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Scientific workflow systems often operate in highly unreliable, heterogeneous and dynamic environments, and have accordingly incorporated different fault tolerance techniques. We propose an exception‐handling mechanism, based on techniques adopted in programming languages, for modifying at run‐time the structure of a workflow. In contrast to other proposals that achieve the required flexibility by means of the infrastructure, our proposal expresses the exception‐handling mechanism within the workflow language—primarily as two exception‐handling patterns that are exclusively based on the Reference Nets‐within‐Nets formalism (a specific type of Petri nets). When an exception is detected, a workflow in our approach can be re‐written (replaced), based on the particular failure condition that has been detected. This enables workflow users to have better control and understanding of the behaviour of their …