We’re witnessing the era of Data-Oriented Science, where investigations routinely involve computational data analysis. The research lifecycle has now become more elaborate to support the sharing and re-use of scientific data. To establish the veracity of shared data, scientific communities aim for systematising 1) the process of analysing data, and, 2) the reporting of analyses and results. Scientific workflows are a prominent mechanism for systematising analyses by encoding them as automated processes and documenting process executions with Workflow Provenance. Meanwhile, systematic reporting calls for discipline-specific Experimental Metadata to be provided outlining the context of data analysis such as source/reference datasets and community resources used, analytical methods and their parameter settings. A natural expectation would be that investigations, which adopt a systematic, workflow-based approach to the analysis can be advantageous at the time of reporting. This premise holds weakly. While workflow provenance supports streamlined enactment of analyses, their auditability and verifiability, we conjecture that it has limited contribution to reporting. This dissertation focuses on eliciting the apparent disconnect of Workflow Provenance and Experimental Metadata as the provenance gap. We identify complexity, mixed granularity, and genericity as characteristics of workflow provenance that underlie this gap. In response we develop techniques for provenance abstraction, analysis and annotation. We argue that workflow provenance is accompanied with implicit information, that can be made explicit to inform these techniques. Through empirical evidence we show that workflow steps have common functional characteristics, which we capture in a taxonomy of Workflow Motifs. We show how formally defined Graph Transformations can exploit Motifs to identify causes of complexity in workflows and abstract them to structurally simpler forms. We build on insight from prior research to show how execution and provenance collection behaviour of a workflow system can anticipate the granularity characteristics of provenance. We provide declarative anticipatory rules for the static-analysis of workflows of the Taverna system. We observe that scientific context is often available in embedded form in data and argue that data can be lifted to become metadata by discipline-specific metadata extractors. We outline a framework, that can be plugged with extractors and provide operators that encapsulate generic procedures to annotate workflow provenance. We implement our techniques with technology-independent provenance models and we showcase their benefit using real-world workflows.

An enterprise is composed of different departments, and these departments work together to achieve goals of business processes collaboratively. However, most of these business processes comprise loose operations, and information can¡¦t be passed efficiently among them. Hence, if an enterprise wants to promote competence, the problem of inefficient execution of processes must be improved. And, if workflows could have more flexibility, it will bring more benefits for enterprises. In this study, there are four parts to discuss flexible workflows. Firstly, we discussed workflows including the definitions of flexible workflows. Secondly, we discussed resource management including workflows with resource management and constraints programming. Thirdly, we discussed project management including the definition of project management and techniques. Finally, we discussed medical flows including three kinds of medical flows. We propose a prototyping system architecture including workflow management, resource management and project management to implement flexible workflows. In the experiment, we use a medical flow to explain how this system works. And, this system can produce a feasible schedule by a constraint solver.

The goal of this thesis was to design and implement a graphical editor for workflow modelling, focusing on productivity, simplicity and usability for the common user. The resulting application is integrated into the FlowOpt project, in which the workflows can be used to manage manufacturing processes in small and medium size factories. The workflow editor should serve among other things as a proof of concept of practical usability of the Nested TNA workflow model. The main parts of the thesis include a working implementation of the editor, a procedure for automatic verification of the workflows and support of the XPDL (BPMN) standard for saving workflows.

Workflow management is more and more popular and its technologies are becoming more and more mature. However, an important feature that is essential to many business process are left unsolved ¡V namely the unexpected exception handling. Not only does unexpected exceptions degrade the performance of WFMS, it also reflects the defects of workflow design. Our research proposes a framework that uses case-based reasoning to find exception handling rules from historical exception instances. These exception handling rules can help both improving exception handling performance and enabling workflow evolution. Our framework includes an exception taxonomy, an exception case base, and a set of exception naïve models. When an exception occurs, it is classified into a particular category according to the exception taxonomy. Within the category a number of attributes are compared and a naïve model that best represents the incoming exception is identified. It is then adapt to the current environment for an appropriate handling approach. We discuss in the thesis how to discover naïve models from a set of exception instances. A case is finally studied to demonstrate the feasibility of our framework and address the issues of some subtle considerations.

