Workflow systems aim to provide automated support for the conduct of certain business processes. Workflow systems are driven by workflow specifications which among others, capture the execution interdependencies between various activities. These interdependencies are modelled by means of different control flow constructors, e.g., sequence, choice, parallelism and synchronisation. It has been shown in the research on workflow patterns that the support for and the interpretation of various control flow constructs varies substantially across workflow systems. Two of the most problematic patterns relate to the OR-join and to cancellation. An OR-join is used in situations when we need to model " wait and see" behaviour for synchronisation. Different approaches assign a different (often only intuitive) semantics to this type of join, though they do share the common theme that synchronisation is only to be performed for active paths. Depending on context assumptions this behaviour may be relatively easy to deal with, though in general its semantics is complicated, both from a definition point of view (in terms of formally capturing a desired intuitive semantics) and from a computational point of view (how does one determine whether an OR-join is enabled?). Many systems and languages struggle with the semantics and implementation of the OR-join because its non-local semantics require a synchronisation depending on an analysis of future execution paths. This may require some non-trivial reasoning. The presence of cancellation features and other OR-joins in a workflow further complicates the formal semantics of the OR-join. The cancellation feature is commonly used to model external events that can change the behaviour of a running workflow. It can be used to either disable activities in certain parts of a workflow or to stop currently running activities. Even though it is possible to cancel activities in workflow systems using some sort of abort function, many workflow systems do not provide direct support for this feature in the workflow language. Sometimes, cancellation affects only a selected part of a workflow and other activities can continue after performing a cancellation action. As cancellation occurs naturally in business scenarios, comprehensive support in a workflow language is desirable. We take on the challenge of providing formal semantics, verification techniques as well as an implementation for workflows with those features. This thesis addresses three interrelated issues for workflows with cancellation regions and OR-joins. The concept of the OR-join is examined in detail in the context of the workflow language YAWL, a powerful workflow language designed to support a collection of workflow patterns and inspired by Petri nets. The OR-join semantics has been redesigned to represent a general, formal, and decidable approach for workflows in the presence of cancellation regions and other OR-joins. This approach exploits a link that is proposed between YAWL and reset nets, a variant of Petri nets with a special type of arc that can remove all tokens from a place. Next, we explore verification techniques for workflows with cancellation regions and OR-joins. Four structural properties have been identified and a verification approach that exploits coverability and reachability notions from reset nets has been proposed. The work on verification techniques has highlighted potential problems with calculating state spaces for large workflows. Applying reduction rules before carrying out verification can decrease the size of the problem by cutting down the size of the workflow that needs to be examined while preserving some essential properties. Therefore, we have extended the work on verification by proposing reduction rules for reset nets and for YAWL nets with and without OR-joins. The proposed OR-join semantics as well as the proposed verification approach have been implemented in the YAWL environment.

Over the past decade, the ubiquity of business processes and their need for ongoing management in the same manner as other corporate assets has been recognized through the establishment of a dedicated research area: Business Process Management (or BPM). There are a wide range of potential software technologies on which a BPM o®ering can be founded. Although there is signi¯cant variation between these alternatives, they all share one common factor { their execution occurs on the basis of a business process model { and consequently, this ¯eld of technologies can be termed Process-Aware Information Systems (or PAIS). This thesis develops a conceptual foundation for PAIS based on the results of a detailed examination of contemporary o®erings including work°ow and case han- dling systems, business process modelling languages and web service composition languages. This foundation is based on 126 patterns that identify recurrent core constructs in the control-°ow, data and resource perspectives of PAIS. These patterns have been used to evaluate some of the leading systems and business process modelling languages. It also proposes a generic graphical language for de¯ning exception handling strategies that span these perspectives. On the basis of these insights, a comprehensive reference language { newYAWL { is developed for business process modelling and enactment. This language is formally de¯ned and an abstract syntax and operational semantics are provided for it. An assessment of its capabilities is provided through a comprehensive patterns-based analysis which allows direct comparison of its functionality with other PAIS. newYAWL serves as a reference language and many of the ideas embodied within it are also applicable to existing languages and systems. The ultimate goal of both the patterns and newYAWL is to improve the support and applicability of PAIS.

