L'identification des interactions survenant au niveau moléculaire joue un rôle crucial pour la compréhension du vivant. L'objectif de ce travail a consisté à développer des méthodes permettant de modéliser et de prédire ces interactions pour le métabolisme et la régulation de la transcription. Nous nous sommes basés pour cela sur la modélisation de ces systèmes sous la forme de graphes et d'automates. Nous avons dans un premier temps développé une méthode permettant de tester et de prédire la distribution du flux au sein d'un réseau métabolique en permettant la formulation d'une à plusieurs contraintes. Nous montrons que la prise en compte des données biologiques par cette méthode permet de mieux reproduire certains phénotypes observés in vivo pour notre modèle d'étude du métabolisme énergétique du parasite Trypanosoma brucei. Les résultats obtenus ont ainsi permis de fournir des éléments d'explication pour comprendre la flexibilité du flux de ce métabolisme, qui étaient cohérentes avec les données expérimentales. Dans un second temps, nous nous sommes intéressés à une catégorie particulière d'ARN non codants appelés sRNAs, qui sont impliqués dans la régulation de la réponse cellulaire aux variations environnementales. Nous avons développé une approche permettant de mieux prédire les interactions qu'ils effectuent avec d'autres ARN en nous basant sur une prédiction des interactions, une analyse par enrichissement du contexte biologique de ces cibles, et en développant un système de visualisation spécialement adapté à la manipulation de ces données. Nous avons appliqué notre méthode pour l'étude des sRNAs de la bactérie Escherichia coli. Les prédictions réalisées sont apparues être en accord avec les données expérimentales disponibles, et ont permis de proposer plusieurs nouvelles cibles candidates. / The identification of the interactions occurring at the molecular level is crucial to understand the life process. The aim of this work was to develop methods to model and to predict these interactions for the metabolism and the regulation of transcription. We modeled these systems by graphs and automata.Firstly, we developed a method to test and to predict the flux distribution in a metabolic network, which consider the formulation of several constraints. We showed that this method can better mimic the in vivo phenotype of the energy metabolism of the parasite Trypanosoma brucei. The results enabled to provide a good explanation of the metabolic flux flexibility, which were consistent with the experimental data. Secondly, we have considered a particular class of non-coding RNAs called sRNAs, which are involved in the regulation of the cellular response to environmental changes. We developed an approach to better predict their interactions with other RNAs based on the interaction prediction, an enrichment analysis, and by developing a visualization system adapted to the manipulation of these data. We applied our method to the study of the sRNAs interactions within the bacteria Escherichia coli. The predictions were in agreement with the available experimental data, and helped to propose several new target candidates.

Apresenta uma análise da estimação de custos em sistemas de manufatura utilizando rede de Petri (PN), ferramenta gráfica e matemática para modelagem e simulação. Esta análise permite a apresentação de um sistema aplicável à programação e otimização de processos de fabricação aliadas à estimação dos custos ao longo do processo. Para uma determinada peça, a partir de conceitos sobre custeio de produtos, é proposto um modelo que visa conectar as transições da PN com as informações de custos de produção. O estudo de caso mostra que informações importantes à tomada de decisão podem ser obtidas através do uso de uma metodologia que incorpore planejamento de processos, métodos de custeio e redes de Petri. Finalmente, traz sugestão de um trabalho subseqüente: a partir do modelo proposto, implementar um template no editor/simulador de redes de Petri, Petri Net Tools 2000, capaz de realizar os cálculos necessários para estimativas de custo e fornecer resultados relevantes para um planejamento real. / This work presents a cost estimation analysis in manufacturing systems based in Petri net (PN), which is a graphical and mathematical tool. This analysis allows the presentation of a system, applicable to the programming and optimizing of manufacturing processes joined with cost estimation. A cost model is proposed using concepts of product costing. It seeks for connecting PN transitions to the data manufacturing cost of a certain part. The case study shows that important information to decision support can be found through the use of a methodology which joins process planning, costing systems and Petri nets. There is also a suggestion of a later work: a template implementation, on Petri Net Tools 2000 editor/simulator of PN models, which is able to accomplish the necessary calculations for cost estimates and, to supply important results to a real planning.

