Mike at Bioinformatics Zen has a post on good practices for file naming and directory hygiene that could help ease confusion when you're running scripts involving several files. "For the last year I’ve been working with Ruby on Rails, and I think many of the techniques used in this framework are also applicable to bioinformatics experiment structuring," Mike writes. He elaborates on his recommendations, which include using a database and relational management library instead of flat files and performing validation to verify data, among others.
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