Set up a file system and runtime environment for the Borph on the control FPGA.
Here's how to set up the BEE2. I'm assuming that it has been powered up and tested, and all the relevant parts work.
First, some preliminaries. You'll need root access to your host to set up the NFS root for the bee. Or a friendly system administrator to sit with you and help when needed.
Follow the instructions at http://bee2.eecs.berkeley.edu/wiki/Bee2Setup.html to connect up your hardware and ensure it works. Once that's done, you need to create a bootable compact flash disk.