in the middle despite being a scientist. I try to write the best code I can, and keep up on best practices, but try to keep things simple. A lot of the scientific code out there in research papers is so bad, that when you look at it, you realize the whole paper is actually B.S.. What the paper claims was never even implemented, but they just did the most kludgy and quick thing possible to produce the plots in the paper. The whole paper will often hinge on the idea that they did something that generalizes, and are showing specific examples, when actually they just skipped to producing those specific examples - cherry picked no doubt from other ones that they couldn't get to work - and did nothing else. As a reviewer if I notice this and really tear into the authors, it will usually get published and not fixed anyways. This happens because you get inexperienced new people doing the actual coding work without any proper mentors or instruction, and then they're under enormous pressure for results from a PI that doesn't understand or care about coding at all. It makes the whole thing a house of cards. Trying to do it 'properly' as a scientist is an uphill battle, because funders, collaborators, etc. expect the quick (and fake) stuff other people seem to be doing. The realities of developing good reusable software and maintaining it long term are not possible to fund through scientific grants. People writing usable code in academia are doing it for free on the weekends.
patrulek 2y ago
No kidding. Most of the academic/scientist's code is such a mess i would rather go through the paper and reimplement algorithm by myself :P

dlisboa 2y ago

A lot of the code written in math, physics or data analysis settings is really written for the authors alone to understand. They benefit from tens of pages of documentation (papers) plus decades of previous experience from the readers. None of which commercial software systems have.

_yb2s 2y ago

I agree- I'd like to think I'm somewhere in the middle despite being a scientist. I try to write the best code I can, and keep up on best practices, but try to keep things simple. A lot of the scientific code out there in research papers is so bad, that when you look at it, you realize the whole paper is actually B.S.. What the paper claims was never even implemented, but they just did the most kludgy and quick thing possible to produce the plots in the paper. The whole paper will often hinge on the idea that they did something that generalizes, and are showing specific examples, when actually they just skipped to producing those specific examples - cherry picked no doubt from other ones that they couldn't get to work - and did nothing else. As a reviewer if I notice this and really tear into the authors, it will usually get published and not fixed anyways. This happens because you get inexperienced new people doing the actual coding work without any proper mentors or instruction, and then they're under enormous pressure for results from a PI that doesn't understand or care about coding at all. It makes the whole thing a house of cards. Trying to do it 'properly' as a scientist is an uphill battle, because funders, collaborators, etc. expect the quick (and fake) stuff other people seem to be doing. The realities of developing good reusable software and maintaining it long term are not possible to fund through scientific grants. People writing usable code in academia are doing it for free on the weekends.

patrulek 2y ago

No kidding. Most of the academic/scientist's code is such a mess i would rather go through the paper and reimplement algorithm by myself :P