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2 Fundamenta Informaticae

2 2009

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Towards a Formal Semantics for the Process Model of the Taverna Workbench. Part I

Sroka J., Hidders J.

Fundamenta Informaticae

2009

Vol. 92, nr 3

279-299

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 first of two. It defines, explains and discusses fundamental notions for describing Scufl graphs and their semantics. Then, 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.

Towards a Formal Semantics for the Process Model of the Taverna Workbench. Part II

Sroka J., Hidders J.

Fundamenta Informaticae

2009

Vol. 92, nr 4

373-396

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.