The team of engineers designing and implementing distributed control system software must communicate within a multidisciplinary environment. One of the main problems is the interaction between hardware and software solutions. Software project presumptions may not be based only on minimum hardware requirements and on technology rules. Modern distributed control systems embrace all aspects of a complex and widespread object. Hence, every modification within any discipline requires interference into the system and validation of its new features, which in turn constraints effectiveness of designing. This paper discusses how to increase effectiveness and speed up validation, in a standardised CAD environment, by using: MultiAgent System in order to limit the number of interactions between particular subsystems, ontology for assisting topology description and properties of system entropy for assessment of introduced solutions. The proposed system was implemented and worked out in a biotechn...