Psst! I've posted some details about my notebook setup here.

Super simple reverse-complement aware DNA sequence search with rcgrep

There are many wonderfully elegant and efficient tools for performing all sorts of exact and inexact searches on large collections of DNA sequences. Experience has shown, however, that these tools are usually very rigid with respect to their assumptions about input data. If input files are compressed in a certain way, or stored in a non-standard format, there is usually ...

more…

Thoughts on research software from the PSRN workshop

In which I ramble on about experimental science, research software, and cyberinfrastructure engineering.

more…

Reading roundup

Roundup of links from the last week's worth of interesting reads.

more…

Reading roundup

Roundup of links from the last week's worth of interesting reads.

more…

Misconceptions about research software

I stumbled across the following question the other day in an email digest from Quora.

I have 5 years of working experience, but I still code very slow. How can I code faster? What should I learn?

Most of the responses don't answer the question directly, but instead make the point that speed is a very poor metric by ...

more…