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Increased use of sensors and social data collection methods have provided cites with unprecedented amounts of data. Yet, data alone is no guarantee that cities will make smarter decisions and many of what we call smart cities would be more accurately described as data-driven cities. Parallel advances in theory are needed to make sense of those novel data streams and computationally intensive decision support models are needed to guide decision makers through the avalanche of new data. Fortunately, extraordinary increases in computational ability and data availability in the last two decades have led to revolutionary advances in the simulation and modeling of complex systems. Techniques, such as agent-based modeling and systems dynamic modeling, have taken advantage of these advances to make major contributions to diverse disciplines such as personalized medicine, computational chemistry, social dynamics, or behavioral economics. Urban systems, with dynamic webs of interacting human, institutional, environmental, and physical systems, are particularly suited to the application of these advanced modeling and simulation techniques. Contributions to this special issue highlight the use of such techniques and are particularly timely as an emerging science of cities begins to crystallize.