Randy Olson, who is watching amusedly from the side lines as I struggle once again to teach programming to graduate students in biology, asked a really good question (it's rare, yes, but it should be acknowledged for encouragement) --
read moreHad a student from your class ask me today if it's typical …
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At BOSC 2012, we heard a report from Richard Holland on the Pistoia Alliance Sequence Squeeze competition. I'd run across this a couple of times before -- most notably in the Quip paper -- and was interested in hearing the results.
What was the problem being tackled? To quote,
read moreThe volume of …
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After yet another round of futile Twittering on the subject of research software, I thought I'd share a deeply personal story -- a story that explains some of my rather adamant stance that most research scientists need to think more critically about their code, and should adopt at least some of …
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One of my favorite in-class exercises is The Assembly Exercise, in which I provided "shotgun sequence" from some English text and ask the students to assemble it. Normally I provide a printout of about 10-20 pages of reads with range of read lengths, error rates, and single/paired end sequences …
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The IPython Notebook (or 'ipynb' for short) is one of the most exciting technologies for teaching and research that I've seen in recent years. It is a completely open source, well architected, and fairly stable system for scientific computing and data exploration.
I've now been using it for teaching for …
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These talk notes are for my talk at the 2012 Argonne Soil Metagenomics Workshop.
The slides are available for viewing and download here, on Slideshare.
I'm going to be talking about our assembly pipeline for soil metagenomes.
Much of this work was done by …
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I just finished reading The Idea Factory: Bell Labs and the Great Age of American Innovation, by Jon Gertner, an absolutely fabulous book on Bell Labs, and their invention of the transistor, the laser, and almost everything to do with modern telecommunications and computers ;).
The final chapter is about the …
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