The iCycler contains a software system that uses protocol files to control some of the parameters of the experiment. The protocol files have the file extension ".tmo." The Plate Setup files, which are also used to control some parameters, have the file extension ".pts."
The analyst using the iCycler uses the protocol files to set the parameters of the thermal cycling step of the PCR reaction, when the DNA is kept at a certain heat for a reaction to occur. The thermal cycle can contain as many as nine steps, and the analyst can choose his own temperatures and times.
The iCycler has a library module where analysts can access protocols that have already been set up. The analyst can edit a particular protocol or create a new protocol from scratch to run his PCR cycle under. He has to ensure any plate setup file being used is suitable to run with his PCR settings.