Tool integration is a very difficult challenge. Problems may arise at different abstraction levels and from several sources such as heterogeneity of manipulated data, incompatible interfaces, or uncoordinated services, to name just a few examples. On the other hand, applications based on the coherent composition of activities, components, services, and data from heterogeneous sources are increasingly present in our everyday lives. Consequently, tool integration takes on increasing significance.

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... In this paper we analyze the tool-integration problem at different abstraction levels and discuss different views on a layered software architecture that we have designed specifically for a middleware that supports the execution of distributed applications for the orchestration of human/system activities. We noticed that the agent paradigm provided a suitable technology for abstraction in tool integration. Throughout the paper, the discussion refers to a case study in the bioinformatics domain.