The Open Provenance Model: Core Specification (v1.1)

The Open Provenance Model is a model of provenance that is designed to meet the following requirements: (1) To allow provenance information to be exchanged between systems, by means of a compatibility layer based on a shared provenance model. (2) To allow developers to build and share tools that operate on such a provenance model. (3) To define provenance in a precise, technology-agnostic manner. (4) To support a digital representation of provenance for any "thing", whether produced by computer systems or not. (5) To allow multiple levels of description to coexist. (6) To define a core set of rules that identify the valid inferences that can be made on provenance representation. This document contains the specification of the Open Provenance Model (v1.1) resulting from a community-effort to achieve inter-operability in the Third Provenance Challenge

Petri net + nested relational calculus = dataflow

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

e-BioFlow: improving practical use of workflow systems in bioinformatics

Workflow management systems (WfMSs) are useful tools for bioinformaticians. As experiences with using WfMSs accumulate, shortcomings of current systems become apparent. In this paper, we focus on practical issues that hinder WfMS users and that arise in the design and execution of workflows, and in access of web services. We present e-BioFlow, a workflow engine that demonstrates in which way a number of these problems can be solved. e-BioFlow offers an improved user interface, can deal with large data volumes, stores all provenance, and has a powerful provenance browser. e-BioFlow also offers the possibility to design and run workflows step by step, allowing its users an explorative research style