Some applications require to generate (or read) digital channels on the host-PC running the GUI. Most commonly, this is needed when closed-loop experiments make use of event detection on the host PC, for example with the phase-detector plugin.
The arduino shield for I/O from the host-pc can generate up to 8 channels of digital I/O. Each channel can be assigned as in or out and assigned to an event channel in the GUI.
On the Arduino, this is implemented via the Firmata firmware (http://playground.arduino.cc/Interfacing/Firmata). This makes it simple for a computer to access the state of the Arduino pins via USB.
Arduino I/O is controlled directly from the Arduino Output sink (in development) in the GUI. Currently, the I/O shield is strictly passive and makes no use of the analog pins. However, you can still access all arduino pins through the headers.