One of the biggest points of friction in my professional life is the disconnect between the design of an experiment and the data that comes out of it. Not in any deep or scientific sense, but in a boringly practical sense of "How do I know what's in file MyRun_F05_039_pXK405.fcs?"
When I'm working with experimentalists and analyzing the data that they've produced, in order to make this connection, I get sent spreadsheets with colored cells and personal shorthands, or unintentionally cryptic emails, or scans of tables with hand-written notes. Then I make my best guess as to what's being encoded there and start organizing file names into scripts to run my analysis. The actual process of analysis is often very fast, only a few minutes, but for a good-sized experiment it can take hours to set it up to be able to run.
Read more of Dr. Beal's post here.