Marios Braindump

Have you ever had the problem of re-finding how you created this particular image or that specific result of your recent bioinformatics project? I did, and not only once.  In his article “A quick guide to organizing computational biology projects“, the distinguished scientist William S. Noble gives great advice on how to organize a research project practically. His key suggestions include:

• use a date-based directory structure for the experiments you perform
• keep a lab-notebook containing documentation and code for each experiment (How about Org-mode?)
• create generate scripts that work on original data and a general runner script for the complete experiment

His work flow is applies mostly to *nix enviroments. One thing I’d like to add: Use symbolic links! Due to huge amounts of data and backup strategies, it might be impractical to have all the project’s data in a single directory. Create subdirectories of your data and result directories according to the naming convention and link them to other network drives using the ‘ln -s’ command.

Tags:english research scripting | Filed on June 8th, 2010 | No Comments »