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There is so little emphasis in production software development in bioinformatics and biostatistics. Despite a lot of groups open sourcing their code it's is nea

by gww 6y ago

There is so little emphasis in production software development in bioinformatics and biostatistics. Despite a lot of groups open sourcing their code it's is nearly unusable and not reproducible due to hard coding, ignoring edge cases, and dumping the majority of the code on a single giant R or python function.

Scandiravian 6y ago
That's my experience as well. My master's is in bioinformatics and I worked for several years in biotech. I got frustrated because my concerns that my team's development practices were causing issues on a regular basis, were ignored. I was continuously able to predict what issues we would run into, but no-one seemed to care - I even had a manager tell me, that it was good that our software was buggy, since the client would continue paying us to fix it I've since left the biotech industry. There's a limit to how many times I want to run my head against that particular wall
natechols 6y ago
It's a real problem, and I've been struggling with it for two decades, but even so I am legitimately impressed (and not in a good way) if they have 170,000 lines of Matlab code in their production software. That takes a really special combination of productivity and cluelessness, even for academic specialists. Regardless of the facts of this particular case, it should be absolutely horrifying that anyone's freedom is left up to a gigantic pile of unaudited Matlab code. (That said I am almost certain he added some zeros to the number, I have a hard time imagining what they're doing that could be that complex.)
- Scandiravian 6y ago
  Choosing MATLAB as a language for software that could potentially lead to people dying (in areas where they still have the death penalty) is a gigantic red-flag I don't know how many job postings ask for a software engineer who knows MATLAB, but I can't recall any

by gww 6y ago

Scandiravian 6y ago

That's my experience as well. My master's is in bioinformatics and I worked for several years in biotech. I got frustrated because my concerns that my team's development practices were causing issues on a regular basis, were ignored. I was continuously able to predict what issues we would run into, but no-one seemed to care - I even had a manager tell me, that it was good that our software was buggy, since the client would continue paying us to fix it I've since left the biotech industry. There's a limit to how many times I want to run my head against that particular wall

natechols 6y ago

It's a real problem, and I've been struggling with it for two decades, but even so I am legitimately impressed (and not in a good way) if they have 170,000 lines of Matlab code in their production software. That takes a really special combination of productivity and cluelessness, even for academic specialists. Regardless of the facts of this particular case, it should be absolutely horrifying that anyone's freedom is left up to a gigantic pile of unaudited Matlab code. (That said I am almost certain he added some zeros to the number, I have a hard time imagining what they're doing that could be that complex.)

Scandiravian 6y ago
Choosing MATLAB as a language for software that could potentially lead to people dying (in areas where they still have the death penalty) is a gigantic red-flag I don't know how many job postings ask for a software engineer who knows MATLAB, but I can't recall any