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

• Autorzy: Sroka J. , Hidders J.
• Języki publikacji: EN

Abstrakty

EN

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.

Słowa kluczowe

EN

formal semantics; Scufl; workflows; Taverna workbench

• Wydawca: IOS Press
• Czasopismo: Fundamenta Informaticae
• Rocznik: 2009
• Tom: Vol. 92, nr 4
• Strony: 373--396
• Opis fizyczny: Bibliogr. 15 poz., wykr.

Twórcy

autor

Sroka J.

autor

Hidders J.

• Institute of Informatics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland,

Bibliografia

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• [13] Sroka, J., Hidders, J.: Towards a formal semantics for the process model of the Taverna workbench. Part I, Fundamenta Informaticae, 92(3) 2009, 279-299.
• [14] Stevens, R., Tipney, H., Wroe, C., Oinn, T., Senger, M., Goble, C., Lord, P., Brass, A., Tassabehji, M.: Exploring Williams-Beuren Syndrome using myGrid, Proceedings of 12th International Conference on Intelligent Systems in Molecular Biology, 2004.
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