The Gimballed Limb Observer for Radiance Imaging of the Atmosphere (GLORIA), a Fourier transform spectrometer based limb spectral imager, operates on high-altitude research aircraft to study the transit region between the troposphere and the stratosphere. It is one of the most sophisticated systems to be flown on research aircraft in Europe, requiring constant monitoring and human intervention in addition to an automation system. To ensure proper functionality and interoperability on multiple platforms, a flexible control and communication system was laid out. The architectures of the communication system as well as the protocols used are reviewed. The integration of this architecture in the automation process as well as the scientific campaign flight application context are discussed.