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Recently, manufacturing companies tried to increase competitiveness in their business collaboration with cooperative companies rather than within their own company. In Korea, more than 600 manufacturing companies are using web-based collaboration systems developed by the government-led project, referred to as i-Manufacturing. The project is being conducted to facilitate on-line collaboration among manufacturing companies since 2004. There are lots of functions and services supported by each collaboration system. In order to re-apply a developed system to other companies, however, we have to modify, upgrade, or newly develop some parts of the system, which is called as customization. During customization processes, we reconfigure functions or services of the system to satisfy user requirements. To facilitate reconfiguration of collaboration systems, therefore, we first define user patterns. Then we introduce an analysis technique to investigate and analyze patterns by using data mining. The analysis technique verifies normal or abnormal patterns(e.g., drastic increase in using a specific function or service), and automatically make the system recognize an abnormal pattern as a new normal pattern when the abnormal pattern continue for a long time. Including the analysis technique, we also suggest a reconfiguration guideline for reorganizing function modules into services in a specific collaboration system.