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The practical feasibility of any proposed algorithm could be tested only by hardware implementation of the algorithm. However, in cases involving wireless infrastructure based networks, hardware implementation may be very costly and time consuming. Hence, software simulations are used for these cases. In this paper, we have discussed the approach to be taken to implement any algorithm in any real time simulator. As a test case, we have implemented a simple infrastructure based centralized cognitive channel allocation algorithm for WiMAX BWA system under QualNet 5.0 software. The performance of the algorithm is then validated in terms of Spectrum Utilization and System Throughput for both Poisson and Pareto Arrival Rate of the end users. The results are further compared with results obtained from MATLAB 7.3.0. Unlike MATLAB, the impact of the lossy environment and layered architecture of the nodes is embedded in the results obtained from Qualnet. A fall of 4% in Spectrum Utilization and 3.8% in Throughput is observed in Qualnet compared to MATLAB.