System and method for loading and/or updating firmware in a device, e.g., an embedded device, operable to be coupled to a host computer system. A first portion of firmware of the device, e.g., a boot loader, may be executable to operate the device, including processing requests from the host computer system and/or enabling the device to execute a second portion of the firmware, e.g., an operating system for the device. The device may be coupled to other devices or instruments. The second portion of the firmware may allow the host computer system to operate and/or control the other devices or instruments through the device. The host computer system may transmit a different version of the second portion of the firmware to the device, e.g., enabling the device to couple to and operate with a specific instrument. The host computer system may not update the first portion of the firmware.