La certification des réseaux avioniques requiert une maîtrise des délais de transmission des données. Cepednant, le multiplexage et le partage des ressource de communications dans des réseaux tels que l'AFDX (Avionics Full Duplex Switched Ethernet) rendent difficile le calcul d'un délai de bout en bout pire cas pour chaque flux. Des outils comme le calcul réseau fournissent une borne supérieure (pessimiste) de ce délai pire cas. Les besoins de communication des avions civils modernes ne cessent d'augmenter et un nombre croissant de flux aux contraintes et aux caractéristiques différentes doivent partager les ressources existantes. Le réseau AFDX actuel ne permet pas de différentier plusieurs classes de trafic : les messages sont traités dans les files des commutateurs selon leur ordre d'arrivée (politique de service FIFO). L'objet de cette thèse est de montrer qu'il est possible de calculer des bornes pire cas des délais de bout en bout avec des politiques de service plus évoluées, à base de priorités statiques (Priority Queueing) ou à répartition équitable de service (Fair Queueing). Nous montrons comment l'approche par trajectoires, issue de la théorie de l'ordonnancement dans des systèmes asynchrones distribués peut s'appliquer au domaine de l'AFDX actuel et futur (intégration de politiques de service plus évoluées permettant la différentiation de flux). Nous comparons les performances de cette approche avec les outils de référence lorsque cela est possible et étudions le pessimisme des bornes ainsi obtenues. / The certification process for avionics network requires guaranties on data transmission delays. However, calculating the worst case delay can be complex in the case of industrial AFDX (Avionics Full Duplex Switched Ethernet) networks. Tools such as Network Calculus provide a pessimistic upper bound of this worst case delay. Communication needs of modern commercial aircraft are expanding and a growing number of flows with various constraints and characteristics must share already existing resources. Currently deployed AFDX networks do not differentiate multiple classes of traffic: messages are processed in their arrival order in the output ports of the switches (FIFO servicing policy). The purpose of this thesis is to show that it is possible to provide upper bounds of end to end transmission delays in networks that implement more advanced servicing policies, based on static priorities (Priority Queuing) or on fairness (Fair Queuing). We show how the trajectory approach, based on scheduling theory in asynchronous distributed systems can be applied to current and future AFDX networks (supporting advanced servicing policies with flow differentiation capabilities). We compare the performance of this approach with the reference tools whenever it is possible and we study the pessimism of the computed upper bounds.

The main theme of this thesis research is concerned with developing a computational pipeline for processing Next-generation RNA sequencing (RNA-seq) data. RNA-seq experiments generate tens of millions of short reads for each DNA/RNA sample. The alignment of a large volume of short reads to a reference genome is a key step in NGS data analysis. Although storing alignment information in the Sequence Alignment/Map (SAM) or Binary SAM (BAM) format is now standard, biomedical researchers still have difficulty accessing useful information. In order to assist biomedical researchers to conveniently access essential information from NGS data files in SAM/BAM format, we have developed a Graphical User Interface (GUI) software tool named SAMMate to pipeline human transcriptome quantification. SAMMate allows researchers to easily process NGS data files in SAM/BAM format and is compatible with both single-end and paired-end sequencing technologies. It also allows researchers to accurately calculate gene expression abundance scores.

