Bioinformatics Zen

One of the differences between researching a scientific problem using a computer, and developing software, is the approach to writing code. If you’re producing a bioinformatics application there is more emphasis on generating high quality, flexible code, as this makes future maintenance easier. On the other hand if you’re trying to find the answer to a biological question using a series of scripts, then the focus is on the results, rather than the standard of code. During my work, the number of scripts I have tends to grow quickly, and this leads to problems with maintaining dependencies across scripts. Examples of this can be database connection parameters, or the file system location of a library I’m calling. This is because the fastest way to get this information into a script, is to cut and paste from an already existing one. However this becomes difficult to manage, when something changes, because I have to go back through all my scripts and update each in turn.

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I guess one of the golden rules of blogging is write about what people are interested in. Here’s the most common questions I get emailed, and my answers to them.

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No post this Monday as I spent Friday evening writing Bio::Blogs. However Shirley Wu has asked me to the mention the PSB session proposal. If you’d like to get involved in the Open Notebook Science movement, this is a good place to begin. Shirley’s post outlines the requirements and there’s a Google Doc for the proposal itself.

This is the February edition of Bio::Blogs, an aggregation of bioinformatics posts from the past month. This issue has a particular focus on Open Notebook Science - researchers sharing their work as they produce it.

For this edition, with the help of Cameron Neylon, Jean-Claude Bradley, and Pedro Beltrao, I’ve tried to write a short essay on open science as well as the open notebook variety. I’ve posted this on my research website.

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