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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I gave a presentation at the BEACON Center's coding group this past Monday; here are my notes and followup links. Thanks to Luiz Irber for scribing!
My short slideshow: here
The khmer project is on github, and we have a tutorial for people who want to try out our development …
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On Tuesday, I wrote a draft blog post in response to Michael Eisen's blog post on how Lior Pachter's blog post was a a model for post-publication peer review (PPPR). (My draft post suggested that scientific bloggers aim for inclusivity by adopting a code of conduct and posting explicit site …
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