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In this paper we propose a calculus that can be used to describe the semantics of collection-oriented scientific workflow systems such as the Taverna workbench. Typically such systems focus on the specification and execution of workflows with a relatively simple control flow and a more complex data flow that involves large nested collections of data. An essential operation in such workflows is the instantiation of a certain nested workflow for each element of a collection. We argue that if such workflows call external services, their semantics must be described not only in terms of input-output behavior but also take side effects into account. Based on this assumption a trace semantics is defined that corresponds to the observational equivalence of two workflow specifications. We show that under such a semantics a relatively small calculus with a structural semantics can be defined and used to describe such workflows. This is demonstrated by giving a translation of Taverna workflows in terms of this calculus.