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so, I got a Arduino Due, but I am somewhat confused about the pin layout.

As a simple setup, I want to have some LEDs blinking. On my host laptop, I use Node and Johnny-five like here: https://github.com/rwaldron/johnny-five/wiki/Getting-Started

But when it comes to the Arduino board, I am confused. I found a board schematic here: http://forum.arduino.cc/index.php?topic=132130.0

But how and where should I connect the LED to have some basic strobe.

arduino due setup

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According to that link you provided:

// Create an Led on pin 13
var led = new five.Led(13);

enter image description here

Connect the LED to pin 13 or any other pin as long as you modify this code.

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    \$\begingroup\$ There is already an onboard LED connected to digital pin 13 so for testing purpose there is no need for an external one. \$\endgroup\$
    – alexan_e
    Commented May 18, 2014 at 18:53

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