Workflow reuse in practice: a study of neuroimaging pipeline users

Workflow reuse is a major benefit of workflow systems and shared workflow repositories, but there are barely any studies that quantify the degree of reuse of workflows or the practical barriers that may stand in the way of successful reuse. In our own work, we hypothesize that defining workflow fragments improves reuse, since end-to-end workflows may be very specific and only partially reusable by others. This paper reports on a study of the current use of workflows and workflow fragments in labs that use the LONI Pipeline, a popular workflow system used mainly for neuroimaging research that enables users to define and reuse workflow fragments. We present an overview of the benefits of workflows and workflow fragments reported by users in informal discussions. We also report on a survey of researchers in a lab that has the LONI Pipeline installed, asking them about their experiences with reuse of workflow fragments and the actual benefits they perceive. This leads to quantifiable indicators of the reuse of workflows and workflow fragments in practice. Finally, we discuss barriers to further adoption of workflow fragments and workflow reuse that motivate further work.

Conservation of Computational Scientific Execution Environments for Workflow-based Experiments Using Ontologies

La reproducibilidad de estudios y resultados científicos es una meta a tener en cuenta por cualquier científico a la hora de publicar el producto de una investigación. El auge de la ciencia computacional, como una forma de llevar a cabo estudios empíricos haciendo uso de modelos matemáticos y simulaciones, ha derivado en una serie de nuevos retos con respecto a la reproducibilidad de dichos experimentos. La adopción de los flujos de trabajo como método para especificar el procedimiento científico de estos experimentos, así como las iniciativas orientadas a la conservación de los datos experimentales desarrolladas en las últimas décadas, han solucionado parcialmente este problema. Sin embargo, para afrontarlo de forma completa, la conservación y reproducibilidad del equipamiento computacional asociado a los flujos de trabajo científicos deben ser tenidas en cuenta. La amplia gama de recursos hardware y software necesarios para ejecutar un flujo de trabajo científico hace que sea necesario aportar una descripción completa detallando que recursos son necesarios y como estos deben de ser configurados. En esta tesis abordamos la reproducibilidad de los entornos de ejecución para flujos de trabajo científicos, mediante su documentación usando un modelo formal que puede ser usado para obtener un entorno equivalente. Para ello, se ha propuesto un conjunto de modelos para representar y relacionar los conceptos relevantes de dichos entornos, así como un conjunto de herramientas que hacen uso de dichos módulos para generar una descripción de la infraestructura, y un algoritmo capaz de generar una nueva especificación de entorno de ejecución a partir de dicha descripción, la cual puede ser usada para recrearlo usando técnicas de virtualización. Estas contribuciones han sido aplicadas a un conjunto representativo de experimentos científicos pertenecientes a diferentes dominios de la ciencia, exponiendo cada uno de ellos diferentes requisitos hardware y software. Los resultados obtenidos muestran la viabilidad de propuesta desarrollada, reproduciendo de forma satisfactoria los experimentos estudiados en diferentes entornos de virtualización. ABSTRACT Reproducibility of scientific studies and results is a goal that every scientist must pursuit when announcing research outcomes. The rise of computational science, as a way of conducting empirical studies by using mathematical models and simulations, have opened a new range of challenges in this context. The adoption of workflows as a way of detailing the scientific procedure of these experiments, along with the experimental data conservation initiatives that have been undertaken during last decades, have partially eased this problem. However, in order to fully address it, the conservation and reproducibility of the computational equipment related to them must be also considered. The wide range of software and hardware resources required to execute a scientific workflow implies that a comprehensive description detailing what those resources are and how they are arranged is necessary. In this thesis we address the issue of reproducibility of execution environments for scientific workflows, by documenting them in a formalized way, which can be later used to obtain and equivalent one. In order to do so, we propose a set of semantic models for representing and relating the relevant information of those environments, as well as a set of tools that uses these models for generating a description of the infrastructure, and an algorithmic process that consumes these descriptions for deriving a new execution environment specification, which can be enacted into a new equivalent one using virtualization solutions. We apply these three contributions to a set of representative scientific experiments, belonging to different scientific domains, and exposing different software and hardware requirements. The obtained results prove the feasibility of the proposed approach, by successfully reproducing the target experiments under different virtualization environments.

