Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Devido à grande diversidade de microrganismos desconhecidos no meio ambiente, 99% deles não podem ser cultivados nos meios de cultura tradicionais dos laboratórios. Para isso, projetos metagenômicos são propostos para estudar comunidades microbianas presentes no meio ambiente, a partir de técnicas moleculares, em especial o seqüenciamento. Dessa forma, para os próximos anos é esperado um acúmulo de seqüências produzidas por esses projetos. As seqüências produzidas pelos projetos genomas e metagenomas apresentam vários desafios para o tratamento, armazenamento e análise, como exemplo: a busca de clones contendo genes de interesse. Este trabalho apresenta uma abordagem algébrica que define e gerencia de forma dinâmica as regras para a seleção de clones em bibliotecas genômicas e metagenômicas, que se baseiam em álgebra de processos. Além disso, uma interface web foi desenvolvida para permitir que os pesquisadores criem e executem facilmente suas próprias regras de seleção de clones em bancos de dados de seqüências genômicas e metagenômicas. Este software foi testado em bibliotecas genômicas e metagenômicas e foi capaz de selecionar clones contendo genes de interesse. / Due to the wide diversity of unknown organisms in the environment, 99% of them cannot be grown in traditional culture medium in laboratories. Therefore, metagenomics projects are proposed to study microbial communities present in the environment, from molecular techniques, especially the sequencing. Thereby, for the coming years it is expected an accumulation of sequences produced by these projects. Thus, the sequences produced by genomics and metagenomics projects present several challenges for the treatment, storing and analysis such as: the search for clones containing genes of interest. This work presents an algebraic approach that defines it dynamically and manages the rules of the selection of clones in genomic and metagenomic libraries, which are based on process algebra. Furthermore, a web interface was developed to allow researchers to easily create and execute their own rules to select clones in genomic and metagenomic sequence database. This software was tested in genomics and metagenomics libraries and it was able to select clones containing genes of interest.

Les infrastructures de calcul scientifique sont en constante évolution, et l’émergence de nouvelles technologies nécessite l’évolution des mécanismes d’ordonnancement qui leur sont associé. Durant la dernière décennie, l’apparition du modèle Cloud a suscité de nombreux espoirs, mais l’idée d’un déploiement et d’une gestion entièrement automatique des plates-formes de calcul est jusque la resté un voeu pieu. Les travaux entrepris dans le cadre de ce doctorat visent a concevoir un moteur de gestion de workflow qui intègre les logiques d’ordonnancement ainsi que le déploiement automatique d’une infrastructure Cloud. Plus particulièrement, nous nous intéressons aux plates-formes Clouds disposant de système de gestion de données de type DaaS (Data as a Service). L’objectif est d’automatiser l’exécution de workflows arbitrairement complexe, soumis de manière indépendante par de nombreux utilisateurs, sur une plate-forme Cloud entièrement élastique. Ces travaux proposent une infrastructure globale, et décrivent en détail les différents composants nécessaires à la réalisation de cette infrastructure :• Un mécanisme de clustering des tâches qui prend en compte les spécificités des communications via un DaaS ;• Un moteur décentralisé permettant l’exécution des workflows découpés en clusters de tâches ;• Un système permettant l’analyse des besoins et le déploiement automatique. Ces différents composants ont fait l’objet d’un simulateur qui a permis de tester leur comportement sur des workflows synthétiques ainsi que sur des workflows scientifiques réels issues du LBMC (Laboratoire de Biologie et Modélisation de la Cellule). Ils ont ensuite été implémentés dans l’intergiciel Diet. Les travaux théoriques décrivant la conception des composants, et les résultats de simulations qui les valident, ont été publié dans des workshops et conférences de portée internationale. / The constant development of scientific and industrial computation infrastructures requires the concurrent development of scheduling and deployment mechanisms to manage such infrastructures. Throughout the last decade, the emergence of the Cloud paradigm raised many hopes, but achieving full platformautonomicity is still an ongoing challenge. Work undertaken during this PhD aimed at building a workflow engine that integrated the logic needed to manage workflow execution and Cloud deployment on its own. More precisely, we focus on Cloud solutions with a dedicated Data as a Service (DaaS) data management component. Our objective was to automate the execution of workflows submitted by many users on elastic Cloud resources.This contribution proposes a modular middleware infrastructure and details the implementation of the underlying modules:• A workflow clustering algorithm that optimises data locality in the context of DaaS-centeredcommunications;• A dynamic scheduler that executes clustered workflows on Cloud resources;• A deployment manager that handles the allocation and deallocation of Cloud resources accordingto the workload characteristics and users’ requirements. All these modules have been implemented in a simulator to analyse their behaviour and measure their effectiveness when running both synthetic and real scientific workflows. We also implemented these modules in the Diet middleware to give it new features and prove the versatility of this approach.Simulation running the WASABI workflow (waves analysis based inference, a framework for the reconstruction of gene regulatory networks) showed that our approach can decrease the deployment cost byup to 44% while meeting the required deadlines.

