A system and method are provided for managing applications over a network between a server system and client computers. In one example, the method involves receiving user login information from a client computer, then accessing on the server system a user profile associated with the login information. The user profile includes a user environment configuration for a client environment. Transport protocols are selected based on the user profile. The transport protocols are protocols for transporting information between the server system and the client computer. The user environment configuration stored on the server system is then synchronized with a client environment configuration on the client computer.