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Some modern distributed applications require cooperation among multiple geographically separated computing facilities to perform intensive computing at the end sites and large-scale data transfers in the wide area network. It has been widely recognized that WDM networks are cost-effective means to support data transfers in this type of data-intensive applications. However, neither the traditional approaches to establishing lightpaths between given source destination pairs nor the existing application-level approaches that only consider computing resources but take the underlying connectivity for granted are sufficient. In this article we identify key limitations and issues in existing systems, and focus on joint resource allocation of both computing resources and network resources in federated computing and network systems. A variety of resource allocation schemes that provide modern distributed computing applications with performance and reliability guarantees are presented.