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Network-on-chip (NoC) based multi-processor systems-on-chip (MPSoCs) are promising candidates for future multi-processor embedded platforms, which are expected to be composed of hundreds of heterogeneous processing elements (PEs) to potentially provide high performances. However, together with the performances, the systems complexity will increase, and new high level design techniques will be needed to efficiently model, simulate, debug and synthesize them. System-level design (SLD) is considered to be the next frontier in electronic design automation (EDA). It enables the description of embedded systems in terms of abstract functions and interconnected blocks. A promising complementary approach to SLD is the use of models of computation (MoCs) to formally describe the execution semantics of functions and blocks through a set of rules. However, also when this formalization is used, there is no clear way to synthesize system-level models into software (SW) and hardware (HW) towards a NoC-based MPSoC implementation, i.e., there is a lack of system design automation (SDA) techniques to rapidly synthesize and prototype system-level models onto heterogeneous NoC-based MPSoCs. In addition, many of the proposed solutions require large overhead in terms of SW components and memory requirements, resulting in complex and customized multi-processor platforms. In order to tackle the problem, a novel model-based SDA flow has been developed as part of the thesis. It starts from a system-level specification, where functions execute according to the synchronous MoC, and then it can rapidly prototype the system onto an FPGA configured as an heterogeneous NoC-based MPSoC. In the first part of the thesis the HeartBeat model is proposed as a model-based technique which fills the abstraction gap between the abstract system-level representation and its implementation on the multiprocessor prototype. Then details are provided to describe how this technique is automated to rapidly prototype the modeled system on a flexible platform, permitting to adjust the system specification until the designer is satisfied with the results. Finally, the proposed SDA technique is improved defining a methodology to automatically explore possible design alternatives for the modeled system to be implemented on a heterogeneous NoC-based MPSoC. The goal of the exploration is to find an implementation satisfying the designer's requirements, which can be integrated in the proposed SDA flow. Through the proposed SDA flow, the designer is relieved from implementation details and the design time of systems targeting heterogeneous NoC-based MPSoCs on FPGA is significantly reduced. In addition, it reduces possible design errors proposing a completely automated technique for fast prototyping. Compared to other SDA flows, the proposed technique targets a bare-metal solution, avoiding the use of an operating system (OS). This reduces the memory requirements on the FPGA platform comparing to related work targeting MPSoC on FPGA. At the same time, the performance (throughput) of the modeled applications can be increased when the number of processors of the target platform is increased. This is shown through a wide set of case studies implemented on FPGA. / <p>QC 20140609</p>