Custom Board using ATSAM3S

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http://forum.allaboutcircuits.com – I've recently made a custom board with an AT91SAM3S chip. The hardware is ready but the chip has nothing inside yet. I need to be able to code into the chip just like coding into any other commercial MCU board (e.g. arduino). I'm going to use the Atmel SAM-ICE over JTAG to interface my board to my PC. Could anyone please share the steps to get started working on the software using Atmel Studio? Or are there anything else I need to touch on before I move to Atmel Studio? (Embedded)