Submitted by Renata Lopes (renatasil82@gmail.com) on 2017-06-07T18:08:54Z No. of bitstreams: 1 brunofernandesbastos.pdf: 2778109 bytes, checksum: 078e98ab953377165b30e0e21520c35c (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-06-24T13:49:46Z (GMT) No. of bitstreams: 1 brunofernandesbastos.pdf: 2778109 bytes, checksum: 078e98ab953377165b30e0e21520c35c (MD5) / Made available in DSpace on 2017-06-24T13:49:46Z (GMT). No. of bitstreams: 1 brunofernandesbastos.pdf: 2778109 bytes, checksum: 078e98ab953377165b30e0e21520c35c (MD5) Previous issue date: 2015-08-20 / Workflows científicos vêm sendo utilizados para resolver problemas complexos em diferentes áreas. Sistemas Gerenciadores de Workflows Científicos (SGWfCs) são utilizados para a especificação e gerenciamento desses workflows. Porém, cada SGWfC pode possuir características diferentes e uma linguagem de especificação de workflows própria, dificultando o reuso dos workflows entre diferentes SGWfCs. A inexistência de uma padronização semântica dificulta ainda mais esse reuso, uma vez que elementos de modelagem de workflow presentes em alguns SGWfCS podem não ser mapeáveis em outros SGWfCs. O uso de uma linguagem intermediária para o intercâmbio de workflows científicos facilita o reuso de workflows desenvolvidos em diferentes SGWfCs ao permitir a definição de um arcabouço comum para esses SGWfCs. No entanto, uma linguagem desse tipo não impede que haja perda de informação semântica durante um processo de transformação de especificações entre esses SGWfCs, uma vez que essa linguagem deve ser robusta o suficiente para representar a semântica de diversos workflows desenvolvidos em diferentes SGWfCs. A existência de padrões (patterns) em workflows científicos pode ajudar a explicitar as informações semânticas mais importantes para a construção desses workflows. Assim a proposta deste trabalho é oferecer uma abordagem baseada em padrões para o intercâmbio entre especificações de workflows científicos, empregando uma linguagem intermediária com suporte a informações semânticas obtidas através da descrição dos padrões. Esta dissertação analisa os resultados obtidos com essa proposta a partir da aplicação da abordagem em especificações de workflows armazenadas no repositório myExperiment. / Scientific workflows have been used to solve complex problems in different areas. Scientific Workflow Management Systems (SWfMSs) are used for specifying and managing these workflows. Nevertheless, each SWfMS may have different characteristics and its own workflow specification language, making its reuse accross different SWfMSs a difficult process. The lack of semantic standardization makes this reuse even more difficult, since the workflow modeling elements available in some SWfMSs may not be mapped onto others SWfMSs. The use of an intermediate language for the interchange of scientific workflows may help with the reuse of workflows developed in different SWfMSs, as it allows for the definition of a common framework for these SWfMSs. Nonetheless, such a language does not prevent the loss of some semantic information during a specification transformation process between different SWfMSs, since this language must be robust enough to represent the semantics of diverse workflows developed in different SWfMSs. The identification of scientific workflow patterns may help to describe the most important semantic information for the construction of these workflows. Thus, the purpose of this study is to provide a pattern-based approach for the interchange of scientific workflow specifications, using an intermediate language that supports semantic information obtained through the description of workflow patterns. This thesis also analyses the results obtained with the proposed approach being applied to workflow specifications stored in the myExperiment repository.

