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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The 2012 MSU Next-gen Sequence Analysis course application period just closed, and we received 168 applicants. Last year, we received 133, and the year before that we received 33.
We can take 24.
I was also invited to go teach a ~1 week workshop at two other universities on these …
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I'm putting together a computational pipeline for a paper - a Makefile that runs a ton of stuff and outputs files, combined with an ipython notebook file that takes those output files and turns them into figures for inclusion in a LaTeX file. (Yes, very 2000, except for the ipython notebook …
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At PyCon 2012, I took a tutorial on the IPython Notebook, which I'd already been using for a month or two (ever since Wes McKinney (the author of pandas) introduced me to it). The tutorial blew me away -- these guys have done a great job with the notebook so far …
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If you're like me, we pretend to care about the science in bioinformatics software. But what we really do is try to find reasons not to outright loathe the software -- because, lud knows, there are usually plenty of reasons to hate it.
In no particular order, here are the top …
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