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Attempting to optimize the design of a complex enterprise system is extremely difficult at best. The interconnections and human elements inherent in these systems make determining the impact of design elements and changes to these elements challenging. We suggest that a combination of sophisticated modeling and simulation techniques, including the use of agent- based models, and biologically inspired optimization techniques can be used to address the aforementioned difficulties. Finally, we discuss visualization techniques for these types of systems that enhance the ability of subject matter experts and decision-makers to understand the results.