We've just posted a new paper to arXiv: "These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure." We'll be submitting it to PLoS One after we wait a few days for comments from the Twittersphere and/or on Haldane's Sieve.
The …
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The paper Howison et al., 2013, just appeared in early form in Bioinformatics. Here is my first round review, which they handily addressed in their revisions; since I was quite positive I felt I might as well post the whole thing, though.
Note that a relevant paper from Mihai Pop …
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So, we've been running this course on NGS data analysis. And it's been fun and all. But a lot of work.
About a year ago, I thought hard about whether or not I wanted to apply for renewal, and ended up applying again. You can see the final grant if …
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Two papers on the Haemonchus contortus genome just came out (Schwarz et al. and Laing et al.), and I'm an author on one of them (Schwarz et al.). H. contortus, or Haemonch (as I affectionately called it) is a nasty parasitic nematode that feasts on the mucosal blood of ruminants …
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In my post on proselytizing version control, an underlying and implicit assumption was that version control was not fulfilling the function of a lab notebook. But I didn't make that explicit. And then someone asked in the comments. So now I'm making it explicit.
tl; dr? Version control's a really …
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I gave a talk yesterday at the 2013 BEACON Congress titled "How to build an enduring online research presence using social networking and open science." The talk slides are here.
This talk was a combined survey of sites and personal perspective on how social media has helped shape the last …
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Since I attended the entire STAMPS course at MBL this year, which was an entirely computational course, I had the opportunity to proselytize computational reproducibility and good practice to a number of people.
Now, with students I'm usually fairly gentle about this kind of thing, and try to get my …
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