A test system for testing prototype designs includes a host workstation, multiple interface devices, and multiple prototype boards. The prototype boards include programmable devices which implement one or more partitions of a user design and an associated verification modules. The verification modules probe signals of the partitions and transmit the probed signals to the interface devices. The verification modules can also transmit output signals generated by one or more partitions on the prototype boards to the host workstation via the interface devices, and transmit input signals, which are received from the host workstation via the interface devices, to one or more partitions on the prototype boards.