I'm Vince Buffalo, a Ph.D. student in Graham Coop's lab studying evolutionary and population genetics at UC Davis in the Center for Population Biology. Previously, I worked as a bioinformatician at the UC Davis Genome Center and in the Dubcovsky and Ross-Ibarra labs. I wrote Bioinformatics Data Skills published by O'Reilly Media in July 2015. I use statistics, probability, and computers to learn about evolution. » read more
It’s hard not to fall in love with Unix as a bioinformatician. In a past post I mentioned how Unix pipes are an extremely elegant way to interface bioinformatics programs (and do inter-process communication in general). In exploring other ways of interfacing programs in Unix, I’ve discovered two great but overlooked ways of interfacing programs: the named pipe and process substitution.
A few weeks ago I stumbled across a great talk by Gary Bernhardt entitled The Unix Chainsaw. Bernhardt’s “chainsaw” analogy is great: people sometimes fear doing work in Unix because it’s a powerful tool, and it’s easy to screw up with powerful tools. I think in the process ...continue reading→