Os sistemas de manufatura há muito vêm sendo objeto de interesse por profissionais e pesquisadores devido à busca de melhores técnicas visando o aumento da produtividade bem como pelo aumento da competitividade empresarial ao longo dos anos. Dentre seus componentes, o sistema de movimentação de materiais merece atenção especial pois, apesar de não aumentar o valor do produto, é responsável por manter o fluxo de materiais entre máquinas, células de manufatura, centros de custos ou mesmo entre empresas, que é imprescindível para qualquer sistema produtivo. Neste contexto, o presente trabalho propõe uma metodologia para a modelagem de sistemas flexíveis de movimentação de materiais e partes em ambiente fabril, focando-se em sistemas cuja movimentação possa ser realizada por VATs (Veículos Autônomos de Transporte). Considerando-se o sistema de movimentação de materiais como sendo um sistema a eventos discretos (SEDs), pode-se empregar técnicas derivadas das Redes de Petri como o PFS (Production Flow Schema) e o E-MFG (Enhanced Mark Flow Graph) na modelagem de tais sistemas. Para tanto, foram introduzidos conceitos de orientação a objetos ao E-MFG de forma a ampliar sua capacidade de modelagem, possibilitando a migração de um paradigma de modelagem orientada a processos para um de modelagem híbrida orientada a processos e a objetos. Como estudo de caso, apresenta-se a modelagem de uma simplificação do sistema de movimentação de materiais da Mercedes Benz do Brasil, situada em São Bernardo do Campo, São Paulo, para a qual se aplica a metodologia proposta. / Manufacturing systems have been object of interest of many professionals and researchers through the years due to the search of better methods for raising goods productivity and managerial competitiveness. Among its components, the material movement system deserves special attention because even not increasing the product value, it is responsible for keeping the flow of materials between machines, manufacturing cells, cost centers and also between companies, which is indispensable for any productive system. In this context, this work proposes a methodology for modeling flexible systems for materials and parts movement in the industrial environment, focusing on systems whose movement can be performed by AGVs (Autonomous Guided Vehicles). Considering the materials movement system as a Discrete Event System (DES), techniques derived from Petri Nets as PFS (Production Flow Schema) and E-MFG (Enhanced Mark Flow Graph) can be used for modeling those systems. To this purpose, concepts of object orientation are introduced to E-MFG in order to increase its modeling capacity, allowing the migration from the process oriented modeling paradigm to an hybrid object and process oriented modeling. A simplification of the materials movement system of the plant of "Mercedes Benz do Brasil", which is located in São Bernado do Campo, São Paulo, was used as a study case to illustrate the methodology presented.

A arquitetura IP Multimedia Subsystem, proposta pelo consórcio 3rd Generation Partnership Project como base para o suporte à convergência entre telefonia móvel e a Internet, define uma série de elementos arquiteturais, entre os quais, o componente Call Session Control Function e o protocolo Session Initiation Protocol. Session Initiation Protocol é um protocolo da camada de aplicação utilizado para estabelecer, modificar e terminar sessões multimídia entre dispositivos. Em redes baseadas na arquitetura IP Multimedia Subsystem, o Session Initiation Protocol é o responsável pela comunicação entre dispositivos e a rede, e entre os componentes responsáveis pelo gerenciamento de sessão. Nos últimos anos, estudos detectaram degradação de desempenho em redes baseadas na arquitetura IP Multimedia Subsystem em função das características centralizadas do Session Initiation Protocol e dos componentes de gerenciamento de sessão. Este trabalho apresenta uma arquitetura distribuída para redes baseadas em IP Multimedia Subsystem, tendo como fundamento o paradigma de computação paralela baseado em espaço de tuplas onde os servidores são organizados em uma rede P2P, com objetivo de prover uma infraestrutura escalável e tolerante a falhas. A validação da arquitetura em termos de desempenho e escalabilidade se deu através de modelagem formal e simulação com Redes de Petri Coloridas. / The IP Multimedia Subsystem architecture, proposed by the 3rd Generation Partnership Project consortium as basis to support the convergence between mobile networks and the Internet, defines a set of architectural elements, among them, the Call Session Control Function and the Session Initiation Protocol. The Session Initiation Protocol is an application layer protocol used to establish, modify and terminate sessions between devices. On the IP multimedia subsystem based network, the Session Initiation Protocol play a key role on the communication between devices and the network, and between session management components. In the last years, studies have detected a performance bottleneck on IP multimedia subsystem networks due to centralized characteristic of the Session Initiation Protocol and in Session Control components. This work shows a distributed architecture for IP Multimedia Subsystem networks based on the tuple space paradigm, and the servers structured in a P2P network, aiming to achieve a scalable and fault-tolerant infrastructure. The validation of the architecture on the performance and scalability took place through the Coloured Petri Net formal modeling and simulation.

