After my recent next-gen sequencing course, which was supposed to tie into the whole software carpentry (SWC) effort but didn't really succeed in doing so the first time through, I started thinking about the Right Way to tie in the SWC material. In particular, how do you both motivate scientists …
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So, I'm running this summer course and I am trying to figure out how to organize the notes for students. I'd like to mix curriculum-specific notes ("here's what we're doing today, and here are some problems to work on") with tutorials (material independent of a single course, like "here's how …
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In conversation with a colleague the other day, I found myself making a surprising prediction: the age of the big sequencing centers (Broad Institute, WUSTL, Baylor, DOE JGI, etc.) is coming to an end. In 5 years they will no longer exist.
This prediction is obvious in hindsight.
That is …
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Dear NSF,
I am happy to respond to your request for a 2-page Data Management Plan.
First of all, let me say how enthusiastic I am that you have embraced this new field of "large scale data analysis". Ever since I started working with large Avida data sets in 1993 …
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Just got news that the BEACON NSF Science and Technology Center for the study of Evolution in Action funded Chris Adami to come do a sabbatical here at Michigan State University for the next year. This puts me, Chris, and Charles Ofria at the same institution (now MSU, then Caltech …
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I've been doing some more focused bioinformatics programming recently, and as I'm thinking about how to teach biologists about data analysis, I realize more and more how much backstory goes into even relatively simple programming.
The problem: given a reference genome, and a very large set of short, error-prone, random …
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These days, molecular biologists are dealing with lots and lots of sequences, largely due to next-gen sequencing technologies. For example, the Illumina GA2 is producing 100-200 million DNA sequences, each of 75-125 bases, per run; that works out to 20 gb of sequence data per run, not counting metadata such …
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