Abstract
In this paper we propose a formal, graphical workflow language for dataflows, i.e., workflows where large amounts of complex data are manipulated and the structure of the manipulated data is reflected in the structure of the workflow. It is a common extension of
-
Petri nets, which are responsible for the organization of the processing tasks, and
-
Nested relational calculus, which is a database query language over complex objects, and is responsible for handling collections of data items (in particular, for iteration) and for the typing system.
We demonstrate that dataflows constructed in hierarchical manner, according to a set of refinement rules we propose, are sound: initiated with a single token (which may represent a complex scientific data collection) in the input node, terminate with a single token in the output node (which represents the output data collection). In particular they always process all of the input data, leave no ”debris data” behind and the output is always eventually computed.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
van der Aalst, W.: The application of petri nets to workflow management. The Journal of Circuits, Systems and Computers, 21–66 (1998)
Valk, R.: Object Petri nets: Using the nets-within-nets paradigm. In: Lectures on Concurrency and Petri Nets, pp. 819–848 (2003)
Valk, R.: Self-modifying nets, a natural extension of Petri nets. In: ICALP, pp. 464–476 (1978)
Oberweis, A., Sander, P.: Information system behavior specification by high level petri nets. ACM Trans. Inf. Syst. 14, 380–420 (1996)
Buneman, P., Naqvi, S., Tannen, V., Wong, L.: Principles of programming with complex objects and collection types. Theoretical Computer Science, 3–48 (1995)
Moggi, E.: Notions of computation and monads. Information and Computation, 55–92 (1991)
Oinn, T., Addis, M., Ferris, J., Marvin, D., Greenwood, M., Carver, T., Wipat, A., Li, P.: Taverna: A tool for the composition and enactment of bioinformatics workflows. Bioinformatics (2004)
Object Management Group: Unified modeling language resource page, http://www.uml.org/
Altschul, S., Gish, W., Miller, W., Myers, E., Lipman, D.: Basic local alignment search tool. J. Mol. Biol., 403–410 (1990)
Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M., Estreicher, A., et al.: The swiss-prot protein knowledgebase and its supplement trembl in 2003. Nucleic Acids Research 31, 365–370 (2003)
Rice, P., Longden, I., Bleasby, A.: Emboss: The european molecular biology open software suite. Trends in Genetics 16, 276–277 (2000)
Chrząstowski-Wachtel, P., Benatallah, B., Hamadi, R., O’Dell, M., Susanto, A.: A top-down petri net-based approach for dynamic workflow modeling. In: van der Aalst, W.M.P., ter Hofstede, A.H.M., Weske, M. (eds.) BPM 2003. LNCS, vol. 2678, pp. 336–353. Springer, Heidelberg (2003)
Gambin, A., Hidders, J., Kwasnikowska, N., Lasota, S., Sroka, J., Tyszkiewicz, J., Van den Bussche, J.: NRC as a formal model for expressing bioinformatics workflows. Poster at ISMB 2005 (2005)
Dumont, D., Noben, J.P., Raus, J., Stinissen, P., Robben, J.: Proteomic analysis of cerebrospinal fluid from multiple sclerosis patients. Proteomics 4 (2004)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Hidders, J., Kwasnikowska, N., Sroka, J., Tyszkiewicz, J., Van den Bussche, J. (2005). Petri Net + Nested Relational Calculus = Dataflow. In: Meersman, R., Tari, Z. (eds) On the Move to Meaningful Internet Systems 2005: CoopIS, DOA, and ODBASE. OTM 2005. Lecture Notes in Computer Science, vol 3760. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11575771_16
Download citation
DOI: https://doi.org/10.1007/11575771_16
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-29736-9
Online ISBN: 978-3-540-32116-3
eBook Packages: Computer ScienceComputer Science (R0)