In many practical problems, both decision and estimation are involved. This dissertation intends to study the relationship between decision and estimation in these problems, so that more accurate inference methods can be developed. Hybrid estimation is an important formulation that deals with state estimation and model structure identification simultaneously. Multiple-model (MM) methods are the most widelyused tool for hybrid estimation. A novel approach to predict the Internet end-to-end delay using MM methods is proposed. Based on preliminary analysis of the collected end-to-end delay data, we propose an off-line model set design procedure using vector quantization (VQ) and short-term time series analysis so that MM methods can be applied to predict on-line measurement data. Experimental results show that the proposed MM predictor outperforms two widely used adaptive filters in terms of prediction accuracy and robustness. Although hybrid estimation can identify model structure, it mainly focuses on the estimation part. When decision and estimation are of (nearly) equal importance, a joint solution is preferred. By noticing the resemblance, a new Bayes risk is generalized from those of decision and estimation, respectively. Based on this generalized Bayes risk, a novel, integrated solution to decision and estimation is introduced. Our study tries to give a more systematic view on the joint decision and estimation (JDE) problem, which we believe the work in various fields, such as target tracking, communications, time series modeling, will benefit greatly from. We apply this integrated Bayes solution to joint target tracking and classification, a very important topic in target inference, with simplified measurement models. The results of this new approach are compared with two conventional strategies. At last, a surveillance testbed is being built for such purposes as algorithm development and performance evaluation. We try to use the testbed to bridge the gap between theory and practice. In the dissertation, an overview as well as the architecture of the testbed is given and one case study is presented. The testbed is capable to serve the tasks with decision and/or estimation aspects, and is helpful for the development of the JDE algorithms.

O presente trabalho tem como principal objetivo estudar a influência da consultoria em iniciativas de Fuzzy Front End (FFE). Para tanto, conceituam-se os principais constructos que sustentam a análise, quais sejam: FFE, Nebulosidade, Modelo de Gestão de FFE e Modelo de Tomada de Decisão. Com o intuito de entender melhor o fenômeno em questão, o FFE, avalia-se, através de revisão bibliográfica, quais sãos os principais elementos capacitadores em gestão de FFE para os processos de inovação de produtos em empresas. Nesse sentido, foi elaborado um modelo de gestão FFE, com base em modelo preexistente, aprimorado com modelos de tomada de decisão. Foram empregados a metodologia de Estudo de Caso e o método de Extended Case Method, aplicado a consultorias que executam iniciativas de FFE em empresas clientes. A questão de pesquisa a ser respondida foi: Qual a influência das consultorias em iniciativas de FFE de empresas clientes? Foi construído também um modelo de geração de ideia para entender a gênese do surgimento da ideia em iniciativas de FFE. Da mesma forma, foi realizado o mapeamento do FFE dentro da ciência da administração, mostrando que o FFE deve ser entendido como o motor de geração e seleção de ideias para quaisquer tipos de mudança, e, para isso, recorreu-se à Teoria da Decisão, a fim de fazer a integração do FFE com os demais temas de ciências. Como resultado, este trabalho traz uma visão do FFE, verificando a aplicabilidade prática dos elementos capacitadores levantados na revisão da literatura; um modelo de gestão da dinâmica de interação e geração de competência entre consultorias e empresas clientes; bem como o reconhecimento do valor gerado pelas consultorias em iniciativas de FFE. / The main objective of this work is to study the influence of consulting on Fuzzy Front End initiatives (FFE). For this, the main constructs that support the analysis are: FFE, Fuzziness, FFE Management Model, Decision Making Model and Consulting. In order to better understand the phenomenon in question, the FFE, it is evaluated, through a bibliographic review, which are the main enablers in FFE management for the processes of product innovation in companies. In this sense, an FFE management model was elaborated, based on a preexisting model, improved with decision-making models. We used the Case Study methodology and the Extended Case Method, applied to consultancies that execute FFE initiatives in client companies. The research question is: What is the influence of consulting companies in FFE of client\'s enterprises? A model of idea generation was also designed to understand the genesis of the idea\'s emergence in FFE initiatives. In the same way, the mapping of the FFE within the science of administration was carried out, showing that the FFE should be understood as the engine of generation and selection of ideas for any type of change, and for this, we used Decision Theory, In order to integrate the FFE with other science subjects. As a result, this work brings a complete view of the FFE, verifying the practical applicability of the enablers in the literature; A management model of interaction dynamics and competence generation between consultancies and client companies; as well as the recognition of the value generated by consultancies in FFE initiatives.

