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Summary: Honeycomb is a distributed smart building system that is robust, flexible, and portable. Here, we present a protocol that uses semi-physical simulation to construct a Honeycomb prototype. We describe steps for software and hardware preparation, as well as the implementation of a video-based occupancy detection algorithm. Besides, we provide examples and scenarios of distributed applications, including node failure and recovery. We further provide guidance on data visualization and analysis to facilitate the design of distributed applications for smart buildings.For complete details on the use and execution of this protocol, please refer to Xing et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.