A beginner’s guide to BioRuby development

I’m the “biologist-turned-programmer” type of bioinformatician which makes me a hacker, not a developer. Most of the day-to-day coding that I do goes something like this:

Colleague: Hey Neil, can you write me a script to read data from file X, do Y to it and output a table in file Z?
Me: Sure… (clickety-click, hackety-hack…) …there you go.
Colleague: Great! Thanks.

I’m a big fan of the Bio* projects and have used them for many years, beginning with Bioperl and more recently, BioRuby. And I’ve always wanted to contribute some code to them, but have never got around to doing so. This week, two thoughts popped into my head:

  • How hard can it be?
  • There isn’t much introductory documentation for would-be Bio* developers

The answer to the first question is: given some programming experience, not very hard at all. This blog post is my attempt to address the second thought, by writing a step-by-step guide to developing a simple class for the BioRuby library. When I say “beginner’s guide”, I’m referring to myself as much as anyone else.
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