I recently described our group's current status in this post: We have the minimum of everything required for bioinformatics analysis; why do we need more?
This is a follow-up to one of those points, namely the data management issue. Would someone be able to give me good arguments for why it is better to switch over to database-based data management? What are the advantages of this, that I would not be able to do by just keeping everything in files?
Well, you will have to define more clearly what you would want to store in such a databases. Generally speaking, databases are good for relational data.
Also, I don't think it makes sense to explicitly use either.
Perhaps not a strictly bioinformatics-related question, this, but it is so tightly connected to what we need to do in bioinformatics that I still consider it appropriate for this forum. Please let me know if I am wrong about this.
You posed and answered your question in the same sentence: "not a strictly bioinformatics-related question" yet "so tightly connected to what we need to do in bioinformatics". I consider activities connected to bioinformatics to be the subject of bioinformatics questions. So, I think this question is completely appropriate here.
As to the question itself, without a database, what method would you suggest for making queries across all your projects? A script that scans directories and reads standardized flat files? The "management" part implies the ability to gain and navigate some kind of overview. I employ both methods due to a generally un-directed and historically messy design process, but seldom hear about how to "manage" data overviews without a database.
A friend of mine made a suggestion to me just earlier today, that if I'm talking about a rare query that I'm interested in doing across projects, then it might be better to just stick with flat files. He was suggesting that maintaining a database with all its hassles might be a bit excessive for what I would need it for.
http://stackoverflow.com/questions/2356851 "database vs. flat files" ; http://stackoverflow.com/questions/6853482 "Flat file vs database - speed?"; etc...