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Using the Arduino Due board within Atmel Studio 6: 
  1. Starting a New Project
  2. Uploading Code to Due
  3. Integrating Programming tool in AtmelStudio
  4. J-Link with Arduino Due



Other related pages:

https://sites.google.com/site/arduinofocus/home
https://sites.google.com/site/yaeuls/home
https://sites.google.com/site/taiglathe/

Using the Open Logic Sniffer  a low cost Logic-Analyser :  https://sites.google.com/site/openlogicsniffer/home