Submitted by Maria Cristina (library@lncc.br) on 2015-04-07T14:04:08Z No. of bitstreams: 1 thesis_RLC.pdf: 14146223 bytes, checksum: 3e764cd68f4c65f0572940fb339e5708 (MD5) / Approved for entry into archive by Maria Cristina (library@lncc.br) on 2015-04-07T14:04:34Z (GMT) No. of bitstreams: 1 thesis_RLC.pdf: 14146223 bytes, checksum: 3e764cd68f4c65f0572940fb339e5708 (MD5) / Made available in DSpace on 2015-04-07T14:04:50Z (GMT). No. of bitstreams: 1 thesis_RLC.pdf: 14146223 bytes, checksum: 3e764cd68f4c65f0572940fb339e5708 (MD5) Previous issue date: 2014-10-31 / Recent developments in molecular assays to study the transcriptome associated with statistical, mathematics and computational methods, introduced great advances in the comprehension of biological systems, in understanding the viral infectious process associated with immune response and the choice of targets for the development of vaccines and antiviral therapies. On one hand side, the modelling process involves different stages, including transcriptome acquisition, the integration with information available in biological databases and the visualization and analysis of networks therein obtained. On the other hand side, during the modelling process, many software systems are employed with differences in structure, design assumptions and heterogeneity in input data, making the whole analysis process, besides laborious and fragmented, error-prone. In this context, infrastructure to support e-science such as scientific workflows and databases are used in automating, structuring, execution, organization and management of scientific experiments in silico. In this thesis, we studied gene expression data (DNA microarray) of primates infected with SIV (Simian Virus Imunodeficiency) composing a time-series reflecting the evolution of infection. SIV infects more than 40 species in African continent that are known as natural hosts, as they do not develop the immunodeficiency syndrome (AIDS). However, when SIV strains infect non African primates, known as non-natural hosts, among them Asian rhesus monkey (Macaca mulatta), they develop a syndrome similar to the human immunodeficiency virus HIV. The evolutionary closeness of the virus, SIV and HIV, and between the hosts, human and non-human primates, enables biological studies in non-human models relevant to understanding the biological mechanisms of various innate and adaptive immunity in the host. Thus, we used data corresponding to sampling points in three different stages of SIV infection: before infection, acute and chronic phases of infection. Data process analysis was based on systems biology approaches. These analyzes included steps such as, data normalization, filtering, annotation, clustering, enrichment, interactions biological database and visualizations of the results in gene interaction networks. Among the main biological results, we selected: identification of co-expressed genes; functional characterization profiles from ontologies related to biological processes; interactions between genes host-host and virus-host and differences in the timing of immune responses during acute phase of infection between the different types of hosts. We implemented the analytical process described above in a framework denominated GenNet that consisting of a scientific workflow, GenNet.W, responsible for the automation of scientific experiments in silico and a database, GenNet.DB. The database adopted a graph data model, within a NoSQL based system, to store the inferred gene interaction networks, as well as other information generated by the scientific workflow. The graph data model natively supports the representation of gene interaction networks and enables the comparison between different inferred networks, as much as path explorations such as co??