(This project is a collaboration with Jason Pell and Adina Howe)
A few weeks ago I posted about a k-mer filtering approach that we were using to remove low-abundance k-mers from metagenomic data sets, prior to assembly. This technique is working well, and we've managed to do some assembly of …
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The Terabase Metagenomics meeting was good fun, but I most valued the computational component (because that's what I do). Rachel Mackelprang and Rob Knight and I wrote down a list of the computational issues involved in a petabase metagenomics project, and that list will help direct my future research. I'll …
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I'm on my way back from the Terabase Metagenomics meeting in Snowbird, UT, and I'm buzzing with ideas about how to move forward in metagenomics and bioinformatics research. Metagenomics, the use of genomics approaches to study microbial communities, has been opening up as sequencing drops in price. With sequencing becoming …
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(Everyone needs an "I'm wonderful" wall, right? Here's mine!)
My rather snarky post on data management made it into Episode 34 of the Coast to Coast Bio Podcast.
Turns out I'm now a leading evangelist for cloud computing in genomic research, which I guess is true if evangelism is relative …
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I've spent the last few weeks working on a simple solution to a challenging problem in DNA sequence assembly, and I think we've got a nice simple theoretical solution with an actual implementation. I'd be interested in comments!
Briefly, the algorithmic challenge is this:
We have a bunch of …
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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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Laurie Dillon just posted the SIGPLAN eduction board article on Why Undergraduates Should Learn the Principles of Programming Languages to our faculty mailing list at the MSU Computer Science department. One question that came up in the ensuing conversation was: what functional programming language(s) would/should we teach?
I …
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