A Semantic Workflow Mechanism to Realize Experimental Goals and Constraints

Postprint

Facilitating cross-organisational workflows with a workflow view approach

Interconnecting business processes across systems and organisations is considered to provide significant benefits, such as greater process transparency, higher degrees of integration, facilitation of communication, and consequently higher throughput in a given time interval. However, to achieve these benefits requires tackling constraints. In the context of this paper these are privacy-requirements of the involved workflows and their mutual dependencies. Workflow views are a promising conceptional approach to address the issue of privacy; however this approach requires addressing the issue of interdependencies between workflow view and adjacent private workflow. In this paper we focus on three aspects concerning the support for execution of cross-organisational workflows that have been modelled with a workflow view approach: (i) communication between the entities of a view-based workflow model, (ii) their impact on an extended workflow engine, and (iii) the design of a cross-organisational workflow architecture (CWA). We consider communication aspects in terms of state dependencies and control flow dependencies. We propose to tightly couple private workflow and workflow view with state dependencies, whilst to loosely couple workflow views with control flow dependencies. We introduce a Petri-Net-based state transition approach that binds states of private workflow tasks to their adjacent workflow view-task. On the basis of these communication aspects we develop a CWA for view-based cross-organisational workflow execution. Its concepts are valid for mediated and unmediated interactions and express no choice of a particular technology. The concepts are demonstrated by a scenario, run by two extended workflow management systems. (C) 2004 Elsevier B.V. All rights reserved.

Managing change and time in dynamic workflow processes

Business environments have become exceedingly dynamic and competitive in recent times. This dynamism is manifested in the form of changing process requirements and time constraints. Workflow technology is currently one of the most promising fields of research in business process automation. However, workflow systems to date do not provide the flexibility necessary to support the dynamic nature of business processes. In this paper we primarily discuss the issues and challenges related to managing change and time in workflows representing dynamic business processes. We also present an analysis of workflow modifications and provide feasibility considerations for the automation of this process.

Relationships between quality of experience and participation in diverse performance settingshttp://espace.library.uq.edu.au/workflow/edit_metadata.php?id=382160&wfs_id=778

The flow concept describes a model of enjoyment that has relevance for understanding participation and experience across a wide range of activities (Csikszentmihalyi, 1997). The basic premise of the flow concept is that when challenges and skills are simultaneously balanced and extending the individual, a state of total absorption can occur. Research by Jackson and colleagues has examined the utility of the flow concept to understanding participation and performance in sport settings. Recently, Jackson and Eklund have examined flow in a range of performance settings: sport, exercise, dance, creative and performing arts, and music. In this paper, we present descriptive and construct validity data on how participants in these activities experienced flow, as assessed by the recently revised flow scales: The Dispositional Flow Scale-2 (DFS-2) and Flow State Scale-2 (FSS-2) (Jackson & Eklund, 2002). The fmdings will be discussed in relation to the utility of the flow concept to understanding participation across performance settings.

Data flow and validation in workflow modelling

A complete workflow specification requires careful integration of many different process characteristics. Decisions must be made as to the definitions of individual activities, their scope, the order of execution that maintains the overall business process logic, the rules governing the discipline of work list scheduling to performers, identification of time constraints and more. The goal of this paper is to address an important issue in workflows modelling and specification, which is data flow, its modelling, specification and validation. Researchers have neglected this dimension of process analysis for some time, mainly focussing on structural considerations with limited verification checks. In this paper, we identify and justify the importance of data modelling in overall workflows specification and verification. We illustrate and define several potential data flow problems that, if not detected prior to workflow deployment may prevent the process from correct execution, execute process on inconsistent data or even lead to process suspension. A discussion on essential requirements of the workflow data model in order to support data validation is also given..

Pockets of flexibility in workflow specification

Workflow technology is currently being deployed in quite diverse domains. However, the element of change is present in some degree and form in almost all domains. A workflow implementation that does not support the process of change will not benefit the organization in the long run. Change can be manifested in different forms in workflow processes. In this paper, we first present a categorization of workflow change characteristics and divide workflow processes into dynamic, adaptive and flexible processes. We define flexibility as the ability of the workflow process to execute on the basis of a loosely, or partially specified model, where the full specification of the model is made at runtime, and may be unique to each instance. To provide a modeling framework that offers true flexibility, we need to consider the factors, which influence the paths of (unique) instances together with the process definition. We advocate an approach that aims at making the process of change part of the workflow process itself. We introduce the notion of an open instance that consists of a core process and several pockets of flexibility, and present a framework based on this notion, which makes use of special build activities that provide the functionality to integrate the process of defining a change, into the open workflow instance.