Thoughts on bioinformatics training suites

I’ve started to think more broadly about bioinformatics training, and after some conversations with Vicky Schneider-Gricar at TGAC, Terri Atwood at GOBLET, and others, I thought I’d write down some thoughts on bioinformatics classrooms. In particular, what kind of compute infrastructure is needed? Before I get started, my assumptions and interests are as follows: Many …

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Install gplots in R 2.1X

I’ve been using EBSeq for a few things lately, and have had trouble getting some of the dependencies installed — in particular, gplots doesn’t seem to be readily available for R 2.14, 2.15, etc. Judging by my Google searches, others have been having the same problems; see e.g. http://stackoverflow.com/questions/16091096/can-not-install-ggplot-package-in-r-2-14-1 The general error message is of …

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The Cost of Open Science

I just finished reading The Immortal Life of Henrietta Lacks, an excellent book about the HeLa cell line cultured from cancerous cells taken from Henrietta Lacks. In addition to raising some really interesting and astonishing questions about the appropriate (mis)use of patients’ tissue samples, a section about George Gey caught my eye and made me …

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Why do I Blog?

Why do I blog? I’ve been blogging now for almost 8 years, since around when Grig Gheorghiu started the Southern California Python Interest Group. Since then I’ve gotten a PhD, taken a postdoc, had one child, started a faculty position, had another child, and basically gotten way, way busier. Why do I keep it up? …

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