-expression genes in high-level declarative query language. / O recente desenvolvimento de ensaios moleculares para estudo do transcriptoma, associados a métodos estatísticos, matemáticos e computacionais, trouxeram grandes avanços no entendimento de sistemas biológicos, dentre os quais, a compreensão de processos infecciosos virais associados à resposta imune e escolha de alvos para o desenvolvimento de vacinas e terapias antivirais. De um lado, o processo de modelagem envolve diferentes etapas, desde a aquisição dos dados de transcriptoma, integração de informações disponíveis em bancos de dados biológicos até visualizações e análises das redes obtidas. Por outro lado, durante o processo de modelagem, são utilizados diversos sistemas de software com diferentes pressupostos de organização e forma de dados de entrada, fazendo com que todo esse processo seja, além de trabalhoso e fragmentado, passível de erros. Nesse sentido, infraestruturas de apoio a e-science como workflows científicos e banco de dados são utilizados na automação, estruturação, execução, organização e gerenciamento de experimentos científicos in silico. Nessa tese, utilizamos diferentes dados de séries temporais de expressão gênica (microarranjo de DNA) em primatas infectados pelo SIV (do inglês, Simian Imunodeficiency Virus). O SIV infecta várias espécies de primatas africanos, conhecidos como hospedeiros naturais, que não desenvolvem doença. Entretanto, quando linhagens de SIV infectam primatas não africanos, conhecidos como hospedeiros não naturais, dentre os quais o macaco asiático rhesus (Macaca mulatta), esses desenvolvem uma imunodeficiência semelhante a que ocorre em humanos pelo HIV. A proximidade evolutiva entre os vírus, SIV e HIV, e entre os hospedeiros, humanos e primatas não humanos, possibilitam estudos em modelos biológicos não humanos relevantes na compreensão dos diferentes mecanismos da imunidade inata e adaptativa nos hospedeiros. Os dados utilizados corresponderam a pontos amostrais em três diferentes fases da infecção pelo SIV: antes da infecção, fase aguda e fase crônica. O processo de análise desses dados baseou-se em abordagens de biologia de sistemas. Tais análises incluíram etapas de normalização dos dados, filtragem, anotação, agrupamento, enriquecimento, integração com base de dados biológicas e visualização dos resultados em redes de interações gênicas. Dentre os principais resultados biológicos obtidos, selecionamos: a identificação dos genes co-expressos nos perfis de expressão gênica, caracterização funcional a partir das ontologias relacionadas aos processos biológicos, interações entre os genes hopedeiro-hospedeiro e vírus-hospedeiro e diferenças nos tempos das respostas imunes na fase aguda da infecção entre os tipos de hospedeiros. Inserimos o processo analítico descrito acima em uma framework chamada GenNet consistindo de um workflow científico GenNet.W responsável pela automação do experimento científico in silico e um banco de dados GenNet.DB. O banco de dados adotou um modelo de dados em grafos, NoSQL, para armazenar as redes de interações gênicas inferidas, bem como outras informações geradas pelo workflow científico. O modelo de dados em grafo suporta nativamente a representação das redes de interações gênicas e permite a comparação entre diferentes redes inferidas e a exploração de vias de como co-expressão gênica, usando consultas que expressam em alto nível de linguagem que o sistema suporta.

