CAT-Control performs its task by executing a high level program language. The user usually does not need to program himself. He needs to feed the program with variables that his application can run in the desired way. The parameters are entered by the use of excel which places a widely used and well known interface at the users disposal.

CAT-Control uses three levels to interface with the user. The first level we call a ‘Program Application’. This is an excel file containing the principal sequential steps - in which order valves should be opened and closed, when the pump should be running etc. The second level feeds this program application with parameters and is called ‘Sequence’. The parameters are arranged in an Excel sheet and each line represents a step of a peptide syntheses like coupling an amino acid or deprotection of an amino acid.

The third level provides direct access to the individual I/O lines and to the pump.