A controller for controlling a microfluidic device. A first computing device receives commands from a user interface in a relatively high level protocol using a standardized command language, converts the commands from the standardized command language into a relatively mid-level protocol, sends the commands in the relatively mid-level protocol, receiving data, converts the data into the standardized command language, and sends the data to the user interface according to the standardized command language. A second computing device receives the commands from the first computing device in the relatively mid-level protocol, converts the commands from the relatively mid-level protocol to at least one relatively lower level protocol that is understood by a microfluidic device that is connected to the controller, receives data from the microfluidic device, and sends the data to the first computing device.