[pt] Os projetos para estudo de genomas partem de uma fase de sequenciamento onde são gerados em laboratório dados brutos, ou seja, sequências de DNA sem significado biológico. As sequências de DNA possuem códigos responsáveis pela produção de proteínas e RNAs, enquanto que as proteínas participam de todos os fenômenos biológicos, como a replicação celular, produção de energia, defesa imunológica, contração muscular, atividade neurológica e reprodução. As sequências de DNA, RNA e proteínas são chamadas nesta tese de biossequências. Porém, o grande desafio destes projetos consiste em analisar essas biossequências, e obter informações biologicamente relevantes. Durante a fase de análise, os pesquisadores usam diversas ferramentas, programas de computador, e um grande volume de informações armazenadas em fontes de dados de Biologia Molecular. O crescente volume e a distribuição das fontes de dados e a implementação de novos processos em Bioinformática facilitaram enormemente a fase de análise, porém criaram uma demanda por ferramentas e sistemas semi-automáticos para lidar com tal volume e complexidade. Neste cenário, esta tese aborda o uso de workflows para compor processos de Bioinformática, facilitando a fase de análise. Inicialmente apresenta uma ontologia modelando processos e dados comumente utilizados em Bioinformática. Esta ontologia foi derivada de um estudo cuidadoso, resumido na tese, das principais tarefas feitas pelos pesquisadores em Bioinformática. Em seguida, a tese propõe um framework para um sistema de gerência de análises em biossequências, composto por dois sub-sistemas. O primeiro é um sistema de gerência de workflows de Bioinformática, que auxilia os pesquisadores na definição, validação, otimização e execução de workflows necessários para se realizar as análises. O segundo é um sistema de gerência de dados em Bioinformática, que trata do armazenamento e da manipulação dos dados envolvidos nestas análises. O framework inclui um gerente de ontologias, armazenando ontologias para Bioinformática, nos moldes da apresentada anteriormente. Por fim, a tese descreve instanciações do framework para três tipos de ambiente de trabalho comumente encontrados e sugestivamente chamados de ambiente pessoal, ambiente de laboratório e ambiente de comunidade. Para cada um destes ambientes, a tese discute em detalhe os aspectos particulares da execução e otimização de workflows. / [en] Genome projects usually start with a sequencing phase, where experimental data, usually DNA sequences, is generated, without any biological interpretation. DNA sequences have codes which are responsible for the production of protein and RNA sequences, while protein sequences participate in all biological phenomena, such as cell replication, energy production, immunological defense, muscular contraction, neurological activity and reproduction. DNA, RNA and protein sequences are called biosequences in this thesis. The fundamental challenge researchers face lies exactly in analyzing these sequences to derive information that is biologically relevant. During the analysis phase, researchers use a variety of analysis programs and access large data sources holding Molecular Biology data. The growing number of Bioinformatics data sources and analysis programs indeed enormously facilitated the analysis phase. However, it creates a demand for systems that facilitate using such computational resources. Given this scenario, this thesis addresses the use of workflows to compose Bioinformatics analysis programs that access data sources, thereby facilitating the analysis phase. An ontology modeling the analysis program and data sources commonly used in Bioinformatics is first described. This ontology is derived from a careful study, also summarized in the thesis, of the computational resources researchers in Bioinformatics presently use. A framework for biosequence analysis management systems is next described. The system is divided into two major components. The first component is a Bioinformatics workflow management system that helps researchers define, validate, optimize and run workflows combining Bioinformatics analysis programs. The second component is a Bioinformatics data management system that helps researchers manage large volumes of Bioinformatics data. The framework includes an ontology manager that stores Bioinformatics ontologies, such as that previously described. Lastly, instantiations for the Bioinformatics workflow management system framework are described. The instantiations cover three types of working environments commonly found and suggestively called personal environment, laboratory environment and community environment. For each of these instantiations, aspects related to workflow optimization and execution are carefully discussed.

