Today's web applications and their respective business processes reside under the control of different organizations. Establishing federations between these organizations, i.e. bringing these business processes together by transcending organizational and security borders, raises a new class of security questions concerning the management of trust relationships between the autonomous bodies that wish to work together. Based on the WebComposition Architecture Model we provide a modeling approach for federated Web applications. In this paper we present a methodology for formalizing these models using the Ambient Calculus for use in further computation. Based on the results we help the users to identify and detect security related aspects in Web-based federations.