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The proliferation of commercial cloud computing providers has generated significant interest in the scientific computing community. Much recent research has attempted to determine the benefits and drawbacks of cloud computing for scientific applications. Although clouds have many attractive features, such as virtualization, on-demand provisioning, and “pay as you go” usage-based pricing, it is not clear whether they are able to deliver the performance required for scientific applications at a reasonable price. In this paper we examine the performance and cost of clouds from the perspective of scientific workflow applications. We use three characteristic workflows to compare the performance of a commercial cloud with that of a typical HPC system, and we analyze the various costs associated with running those workflows in the cloud. We find that the performance of clouds is not unreasonable given the hardware resources provided, and that performance comparable to HPC systems can be achieved given similar resources. We also find that the cost of running workflows on a commercial cloud can be reduced by storing data in the cloud rather than transferring it from outside.