Bioinformatics Zen


// Sun July 15 2012

This inspiration for this series owes much to Rich Hickey's talk on "Simple made easy". I have aimed to outline the possibilities of applying this in computational research over the previous four posts. My main point has been that building simple workflows from simple tools makes for easier maintenance and creating reproducible computational workflows.

When I first began in bioinformatics I programmed in Java, managed my data using SQL, and created build files with Ant. Later I wrote smaller Ruby scripts, used object relational mapping to connect to the database, and Rake to create reproducible analyses. In the last six months I have changed to creating composable functions in R, Ruby, Clojure or GNU coreutils, storing data in plain-text files, and maintaining reproducibility with GNU make. All of these setups have focused on reproducible bioinformatics workflows. Each time I've varied my tools to reduce the amount of complexity in my projects. Clojure syntax is simpler than Ruby, as is Ruby's when compared to Java, and using a GNU coreutil is simpler that writing something yourself.

The points I have outlined in this series of posts may be obvious to many: plain text files, UNIX pipelines and GNU Make are at the centre of bioinformatics. Using larger and newer tools are however attractive because of their newness and the possibility of potential features. I have often started using new tools after reading about them on blogs or discussion boards. A new tool may offer improved features over a predecessor but at the same time may also tie you to a particular way of working, therefore making it harder to incorporate alternative approaches or tools without significant rewriting or restructuring. The UNIX philosophy instead recommends building tools to do one thing well. The Clojure philosophy recommends combining composable libraries instead of tying yourself to larger frameworks. Building tools and workflows with this philosophy in mind allows for combining and interchanging different tools and approaches more easily and simply.