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The papers in this special section focus on the development of models and data analysis systems for use in the ever growing complex financial markets. Both finance and economics are complex domains, in which multiple components such as investors, trading venues, or intermediary firms frequently interact to generate aggregate outcomes that may be desirable or undesirable, intended or unintended. The behavior of the underlying elements is often adaptive and the aggregate dynamics can be highly nonlinear. The resulting complexity can therefore be difficult to measure, model, and control. The recent financial crisis revealed how interconnections between institutions can provide feedback loops and propagation channels across the financial system, nationally and globally, spilling into the real economy. There is a great need for advances in the ways in which financial and economic systems are modeled, simulated, designed, controlled, and regulated. The techniques and hybrid approaches emerging from the ongoing efforts of the systems community can help address the challenge.