4 ms·

The code is bad because transient Phds and Post-docs are writing it. If there was money in it then the best software developer would already be working on it. S

The code is bad because transient Phds and Post-docs are writing it. If there was money in it then the best software developer would already be working on it. Sadly there is none.

zmmmmm 4y ago
yep .... One of the borderline fraudulent aspects of the field is the pretense that method publications are real software. That is, you come up with a break through statistical or algorithmic method, you get it to run exactly once based on whatever random walk of exploratory code got you to a result that looks better than competing/prior methods, and then you dump your workspace into a script and put it on Github and pretend this is something anybody else could or should responsibly use in your Tier 1 publication. The minute the publication is approved there is zero benefit to the authors in maintaining the software, and in fact its better if nobody can run it because that way they can't disprove your results. Then naturally nobody can get this to work afterwards and 50% of software engineering time and effort is trying to run code that can/never will work outside the context it was created in - but you have to try because this is now the accepted best practice method of doing X or Y based on its publication. The bigger problem is that this whole cycle actually shapes the view of software engineering by academics to the point where they really do think that most software engineering is a waste of time. A small number of 10x engineers manage to prosper in the environment, but it's mainly because they have the sheer technical capability to deal with ALL of that while still doing something useful, and it actually makes the problem worse because the academics then see that as the baseline for software engineering capability.
runeblaze 4y ago
Yes just to second this -- every time I wrote decent code for my bioinformatics software I regret it because my PI does not really care. Sometimes I really don't understand. Much of the field's code does not even have testing, and it is baffling for me to think how the results are believed to be correct in the first place if there is no rigorous testing.

The code is bad because transient Phds and Post-docs are writing it. If there was money in it then the best software developer would already be working on it. Sadly there is none.

zmmmmm 4y ago

yep .... One of the borderline fraudulent aspects of the field is the pretense that method publications are real software. That is, you come up with a break through statistical or algorithmic method, you get it to run exactly once based on whatever random walk of exploratory code got you to a result that looks better than competing/prior methods, and then you dump your workspace into a script and put it on Github and pretend this is something anybody else could or should responsibly use in your Tier 1 publication. The minute the publication is approved there is zero benefit to the authors in maintaining the software, and in fact its better if nobody can run it because that way they can't disprove your results. Then naturally nobody can get this to work afterwards and 50% of software engineering time and effort is trying to run code that can/never will work outside the context it was created in - but you have to try because this is now the accepted best practice method of doing X or Y based on its publication. The bigger problem is that this whole cycle actually shapes the view of software engineering by academics to the point where they really do think that most software engineering is a waste of time. A small number of 10x engineers manage to prosper in the environment, but it's mainly because they have the sheer technical capability to deal with ALL of that while still doing something useful, and it actually makes the problem worse because the academics then see that as the baseline for software engineering capability.

runeblaze 4y ago

Yes just to second this -- every time I wrote decent code for my bioinformatics software I regret it because my PI does not really care. Sometimes I really don't understand. Much of the field's code does not even have testing, and it is baffling for me to think how the results are believed to be correct in the first place if there is no rigorous testing.