Thank you for your answer @graykevinb .
But I also saw that there is ISP header on the GoPiGo board to program the AT328 :
So with a USB ISP programmer compatible with ATMEGA328, it is possible to change the program on the AT328.
I want to do this in order to implement a complete PID motion control for the GoPiGo. The PID which is currently implement on the official firmware is too basic and doesn't fit with my need.