La validation des systèmes est un des aspects critiques dans les phases de développement. Cette validation est d'autant plus importante pour les systèmes embarqués, dont le fonctionnement doit être autonome, mais aussi contraint par des limitations physiques et techniques. Avec la complexification des systèmes embarqués ces dernières années, l'applications de méthodes de validation durant le développement devient trop couteux, et la mise en place de mécanismes de vérification post-conception est nécessaire. L'utilisation de traces d'exécution, permettant de capturer le comportement du système lors de son exécution, se révèle efficace pour la compréhension et la validation des systèmes observés. Cependant, les outils d'exploitation de traces actuels se confrontent à deux défis majeurs, à savoir, la gestion de traces pouvant atteindre des tailles considérables, et l'extraction de mesures pertinentes à partir des informations bas-niveau contenues dans ces traces. Dans cette thèse, faite dans le cadre du projet FUI SoC-TRACE, nous présentons trois contributions. La première concerne la définition d'un format générique pour la représentation des traces d'exécution, enrichi en sémantique. La seconde concerne une infrastructure d'analyse utilisant des mécanismes de workflow permettant l'analyse générique et automatique de traces d'exécution. Cette infrastructure répond au problème de gestion des traces de tailles considérables textit{via} des mécanismes de streaming, permet la création d'analyses modulaires et configurables, ainsi qu'un enchainement automatique des traitements. Notre troisième contribution propose une méthode générique pour l'analyse de performances de systèmes Linux. Cette contribution propose à la fois la méthode et les outils de collecte de traces, mais aussi le workflow permettant d'obtenir des profils unifiés pour les traces capturées. La validation de nos propositions ont été faites d'une part sur des traces issues de cas d'usages proposés par STMicroelectronics, partenaire du projet, et d'autre part sur des traces issues de programmes de benchmarks. L'utilisation d'un format enrichi en sémantique a permis de mettre en évidence des anomalies d'exécutions, et ce de manière semi-automatique. L'utilisation de mécanismes de streaming au sein de notre infrastructure nous a permis de traiter des traces de plusieurs centaines de gigaoctets. Enfin, notre méthode d'analyse générique nous a permis de mettre en évidence, de manière automatique et sans connaissances a priori des programmes, le fonctionnement interne de ces différents benchmarks. La généricité de nos solutions a permis d'observer le comportement de programmes similaires sur des plates-formes et des architectures différentes, et d'en montrer leur impact sur les exécutions. / Validation process is a critical aspect of systems development. This process is a major concern for embedded systems, to assess their autonomous behavior, led by technical and physical constraints. The growth of embedded systems complexity during last years prevents the use of complex and costly development processes such as formal methods. Thus, post-conception validations must be applied. Execution traces are effective for validation and understanding as they allow the capture of systems behavior during their executions. However, trace analysis tools face two major challenges. First, the management of huge execution traces. Second, the ability to retrieve relevant metrics, from the low-level information the trace contains. This thesis was done as part of the SoC-TRACE projet, and presents three contributions. Our first contribution is a definition of a generic execution trace format that expresses semantics. Our second contribution is a workflow-based infrastructure for generic and automatic trace analysis. This infrastructure addresses the problem of huge traces management using streaming mechanisms. It allows modular and configurable analyses, as well as automatic analyses execution. Our third contribution is about the definition of a generic performance analyses for Linux systems. This contribution provides methods and tools for trace recording, and also analysis workflow to obtain unified performance profiles. We validate our contributions on traces from use cases given by STMicroelectronics, partner of the project, and also on traces recorded from benchmarks executions. Our trace format with semantics allowed us to automatically bring out execution problems. Using streaming mechanisms, we have been able to analyze traces that can reach several hundreds of gigabytes. Our generic analysis method for systems let us to automatically highlight, without any prior knowledge, internal behavior of benchmark programs. Our generic solutions point out a similar execution behavior of benchmarks on different machines and architectures, and showed their impact on the execution.

[pt] Os sistemas de gerência de workflow são freqüentemente utilizados para modelagem, monitoramento e execução coordenada de atividades realizadas por grupos de usuários em diferentes contextos. Com a atual proliferação de computadores portáteis e seu crescente poder de computação, os sistemas tradicionalmente desenvolvidos têm se mostrado, muitas vezes, excessivamente rígidos, limitando o grau de autonomia dos usuários. O objetivo deste trabalho é identificar e analisar diferentes técnicas de flexibilização e mecanismos que possam ser empregados em um sistema de gerência de work-flow destinado a dar suporte à operação desconectada. O principal desafio é garantir um nível de independência satisfatório entre grupos de pessoas trabalhando de forma conjunta que possibilite a realização coordenada de tarefas, com um objetivo global comum, em ambientes com desconexão. Para testar a viabilidade das idéias discutidas nesta dissertação, foi construído um sistema cujo projeto levou em conta os vários requisitos apresentados e que permite explorar características específicas de diferentes tipos de work-flow, buscando flexibilizar sua execução, sem comprometer a estruturação preestabelecida. / [en] Workflow management systems are frequently used for modeling, monitoring and controlling the coordinated execution of activities performed by workgroups in a variety of contexts. With the widespread use of portable computers and their growing computational power, conventional systems have often proved to be overly restrictive, effectively limiting the level of autonomy of the users involved. The primary goal of this work is to identify and analyze different flexibilization techniques and mechanisms that can be employed in a workflow management system aimed at supporting disconnected operation. The main challenge is to provide a satisfactory degree of independence among individuals in cooperating teams who share a common goal and work in disconnected environments. In order to test the viability of the ideas discussed in this dissertation, a system was built whose design met the requirements presented in the text and which allows the exploration of specific features of different kinds of workflow so as to enhance execution flexibility, without compromising the predefined structure.

