Workflows for Heliophysics

In this paper we describe how we have introduced workflows into the working practices of a community for whom the concept of workflows is very new, namely the heliophysics community. Heliophysics is a branch of astrophysics which studies the Sun and the interactions between the Sun and the planets, by tracking solar events as they travel throughout the Solar system. Heliophysics produces two major challenges for workflow technology. Firstly it is a systems science where research is currently developed by many different communities who need reliable data models and metadata to be able to work together. Thus it has major challenges in the semantics of workflows. Secondly, the problem of time is critical in heliophysics; the workflows must take account of the propagation of events outwards from the sun. They have to address the four dimensional nature of space and time in terms of the indexing of data. We discuss how we have built an environment for Heliophysics workflows building on and extending the Taverna workflow system and utilising the myExperiment site for sharing workflows. We also describe how we have integrated the workflows into the existing practices of the communities involved in Heliophysics by developing a web portal which can hide the technical details from the users, who can concentrate on the data from their scientific point of view rather than on the methods used to integrate and process the data. This work has been developed in the EU Framework 7 project HELIO, and is being disseminated to the worldwide Heliophysics community, since Heliophysics requires integration of effort on a global scale.     

Common motifs in scientific workflows: An empirical analysis

Workflow technology continues to play an important role as a means for specifying and enacting computational experiments in modern science. Reusing and re-purposing workflows allow scientists to do new experiments faster, since the workflows capture useful expertise from others. As workflow libraries grow, scientists face the challenge of finding workflows appropriate for their task, understanding what each workflow does, and reusing relevant portions of a given workflow. We believe that workflows would be easier to understand and reuse if high-level views (abstractions) of their activities were available in workflow libraries. As a first step towards obtaining these abstractions, we report in this paper on the results of a manual analysis performed over a set of real-world scientific workflows from Taverna, Wings, Galaxy and Vistrails. Our analysis has resulted in a set of scientific workflow motifs that outline (i) the kinds of data-intensive activities that are observed in workflows (Data-Operation motifs), and (ii) the different manners in which activities are implemented within workflows (Workflow-Oriented motifs). These motifs are helpful to identify the functionality of the steps in a given workflow, to develop best practices for workflow design, and to develop approaches for automated generation of workflow abstractions.     

A new optimization phase for scientific workflow management systems

Scientific workflows have emerged as an important tool for combining the computational power with data analysis for all scientific domains in e-science, especially in the life sciences. They help scientists to design and execute complex in silico experiments. However, with rising complexity it becomes increasingly impractical to optimize scientific workflows by trial and error. To address this issue, we propose to insert a new optimization phase into the common scientific workflow life cycle. This paper describes the design and implementation of an automated optimization framework for scientific workflows to implement this phase. Our framework was integrated into Taverna, a life-science oriented workflow management system and offers a versatile programming interface (API), which enables easy integration of arbitrary optimization methods. We have used this API to develop an example plugin for parameter optimization that is based on a Genetic Algorithm. Two use cases taken from the areas of structural bioinformatics and proteomics demonstrate how our framework facilitates setup, execution, and monitoring of workflow parameter optimization in high performance computing e-science environments.     

A comparison of using Taverna and BPEL in building scientific workflows: the case of caGrid

When the emergence of ‘service‐oriented science,’ the need arises to orchestrate multiple services to facilitate scientific investigation—that is, to create ‘science workflows.’ We present here our findings in providing a workflow solution for the caGrid service‐based grid infrastructure. We choose BPEL and Taverna as candidates, and compare their usability in the lifecycle of a scientific workflow, including workflow composition, execution, and result analysis. Our experience shows that BPEL as an imperative language offers a comprehensive set of modeling primitives for workflows of all flavors; whereas Taverna offers a dataflow model and a more compact set of primitives that facilitates dataflow modeling and pipelined execution. We hope that this comparison study not only helps researchers to select a language or tool that meets their specific needs, but also offers some insight into how a workflow language and tool can fulfill the requirement of the scientific community. Copyright © 2009 John Wiley & Sons, Ltd.     

A tool for minimizing update errors for workflow applications: The CARD model

Product Data Management, the ASP (application service provider) model of e-business, and other information enterprises involve complex database-driven processes that change frequently. Workflow management for these enterprises requires analysis of the causality of updates on the control logic of the processes and the semantics of the databases involved. Previous workflow analysis tends to focus on the former and leave the details of the database control to application developers. This practice could lead to inconsistent applications when the processes evolve and/or the underlying data and rules change. The field still needs an integrated causality analysis tool to facilitate the update problem. In this research, we develop a Control-Activity-Rule-Data (CARD) model of a decision support tool that helps workflow administrators analyze the effects of update in processes and/or databases on both control flow and data/rules flow. The CARD model contributes a new Workflow Information Resources Dictionary which represents data, rules, activities and control in a mutually independent but collectively integrated way to achieve the goal. An extended Workflow Causality Graph capable of representing workflow integrity rules enables the CARD model for implementation. An empirical validation of the model using three representative Product Data Management workflow cases at Samsung Electronics Corporation shows its correctness and relevance for practical applications.     

