Update: A representative of Omega responded to my request for a communications manual: "The OM-92 is designed and marketed for use only with the provided software. The command set is not available and considered proprietary." Regardless of this, I am still interested in good techniques for reverse engineering serial devices, but will be proceeding in my project with different sensors.
Background: I have an OM-92 temperature and humidity logger that I am trying to communicate with over serial. There doesn't seem to be any documentation about the communication protocol it uses. It comes with a GUI to download data from the device, but I'm trying to record data from this device automatically and the GUI just gets in the way. Additionally, the GUI software only works on Mac and Windows (I am using Ubuntu on a Beagle Bone Black).
Question: How can I determine the communication protocol it uses? How can I determine the command instruction set?
Theories: I have a hunch that it uses Modbus (because the Omega controllers do). All I know for sure is that it connects the the PC with a standard via USB.