Computer simulations and rule-based modelling can be effective methodologies to describe complex systems and understand or control their behaviour. As many complex biological systems encompass several spatial and temporal scales, as well as several elementary components they cannot be described by a single homogenous model. COAST is developing a multi-scale, multi-science framework coined ‘Complex Automata’ for modelling and simulation of complex systems. The key tenet of COAST is that a multi-scale system can be decomposed into a number of single-scale Cellular Automata or agent-based models that mutually interact across the scales. Decomposition is facilitated by building a Scale Separation Map (SSM) on which each single-scale system is represented according to its spatial and temporal characteristics. Processes having well-separated scales are thus easily identified as the fundamental components of the multi-scale model.