Cloud resources promise to be an avenue to address new categories of scientific applications including data-intensive science applications, on-demand/surge computing, and applications that require customized software environments. However, there is a limited understanding on how to operate and use clouds for scientific applications. Magellan, a project funded through the Department of Energy's (DOE) Advanced Scientific Computing Research (ASCR) program, is investigating the use of cloud computing for science at the Argonne Leadership Computing Facility (ALCF) and the National Energy Research Scientific Computing Facility (NERSC). In this paper, we detail the experiences to date at both sites and identify the gaps and open challenges from both a resource provider as well as application perspective.