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This paper presents an adaptive setup planning system that considers both the availability and capability of machines on a shop floor. It integrates scheduling functions at setup planning stage, and utilises a two-step decision-making strategy for generating machine-neutral and machine-specific optimal setup plans. The objective is to enable adaptive setup planning for dynamic job shop operations. Particularly, this paper documents basic algorithms and architecture of the setup planning system for dynamically assigned machines. It is then validated through a case study.