Notebook software

Bioinformatics Twitter is having...a moment. What began as one man's exasperated rant against poorly documented and distributed code has bloomed into a protracted debate about what constitutes "good" bioinformatics software and which kind(s) of interfaces developers should be expected to provide if they "really" want people to use their software. For those that have been around a while …

I contend that you should be treating your solo software projects like a collaborative project and using pull requests, an issue tracker, and other social development tools.

A primer on software testing for scientists and researchers.

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 …

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

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

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

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 which …