Agent-based complex systems are dynamic networks of many interacting agents; examples include ecosystems, financial markets, and cities. The search for general principles underlying the internal organization of such systems often uses bottom-up simulation models such as cellular automata and agent-based models. No general framework for designing, testing, and analyzing bottom-up models has yet been established, but recent advances in ecological modeling have come together in a general strategy we call patternoriented modeling. This strategy provides a unifying framework for decoding the internal organization of agent-based complex systems and may lead toward unifying algorithmic theories of the relation between adaptive behavior and system complexity. What makes James Bond an agent? He has a clear goal, he is autonomous in his decisions about achieving the goal, and he adapts these decisions to his rapidly changing situation. We are surrounded by such autonomous, adaptive agents: cells of the immune system, plants, citizens, stock market investors, businesses, etc. The agent-based complex systems (1) (ACSs) around us are made up of myriad interacting agents. One of the most important challenges confronting modern science is to understand and predict such systems. Bottom-up simulation modeling is one tool for doing so: We compile relevant information about entities at a lower level of the system (in Bagent-based models,[ these are individual agents), formulate theories about their behavior, implement these theories in a computer simulation, and observe the emergence of system-level properties related to particular questions (2, 3).Bottom-up models have been developed for many types of ACSs (4), but the identification of general principles underlying the organization of ACSs has been hampered by the lack of an explicit strategy for coping with the two main challenges of bottom-up modeling: complexity and uncertainty (5, 6). Consequently, model structure often is chosen ad hoc, and the focus is often on how to represent agents without sufficient emphasis on analyzing and validating the applicability of models to real problems (5, 7).A strategy called pattern-oriented modeling (POM) attempts to make bottom-up modeling more rigorous and comprehensive (6,(8)(9)(10). In POM, we explicitly follow the basic research program of science: the explanation of observed patterns (11). Patterns are defining characteristics of a system and often, therefore, indicators of essential underlying processes and structures. Patterns contain information on the internal organization of a system, but in a Bcoded[ form. The purpose of POM is to Bdecode[ this information (10).The motivation for POM is that, for complex systems, a single pattern observed at a specific scale and hierarchical level is not sufficient to reduce uncertainty in model structure and parameters. This has long been known in science. For example, Chargaff_s rule of DNA base pairing was not sufficient to decode the structure of DNA-until combined with patterns from x-ray...