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comment by thundara
thundara  ·  4077 days ago  ·  link  ·    ·  parent  ·  post: A farewell to bioinformatics

In my last project, I was advised that, while writing good code is beneficial in the long run, the cutting edge is all about prototyping fast, finding out what works, and not getting invested in ideas that don't. Now, I am of the opinion that poor software engineering practices cost a price in the long run. Also, frequently code that was never meant for production finds its way onto many other scientists' computers.

Personally, I blame it on a lack of experience and general computational education. It's not that hard to add docstrings to python code. Hell, it's easier to use standard modules than to roll your own format parser. I'm regularly able to compress code bases in half by just adhering to the best practices of the language being used.

But that doesn't win grants.





temple  ·  4077 days ago  ·  link  ·  

There's several examples that I know of that were the one-off prototype code written by the physicists that turned into production code. They were used for years but would take hours to run.

We look at it and fix it for them. Usually takes less than a week. Now, the codes now run in minutes instead of hours. That's a lot of wasted scientist time.

Though, I get that it's hard to get software engineers or computer scientists on the grants, anyways, because no one wants to pay for them, even if there is a large computational portion of the research.

thundara  ·  4077 days ago  ·  link  ·  

    Though, I get that it's hard to get software engineers or computer scientists on the grants, anyways, because no one wants to pay for them, even if there is a large computational portion of the research.

Easy argument against it is that funds are spread paper thin already, and when you have to choose between a grant to optimize an already-built program and one to write a completely novel one, well, the choice is clear.

Now, if everyone wasn't spending every waking minute stressing about grants...but I don't think anyone will disagree with me that that's already a known and well documented problem. ;)

I personally think it would be worthwhile in the long run, economically, to add a short subject on good programming practices to conferences / workshops, but I'm not the one scheduling them.

mk  ·  4077 days ago  ·  link  ·  

    But that doesn't win grants.

Few things do these days. :/