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The paper discusses an FPGA-based prototyping system with both wired and wireless programming and data exchange facilities. The system can be efficiently used for different types of portable devices. For example, it can supply additional interfaces to mobile computers; can be seen as a hardware accelerator for solving computationally complex problems or serve as a base for portable embedded applications. The system includes an extendable core prototyping board, development tools and supplementary software. The board is designed in such a way that it provides direct support for reconfiguration and self-reconfiguration. It can also be employed for virtual prototyping systems that require more resources that the capacity of the onboard FPGA. The supplementary software includes all necessary drivers and interfaces to interact with the board. The development tools are targeted to design space exploration and they consist of hardware description language libraries, design templates, IP cores, software models and multimedia applications. The latter are mainly used for different types of experiments and for hardware/software partitioning.