Root and Hanna were playing Oregon Trail on an Apple IIe computer. Oregon Trail was developed for the Minnesota Education Computing Consortium (MECC), and used by elementary schools to teach school children about the realities of 19th century pioneer life on the Oregon Trail.
The book Flowers for Algernon, which is a plot point in the story, was not chosen accidentally. That story is about a man with a low IQ who has brain surgery in attempt to boost his IQ. It succeeds beyond everyone's wildest dream, but it eventually produces unexpected consequences. At this point of the show Root is still an unknown figure, but her story line during the course of the show would begin to parallel the character in Flowers for Algernon.
Jonathan Nolan's wife suggested Amy Acker for the role of Root, as she was a big fan of Acker's from Angel. She noted that Acker can appear innocent, and at the same time be very slippery, which showed great depth as an actor.
One of the accounts that Root created for herself was in the name of Von Neuman. John Von Neuman is one of the founding figures in computer science.
Denton Weeks told Root that the machine was loaded to a train in Des Moines, headed to Utah and then loaded up on another train belonging to Union Pacific Railway. This means that the machine followed a similar route to historical Oregon Trail. Throughout the episode, Root and her friend Hannah are shown play Oregon Trail during their childhood with flashbacks.