Note: Last week, I submitted my review of Stephen R. Piccolo, Adam B. Lee, and Michael B. Frampton's paper, Tools and techniques for computational reproducibility. Soon after, Dan Katz wrote a blog post about notebooks, and in a comment I mentioned Piccolo's paper; and, after dropping a note to Dr …
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This is a response to (parts of) Dr. Lior Pachter's post, "The myths of bioinformatics software". (You can also see my post on bioinformatics software licensing for at least some of the background arguments.)
I agree with a lot of what Lior says: most bioinformatics software is not very good …
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If a piece of bioinformatics software is not fully open source, my lab and I will generally seek out alternatives to it for research, teaching and training. This holds whether or not the software is free for academic use.
If a piece of bioinformatics software is only available under the …
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(This is a review of Large-Scale Search of Transcriptomic Read Sets with Sequence Bloom Trees, Solomon and Kingsford, 2015.)
In this paper, Solomon and Kingsford present Sequence Bloom Trees (SBTs). SBT provides an efficient method for indexing multiple sequencing datasets and finding in which datasets a query sequence is present …
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We just submitted our review of the paper Large-Scale Search of Transcriptomic Read Sets with Sequence Bloom Trees., by Brad Solomon and Carl Kingsford.
The paper outlines a fairly simple and straightforward way to query massive amounts of sequence data (5 TB of mRNAseq!) in very small disk (~70 GB …
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Yesterday morning, we announced a Software Carpentry workshop here at UC Davis, running July 6-7 -- see the Web site for more information. I'm organizing, and Easton White and Noam Ross are co-lead instructors. (This is the first workshop I'm running since we became an affiliate!)
I'd love it if you …
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Some background: I'm a white, male, tenured faculty member at UC Davis, and a 3rd generation academic. I work in relatively uncontroversial areas of science (primarily bioinformatics & genomics) at a university that is about as protective of academic freedom as you can get these days. I also live in a …
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