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Distributed atmospheric data are often stored and managed in diverse regional and global repositories. The scientific process requires composition of these resources to solve a specific atmospheric science problem. A challenge is how to harvest data and models for designing and executing experiments in a seamless manner. Moreover, data intensive scientific experiments with large-scale scientific data processing are iterative, dynamic and human centered. In particular, the atmospheric scientific experiments usually include some fixed steps, such as data discovery, access, preprocessing, transformation, visualization. A Web service enabled workflow system is a flexible tool for accessing distributed scientific data, and executing complex analysis on it. In this paper, we describe a four-layered architecture of the workflow system, which consists of Web interaction layer, workflow engine layer, workflow components layer and resource layer. We also develop an intuitive and easy-to-use Web based toolkit and apply it to atmospheric data processing.