A Case Study into Using Common Real-Time Workflow Monitoring Infrastructure for Scientific Workflows

Scientific workflow systems support various workflow representations, operational modes, and configurations. Regardless of the system used, end users have common needs: to track the status of their workflows in real time, be notified of execution anomalies and failures automatically, perform troubleshooting, and automate the analysis of the workflow results. In this paper, we describe how the Stampede monitoring infrastructure was integrated with the Pegasus Workflow Management System and the Triana Workflow Systems, in order to add generic real time monitoring and troubleshooting capabilities across both systems. Stampede is an infrastructure that provides interoperable monitoring using a three-layer model: (1) a common data model to describe workflow and job executions; (2) high-performance tools to load workflow logs conforming to the data model into a data store; and (3) a common query interface. This paper describes the integration of Stampede monitoring architecture with Pegasus and Triana and shows the new analysis capabilities that Stampede provides to these workflow systems. The successful integration of Stampede with these workflow engines demonstrates the generic nature of the Stampede monitoring infrastructure and its potential to provide a common platform for monitoring across scientific workflow engines.     

On design,verification, and dynamic modification of the problem-based scientific workflow model

A science process is a process to solve complex scientific problems which usually have no mature solving methods. Science processes if modeled in workflow forms, i.e. scientific workflows, can be managed more effectively and performed more automatically. However, most current workflow models seldom take account of specific characteristics of science processes and are not very suitable for modeling scientific workflows. Therefore, a new workflow model named problem-based scientific workflow model (PBSWM) is proposed in this paper to accommodate those specific characteristics. Corresponding soundness verification and dynamic modification are discussed accordingly based on the new modelling method. This paper makes three main contributions: (1) three new constructs are proposed for special logic semantics in science processes; (2) verification is deployed with the consideration from both data-specific perspective and control-specific perspective; and (3) a set of rules are provided to automatically infer passive modifications caused by other modifications.     

基于过程模型的工作流执行语义研究

针对现有工作流建模语言难以兼顾语言的可理解性、执行语义的形式化和描述维度的单一性等问题,提出利用可视化的过程模型作为工作流建模语言。过程模型能从过程、数据、资源、组织等多个角度描述企事业的业务工作流程。根据过程模型的语法和工作流系统的特点,定义形式化执行语义,为过程模型的分析、验证和执行提供理论依据。     

基于ECA规则和活动分解的工作流模型

企业在面临电子商务的挑战中,越来越重视业务过程重组.建立一种合理的流程模型是成功开展BPR(business process re-engineering)的关键.这样的模型应该可以集成企业许多业务相关的信息并且是可被系统解释执行的.在参考WfMC(workflow management coalition)元模型基础上建立了一种基于ECA(event-condition-action)规则和活动分解的工作流模型.ECA规则反映活动之间的执行依赖关系,通过重写办法把ECA模型变为触发器形式的TA(trig     

Nondeterministic Probabilistic Petri Net — A New Method to Study Qualitative and Quantitative Behaviors of System

There are many variants of Petri net at present,and some of them can be used to model system with both function and performance specification,such as stochastic Petri net,generalized stochastic Petri net and probabilistic Petri net.In this paper,we utilize extended Petri net to address the issue of modeling and verifying system with probability and nondeterminism besides function aspects.Using probabilistic Petri net as reference,we propose a new mixed model NPPN(Nondeterministic Probabilistic Petri Net) system,which can model and verify systems with qualitative and quantitative behaviours.Then we develop a kind of process algebra for NPPN system to interpret its algebraic semantics,and an actionbased PCTL(Probabilistic Computation Tree Logic) to interpret its logical semantics.Afterwards we present the rules for compositional operation of NPPN system based on NPPN system process algebra,and the model checking algorithm based on the action-based PCTL.In order to put the NPPN system into practice,we develop a friendly and visual tool for modeling,analyzing,simulating,and verifying NPPN system using action-based PCTL.The usefulness and effectiveness of the NPPN system are illustrated by modeling and model checking an elaborate model of travel arrangements workflow.     

Norm驱动的网格工作流状态机模型

动态的网格环境赋予了网格工作流新的特征,从而进一步增加了工作流程的不确定性和复杂性.提出了Norm驱动的网格工作流状态机模型——GridWSM,利用Norm丰富的语义表达能力和适于描述复杂系统的特征来描述网格工作流系统中任务的动态调度,并利用其推理功能来完善Norm描述、检验Norm的语义冲突,不仅确保了Norm描述的完备性,而且反映了工作流程的实时变化,为系统仿真提供了理论基础.模型的原型系统NormTools验证了网格排序流程的Norm描述,检查出所有的错误.     

