You connect the Moteino/Arduino to the RPi using USB. Your code running 
on the RPi opens /dev/ttyUSB0 (or whatever it shows up as) and talks to 
the uC on the Moteino/Arduino like if it were using a true serial port 
(/dev/ttyUSB0 behaves like a true serial port for all intents and 
purposes). You don't have to use /dev/ttyAMA0 (the Broadcom UART) to 
talk to the Moteino/Arduino. In fact, you cannot because the Rx and Tx 
pins of the uC are connected to the FTDI chip, so USB is the only option 
to talk to an Arduino via serial (unless the Arduino is one of the 
recent generations that supports more than one serial port), in which 
you don't have to use USB and can use the RPi serial port directly.

On 02/11/2014 03:19 PM, Colin Reese wrote:

> Yes, but we'd connect directly to the serial connection on the Pi after
> disabling the console, not go through USB.
>
>
> On Tue, Feb 11, 2014 at 12:11 PM, Eloy Paris <[email protected]
> <mailto:[email protected]>> wrote:
>
>     On 02/11/2014 02:58 PM, Colin Reese wrote:
>
>       > I have very little Arduino experience, but I was under the
>     impression
>       > that the serial console over the FTDI was typically just used
>     for debug.
>
>     What's the difference between sending a debug message to the PC or RPi
>     through the serial port/USB connection and sending a temperature value
>     received from a remote wireless sensor? It's all about how the data is
>     interpreted on the PC side, right? ;-)
>
>     The Arduino/Moteino/uC will also be able to read data sent to it by the
>     RPi through the USB connection.
>
>     Cheers,
>
>     Eloy Paris.-


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