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Is it possible to format an SPI EEPROM (such as AT24C128) to be used as an SD card? So format it with FAT 32 and have a 16MB drive appear in windows?

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Yes, it is possible, but you'd need some kind of controller, you couldn't just wire the eeprom directly. This is because the EEPROM does not speak SD card protocol. I would probably bypass SD completely, and just use USB. So something like:

SPI EEPROM <-SPI-> AVR <-USB-> PC

Look into the examples provided with the AVR USB library, Lufa, one of the examples shows exactly the above setup...except it's using an Atmel DataFlash instead of a SPI EEPROM. But it's possible, you'd just need to change the code which accesses the Flash to instead access the EEPROM.

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Microchip also has an example of how to implement a USB mass storage device.

AN1189 - Implementing a Mass Storage Device

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