I write a Rails server for each of my experiments. Rake tasks are GREAT for bioinformatics pipelines, and migrations and database backups make it incredibly easy to save old experiments.

Plus, various Ruby gems (starling, workling) enable me to farm out long-running experiments to a variety of lab machines. I can use Rice to write C++ Ruby extensions that are compiled individually on different machines.

And all of this is stored in a PostgreSQL database. (MySQL is slow for complex joins, which you sometimes have to write in bioinformatics.)

Well, you could, but it might take a pretty long while to do it by hand. And it wouldn't do you much good, either.