Greg Wilson, Ethan White and I have been talking a bit about what Responsible Conduct of Research (RCR) standards would look like for computational science. I'm having trouble coming up with more than the below standards, which are largely related to publication.
Note, if you regard these as obvious, that's …
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Brad Chapman (@chapmanb on twitter) wrote and signed a nice review of my submission to the Bioinformatics Open Source Conference. In his review, he said
My only small suggestion is to include some discussion about your reproducibility work during the talk: the Amazon AMI, documentation and reproducible ipython workflows. This …read more
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I'm a pretty big advocate of anything open -- open source, open access, and open science, in particular. I always have been. And now that I'm a professor, I've been trying to figure out how to actually practice open science effectively
What is open science? Well, I think of it as …
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I'm going to pick on Mick Watson today. (It's OK. He's just a foil for this discussion, and I hope he doesn't take it too personally.)
Mick made the following comment on my earlier Big Data Biology blog post:
read moreI do wonder whether there is just a bit too much …
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I'm out at a Cloud Computing for the Human Microbiome Workshop and I've been trying to convince people of the importance of digital normalization. When I posted the paper the reaction was reasonably positive, but I haven't had much luck explaining why it's so awesome.
At the workshop, people were …
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I'm pretty proud of our most recently posted paper, which is on a sequence analysis concept we call digital normalization. I think the paper is pretty kick-ass, but so is the way in which we're approaching replication. This blog post is about the latter.
(Quick note re "replication" vs "reproduction …
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We just posted a pre-submission paper to arXiv.org:
A single pass approach to reducing sampling variation, removing errors, and scaling de novo assembly of shotgun sequences
Authors: C. Titus Brown, Adina Howe, Qingpeng Zhang, Alexis B. Pyrkosz, and Timothy H. Brom
Paper Web site, with source code …
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