to postdoc or not to postdoc: from PhD to industry

After finishing my PhD, I did an academic postdoc for about 2 years, then recently moved to a small company in private industry. A friend recently asked whether I thought the academic postdoc was worthwhile and if I had any advice for getting into industry. Here's what I said.

How systems programming is like biochemistry

Recently I've been taking a lot of classes in computer architecture and systems programming, someone asked me why, with a biology background, I would be interested in such things. Here's what I said.

compiling Codon Optimizer on ubuntu 18.04

There is a cool old piece of software for codon optimization, inventively named "Codon Optimizer"

http://www.cs.ubc.ca/labs/beta/Projects/codon-optimizer/

It's not really very useful from a practical standpoint because its codon optimization strategy is to try to replace every codon with the highest CAI codon for the same amino acid. Which turns out to not be a very good strategy in practice. The software also can only optimize for E. coli, and has the translation tables and codon frequency tables hard-coded in.

Nevertheless, it's one of the few Open Source programs for codon optimization, so it might be useful to use as a starting point for a more fully-featured program, by adding more tables or some alternative algorithms for picking codons to use.

Unfortunately, it won't compile on Ubuntu 18.04.

To get it to compile, I had to do the following:

Minimalist shoes: a journey

The idea of minimalist footwear appeals to me from a number of perspectives. Aesthetically, I like the idea of having as little as possible on my feet. Minimalist shoes also tend to be cheaper than other shoes, particularly other running shoes. I also like the fact that I can (try to) make my own minimalist shoes, whereas trying to make a pair of padded, heel-raised shoes seems like it would be a nightmare.