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The integration of Software Fault Tree (SFT), which describes intrusions and Coloured Petri Nets (CPNs) that specifies design, is examined for an Intrusion Detection System (IDS). The IDS under development is a collection of mobile agents that detect, classify, and correlate the system and network activities. SFTs, augmented with nodes that describe trust, temporal and contextual relationships, are used to describe intrusions. CPNs for intrusion detection are built using CPN templates created from the augmented SFTs. Hierarchical CPNs are created to detect critical stages of intrusions. The agentbased implementation of the IDS is then constructed from the CPNs. Examples of intrusions and descriptions of the prototype implementation are used to demonstrate how the CPN approach has been used in the development of the IDS. The main contribution of this paper is an approach to systematic specification, design …