O uso de técnicas e métodos formais contribui para o desenvolvimento de sistemas confiáveis. No entanto, apesar do rigor obtido, em geral, é necessário que essas técnicas sejam complementadas com atividades de teste e validação. Deve-se ressaltar que o custo para eliminar erros encontrados nas etapas iniciais de desenvolvimento é menor do que quando esses erros são encontrados nas fases posteriores. Dessa forma, é essencial a condução de atividades de VV&T - Verificação, Validação e Teste - desde as primeiras fases de desenvolvimento. Critérios de teste, como uma forma sistemática de avaliar e/ou gerar casos de teste de qualidade e, dessa forma, contribuir para aumentar a qualidade da atividade de teste, têm sido investigados para o teste de especificação de Sistemas Reativos. A técnica Redes de Petri Coloridas tem sido constantemente utilizada para a especificação do aspecto comportamental de Sistemas Reativos. Apesar de existirem diversas técnicas de análise, um aspecto não considerado é a cobertura alcançada, visto que, em geral, a aplicação exaustiva não é viável devido ao alto custo. Considerando a relevância do estabelecimento de métodos sistemáticos para o teste e validação dessas especificações, este trabalho propõe a aplicação do critério de teste Análise de Mutantes para o teste de Redes de Petri Coloridas. Neste trabalho foram almejados três objetivos principais, os quais podem ser divididos em estudos teóricos, estudos empíricos e automatização. No contexto de estudos teóricos, foi realizada a definição e embasamento teórico para possibilitar a aplicação da Análise de Mutantes no contexto de Redes de Petri Coloridas. Além disso, investigaram-se mecanismos genéricos para a descrição e geração de mutantes. Definiu-se um algoritmo para a geração de casos de teste baseado na Análise de Mutantes. No contexto de estudos empíricos, foram conduzidos estudos de caso para avaliar a aplicabilidade e eficácia dos resultados teóricos obtidos. Finalmente, no contexto de automatização, foram desenvolvidas ferramentas de apoio à aplicação da Análise de Mutantes. / The usage of formal methods and techniques contributes to the development of highly reliable system, but, in spite of the achieved rigour, these techniques must be complemented with testing and validation activities. It should be highlighted that the cost to eliminate errors found in the early phases of development is smaller than when those errors are found in the later phases. Therefore, the accomplishment of VV&T activities - Verification, Validation and Test - starting at the first development phases is essential. Testing criteria, as a systematic way to evaluate and/or generate test cases, contributing, therefore, to improve the quality of the test activity, have been proposed for testing reactive systems specifications. A technique that has been steadily employed for specifying the behavioural aspect of reactive systems is the coloured Petri nets. Although there are several analysis and validation techniques, a usually neglected aspect is the achieved coverage, given that, in general, the exhaustive application is not feasible due to its high cost. Considering the relevance of establishing systematic methods for the test and validation of coloured Petri nets based specification, this work proposes the investigation of the viability of applying Mutation Testing to test coloured Petri nets. In this work three main goals were pursued, which can be grouped in: theoretical studies, empirical studies and tool development. In the context of theoretical studies, it was accomplished the definition of theoretical concepts to enable the application of Mutant Analysis in the context of coloured Petri nets. Moreover, a mutation-based algorithm was defined to generate test sequences for Petri nets. In the context of empirical studies, case studies were carried out to evaluate the applicability and effectiveness of the achieved theoretical results. Finally, in the context of tool development, tools for supporting the application of Mutation Testing were developed.