The role of provenance information in data-intensive research is a significant topic of discussion among technical experts and scientists. Typical use cases addressing traceability, versioning and reproducibility of the research findings are extended with more interactive scenarios in support, for instance, of computational steering and results management. In this thesis we investigate the impact that lineage records can have on the early phases of the analysis, for instance performed through near-real-time systems and Virtual Research Environments (VREs) tailored to the requirements of a specific community. By positioning provenance at the centre of the computational research cycle, we highlight the importance of having mechanisms at the data-scientists' side that, by integrating with the abstractions offered by the processing technologies, such as scientific workflows and data-intensive tools, facilitate the experts' contribution to the lineage at runtime. Ultimately, by encouraging tuning and use of provenance for rapid feedback, the thesis aims at improving the synergy between different user groups to increase productivity and understanding of their processes. We present a model of provenance, called S-PROV, that uses and further extends PROV and ProvONE. The relationships and properties characterising the workflow's abstractions and their concrete executions are re-elaborated to include aspects related to delegation, distribution and steering of stateful streaming operators. The model is supported by the Active framework for tuneable and actionable lineage ensuring the user's engagement by fostering rapid exploitation. Here, concepts such as provenance types, configuration and explicit state management allow users to capture complex provenance scenarios and activate selective controls based on domain and user-defined metadata. We outline how the traces are recorded in a new comprehensive system, called S-ProvFlow, enabling different classes of consumers to explore the provenance data with services and tools for monitoring, in-depth validation and comprehensive visual-analytics. The work of this thesis will be discussed in the context of an existing computational framework and the experience matured in implementing provenance-aware tools for seismology and climate VREs. It will continue to evolve through newly funded projects, thereby providing generic and user-centred solutions for data-intensive research.

Trabalho com suporte da CAPES. / This work presents a new model of process definition in workflow systems, the PDBC model. We also present a prototype of a workflow system whicli implements the PDBC model, the Tucupi server. The proposal of this new model is to allow flexibility in workflow systems. For this, we will use what we call partia! workflow, which is a partially deüned workflow whose complete definition is carried through during the execution of workflow. Partia! Workflow is deüned as a set of constraints and activities. Moreover, another way for a workflow system to get flexibility is through an exception handling mechanism. In this work we consider such mechanism through the use of overriden constraints, that is, constraints that can be violated in determined circumstances. For this we present the WRBAC, a model of access control for workflow systems, used to provide an adequate mechanism of violation of the overriden constraints used in the definition of a workflow. / Em domínios de aplicação como a área médica e engenharia de software os sistemas de workflow existentes são inadequados, pois a definição dos processos nesses sistemas é inflexível. No exemplo da área médica, ninguém sabe quais as ações devem ser tomadas durante a abordagem de um paciente, ou seja, ninguém conhece um processo de tratamento para paciente no instante em que ele é admitido no hospital. Portanto, uma nova forma de interação com os sistemas de workflow se faz necessário. Nesta nova forma de interação um usuário pergunta ao sistema o que deve ser feito para que uma atividade (atividade objetivo) seja executada. Por exemplo, para um médico realizar uma cirurgia em um paciente que procedimentos devem ser executados antes ou mesmo depois? Nesta nova abordagem, o sistema de workflow cumpre, além do papel de despachante de atividades aos usuários, como nos sistemas de workflow atuais, o papel de ajudante do usuário, pois indica ao usuário quais atividades executar antes e depois de executar uma atividade objetivo. Este trabalho apresenta um novo modelo de definição de processos em sistemas de workflow, o modelo PDBC. Apresentamos também um protótipo de um sistema de workflow que implementa o modelo PDBC, o servidor Tucupi. A proposta deste novo modelo é permitir que os sistemas de workflow manipulem workflows mais flexíveis. Para isso usaremos o que chamamos de workflow parcial, que é um workflow parcialmente definido cuja definição completa é realizada apenas durante a execução do workflow. O workflow parcial é definido como um conjunto de restrições e atividades. Outra maneira de se obter flexibilidade em sistemas de workflow é através de um mecanismo de tratamento de exceções adequado. Neste trabalho propomos um mecanismo de tratamento de exceções através do uso de restrições violáveis, ou seja, restrições que podem ser violadas em determinadas circunstâncias. Para isso apresentamos o WRBAC, um modelo de controle de acesso para sistemas de workflow, utilizado para provê um mecanismo adequado de sobrecarga das restrições utilizadas na definição de um processo.

