Actually using the USB port of the BeMicro kit...

[Altera_Forum]

This is a **really** newbie-esque question, but I haven't found a clear answer elsewhere, so here goes: 

 I know that the USB connection on the BeMicro eval kit is usually just used for downloading to the device and debugging, but can it also be incorporated into my actual design?  For example, if I wanted to set the device up as some sort of USB... like a thumbdrive or something like that.  Thanks.

[Altera_Forum]

The USB port is connected to the FTDI driver chip, which connects to very small max2 device. 

The max2 device decode the USB signal and translate it to jtag signal. The jtag signal goes to the FPGA finally.  So, if you can modify the small max2 program, then you can use the USB as just USB. Otherwise, the USB port always works as USB Blaster.  User can program or control the BeMicro by using Altera tool sets, such as system console or Jtag-Uart. The system console does have API for JAVA. So if you can understand how to use JAVA, you can control most of stuff via that.

[Altera_Forum]

Are you referring to the Cyclone III or Cyclone IV BeMicro? The latter has an embedded MAXII USB Blaster, the former connects the FTDI chip to JTAG directly and exposes and additional UART channel.