I am communicating with two Arduino Unos, using my Raspberry Pi 3 via the UART interface. I have established serial communication between them. But I was wondering if there was a way to use this to upload new sketches on the fly to the Arduino(s).

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    The standard method of programming an Arduino Pro Mini, which has no USB, is via a serial interface, so this should be possible. You need to manually control reset etc. A better option is ICSP interface. In all cases you need to be aware of the 5V vs 3.3V differences. You should ask on the Arduino site. – Milliways Jun 12 '17 at 6:52

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