Bioinformatics Zen

Deepak, Neil, and Cameron have set up life streams which aggregate the feeds from services from sites like Last.fm and Flickr into a single set of posts. I’m a bit wary of this doing this because I already get easily distracted by Ruby and bioinformatics blogs, but Neil gave me an idea when he wrote about using these technologies to track research. I currently use Subversion to back up my project files, and I noticed Twitter status updates are very similar in length to subversion log messages. I created a short script so that every time I do a subversion repository check in, the message is also sent to Twitter.

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A common practice in any computationally based field is writing code where the intended functionality has already been produced by someone else. This is usually called reinventing the wheel. This isn’t very useful since you’re spending time on an intermediate step, when instead you can use existing code and jump ahead to the next step in your research. Of course, it’s easy for me to shout bad practice on my blog, but I’m the worst person for doing this. I work in bioinformatics because I like writing code to solve problems, and my first response is to start coding, rather than look to see if someone has created a solution already. On the other hand, the benefit of using existing libraries is that you can build new things on what has already been done.

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