La petite planète

Posted on October 2, 2020October 9, 2020 by spencer

The little prince looked around his asteroid. Everything seemed to be in its place; his flower was watered, the baobabs had been weeded, and he had cleaned out both the active volcanoes and the extinc... Read More

Ripping Video CDs

Posted on August 3, 2020 by spencer

I recently acquired some movies in Video CD format. These are from before DVD readers were common, and so a full length film would be split across two CDROMs. I normally rip DVDs on my mac using Handb... Read More

Raspberry Pi IP notifications using Telegram

Posted on November 7, 2017 by spencer

One of the issues when using Raspberry Pi computers is that you have to hook up a monitor to find the IP address when plugging in to a new network, even if you really only need ssh access. To get arou... Read More

Protein words

Posted on December 7, 2016September 29, 2020 by spencer

In my post about creating a DNA font, I mentioned the idea of doing a similar thing for proteins. There are 20 standard amino acids, each with a single character abbreviation. When combined with symbo... Read More

CE-CP

Posted on April 13, 2015 by spencer

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

Posted on April 10, 2015 by spencer

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

A PDB-wide, evolution-based assessment of protein–protein interfaces

Posted on October 21, 2014 by spencer

My first paper in collaboration with the Capitani team has been published online: Kumaran Baskaran, Jose M Duarte, Nikhil Biyani, Spencer Bliven and Guido Capitani. (2014) A PDB-wide, evolution-based ... Read More

Regiomeeting at Mont Sainte-Odile

Posted on October 1, 2014 by spencer

Last week I attended the Rhine-Knee Regional Meeting on Biocrystallography at the Hohenburg Abbey on Mont Sainte-Odile, France. It’s a smaller conference, with a focus on short PhD and Postdoc p... Read More

ISMB 2014

Posted on July 24, 2014 by spencer

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

Babies

Posted on July 23, 2014December 7, 2016 by spencer

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