In addition to entertainment, simulation is often used for education and training. The purpose of training is to improve the performance of the “pilot module” whereas the purpose of scientific simulation is to improve one of the other modules – such as the autopilot, flight model, etc.
The uses above are developing/improving modules for navigation, autopilot, checklist and instrument panel. Scientific work on flight data models tends to be scripted so JSBSim for example would run independently of FlightGear. Since JSBSim can run as a FlightGear module as well as a standalone program, the aircraft models that result from the simulation can subsequently be immersively flown by pilots for a qualitative evaluation.