Verifying workflow processes: a transformation-based approach

Workflow modeling is a challenging activity and designers are likely to introduce errors, especially in complex industrial processes. Effective process verification is essential at design time because the cost of fixing errors during runtime is substantially higher. However, most user-oriented workflow modeling languages lack formal semantics that hinders such verification. In this paper, we propose a generic approach based on the model transformation to verify workflow processes. The model transformation includes two steps: first, it formalizes the desirable semantics of each modeling element; secondly, it translates a workflow process with clear semantics to an equivalent Petri net. Thus, we can verify the original workflow process using existing Petri net theory and analysis tools. As a comprehensive case study, verifying workflow processes in an industrial modeling language (TiPLM) is presented. Experimental evaluations on verifying real-world business processes validate our approach.     

ECA规则在工作流管理系统中的应用

针对工作流管理系统的实现复杂性及模型可靠性的验证问题,提出了一种结合工作流网和ECA规则来创建工作流管理系统的方法。这种基于ECA规则的工作流描述和执行机制较好地实现了工作流网模型的语义描述和控制的统一。通过建立基于ECA规则的工作流描述表,将ECA 规则引入到工作流路由机制中,灵活地控制了工作流的流程。通过事件触发和消息处理机制,工作流描述表处理可以被实际系统加以执行和控制。     

Mediator approach to direct workflow simulation

This paper presents a direct workflow simulation method with which the future enactment service processes of a BPM system can be simulated directly (i.e., without a model conversion). The proposed method may easily be implemented on a commercial BPM system by plugging in a couple of software modules (no internal modification of the BPM system is required). Previous researches on workflow simulation relied mostly on conversion methods in which process definition models (PDMs) are converted to simulation models and the simulation is performed by a separate simulator. More recently, a direct workflow simulation method based on the concept of listener was proposed. However, with the listener approach, (1) some internal modification of the BPM system is required, (2) PDMs have to be modified slightly, and (3) reliable simulation is not guaranteed. The direct workflow simulation approach proposed in this paper, which we call the mediator approach, is free of these shortcomings. Moreover, the mediator approach is suitable for workflow simulation involving multiple BPM systems. In a ‘direct’ workflow simulation, (1) the work-list handler of each participant is replaced by a participant simulator, (2) simulation is carried out by the workflow engine of the BPM system, and (3) a software module called synchronization manager (mediator or listener) handles time synchronization during simulation. In this paper, the architecture and detailed logic of the mediator are described as DEVS models. The behaviors of participant simulators are also described as DEVS models. The proposed workflow simulation method has been implemented on a commercial BPM system as well as on an academic BPM system, and an illustrative workflow simulation example is provided.     

Structured design,consistency analysis and failure reasoning of business workflows with activity-control templates and causal ordering

The design, analysis, control and diagnosis of business workflows have been major challenges for enterprise information system designers. We propose a structured framework for workflow design, formal semantics, consistency analysis, execution automation and failure reasoning targeting E-commerce applications. A business workflow is modeled by using a visual tool named activity-control (AC) diagram. Frequently occurring business procedures are captured by the adoptions of reusable AC templates. With formally defined semantics by a combination of first-order logic and happen-before causal ordering in distributed system theory, workflow consistency can be mechanically analyzed at design time while failure reasoning can be applied at execution time for problem diagnosis. A completely specified model is automatically converted to a workflow by an iterative traversal algorithm that maps an AC diagram to an XML workflow specification which can then be executed automatically by an XML workflow engine. A failure reasoning and diagnosis algorithm is devised to find all possible causes of a failed execution when problems occur. Preliminary proof-of-concept implementation and evaluation results demonstrate the feasibility and effectiveness of our framework and techniques.     

基于构件设计的正确性验证

本文研究基于构件设计的正确性问题,我们首先建立一个构件描述的模型：（１）接口：通过对ＣＯＲＢＡ的ＩＤＬ进行扩展,使其能够在构件的接口中同时描述构件的语法和语义信息,（２）实现,通过引入一个简单的程序模型,阐述如何利用子构造一个新的构件,然后我们考虑如何将构件的接口和实现联系起来,利用Ｈｏａｒｅ逻辑,验证一个构件的实现是否满足其接口中所给出的语义要求。     

UML活动图描述工作流模型的执行语义

UML是软件工程中广泛应用的建模语言,但其主要问题是缺少严格的形式化语义,因而描述的模型容易产生歧义.根据UML活动图的语法和工作流系统的特点,为UML活动图定义了一种执行语义.基于时间转变系统模型,将工作流系统的执行描述为时间转变和数据转变两个交替进行的过程.时间转变描述时间的前进,数据转变修改工作流案例的状态,这种语义比层次状态图具有更强的描述并行的能力,比Petri网和进程代数更适合描述工作流模型.     

Tool support for verifying UML activity diagrams

We describe a tool that supports verification of workflow models specified in UML activity diagrams. The tool translates an activity diagram into an input format for a model checker according to a mathematical semantics. With the model checker, arbitrary propositional requirements can be checked against the input model. If a requirement fails to hold, an error trace is returned by the model checker, which our tool presents by highlighting a corresponding path in the activity diagram. We summarize our formal semantics, discuss the techniques used to reduce an infinite state space to a finite one, and motivate the need for strong fairness constraints to obtain realistic results. We define requirement-preserving rules for state space reduction. Finally, we illustrate the whole approach with a few example verifications.