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I agree. They also need a lot of help with basic software engineering, versioning, specifications, databases, documenting....
by yread 13y ago
I agree. They also need a lot of help with basic software engineering, versioning, specifications, databases, documenting....
- w1ntermute 13y agoExactly. Someone who is only considered mediocre in a software company will be seen as an amazing software engineer if they are working with scientists. Many of these scientists are not using version control. They don't have proper websites for their software. The codebases are a mess, and the software is very buggy. This is all low-hanging fruit that most software developers will be able to fix (if the scientists whose code it is are amenable to those fixes - many times they are not).
- dekhn 13y agoActually, these days, most scientists who are at the forefront of computational biology have mastered github. They use markdown for README files, and produce md5summed data sets and command lines so you can repro their work. From what I can tell, this started 3-5 years ago when the kids coming into grad school picked up what the open source hackers were doing. To be clear: none of this is properly incentivized by the funders, so there's not much selection for this behavior.
- yread 13y agoWhat use is an MD5 of dataset if its semantics should be clear from table and column names?
- dekhn 13y agoFileset checksumming addresses a different concern from the semantic content of the data. It's merely a way to ensure that two people send the exact same input files to a routine. It's a critical control.
- a_bonobo 13y agoIt sounds as if http://www.software-carpentry.org http://www.software-carpentry.org might be something to join for most participants in this thread - a non-profit organization that runs bootcamps for scientists to learn proper coding, version control etc. I think they're always looking for more volunteers.