In dieser Arbeit geht es um die schrittweise Verfeinerung verteilter Algorithmen. Dabei wird ein einfacher Algorithmus, der einige gewünschte Eigenschaften hat, Schritt für Schritt zu einem komplexen Algorithmus verfeinert, der konkrete Implementationsanforderungen erfüllt, so daß in jedem Schritt die gewünschten Eigenschaften erhalten bleiben. Wir stellen einen neuen eigenschaftserhaltenden Verfeinerungsbegriff vor, der auf der kausalen Ordnung der Aktionen eines Algorithmus basiert. Diesen Begriff definieren wir als Transitionsverfeinerung für elementare Petrinetze und diskutieren Beweiskriterien. Danach definieren und diskutieren wir die simultane Verfeinerung mehrerer Transitionen. Zur Modellierung komplexer verteilter Algorithmen sind elementare Petrinetze oft nicht adäquat. Wir benutzen deshalb algebraische Petrinetze. Wir definieren Transitionsverfeinerung für algebraische Petrinetze und stellen einen Zusammenhang zur simultanen Verfeinerung von Transitionen in elementaren Petrinetzen her. Transitionsverfeinerung ist besonders für Verfeinerungsschritte geeignet, in denen synchrone Kommunikation zwischen Agenten durch asynchronen Nachrichtenaustausch ersetzt wird. Wir zeigen dies am Beispiel eines komplexen verteilten Algorithmus, zur Berechnung des minimalen spannenden Baumes in einem gewichteten Graphen. Wir zeigen die Korrektheit dieses Algorithmus in mehreren Schritten, von denen einige Schritte Transitionsverfeinerungen sind. In anderen Schritten sind klassische Verfeinerungsbegriffe ausreichend. Wir übertragen deshalb auch einen klassischen Verfeinerungsbegriff in unser formales Modell. / The topic of this PhD thesis is the stepwise refinement of distributed algorithms. Stepwise refinement starts with a simple algorithm with certain desired properties. This algorithm is refined step by step such that the desired properties are preserved in each refinement step. The result is a complex distributed algorithm which satisfies concrete implementation requirements and which still has the desired properties. We propose a new property preserving notion of refinement which is based on the causal ordering of actions of an algorithm. We call this notion transition refinement and we define it first for elementary Petri nets. Furthermore, we discuss proof criteria. Then, we define and discuss the simultaneous refinement of several transitions. For modelling complex distributed algorithms, we use algebraic Petri nets instead of elementary Petri nets. We define transition refinement for algebraic Petri nets, and we show its relationship to simultaneous transition refinement in elementary Petri nets. Transition refinement is particularly suitable for refinement steps in which synchronous communication between agents is replaced by asynchronous message passing. We show this by means of a complex distributed algorithm for determining the minimal spanning tree of a weighted graph. We prove the correctness of this algorithm in several steps. Some of these steps are transition refinements. For other steps, well-known notions of refinement are sufficient. Therefore, we also carry over a well-known notion of refinement into our formal model.

La surveillance d'entrepôts de produits chimiques est une opération délicate dans le sens où elle passe par une connaissance de la nature de chaque produit stocké, sur leur localisation, sur leur possible interaction et sur les actions à mettre en oeuvre en cas d'alerte. Pour faciliter cette gestion de stockage, cette thèse propose d'utiliser le concept de l'ambiant où le produit possède son propre système d'information et de communication sans fil de façon à le rendre intelligent et autonome. Cette thèse propose et développe un modèle de comportement interne de produit actif permettant une approche distribuée de sécurité active. Celui-ci permet d'aboutir à un protocole de communication de niveau applicatif à embarquer dans les produits actifs. Ce protocole est évalué de façon formelle en utilisant les Réseaux de Petri colorés hiérarchiques. Finalement, ce protocole est implémenté dans le simulateur Castalia/Omnet++ pour l'analyser dans plusieurs scénarii et aussi pour l'éprouver lors du passage à l'échelle. Les résultats montrent l'intérêt et la faisabilité du concept de produit actif / Monitoring of chemical product storage is a delicate operation in the sense that it requires knowledge of the nature of each stored product, their location, their interaction and possible actions to be implemented in case of emergency. To facilitate the storage management, this thesis proposes to use the concept of ambient where the product has its own information system and wireless communication so as to make it intelligent and autonomous. This thesis proposes and develops a model of internal behavior of active product that allows a distributed approach of active security. This can lead to a communication protocol of application level to embed the active products. This protocol is formally assessed using hierarchical colored Petri nets. Finally, this protocol is implemented in the simulator Castalia/Omnet++ to analyze it in several scenarios and also for the experience when going to scale. The results show the usefulness and feasibility of the concept of active product

