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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Dear <student>,
I'd be happy to, but I do have a few conditions/requests based on prior experience with students!
First, please schedule all of your meetings at least 2 months in advance :)
Second, a condition for my signing off on your thesis will be that, for any paper for …
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It's not often that someone perfectly and thoroughly summarizes the challenges inherent in data science being confronted by academic institutions, but that's just what Fernando Perez did in this blog post. Just... just go read it, trust me :)
The new data driven discovery centers being funded by Sloan & Moore are …
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