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The human immune system is a complex system of cells, molecules, tissues, and diverse organs that can provide us with primary defense against pathogenic organisms. These components are highly interactive and execute the immune response in a coordinated and specific manner. This paper presents a formal mathematical model of an artificial immune system (AIS)-based control framework. The framework aims to provide an integrated solution to control and coordinate complex distributed systems with a large number of autonomous agents such as automated warehouses, distribution centers, and automated material-handling systems. The control framework consists of a set of AIS agents working in response to the changing environment and the occurrence of tasks. The AIS agents manipulate their capabilities to derive appropriate responses to tackle different problems. A methodology describing the response-manipulation algorithm of the AIS agents and their ability to generate new capabilities is discussed in this paper. Through response manipulation and knowledge building, a self-organized and fully distributed system with agents that are able to adapt and accommodate in a dynamic environment via distributed decision making and interagent communication is achieved.