The term Facility Management describes one part of business management with the goal of supporting the management activities through the delivery of infrastructure, technology and services. It covers the whole life cycle of a structural facility. An integration of facility management in the active processes of an enterprise or an enterprise group will be substantially supported by the introduction of an efficient, flexible and future-safe computer aided facility management system. But still no universal standards were established in this area. With high expenditure adapted single solutions are the rule, harm however the demand for a save investment independently of proprietary special solutions of individual manufacturers. An analysis of existing business standards shows that these solutions are suitable only partly for combining the existing isolated solutions in a virtual enterprise group in order to create a sustainable architectural approach for a process oriented facility management. In doing so the communication must not be reduced to pure data exchange, but only stable interface definitions and accurately specified document formats can lead to a continuous solution. In order to make these solutions for developers and end users in the phases of the design, the implementation and maintenance equally clear, a common vocabulary of concepts is necessary. The usage of the Unified Modeling Language gives thereby a promising basis. The concrete models with the contained types and their relations to each other are described over meta models. The usage of XML as means to data exchange between the individual components and for the description of the meta models guarantees a flexible and future-safe development basis. In the context of the work based on use cases the conception for a framework with core components for process oriented facility management in distributed environments is designed. The framework Simplix conceived by the author integrates meta models for the description of concrete data, workflow and access schemes. The designed modules are embedded into a component-based architecture, in order to obtain a greatest possible flexibility for the deployment in heterogeneous IT environments. The framework Simplix covers four core components. The SchemaService describes the concrete product models, the associated processes are represented by the WorkflowService. The realization of the access rules is realized by the SecurityService. The exchange of workflow messages with the encapsulated project data is done by the ExchangeService in XML. The presented design focuses on the integration of existing business and IT standards. The design of the four core components describes a possibility of standardization in the area of CAFM, which connects only the relevant data over processes detached from conventional export/import scenarios: <ul> <li>Reduction of the complexity of conventional product models by a standardization over meta models, the actual product and process models can be designed for end users and to their vocabulary of concepts adapted</li> <li>Support of the Ad-Hoc-manipulation of concrete product and process models, only thereby can be achieved an integration of different vocabulary of concepts</li> <li>The usage of standardized methods in the analysis and design phases makes a fast technical implementation of the individual services possible, especially during the integration of external software systems as always necessary in the CAFM sector</li> <li>Due to a clear interface specification external offers for individual services can be provided and used, the continuous use of XML makes an effective long-term data storage in a standardized, self-describing language possible</li></ul> / Der Begriff Facility Management bezeichnet eine Facette des unternehmerischen Managements, die es zum Ziel hat, die unternehmerischen Aktivitäten durch die Bereitstellung von Infrastruktur, Technologien und Diensten zu unterstützen und umfaßt den gesamten Lebenszyklus einer baulichen Anlage. Eine Einbettung von Facility Management in die laufenden Prozesse eines Unternehmens oder eines Unternehmensverbundes wird durch die Einführung eines leistungsfähigen, flexiblen und zukunftssicheren Computer Aided Facility Management Systems wesentlich unterstützt. Allerdings haben sich auf diesem Gebiet noch keine durchgängigen Standards etabliert, mit hohem Aufwand angepaßte Einzellösungen sind die Regel, verletzen aber die Forderung nach Investitionssicherheit unabhängig von den proprietären Speziallösungen einzelner Hersteller. Eine Analyse vorhandener