Ce mémoire, réalisé dans le cadre d’une thèse sous convention CIFRE avec la société Schneider-Electric et l’Université de Lorraine à travers le laboratoire du CRAN, porte sur l’évaluation des performances temporelles des architectures de contrôle-commande distribuées sur un réseau de communication. Le besoin industriel s’exprime sous la forme d’un outil d’aide au dimensionnement des architectures en phase d’avant-vente caractérisée par une connaissance partielle de ces dernières. Le problème scientifique sous-jacent est relatif à la génération automatique des modèles servant de support à l’évaluation. En effet, l’évaluation des performances doit être réalisée pour un ensemble important d’architectures, dans un temps court, difficilement compatible avec une construction manuelle des modèles. Notre contribution porte sur la définition formelle, à l’aide de réseaux de Petri colorés et temporisés, d’un modèle « constructeur » d’architectures embarquant des mécanismes de configuration, d’instanciation et de paramétrage. Plusieurs algorithmes sont proposés pour, d’une part, construire automatiquement le modèle d’une architecture donnée, à partir d’une description formelle de sa topologie et d’une librairie de modèles d’équipements de contrôle-commande, et, d’autre part, pour générer les observateurs requis à partir d’une description formelle des performances à évaluer. Ces différents algorithmes ont été implantés dans un outil interfacé, d’une part avec l’outil Schneider de description des architectures, et, d’autre part avec le simulateur de l’outil CPN Tools qui fournit une estimation des performances via des simulations de Monte-Carlo. L’intérêt de cette approche a été illustrée sur la base de quelques architectures types fournies par la société Schneider-Electric / This PhD dissertation, supported by CIFRE convention between the company Schneider-Electric and the University of Lorraine through the CRAN laboratory, deals with the assessment of temporal performances for a networked distributed control system. The industrial need was the development of a quotation and sizing tool of industrial control architecture during pre-sales stage. This stage is characterized by limited information about the process and the customers’ needs. The underlying scientific problematic was the ability to generate automatically models serving as support for the evaluation. In fact, performance assessment is realized for a wide range of architecture during a small amount of time, which is not compliant with a manual definition of the models. Our contribution is mainly based on a formal definition of a “builder” model with Colored and Timed Petri Nets which embeds mechanisms for configuration, instantiation and parameters setting of the architecture models. Several algorithms have been proposed for firstly build automatically the architecture Petri Nets model from a formal description of the topology and from a component model library and, secondly, for generating performance observers. Theses algorithms have been implemented on a tool gathering a user interface developed by Schneider –Electric and the Petri Nets simulator called CPN Tools which provides the performance assessment through Monte-Carlo simulation. The added value of this approach has been illustrated through case studies provided by Schneider-Electric

La méthodologie HILECOP a été élaborée pour la conception formelle de systèmes numériques complexes critiques ; elle couvre donc l'intégralité du processus, allant de la modélisation à la génération de code pour l’implantation sur la cible matérielle (composant électronique de type FPGA), en passant par la validation formelle. Or, si le modèle formel, les réseaux de Petri en l'occurrence, est par essence asynchrone, il est néanmoins exécuté de manière synchrone sur la cible. De fait, les approches d'analyse usuelles ne sont pas adaptées au sens où elles construisent des graphes d'états non conformes à l'évolution d'états réelle au sein de la cible. Dans l'objectif de gagner en confiance quant à la validité des résultats de l’analyse formelle, ces travaux visent à capturer les caractéristiques dites non-fonctionnelles, à les réifier sur le modèle et enfin à considérer leur impact à travers l’analyse. En d’autres termes, l’objectif est d’améliorer l’expressivité du modèle et la pertinence de l'analyse, en considérant des aspects comme la synchronisation d'horloge, le parallélisme effectif, le risque de blocage induit par l'expression conjointe d'un événement (condition) et d'une fenêtre temporelle d'occurrence, sans omettre la gestion des exceptions. Pour traiter tous ces aspects, nous avons proposé une nouvelle méthode d'analyse pour les réseaux de Petri temporels généralisés étendus interprétés exécutés en synchrone, en les transformant vers un formalisme équivalent analysable. Ce formalisme est associé avec une sémantique formelle intégrant toutes les aspects particuliers de l'exécution et un algorithme de construction d'un graphe d'états spécifique : le Graphe de Comportement Synchrone. Nos travaux ont été appliqués à un cas industriel, plus précisément à la validation du comportement de la partie numérique d'un neuro-stimulateur. / The HILECOP methodology has been developed for the formal design of critical complex