Scientific exploration demands heavy usage of computational resources for large-scale and deep analysis in many different fields. The complexity or the sheer scale of the computational studies can sometimes be encapsulated in the form of a workflow that is made up of numerous dependent components. Due to its decomposable and parallelizable nature, different components of a scientific workflow may be mapped over a distributed resource infrastructure to reduce time to results. However, the resource infrastructure may be heterogeneous, dynamic, and under diverse administrative control. Workflow management tools are utilized to help manage and deal with various aspects in the lifecycle of such complex applications. One particular and fundamental aspect that has to be dealt with as smooth and efficient as possible is the run-time coordination of workflow activities (i.e. workflow orchestration). Our efforts in this study are focused on improving the workflow orchestration process in such dynamic and distributed resource environments. We tackle three main aspects of this process and provide contributions in each of them. Our first contribution involves increasing the scalability and site autonomy in situations where the mapped components of a workflow span across several heterogeneous administrative domains. We devise and implement a generic decentralization framework for orchestration of workflows under such conditions. Our second contribution is involved with addressing the issues that arise due to the dynamic nature of such environments. We provide generic adaptation mechanisms that are highly transparent and also substantially less intrusive with respect to the rest of the workflow in execution. Our third contribution is to improve the efficiency of orchestration of large-scale parameter-sweep workflows. By exploiting their specific characteristics, we provide generic optimization patterns that are applicable to most instances of such workflows. We also discuss implementation issues and details that arise as we provide our contributions in each situation.

Je weiter die Zivilisation vorranschreitet, um so komplexer werden deren Errungenschaften. Die Herstellungsprozesse ziehen auch ein komplexes Management während der Produktion nach sich, da viele Menschen und Maschinen am Produktionsprozess beteiligt sind. Der Manager stellt hier einen "Single Point of Failure" dar. Das bedeutet, dass die erfolgreiche Produktion nun abhängig von der Qualität und der Fehlerfreiheit des Managers bzw. des leitetenden Personals ist. Um diesen Mangel zu beseitigen, lohnt es sich auch an dieser Stelle gewisse Prozesse zu automatisieren. Man erreicht dadurch einen höheren Grad an Fehlerfreiheit und Zuverlässigkeit. Um dies zu realisieren, werden unter anderem die Prinzipien des Workflow-Managements benutzt. Je komplexer ein Workflow wird, um so mehr Rechenleistung wird benötigt, um diesen in einem Workflow-Management-System auszuführen. Eine technische Möglichkeit dieses Problem zu lösen, stellt die Verteilung der Workflow-Management-Software dar. Verteilung bedeutet im gleichen Atemzug eine Verkomplizierung der Softwarearchitektur, wodurch sie wiederum komplizierter zu entwickeln ist. Komplexe Softwaresysteme ziehen komplexe Testprogramme und Simulationsumgebungen nach sich. Um die Entwicklung eines verteilten Workflow-Management-Systems zu unterstützen, wird in dieser Arbeit ein Simulationssystem für Workflow-Management-Systeme entworfen und implementiert. Es wird den Entwicklern eines verteilten Workflow-Management- Systems ein wertvolles Tool während der Implementierung der Software sein.

Modern enterprise organisations rely on dynamic processes. Generally these processes cannot be modelled once and executed repeatedly without change. Enterprise processes may evolve unpredictably according to situations that cannot always be prescribed. However, no mechanism exists to ensure an updated process does not violate any compliance requirements. Typical workflow processes may follow a process definition and execute several thousand instances using a workflow engine without any changes. This is suitable for routine business processes. However, when business processes need flexibility, adaptive features are needed. Updating processes may violate compliance requirements so automatic verification of compliance checking is necessary. The research work presented in this Thesis investigates the problem of current workflow technology in defining, managing and ensuring the specification and execution of business processes that are dynamic in nature, combined with policy standards throughout the process lifycle. The findings from the literature review and the system requirements are used to design the proposed system architecture. Since a two-tier reference process model is not sufficient as a basis for the reference model for an adaptive and compliance workflow management system, a three-tier process model is proposed. The major components of the architecture consist of process models, business rules and plugin modules. This architecture exhibits the concept of user adaptation with structural checks and dynamic adaptation with data-driven checks. A research prototype - Adaptive and Compliance Workflow Management System (ACWfMS) - was developed based on the proposed system architecture to implement core services of the system for testing and evaluation purposes. The ACWfMS enables the development of a workflow management tool to create or update the process models. It automatically validates compliance requirements and, in the case of violations, visual feedback is presented to the user. In addition, the architecture facilitates process migration to manage specific instances with modified definitions. A case study based on the postgraduate research process domain is discussed.

