Computational models and tools provide increasingly solid foundations for the study of cognition and model-based reasoning, with knowledge generation in different types of cognizing agents, from the simplest ones like bacteria to the complex human distributed cognition. After the introduction of the computational turn, we proceed to models of computation and the relationship between information and computation. A distinction is made between mathematical and computational (executable) models , which are central for biology and cognition. Computation as it appears in cognitive systems is physical, natural, embodied, and distributed computation, and we explain how it relates to the symbol manipulation view of classical computationalism . As present day models of distributed, asynchronous, heterogeneous, and concurrent networks are becoming increasingly well suited for modeling of cognitive systems with their dynamic properties, they can be used to study mechanisms of abduction and scientific discovery. We conclude the chapter with the presentation of software modeling with computationally automated reasoning and the discussion of model transformations and separation between semantics and ontology.