Recently a few people have been working on various methods of interfacing their Raspberry Pi computer with the Arduino boards - for control of the GPIO, interfacing with other objects using the Arduino as the medium and so on. One interesting example of this is from the Mitchtech blog, where they demonstrate sending data from the Raspberry Pi to the Arduino via the SPI bus. The Arduino is set as a slave SPI device and the code demonstration is written in C for the RPi.
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If you're looking to embed an Arduino-compatible board in your projects driven by Raspberry Pi or other computers, consider embedding the Freetronics LeoStick. Apart from being one of the smallest Arduino-compatibles on the market with USB, it also has an onboard RGB LED and piezo for an alarm clock, and it's own form of knock detection to use as a snooze button: