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Recent advances in network coding have shown great potential for efficient information multicasting in communication networks, in terms of both network throughput and network management. In this paper, the problem of flow control at end-systems for network-coding-based multicast flows is addressed. Optimization-based models are formulated for network resource allocation, based on which two sets of decentralized controllers at sources and links/nodes for congestion control are developed for wired networks with given coding subgraphs and without given coding subgraphs, respectively. With random network coding, both sets of controllers can be implemented in a distributed manner, and work at the transport layer to adjust source rates and at network layer to carry out network coding. The convergence of the proposed controllers to the desired equilibrium operating points is proved, and numerical examples are provided to complement the theoretical analysis. The extension to wireless networks is also briefly discussed.