The extruder controller is a compact little board based on the Arduino Diecimila. This board contains all the electronics required to drive one extruder, as well as extra electronics to drive a heated/automated build platform. It has built-in USB, so you can talk to it and program it with a normal USB cable. It has been redesigned with much higher power needs, so it has an ATX power header to provide the power. This means power is not coming over the RS485 cable which has the side effect of reducing noise.

Full instructions here: http://wiki.makerbot.com/thingomatic-doc:extruder-controller-3-6