One of the most important jobs a professor has is to pay it forward: that is, to teach, train, mentor, support, and open up opportunities for their students and postdocs. It's a job that is undervalued by those who focus on the short term -- the administrators and review committees that …
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During our next-gen course, a "student" (really a professor from Australia ;) asked me if I could provide some guidance on what computational infrastructure was necessary to handle next-gen sequencing data. While we used Amazon Web Services during the course, she was interested in finding out if they could use their …
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For anyone who actually wants to know what it is I do, I've updated my lab Web site, http://ged.msu.edu/, to be a bit more representative of what it is we're doing these days. (I wrote it over three years ago, so it's been becoming increasingly dated.) In …
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I just flew back from Montreal, where I gave a talk at the International Tunicate Meeting on the Molgula project. This is a project wherein we are doing quantitative mRNA sequencing on two species of ascidians, or sea squirts -- specifically, on M. oculata (tailed), M. occulta (tailless) -- and their hybrids …
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The second iteration of our bioinformatics summer course, Analyzing Next-Generation Sequencing Data, just finished. It was a great success, at least judging from the comments that people made to us personally; the evaluations aren't yet complete.
The what: a two week course on analyzing next-gen sequencing data, using the Amazon …
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I desperately need something to run and test things at the command line, both for course documentation (think "doctest" but with shell prompts) and for script testing (as part of scientific pipelines). At the 2011 testing-in-python BoF, Augie showed us cram, which is the mercurial project's internal test code ripped …
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