Most organizations have traditionally been organized by function, and most coordination is intrafunctional rather than interfunctional. However, many organizations are finding that they must also manage processes - such as order fulfillment, new product development, and interorganizational supply chain management - that span their separate functional units and that integrate their activities with those of other organizations. These processes are essential to the well-being of organizations in a dynamic competitive environment.In response to this, organizations are deploying large-scale enterprise information systems in order to support operational, tactical, and strategic decision making, along with information management. However, deployment of such information systems has not realized the requisite benefits due to issues such as lack of interoperability among applications due to technological evolution, constant changes to the business processes, evolving organizational structures, inherent complexity in management of distributed knowledge and resources.To ameliorate such issues, a recent technological trend is the adoption of support tools such as Workflow Management Systems (WFMS) and groupware to support coordination between individual and group knowledge worker activities respectively. While WFMSs mostly deal with tasks involving very structured information, groupware tools deal with tasks involving unstructured information. Due to these differences, such tools are used in a fragmented manner, causing information loss. The overall guiding design principles that can be used by such process support systems are minimal, resulting in costly overheads for organizations.This dissertation deals with the problems highlighted above from a organizational process design standpoint. The goal of the dissertation is to provide process designers with guidelines and tools that can assist them in modeling flexible and adaptable processes. The following two research questions are central to the work described in this dissertation: (1) How can organizational processes be designed to be flexible andadaptable in dynamic environments? (2) How can collaborative activities be designed to facilitate integration with individual activities in organizational processes?In this regard, this dissertation reports on the development of a conceptual framework to support design of organizational processes considering both individual and collaboration tasks in a unified manner. A business process is modeled as a problem solving mechanism consisting of a series of steps (also termed as process model, process definition or plan), each of which may be an individual or group activity. The task of designing business processes is considered as the development of an effective plan to solve a business process problem by searching the design space. We employ declarative formalisms from recent advances in Artificial Intelligence (AI) planning to support the task of process design. Similarly, we build on research in the field of Collaboration Engineering (CE), to propose an approach for collaborative task design. The feasibility and benefits of the approach are evaluated by prototyping intelligent build time tools for process design, and utilizing the same in the design of processes such as loan processing, and new drug discovery.

Epigenetics is the study of factors that can change DNA and passed to next generation without change to DNA sequence. DNA methylation is one of the categories of epigenetic change. DNA methylation is the attachment of methyl group (CH3) to DNA. Most of the time it occurs in the sequences that G is followed by C known as CpG sites and by addition of methyl to the cytosine residue. As science and technology progress new data are available about individual’s DNA methylation profile in different conditions. Also new features discovered that can have role in DNA methylation. The availability of new data on DNA methylation and other features of DNA provide challenge to bioinformatics and the opportunity to discover new knowledge from existing data. In this research multiple data series were used to identify classes of methylation DNA to CpG sites. These classes are a) Never methylated CpG sites,b) Always methylated CpG sites, c) Methylated CpG sites in cancer/disease samples and non-methylated in normal samples d) Methylated CpG sites in normal samples and non-methylated in cancer/disease samples. After identification of these sites and their classes, an analysis was carried out to find the features which can better classify these sites a matrix of features was generated using four applications in EMBOSS software suite. Features matrix was also generated using the gUse/WS-PGRADE portal workflow system. In order to do this each of the four applications were grid enabled and ported to BOINC platform. The gUse portal was connected to the BOINC project via 3G-bridge. Each node in the workflow created portion of matrix and then these portions were combined together to create final matrix. This final feature matrix used in a hill climbing workflow. Hill climbing node was a JAVA program ported to BOINC platform. A Hill climbing search workflow was used to search for a subset of features that are better at classifying the CpG sites using 5 different measurements and three different classification methods: support vector machine, naïve bayes and J48 decision tree. Using this approach the hill climbing search found the models which contain less than half the number of features and better classification results. It is also been demonstrated that using gUse/WS-PGRADE workflow system can provide a modular way of feature generation so adding new feature generator application can be done without changing other parts. It is also shown that using grid enabled applications can speedup both feature generation and feature subset selection. The approach used in this research for distributed workflow based feature generation is not restricted to this study and can be applied in other studies that involve feature generation. The approach also needs multiple binaries to generate portions of features. The grid enabled hill climbing search application can also be used in different context as it only requires to follow the same format of feature matrix.

