Popping the open source/open science bubble.

"One of the things that became clear to me over the last two weeks is just how much of a open source/open science bubble my blog and Twitter commenters live in. Don't take that as a negative -- I'm in here with you, and it's a great place to live :). But it's still a bubble. Two specific points brought this home to me. First, a lot of the Twitter and blog commentary on Please destroy this software after publication. kthxbye. expressed shock and dismay that I would be OK with non-OSS software being published. (Read Mick Watson's blog post and Kai Blin's comment.) Many really good reasons why I was wrong were brought up, and, well, I have to say it was terrifically convincing and I'm going to change my own policy as a reviewer. So far, so good. But it turns out that only a few journals require an actual open source license (Journal of Open Research Software and Journal of Statistical Software). So there is a massive disparity between what some of my tweeps (and now me) believe, and what is codified practice. Second, many eloquent points were made about software as a major product and enabler of research -- see especially the comments on 'software as communication' and 'software as experimental design' by others (linked to here - see 'Software as...' section). These points were very convincing as well, although I'm still trying to figure out how exactly to evolve my own views. And yet here again I think we can be quite clear that most biologists and perhaps even some bioinformaticians would have either no considered opinion on software, or be outright dismissive of the idea that software itself is intellectual output. Again, very different from what the people on Twitter and my blog think. I was already pretty surprised with how strong the case was for open source software as a requirement (go read the links above). I was even more surprised with how eloquently and expansively people defended the role of software in research. Many, many strong arguments were put forth. So, how do we evolve current practice?? ..."