Causality and the semantics of provenance

Provenance, or information about the sources, derivation, custody or history of data, has been studied recently in a number of contexts, including databases, scientific workflows and the Semantic Web. Many provenance mechanisms have been developed, motivated by informal notions such as influence, dependence, explanation and causality. However, there has been little study of whether these mechanisms formally satisfy appropriate policies or even how to formalize relevant motivating concepts such as causality. We contend that mathematical models of these concepts are needed to justify and compare provenance techniques. In this paper we review a theory of causality based on structural models that has been developed in artificial intelligence, and describe work in progress on a causal semantics for provenance graphs.Comment: Workshop submissio

E-BioFlow: Different Perspectives on Scientific Workflows

We introduce a new type of workflow design system called\ud e-BioFlow and illustrate it by means of a simple sequence alignment workflow. E-BioFlow, intended to model advanced scientific workflows, enables the user to model a workflow from three different but strongly coupled perspectives: the control flow perspective, the data flow perspective, and the resource perspective. All three perspectives are of\ud equal importance, but workflow designers from different domains prefer different perspectives as entry points for their design, and a single workflow designer may prefer different perspectives in different stages of workflow design. Each perspective provides its own type of information, visualisation and support for validation. Combining these three perspectives in a single application provides a new and flexible way of modelling workflows

Parallel computation of the reachability graph of petri net models with semantic information

Formal verification plays a crucial role when dealing with correctness of systems. In a previous work, the authors proposed a class of models, the Unary Resource Description Framework Petri Nets (U-RDF-PN), which integrated Petri nets and (RDF-based) semantic information. The work also proposed a model checking approach for the analysis of system behavioural properties that made use of the net reachability graph. Computing such a graph, specially when dealing with high-level structures as RDF graphs, is a very expensive task that must be considered. This paper describes the development of a parallel solution for the computation of the reachability graph of U-RDF-PN models. Besides that, the paper presents some experimental results when the tool was deployed in cluster and cloud frameworks. The results not only show the improvement in the total time required for computing the graph, but also the high scalability of the solution, which make it very useful thanks to the current (and future) availability of cloud infrastructures

Work flows in life science

The introduction of computer science technology in the life science domain has resulted in a new life science discipline called bioinformatics. Bioinformaticians are biologists who know how to apply computer science technology to perform computer based experiments, also known as in-silico or dry lab experiments. Various tools, such as databases, web applications and scripting languages, are used to design and run in-silico experiments. As the size and complexity of these experiments grow, new types of tools are required to design and execute the experiments and to analyse the results. Workflow systems promise to fulfill this role. The bioinformatician composes an experiment by using tools and web services as building blocks, and connecting them, often through a graphical user interface. Workflow systems, such as Taverna, provide access to up to a few thousand resources in a uniform way. Although workflow systems are intended to make the bioinformaticians' work easier, bioinformaticians experience difficulties in using them. This thesis is devoted to find out which problems bioinformaticians experience using workflow systems and to provide solutions for these problems.\u

Workflow models for heterogeneous distributed systems

The role of data in modern scientific workflows becomes more and more crucial. The unprecedented amount of data available in the digital era, combined with the recent advancements in Machine Learning and High-Performance Computing (HPC), let computers surpass human performances in a wide range of fields, such as Computer Vision, Natural Language Processing and Bioinformatics. However, a solid data management strategy becomes crucial for key aspects like performance optimisation, privacy preservation and security. Most modern programming paradigms for Big Data analysis adhere to the principle of data locality: moving computation closer to the data to remove transfer-related overheads and risks. Still, there are scenarios in which it is worth, or even unavoidable, to transfer data between different steps of a complex workflow. The contribution of this dissertation is twofold. First, it defines a novel methodology for distributed modular applications, allowing topology-aware scheduling and data management while separating business logic, data dependencies, parallel patterns and execution environments. In addition, it introduces computational notebooks as a high-level and user-friendly interface to this new kind of workflow, aiming to flatten the learning curve and improve the adoption of such methodology. Each of these contributions is accompanied by a full-fledged, Open Source implementation, which has been used for evaluation purposes and allows the interested reader to experience the related methodology first-hand. The validity of the proposed approaches has been demonstrated on a total of five real scientific applications in the domains of Deep Learning, Bioinformatics and Molecular Dynamics Simulation, executing them on large-scale mixed cloud-High-Performance Computing (HPC) infrastructures

