CIS systems, being the most complex yet most reliable technical structures engineered by man, present many challenges throughout their lifecycle. Difficulties in modelling, design, implementation and maintenance come not only from involved, widely distributed technical and organizational structures (comprising both hardware and software resources), but evenmore from complexity of the information processes (data processing, monitoring, resource allocation, dynamic reconfiguration, etc.) which are realized in the operational, often hostile environment. Furthermore, all the issues need to be dealt with taking into account a number of additional factors, such as uncertainties of human interactions, safety criteria and security demands or economic and environmental constrains.