The software program that is used for building energy simulation here at SES is Energy Plus.  This is a description of the program from the U.S. Department of Energy's website:

"EnergyPlus models heating, cooling, lighting, ventilating, and other energy flows as well as water in buildings.  While originally based on the most popular features and capabilities of BLAST and DOE-2, EnergyPlus includes many innovative simulation capabilities such as time steps of less than an hour, modular systems and plant integrated with heat balance-based zone simulation, multizone air flow, thermal comfort, water use, natural ventilation, and photovoltaic systems."

EnergyPlus also utilizes weather data and predicts energy usage for a modeled building.  It is a simulation tool that is accepted by ASHRAE Standard 140 and therefore can be applied to ASHRAE Standard 90.1 (Energy Standard for Buildings except Low-Rise Residential Buildings) and abides by all the parameters and standards provided therein.

Figure 1 is an example of a building that is modeled in EnergyPlus and then imported into Google Sketchup for a better visualizaion of the building. 

Fig. 1: Sketchup Drawing

HVAC components and building construction materials can be altered and/or improved to analyze the changes they make to the system and direct comparisons can be made to optimize the building's performance.