Service Orientation (SO) and grid computing are two computing paradigms that when put together using Internet technologies promise to provide a scalable yet flexible computing platform for a diverse set of distributed computing applications. This practice gives rise to the notion of a computing cloud that addresses some previous limitations of interoperability, resource sharing and utilization within distributed computing. <p>In such a Service Oriented Computing Cloud (SOCC), applications are formed by composing a set of services together. In addition, hierarchical service layers are also possible where general purpose services at lower layers are composed to deliver more domain specific services at the higher layer. In general an SOCC is a horizontally scalable computing platform that offers its resources as services in a standardized fashion. <p>Workflow based applications are a suitable target for SOCC where workflow tasks are executed via service calls within the cloud. One or more workflows can be deployed over an SOCC and their execution requires scheduling of services to workflow tasks as the task become ready following their interdependencies. <p>In this thesis heuristics based scheduling policies are evaluated for scheduling workflows over a collection of services offered by the SOCC. Various execution scenarios and workflow characteristics are considered to understand the implication of the heuristic based workflow scheduling.

Service Orientation (SO) and grid computing are two computing paradigms that when put together using Internet technologies promise to provide a scalable yet flexible computing platform for a diverse set of distributed computing applications. This practice gives rise to the notion of a computing cloud that addresses some previous limitations of interoperability, resource sharing and utilization within distributed computing. <p>In such a Service Oriented Computing Cloud (SOCC), applications are formed by composing a set of services together. In addition, hierarchical service layers are also possible where general purpose services at lower layers are composed to deliver more domain specific services at the higher layer. In general an SOCC is a horizontally scalable computing platform that offers its resources as services in a standardized fashion. <p>Workflow based applications are a suitable target for SOCC where workflow tasks are executed via service calls within the cloud. One or more workflows can be deployed over an SOCC and their execution requires scheduling of services to workflow tasks as the task become ready following their interdependencies. <p>In this thesis heuristics based scheduling policies are evaluated for scheduling workflows over a collection of services offered by the SOCC. Various execution scenarios and workflow characteristics are considered to understand the implication of the heuristic based workflow scheduling.

Rapid advances in electronic communication devices and technologies have resulted in a shift in the way communication applications are being developed. These new development strategies provide abstract views of the underlying communication technologies and lead to the so-called user-centric communication applications. One user-centric communication (UCC) initiative is the Communication Virtual Machine (CVM) technology, which uses the Communication Modeling Language (CML) for modeling communication services and the CVM for realizing these services. In communication-intensive domains such as telemedicine and disaster management, there is an increasing need for user-centric communication applications that are domain-specific and that support the dynamic coordination of communication services commonly found in collaborative communication scenarios. However, UCC approaches like the CVM offer little support for the dynamic coordination of communication services resulting from inherent dependencies between individual steps of a collaboration task. Users either have to manually coordinate communication services, or reply on a process modeling technique to build customized solutions for services in a specific domain that are usually costly, rigidly defined and technology specific. This dissertation proposes a domain-specific modeling approach to address this problem by extending the CVM technology with communication-specific abstractions of workflow concepts commonly found in business processes. The extension involves (1) the definition of the Workflow Communication Modeling Language (WF-CML), a superset of CML, and (2) the extension of the functionality of CVM to process communication-specific workflows. The definition of WF-CML includes the metamodel and the dynamic semantics for control constructs and concurrency. We also extended the CVM prototype to handle the modeling and realization of WF-CML models. A comparative study of the proposed approach with other workflow environments validates the claimed benefits of WF-CML and CVM.