Lastly, the CryptoCape contains an independent microcontroller. This microcontroller is the ATmega328p, which is the same microcontroller on the Arduino UNO. However, because the supply voltage is 3.3V and not 5V like the Arduino UNO, the processor runs at a clock speed of 8MHz versus 16Mhz. In this sense, it is more like the 3.3V Arduino Pro Mini. Shipped from SparkFun, the CryptoCape contains the 3.3V Arduino Pro Mini bootloader. Like any other Arduino-based board, you can reflash the bootloader by attaching an In-System Programming (ISP) programmer to the ISP headers next to the ATmega328p. SparkFun's pocket programmer is an inexpensive tool to perform this task. Just be sure to set the switch to no power target since the CryptoCape is powered from the BBB.
While you can use an ISP programmer, you can also use the BBB as a programmer. The BBB contains both serial UART and SPI; however, only the serial UART, UART 4, is connected to the onboard ATmega328p...