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The paper outlines a framework and software tool intended for simulation of cooperative defence mechanisms against botnets. These framework and software tool are based on agent-oriented approach and packet-level network simulation. They are intended to evaluate and compare different cooperative distributed attacks and defence mechanisms. Botnet and defence components are represented in the paper as a set of collaborating and counteracting agent teams. Agents are supposed to collect information from various network sources, operate different situational knowledge, and react to actions of other agents. The paper describes the results of experiments aimed to investigate botnets and distributed denial of service defence mechanisms. We explore various botnet attacks and counteraction against them on the example of defence against distributed denial of service attacks. Copyright © 2011 John Wiley & Sons, Ltd.