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Simulation is one of the most popular evaluation methods in scientific workflow studies. However, existing workflow simulators fail to provide a framework that takes into consideration heterogeneous system overheads and failures. They also lack the support for widely used workflow optimization techniques such as task clustering. In this paper, we introduce WorkflowSim, which extends the existing CloudSim simulator by providing a higher layer of workflow management. We also indicate that to ignore system overheads and failures in simulating scientific workflows could cause significant inaccuracies in the predicted workflow runtime. To further validate its value in promoting other research work, we introduce two promising research areas for which WorkflowSim provides a unique and effective evaluation platform.