System dynamics validation and analysis methods must be consistent with some unique defining properties of system dynamics. Very briefly, these properties stem from the fact that system dynamics models are causal descriptive models and they are designed for long term policy analysis and design objectives. One of the important results is the fact that system dynamics validity consists of two very different types: structural and behavioral. We present two different validity testing software developed at Boğaziçi University to assist with indirect structure testing (SiS) and behavior pattern testing (BTS II). SiS software does automatic dynamic pattern recognition and indirect structure testing. Our behavior pattern testing (BTS II) software estimates and compares the major dynamic pattern components of the simulated and actual dynamic behaviors. These pattern components are: the trends, periods of oscillations (single or multiple), phases of oscillations, the amplitudes (constant or time-varying), average values, variances (or higher order moments) and finally a single overall discrepancy measure (U). Another issue in dynamic simulation methodology is parameter calibration, assuming that the structure of simulation model constructed by the user is valid. SiS software also does automated parameter calibration with respect to a given (desired) dynamic pattern. This particular feature can also be used in policy analysis and improvement design.