Geschäftsstandards zeigt, daß diese Ansätze nur teilweise dazu geeignet sind, die vorhandenen Insellösungen in einem virtuellen Unternehmensverbund miteinander zu kombinieren, um einen tragfähigen Architekturansatz für ein prozeßorientiertes Facility Management zu schaffen. Dabei darf die Kommunikation nicht auf den reinen Datenaustausch reduziert werden, sondern nur stabile Schnittstellendefinitionen und exakt spezifizierte Dokumentenformate können zu einer durchgehenden Lösung führen. Die konkreten Modelle mit den enthaltenen Typen und deren Beziehungen zueinander werden über Metamodelle beschrieben. Der Einsatz von XML als Mittel zum Datenaustausch zwischen den einzelnen Komponenten und zur Beschreibung der Metamodelle garantiert eine flexible und zukunftssichere Entwicklungsgrundlage. Im Rahmen der Arbeit wird auf der Basis von Anwendungsfällen die Konzeption für ein Framework mit Kernkomponenten zum prozeßorientierten Facility Management in verteilten Umgebungen entworfen. Das vom Autor konzipierte Framework Simplix integriert Metamodelle zur Beschreibung konkreter Daten-, Workflow- und Zugriffsschemata. Die dazu geplanten Module werden in eine komponentenbasierte Architektur eingebettet, um eine größtmögliche Flexibilität beim Einsatz in heterogenen IT-Umgebungen zu erzielen. Das Framework Simplix umfaßt vier Kernkomponenten. Der SchemaService beschreibt die konkreten Produktmodelle, die zugehörigen Prozesse werden über den WorkflowService abgebildet. Die Realisierung der Mechanismen zur Zugriffskontrolle werden vom SecurityService übernommen. Der Austausch von Workflow-Nachrichten mit den gekapselten Projektdaten erfolgt über den ExchangeService in XML. Der vorgestellte Ansatz setzt auf die Integration vorhandener Geschäfts- und IT-Standards. Der Entwurf der vier Kernkomponenten beschreibt eine Möglichkeit der Standardisierung im CAFM-Sektor, die losgelöst von herkömmlichen Export-/Import-Szenarios funktioniert und nur die relevanten Daten über Prozesse verknüpft: <ul> <li>Reduzierung der Komplexität herkömmlicher Produktmodelle durch eine Standardisierung über Metamodelle, die eigentlichen Produkt- und Prozeßmodelle können für die Endanwender entworfen und an deren Begriffswelt angepaßt werden</li> <li>Unterstützung der Ad-Hoc-Manipulation von konkreten Produkt- und Prozeßmodellen, nur dadurch kann eine Integration verschiedener Begriffswelten erreicht werden</li> <li>der Einsatz standardisierter Techniken im Entwurf und dem Design ermöglicht eine schnelle technische Umsetzung der einzelnen Dienste gerade bei der im CAFM immer notwendigen Einbindung von Fremdsoftware</li> <li>auf Grund einer klaren Schnittstellenspezifikation können externe Serviceangebote für einzelne Dienste erstellt und genutzt werden, der durchgehende Einsatz von XML ermöglicht eine effektive Langzeitdatenhaltung in einem standardisierten, selbstbeschreibenden Format</li></ul>

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The distribution of tasks in workflow systems is not a trivial problem. There are two solutions to make this distribution: Push and Pull. These solutions, in general, do not consider the resources aptitude. However, resources that share the same role in the workflow can have different degrees of aptitude to a task. The literature in workflow points the solution based on Pull mechanisms with resources aptitude as ideal to tasks, resulting in a more accurate executions and with more quality. This work shows that, if the resources aptitute is used, the solution based on Push presents a better performance and allows a more tuned balancing, regarding to time and quality of the execution of the business processes. The experiments demonstrate the effectiveness of the used approach. A comparison with traditional solutions shows gains in terms of time and quality of tasks execution. / Distribuir tarefas em sistemas de workflow não é um problema trivial. Há duas soluções para realizar essa distribuição: Push e Pull. Essas soluções, em geral, não consideram a aptidão dos recursos. No entanto, recursos que compartilham o mesmo papel no workflow podem possuir diferentes graus de aptidão a uma tarefa. A literatura de worklfow aponta a solução baseada em Pull, com aptidão dos recursos, como ideal para distribuir tarefas, resultando em execuções mais ágeis e com melhor qualidade. Este trabalho mostra que, se utilizada a aptidão dos recursos, a solução baseada em Push apresenta melhor eficiência do que a Pull e permite um balanceamento mais refinado nos quesitos tempo e qualidade de execução dos processos de negocio. Os experimentos realizados mostram a efetividade da abordagem utilizada. Uma comparação com soluções tradicionais comprova ganhos significativos em termos de tempo e qualidade. / Mestre em Ciência da Computação

