Over the past year of PyCon, #sciox, and other gender imbalance/harassment/sexism discussions that I've seen on Twitter and blogging, I've run into a few posts on these matters that stood out to me in terms of clarity, logic, and/or good instruction for me. I'm sharing them below …
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In 1947 a Bedouin shepherd found a bunch of ancient scrolls in a cave near the Dead Sea. These scrolls, now known as the Dead Sea scrolls, included some of the oldest known Biblical texts as well as other Jewish religious writing. Over the next few decades, these scrolls - of …
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As part of a February visit to the Whitney Marine Lab in Florida, I'm giving a talk for the public. I chose "The Genomic Revolution: How Sequencing Anything and Everything Is Changing the Way We Do Science" as the title. Basically, I want to talk about what the DNA sequencing …
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Over the last year, digital normalization has occupied an increasingly privileged position in sequence analysis: it's a lightweight way to achieve an assembly, one that is computationally cheaper than almost anything else you can do; our software works reasonably well in practice; sequencing data generation capacity is only increasing; and …
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(with Camille Scott, Michael Crusoe, and Leigh Sheneman; Josh Rosenthal contributed to eel-pond; and Adina Howe contributed to kalamazoo)
This summer, I spent a lot of time writing up computational protocols for both mRNAseq and metagenome assembly in the Amazon cloud.
I'm happy to announce that they are now available …
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I've started to think more broadly about bioinformatics training, and after some conversations with Vicky Schneider 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 …
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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 …
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