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Services-oriented architectures hold a lot of promise for grid-enabling scientific applications. In recent times, Web services have gained wide-spread acceptance in the grid community as the standard way of exposing application functionality to end-users. Web services-based architectures provide accessibility via a multitude of clients, and the ability to enable composition of data and applications in novel ways for facilitating innovation across scientific disciplines. However, issues of diverse data formats and styles which hinder interoperability and integration must be addressed. Providing Web service wrappers for legacy applications alleviates many problems because of the exchange of strongly typed data, defined and validated using XML schemas, that can be used by workflow tools for application integration. In this paper, we describe the end-to-end architecture of such a system for biomedical applications that are part of the National Biomedical Computation Resource (NBCR). We present the technical challenges in setting up such an infrastructure, and discuss in detail the back-end resource management, application services, user-interfaces, and the security infrastructure for the same. We also evaluate our prototype infrastructure, discuss some of its shortcomings, and the future work that may be required to address them.