After a fair amount of time thinking about software's place in science (see blog posts 1, 2, 3, and 4), and thinking about khmer's short- and long-term future, we're making some changes to our development process.
Semantic versioning: The first change, and most visible one, is that we are going …
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I finally got a chance to more thoroughly read Mark Stalzer and Chris Mentzel's arxiv preprint, "A Preliminary Review of Influential Works in Data-Driven Discovery". This is a short review paper that discusses concepts highlighted by the 1,000+ "influential works" lists submitted to the Moore Foundation's Data Driven Discovery …
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We just finished teaching the second of my RNAseq workshops at UC Davis -- the fifth workshop I've hosted since I took a faculty position here in VetMed. In order, we've done a Train the Trainers, a Data Carpentry, a reference-guided RNAseq assembly workshop, a mothur (microbial ecology) workshop, and a …
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Note - this was an internal funding request solicited by the Center for Open Science. It's been funded!
Brief: We propose to integrate OSF into Galaxy as a data store. For this purpose, we request 3 months of funding (6 months, half-time) for one developer, plus travel.
Introduction and summary: Galaxy …
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So I wrote this thing that got an awful lot of comments, many telling me that I'm just plain wrong. I think it's impossible to respond comprehensively :). But here are some responses.
In that blog post, I argued that software shouldn't …
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Update - I've written Yet Another blog post, More on scientific software on this topic. I think this blog post is a mess so you should read that one first ;).
This blog post was spurred by a simple question from Pauline Barmby on Twitter. My response didn't, ahem, quite fit in …
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