Low-rate and low-power wireless communications are still the main drivers for innovative industrial automation and the Internet of Things (IoT). Physical mobility is one of the most important challenges for them. Common wireless technologies and protocols, e.g., WirelessHART and ISA100.11a Wireless for industrial process plants, ZigBee for building automation, or 6LoWPAN and 6TiSCH in context of the IoT, are based on the IEEE 802.15.4 standard. Event-based simulation is the method of choice for analyzing network protocols and algorithmic applications of such distributed sensor applications. Performance measurements and holistic evaluations, however, are greatly influenced by the underlying hardware resources, physical layer protocols, and radio channel conditions, which are usually not considered or highly abstracted in network simulations. In this paper we present SEmulate, a hybrid system for seamless (network) simulation and hardware-based emulation for wireless sensor networks based on the IEEE 802.15.4 protocol standard, which takes the hardware aspects into account by applying an Hardware-in-the-Loop (HIL) approach.