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Our latest paper on the CE-CP method for finding protein circular permutations is in this month’s issue of Bioinformatics. Spencer E. Bliven, Philip E. Bourne, and Andreas Prlić. (2015) Detecti... Read More

Using BioJava from R

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I’m a fan of literate programming. When I’m writing a paper, I typically use LaTeX to draft the paper, Java to generate the data, and R to create figures and do basic analysis. With Sweave (or the... Read More

ISMB 2014

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I had a great time at the ISMB conference & related events in Boston last week. As always, it is an exciting event scientifically and socially. First there was the Open Bio Foundation’s Cod... Read More


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I learned some interesting facts about fetal development recently. So interesting, they can only be properly delivered by Doctor McNinja (using the awesome Dinosaur Comic mashup template)... Read More

Castle Panic pieces

I’m quite proud of my recently-released Castle Panic game pieces. Castle Panic is a great game, and it is fun to have some sturdy walls and towers to replace the flimsy cardboard ones it comes w... Read More

TV Oscilloscope Part 2

To further test out my TV oscilloscope, I hooked it up to the output from a small stereo. Changes in dynamics and instrumentation were very apparent in the songs I listened to. I find the blue start a... Read More