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With increased global interconnectivity and reliance on e-commerce, network services and Internet communication, computer security has become a necessity. Organizations must protect their systems from intrusion and computer virus attacks. Such protection must detect anomalous patterns by exploiting known signatures while monitoring normal computer programs and network usage for abnormalities. Current anti-virus and network intrusion detection (ID) solutions can become overwhelmed by the burden of capturing and classifying new viral strains and intrusion patterns. To overcome this problem, a self-adaptive distributed agent-based defense immune system based on biological strategies is developed within a hierarchical layered architecture. A prototype interactive system is designed, implemented in Java and tested. The results validate the use of a distributed-agent biological system approach toward the computer security problems of virus elimination and ID.