Switch from Popen to call in do_research

This automatically wait()s for each process to finish, so we don't end
up with weird results.
Merge branch 'Fall2012' of github.com:petercombs/EisenLab-Code into Fall2012
Turn off Upper Quartile Normalization

It really messes with the FPKMs, giving something not even in the same
range as you'd expect:
http://seqanswers.com/forums/showthread.php?t=20062
Changes to the BayesMatch so they work on server

Mainly things about where various files live, as well as sensible
defaults when no gene set is specified.
Suppress outputs in IPython Notebooks
Does pandas read the significant column as boolean or not?

This is really starting to frustrate me!