A completely automated manufacturing system has been a challenging objective for manufacturing engineers. It is challenging because, from software development point-of-view, it is extremely complex to implement.  A change in the products being manufactured or in the system design can lead to a major revision of the existing control software.  Our research has focused on the design of formal models from which 1) software can be designed that is automatically reconfigurable when product mix or system design changes and 2) the software can recover to maintain control of the system during machine or sensory information failure. The software is implemented in modules (called Agents) that are distributed throughout the manufacturing system. These agents are each responsible for controlling a portion of the manufacturing system and communicating with each other to insure overall coordination. The articles listed under publications describes the research done in this area, including modeling and programming code.