Update software.md

Added Set package at the end.
Update papers.md

Changed "(2010)" to "(2013)" and "Brian Caffo" to "Caffo B," decreased font size for "Preprints," "2014," and "2013," so it would be the same size as the other years.
Update alumni.md

Made small change to my affiliation.
Merge pull request #3 from SiminaB/master

Made some edits to my profile and the reference for our paper, added Set package