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Nowadays, computer systems consist of many components such as servers and clients, protocols, services, and so on. Systems connected to network have become more complex, with research focused on performance and efficiency. While most of the attention in system security has been paid to encryption technology and protocols for securing data transactions, a weakness (security hole) in any component may comprise the whole system. Security engineering is needed for eliminating such holes. This paper outlines some novel challenges of security engineering, as well as their relations to other areas of scientific research.