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We present a system level design methodology for clustered wireless sensor networks based on a semi-random communication protocol called SERAN, a mathematical model that allows to optimize the protocol parameters, and a network initialization and maintenance procedure. SERAN is a two-layer (routing and MAC) protocol. At both layers, SERAN combines a randomized and a deterministic approach. While the randomized component provides robustness over unreliable channels, the deterministic component avoids an explosion of packet collisions and allows our protocol to scale with network size. The combined result is a high reliability and major energy savings when dense clusters are used. Our solution is based on a mathematical model that characterizes performance accurately without resorting to extensive simulations. Thanks to this model, the user needs only to specify the application requirements in terms of end-to-end packet delay and packet loss probability, select the intended hardware platform, and the protocol parameters are set automatically to satisfy latency requirements and optimize for energy consumption.