Dans tous les domaines, le progrès scientifique repose de plus en plus sur la capacité à exploiter des volumes de données toujours plus gigantesques. Alors que leur volume augmente, la gestion de ces données se complexifie. Un point clé est la gestion du cycle de vie des données, c'est à dire les diverses opérations qu'elles subissent entre leur création et leur disparition : transfert, archivage, réplication, suppression, etc. Ces opérations, autrefois simples, deviennent ingérables lorsque le volume des données augmente de manière importante, au vu de l'hétérogénéité des logiciels utilisés d'une part, et de la complexité des infrastructures mises en œuvre d'autre part.Nous présentons Active Data, un méta-modèle, une implémentation et un modèle de programmation qui permet de représenter formellement et graphiquement le cycle de vie de données présentes dans un assemblage de systèmes et d'infrastructures hétérogènes, en exposant naturellement la réplication, la distribution et les différents identifiants des données. Une fois connecté à des applications existantes, Active Data expose aux utilisateurs ou à des programmes l'état d'avancement des données dans leur cycle de vie, en cours d'exécution, tout en gardant leur trace lorsqu'elles passent d'un système à un autre.Le modèle de programmation Active Data permet d'exécuter du code à chaque étape du cycle de vie des données. Les programmes écrits avec Active Data ont à tout moment accès à l'état complet des données, à la fois dans tous les systèmes et dans toutes les infrastructures sur lesquels elles sont distribuées. Nous présentons des évaluations de performance et des exemples d'utilisation qui attestent de l'expressivité du modèle de programmation et de la qualité de l'implémentation. Enfin, nous décrivons l'implémentation d'un outil de Surveillance des données basé sur Active Data pour l'expérience Advanced Photon Source qui permet aux utilisateurs de suivre la progression de leurs données, d'automatiser la plupart des tâches manuelles, d'obtenir des notifications pertinente parmi une masse gigantesque d'événements, ainsi que de détecter et corriger de nombreuses erreurs sans intervention humaine.Ce travail propose des perspectives intéressantes, en particulier dans les domaines de la provenance des données et de l'open data, tout en facilitant la collaboration entre les scientifiques de communautés différentes. / In all domains, scientific progress relies more and more on our ability to exploit ever growing volumes of data. However, as datavolumes increase, their management becomes more difficult. A key point is to deal with the complexity of data life cycle management,i.e. all the operations that happen to data between their creation and there deletion: transfer, archiving, replication, disposal etc.These formerly straightforward operations become intractable when data volume grows dramatically, because of the heterogeneity ofdata management software on the one hand, and the complexity of the infrastructures involved on the other.In this thesis, we introduce Active Data, a meta-model, an implementation and a programming model that allow to represent formally and graphically the life cycle of data distributed in an assemblage of heterogeneous systems and infrastructures, naturally exposing replication, distribution and different data identifiers. Once connected to existing applications, Active Data exposes the progress of data through their life cycle at runtime to users and programs, while keeping their track as it passes from a system to another.The Active Data programming model allows to execute code at each step of the data life cycle. Programs developed with Active Datahave access at any time to the complete state of data in any system and infrastructure it is distributed to.We present micro-benchmarks and usage scenarios that demonstrate the expressivity of the programming model and the implementationquality. Finally, we describe the implementation of a Data Surveillance framework based on Active Data for theAdvanced Photon Source experiment that allows scientists to monitor the progress of their data, automate most manual tasks,get relevant notifications from huge amount of events, and detect and recover from errors without human intervention.This work provides interesting perspectives in data provenance and open data in particular, while facilitating collaboration betweenscientists from different communities.