The Peters Automated Infrared Imaging Telescope (PAIRITEL) is the first meter-class telescope operating as a fully robotic IR imaging system. Dedicated in October 2004, PAIRITEL began regular observations in mid-December 2004 as part of a 1.5 year commissioning period. The system was designed to respond without human intervention to new gamma-ray burst transients: this milestone was finally reached on November 9, 2005 but the telescope had a number of semi-automated sub-10 minute responses throughout early commissioning. When not operating in Target of Opportunity mode, PAIRITEL performs a number of queue scheduled transient monitoring campaigns. To achieve this level of automation, we have developed communicating tools to connect the various sub-systems: an intelligent queue scheduling database, run-time configurable observation sequence software, a data reduction pipeline, and a master state machine which monitors and controls all functions within and affecting the observatory.