I've been invited to present at the Extremely Large Databases (XLDB) 2012 conference as a practicing biologist who occasionally speaks with physicists, and I'm trying to come up with something to say that will explain why physicists and biologists don't often collaborate all that well.
Here are some guesses.
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There's been a lot of discussion about PyCon talks that we do want to see. Here's a brief list of those I don't want to see, for those of you considering a submission -- in no particular order.
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[ Note: I wrote the following e-mail to the Microbiology (MMG) department faculty mailing list here at MSU. I'll post any interesting responses that I get. --titus ]
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Hi all,
I'm an unabashed proponent of Open Access publishing, as well as the idea of decoupling correctness from estimated impact of a paper …
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One of the biggest problems with basic sequence analysis -- some would say the biggest problem -- is the error rate. If our sequencing reads were error-free, both assembly and mapping would be much, much easier. Alas, Illumina reads have a 0.1-1% error rate per base, and PacBio has an error …
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I'm at the MBL STAMPS course, "Strategies and Techniques for Analyzing Microbial Population Structure," and one of the things I needed to address in my morning talk was the role that the k parameter plays in de Bruijn graph assemblers.
In most de Bruijn assemblers that I have used -- Velvet …
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Suppose you have a community that has two organisms in it, at widely varying abundances. What can you do?
Partitioning takes this mixed distribution and, based on graph connectivity, splits the reads into two bins. Thus, you go from this:
to this:
where the reads are …
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