Master of Science / Department of Computing and Information Sciences / John Hatcliff / Like all businesses, clinical care groups and facilities are under a range of pressures to enhance the efficacy of their operations. Though there are a number of ways to go about these improvements, one exciting methodology involves the documentation and analysis of clinical workflows. Unfortunately, there is no industry standard tool which supports this, and many available workflow documentation technologies are not only proprietary, but technologically insufficient as well. Ideally, these workflows would be documented at a formal enough level to support their execution; this would allow the partial automation of documented clinical procedures. However, the difficulty involved in this automation effort is substantial: not only is there the irreducible complexity inherent to automation, but a number of the solutions presented so far layer on additional complication. To solve this, the author introduces Kinerja, a state-of-the-art execution environment for formally specified workflows. Operating on a subset of the academically and industrially proven workflow language YAWL, Kinerja allows for both human guided governance and computer guided verification of workflows, and allows for a seamless switching between modalities. Though the base of Kinerja is essentially an integrated framework allowing for considerable extensibility, a number of modules have already been developed to support the checking and executing of clinical workflows. One such module integrates symbolic execution which greatly optimizes the time and space necessary for a complete exploration of a workflow's state space.

This paper thoroughly examines the production of the thesis short film, Armed With A Heart, from conception to completion. Each area of the film's production is carefully dissected, including the writing, production design, cinematography, editing, sound, technology, workflow, and direction. Each of these areas contain a myriad of decisions that were made in effort to fulfill the overall vision of the movie as being a character driven, psychological thriller produced with a high production value. The aforementioned decisions are discussed at length. Documented feedback from test audiences is also reviewed in an attempt to objectively critique the final film.

A demanda por alto desempenho é um desafio enfrentado por diversas aplicações científicas. Nesse sentido, ambientes para processamento distribuído, tais como, clusters e grades computacionais, têm sido desenvolvidos para prover suporte ao uso de diversos recursos simultaneamente para uma mesma aplicação. Aplicações computacionalmente intensivas são organizadas em workflows e executadas com suporte de middlewares para abstrair a complexidade de uso de tais ambientes. Em ambientes de grade computacional, a execução de workflows contendo tarefas sequenciais e tarefas com paralelismo interno, obtendo bom desempenho, é um desafio, devido à heterogeneidade e comportamento dinâmico do ambiente. Nesse sentido, o escalonamento de workflows em ambientes de grade computacional é essencial. O problema de escalonamento de tarefas, em sua forma geral, é NPCompleto, dessa forma, o estudo do escalonamento de workflows em ambientes de grade computacional é fundamental para aprimorar a execução de aplicações computacionalmente intensivas. O objetivo dessa tese é propor estratégias de escalonamento de workflows, que exploram os seguintes aspectos: Avaliação da possibilidade de executar cada tarefa com paralelismo interno usando recursos de múltiplos clusters; Adaptação de planos de escalonamento no momento da submissão de novos workflows. Foram desenvolvidas duas estratégias: a primeira é uma estratégia para escalonamento estático de workflows, que considera o ambiente dedicado a execução de um workflow. A segunda foi desenvolvida para ser utilizada em conjunto com a primeira, para melhorar o tempo de resposta de múltiplos workflows que podem ser submetidos em diferentes momentos. As estratégias propostas foram avaliadas em um ambiente de simulação. / The demand for high performance is a common problem in many scientific applications. In this sense, distributed processing environments such as cluster, grid computing and multi-cluster environments have been developed to provide support for the use of several resources simultaneously for the same application. Computationally intensive applications are structured as workflows and executed with the support of middleware to abstract the complexity of using such environments. In grid computing environments the execution of workflows containing sequential and parallel tasks, with good performance is a challenge due to the heterogeneity and dynamic behavior of the environment. In this sense, the scheduling of workflows on grid computing environments is essential. The task scheduling problem in its general form is NP-Complete, in this sense, the study concerning workflow scheduling in grid computing environments is fundamental to improve the performance of computationally intensive applications. The aim of this thesis is to propose strategies for scheduling workflows that exploit the following aspects: Explore the possibility of performing single parallel tasks using multiple clusters; Adaptation plans escalation in accordance with the submission of new workflows. Two strategies were developed: the first one is a strategy for static scheduling of workflows, which considers a dedicated environment to the execution of a workflow. The second one was developed to use in conjunction with the first one, in order to improve the response time of multiple workflows that can be submitted at different times. The proposed strategies were evaluated in a simulation environment.