On June 11th, 2010, I remember dropping the last workshop attendee off at the Kalamazoo train station, turning the car towards home, and nearly sobbing in relief that workshop was over and done and I could finally get some sleep now. That workshop was the first of a series of …
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Just as I was moving to UC Davis, a funding call for a training coordination center came out. I got partway down the path of applying for it before realizing that I was overwhelmed with the move, but I did generate some text that I thought was OK. Here it …
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Note: this is a blog post from the DIB Lab journal club.
Jump to Questions and Comments:.
The paper:
http://www.techfak.uni-bielefeld.de/~stoye/dropbox/wabi2015final.pdf
"Bloom Filter Trie: a data structure for pan-genome storage."
by Guillaume Holley, Roland Wittler, and Jens Stoye.
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Note: at the Lab for Data Intensive Biology, we're trying out a new journal club format where we summarize our thoughts on the paper in a blog post. For this blog post, Luiz wrote the majority of the text and the rest of us added questions and comments.
The paper …
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Note: A year ago, I wrote this in response to an editorial request. Ultimately they weren't interested in publishing it, and I got distracted and this languished on my hard disk. So when I remembered it recently, I decided to just push it out to my blog, where I should …
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Note: Last week, I submitted my review of Stephen R. Piccolo, Adam B. Lee, and Michael B. Frampton's paper, Tools and techniques for computational reproducibility. Soon after, Dan Katz wrote a blog post about notebooks, and in a comment I mentioned Piccolo's paper; and, after dropping a note to Dr …
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This is a response to (parts of) Dr. Lior Pachter's post, "The myths of bioinformatics software". (You can also see my post on bioinformatics software licensing for at least some of the background arguments.)
I agree with a lot of what Lior says: most bioinformatics software is not very good …
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