digital systems; it therefore covers the entire design process, ranging from modeling to code generation for implementation on the hardware target (FPGA type electronic component), via formal validation. However, if the formal model, the Petri nets in this case, is inherently asynchronous, it is nevertheless executed synchronously on the target. In fact, the usual analysis approaches are not adapted in the sense that they construct state graphs that do not conform to the real state evolution within the target. In order to gain confidence in the validity of the results of the formal analysis, this work aims to capture the so-called non-functional characteristics, to reify them on the model and finally to consider their impact through the analysis.In other words, the aim is to improve the expressiveness of the model and the relevance of the analysis, considering aspects such as clock synchronization, effective parallelism, the risk of blocking induced by the expression of an event (condition) and a time window of occurrence, without omitting the management of exceptions.To deal with all these aspects, we have proposed a new method of analysis for extended generalized synchronous executed time Petri nets, transforming them into an analysable equivalent formalism. This formalism is associated with a formal semantics integrating all the particular aspects of the execution and dédicated state space construction algorithm: the Synchronous Behavior Graph.Our work has been applied to an industrial case, more precisely to the validation of the behavior of the digital part of a neuro-stimulator.

Os avanços tecnológicos das últimas décadas têm motivado o desenvolvimento dos edifícios inteligentes, visando à criação de ambientes mais confortáveis e seguros para os ocupantes, economicamente vantajosos para os proprietários e ambientalmente corretos. Considerando-se que nestes ambientes emergem novas formas de interação entre os usuários e os sistemas prediais, as quais não são adequadamente tratadas por técnicas convencionais de modelagem, torna-se necessário o estudo de novas soluções que abordem essas interações. Assim, este trabalho apresenta a proposta de uma abordagem sistemática para modelar e simular os sistemas de controle de edifícios inteligentes. Considera-se o sistema de controle como um sistema orientado por eventos discretos, no qual a comunicação entre os dispositivos que o constituem é realizada por meio da troca assíncrona de mensagens. Nesta abordagem, é utilizada a rede de Petri colorida para especificar as funcionalidades do edifício inteligente e a interação entre os dispositivos que constituem o seu sistema de controle. Assim, fornece-se um procedimento estruturado para desenvolver modelos que facilita a especificação do algoritmo de controle dos subsistemas do edifício inteligente. Para avaliar as principais características do procedimento proposto, foi apresentado um exemplo de aplicação que aborda a integração das funcionalidades de um sistema de telefonia distribuído e um sistema de vigilância predial. A abordagem de modelagem possibilitou a identificação das funcionalidades dos dispositivos inteligentes que integram o sistema de controle em diferentes níveis de abstração e as interações que ocorrem durante o seu funcionamento. A realização deste trabalho contribui para o aprimoramento de novas abordagens para o desenvolvimento de sistemas de controle com arquiteturas heterárquicas. Estes sistemas são constituídos por dispositivos inteligentes colaborativos, que possuem um elevado grau de autonomia. / Technological advances in recent decades have motivated the development of intelligent buildings, aimed at creating environments more productive for the occupants, economically advantageous for the owners and environmentally correct. New ways of interaction between users and the buildings systems are emerging from these kinds of systems, which are not adequately treated by conventional modeling techniques. In this sense, it is necessary the study of new approaches which address these new functionalities. Thus, this work presents a proposal for a systematic approach to model and simulate the control system of the intelligent buildings. The control system is considered to be a discrete event system, where the communication between the devices that integrate it is oriented by means of asynchronous messages exchange. This approach uses the colored Petri nets in order to specify the functionalities of the building system and their devices interactions. The approach provides a structured procedure to develop models that facilitate the algorithm specification of the control system. In order to verify the main characteristics of the proposed procedure, it is presented an example that is a control system that integrates a distributed telephony system and a surveillance building system. The approach proposed enabled the identification of the main functionalities and interactions of the intelligent devices constituting the control system. The achievement of this thesis contributes to the development of new approaches to develop heterarchical control system architectures. This kind of system architectures is constituted by collaborative intelligent devices that have a high degree of autonomy.