Novel computational representations, such as simulation models of complex systems and video games for scientific discovery (Foldit, EteRNA etc.), are dramatically changing the way discoveries emerge in science and engineering. The cognitive roles played by such computational representations in discovery are not well understood. We present a theoretical analysis of the cognitive roles such representations play, based on an ethnographic study of the building of computational models in a systems biology laboratory. Specifically, we focus on a case of model-building by an engineer that led to a remarkable discovery in basic bioscience. Accounting for such discoveries requires a distributed cognition (DC) analysis, as DC focuses on the roles played by external representations in cognitive processes. However, DC analyses by and large have not examined scientific discovery, and they mostly focus on memory offloading, particularly how the "use" of existing external representations changes the nature of cognitive tasks. In contrast, we study discovery processes and argue that discoveries emerge from the processes of "building" the computational representation. The building process integrates manipulations in imagination and in the representation, creating a "coupled cognitive system" of model and modeler, where the model is "incorporated" into the modeler's imagination. This account extends DC significantly, and we present some of the theoretical and application implications of this extended account.