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This paper presents a notion of reduction where a WF net is transformed into a smaller net by iteratively contracting certain well-formed subnets into single nodes until no more of such contractions are possible. This reduction can reveal the hierarchical structure of a WF net, and since it preserves certain semantic properties such as soundness, can help with analysing and understanding why a WF net is sound or not. The reduction can also be used to verify if a WF net is an AND-OR net. This class of WF nets was introduced in earlier work, and arguably describes nets that follow good hierarchical design principles. It is shown that the reduction is confluent up to isomorphism, which means that despite the inherent non-determinism that comes from the choice of subnets that are contracted, the final result of the reduction is always the same up to the choice of the identity of the nodes. Based on this result, a polynomial-time algorithm is presented that computes this unique result of the reduction. Finally, it is shown how this algorithm can be used to verify if a WF net is an AND-OR net. [ABSTRACT FROM AUTHOR]

Workflow development and enactment workbenches are becoming a standard tool for conducting in silico experiments. Their main advantages are easy to operate user interfaces, specialized and expressive graphical workflow specification languages and integration with a huge number of bioinformatic services. A popular example of such a workbench is Taverna, which has many additional useful features like service discovery, storing intermediate results and tracking data provenance. We discuss a detailed formal semantics for Scufl - the workflow definition language of the Taverna workbench. It has several interesting features that are notmet in other models including dynamic and transparent type coercion and implicit iteration, control edges, failure mechanisms, and incominglinks strategies. We study these features and investigate their usefulness separately as well as in combination, and discuss alternatives. The formal definition of such a detailed semantics not only allows to exactly understand what is being done in a given experiment, but is also the first step toward automatic correctness verification and allows the creation of auxiliary tools that would detect potential errors and suggest possible solutions to workflow creators, the same way as Integrated Development Environments aid modern programmers. A formal semantics is also essential for work on enactment optimization and in designing the means to effectively query workflow repositories. This paper is the second of two. In the first one [13] we have defined, explained and discussed fundamental notions for describing Scufl graphs and their semantics. Here, in the second part, we use these notions to define the semantics and show that our definition can be used to prove properties of Scufl graphs. [ABSTRACT FROM AUTHOR]