DFL designer: collection-oriented scientific workflows with Petri nets and nested relational calculus

  • Authors:

  • Jacek Sroka;Piotr Włodarczyk;Łukasz Krupa;Jan Hidders

  • Affiliations:

  • University of Warsaw, Poland;University of Warsaw, Poland;University of Warsaw, Poland;Delft University of Technology, The Netherlands

  • Venue:
  • Proceedings of the 1st International Workshop on Workflow Approaches to New Data-centric Science
  • Year:
  • 2010

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Abstract

In this paper we present DFL designer --- a collection-oriented scientific workflow (COSW) tool based on the DFL notation which combines established formalisms from workflow modeling and databases, namely Petri nets and the nested relational calculus (NRC). COSW tools are used in applied sciences like bioinformatics where structured data is processed with the use of specialized services which are made available online by scientific institutions. They make such data processing experiments easier to conduct by the experimentators and easier to comprehend and repeat by the reviewers. The notations, models and techniques used for the construction of COSW tools are similar to the ones known from workflow modeling, but additional emphasis is put on the data manipulation aspects, e.g., the processing of nested collections of data. DFL designer not only allows design and enactment of complicated COSWs with the use of a huge library of supported bioinformatics services, but also provides a set of features for testing and analyzing workflow specifications that is unique for COSWs, including but not limited to interactive firing of transitions, hierarchical analysis of COSWs and translation of side-effect free COSWs to a query language like NRC.