A MULTI-FUNCTIONAL PROVENANCE ARCHITECTURE: CHALLENGES AND SOLUTIONS

In service-oriented environments, services are put together in the form of a workflow with the aim of distributed problem solving. Capturing the execution details of the services' transformations is a significant advantage of using workflows. These execution details, referred to as provenance information, are usually traced automatically and stored in provenance stores. Provenance data contains the data recorded by a workflow engine during a workflow execution. It identifies what data is passed between services, which services are involved, and how results are eventually generated for particular sets of input values. Provenance information is of great importance and has found its way through areas in computer science such as: Bioinformatics, database, social, sensor networks, etc. Current exploitation and application of provenance data is very limited as provenance systems started being developed for specific applications. Thus, applying learning and knowledge discovery methods to provenance data can provide rich and useful information on workflows and services. Therefore, in this work, the challenges with workflows and services are studied to discover the possibilities and benefits of providing solutions by using provenance data. A multifunctional architecture is presented which addresses the workflow and service issues by exploiting provenance data. These challenges include workflow composition, abstract workflow selection, refinement, evaluation, and graph model extraction. The specific contribution of the proposed architecture is its novelty in providing a basis for taking advantage of the previous execution details of services and workflows along with artificial intelligence and knowledge management techniques to resolve the major challenges regarding workflows. The presented architecture is application-independent and could be deployed in any area. The requirements for such an architecture along with its building components are discussed. Furthermore, the responsibility of the components, related works and the implementation details of the architecture along with each component are presented

The Workflow Trace Archive: Open-Access Data from Public and Private Computing Infrastructures -- Technical Report

Realistic, relevant, and reproducible experiments often need input traces collected from real-world environments. We focus in this work on traces of workflows---common in datacenters, clouds, and HPC infrastructures. We show that the state-of-the-art in using workflow-traces raises important issues: (1) the use of realistic traces is infrequent, and (2) the use of realistic, {\it open-access} traces even more so. Alleviating these issues, we introduce the Workflow Trace Archive (WTA), an open-access archive of workflow traces from diverse computing infrastructures and tooling to parse, validate, and analyze traces. The WTA includes ${>}48$ million workflows captured from ${>}10$ computing infrastructures, representing a broad diversity of trace domains and characteristics. To emphasize the importance of trace diversity, we characterize the WTA contents and analyze in simulation the impact of trace diversity on experiment results. Our results indicate significant differences in characteristics, properties, and workflow structures between workload sources, domains, and fields.Comment: Technical repor

Toward guiding simulation experiments

To face the variety of simulation experiment methods, tools are needed that allow their seamless integration, guide the user through the steps of an experiment, and support him in selecting the most suitable method for the task at hand. This work presents techniques for facing such challenges. To guide users through the experiment process, six typical tasks have been identified for structuring the experiment workflow. The M&S framework JAMES II and its plug-in system is exploited to integrate various methods. Finally, an approach for automatic selection and use of such methods is realized

Continuous Workflows: From Model to Enactment System

Workflows are actively being used in both business and scientific domains to automate processes and facilitate collaboration. A workflow management (or enactment) system (WfMS) defines, creates and manages the execution of workflows on one or more workflow engines, which are able to interpret workflow definitions, allocate resources, interact with workflow participants and, where required, invoke the needed tools (e.g., databases, job schedulers, etc.) and applications. Traditional WfMSs and workflow design processes view the workflow as a one-time interaction with the various data sources, i.e., when a workflow is invoked, its steps are executed once and in-order. The fundamental underlying assumption has been that data sources are passive and all interactions are structured along the request/reply (query) model. Hence, traditional WfMS cannot effectively support business or scientific monitoring applications that require the processing of data streams such as those generated by sensing devices as well as mobile and web applications. It is the hypothesis of this dissertation that Workflow Management Systems can be extended to support data stream semantics to enable monitoring applications. This includes the ability to apply flexible bounds on unbounded data streams and the ability to facilitate on-the-fly processing of bounded bundles of data (window semantics). To support this hypothesis this dissertation has produced new specifications, a design, an implementation and a thorough evaluation of a novel Continuous Workflows (CWf) model, which is backwards compatible with currently available workflow models. The CWf model was implemented in a CONtinuous workFLow ExeCution Engine, CONFLuEnCE, as an extension of Kepler, which is a popular scientific WfMS. The applicability of the CWf model in both scientific and business applications was demonstrated by utilizing CONFLuEnCE in Astroshelf to support live annotations (i.e., monitoring of astronomical data), and to support supply chain monitoring and management. The implementation of CONFLuEnCE led to the realization that different applications have different performance requirements and hence an integrated workflow scheduling framework is essential. Towards meeting this need, STAFiLOS, a Stream FLOw Scheduling framework for Continuous Workflows, was designed and implemented, within CONFLuEnCE. The performance of STAFiLOS was evaluated using the Linear Road Benchmark for continuous workflows