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Biomedical research increasingly depends on access to and analysis of distributed medical and biomedical data. In biomedical research, datasets are often collected at multiple locations, as it is difficult to recruit required patient populations at one location. The sensitive nature of these datasets leads to a need for secure sharing methods that can work with distributed databases and image archives. The efficient implementation of such methods is complicated by the fact that the researchers who need to access data are often behind firewalls that prohibit inbound connections. This restriction, combined with large data volumes and many small files, leads to significant data transfer challenges. We present a data management framework suitable for such distributed biomedical research environments and describe its application in the context of FBIRN, a distributed data-sharing system for medical researchers. The framework includes security tools, catalogs for managing datasets, and a secure data transfer service.