The emergence of cloud computing brought the opportunity to use large-scale computational infrastructures for a broad spectrum of scientific applications. As more and more cloud providers and technologies appear, scientists are faced with an increasingly difficult problem of evaluating various offerings, like public and private clouds, and deciding which model to use for their applications' needs. In this paper, we make a performance evaluation of two public and private cloud platforms for scientific computing workloads. We compare the Azure and Nimbus clouds, considering all the primary needs of scientific applications (computation power, storage, data transfers and costs). The evaluation is done using both synthetic benchmarks and a real-life application. Our results show that Nimbus incurs less varaibility and has increased support for data intensive applications, while Azure deploys faster and has a lower cost.