Dans cette thèse, nous proposons une nouvelle approche pour modéliser et estimer les délais de bout-en-bout dans les réseaux de capteurs sans-fil (WSN). Notre approche combine les approches analytiques et expérimentales pour inférer un modèle Markovien modélisant le comportement d'un protocole de contrôle d'accès au médium (MAC) exécuté sur les nœuds d'un réseau de capteurs. À partir de ce modèle Markovien, le délai de bout en bout est ensuite obtenu par une approche analytique basée sur une analyse dans le domaine fréquentiel pour calculer la probabilité de distribution de délais pour un taux d'arrivée spécifique. Afin d’obtenir une estimation du délai de bout en bout, indépendamment du trafic en entrée, la technique de régression non-linéaire est utilisée sur un ensemble d’échantillons limités. Cette approche nous a permis de contourner deux problèmes: 1) la difficulté d'obtenir un modèle Markovien du comportement d’un protocole MAC en tenant compte de son implémentation réelle, 2) l'estimation du délai de bout-en-bout d’un WSN multi-sauts. L'approche a été validée sur un testbed réel (IOT-LAB) et pour plusieurs protocoles (X-MAC, ContikiMAC, IEEE 802.15.4) ainsi que pour un protocole de routage (RPL). / In this thesis, we propose an approach that combines both measurements and analytical approaches for infering a Markov chain model from the MAC protocol execution traces in order to be able to estimate the end to end delay in multi-hop transmission scenarios. This approach allows capturing the main features of WSN. Hence, a suitable Markov chain for modelling the WSN is infered. By means of an approach based on frequency domain analysis, end to end delay distribution for multi-hop scenarios is found. This is an important contribution of our approach with regard to existing analytical approaches where the extension of these models for considering multi-hop scenarios is not possible due to the fact that the arrival distribution to intermediate nodes is not known. Since local delay distribution for each node is obtained by analysing the MAC protocol execution traces for a given traffic scenario, the obtained model (and therefore, the whole end to end delay distribution) is traffic-dependant. In order to overcome this problem, we have proposed an approach based on non-linear regression techniques for generalising our approach in terms of the traffic rate. Results were validated for different MAC protocols (X-MAC, ContikiMAC, IEEE 802.15.4) as well as a well-known routing protocol (RPL) over real test-beds (IOT-LAB).

Product-service systems (PSS), defined as a system of products, services, infrastructure, and networks that aims to satisfy customer needs, support business innovation and has the potential to lead to improved environmental performance. The adoption of PSS requires modifications in the business model of companies or even the creation of new ones. The decision to modify or create business models occurs in the fuzzy front-end through the development of proposals. In this sense, the creation of PSS proposals might assist the adoption of PSS business models in enterprises. However, companies still need support to adopt PSS business models due to three main reasons. First, most of the studies about PSS business models mention its importance but do not explore which content should compose such models. Second, PSS business models are explored considering a partial view of business model dimensions. Finally, there is a lack of methods and tools that support the adoption of PSS business models in the fuzzy front-end. Thereby, the aim of this study is to develop a method, named Configurator of PSS Proposals, to cope with these challenges and assist the creation of PSS proposals for current or new business models. By means of systematic literature review, consulting with experts and an explorative case study, the method was developed. It is composed by eight steps and each step addresses a business model dimension, e.g. value proposition. The steps encompass a range of tasks that must be performed in order to create a PSS proposal. To support carrying out the tasks, a help element is available. This help contains additional information to support the utilization of the method, such as: examples of companies that adopted PSS and hints of practices, methods and tools. To evaluate the method, it was applied through a case study in the context of a research project. The aim was to create a PSS proposal for a bicycle concept and verify whether the method reach its purpose, i.e. is able to support the creation of a PSS proposal. Final considerations include contributions and limitations of this study. An example of contribution of the method is provision of a shared knowledge about PSS between different areas of expertise. As limitation, the lack of application of the method in a real case is highlighted. Additionally, future research is addressed based mainly on the insights gathered in the second case study, e.g. the inclusion of new tasks and relations between them. / Sistema produto-serviço (SPS), definido como um sistema de produtos e serviços, infraestrutura e networks e que visa aumentar a satisfação de clientes, auxilia na inovação nos negócios e tem o potencial de levar à melhoria de desempenho ambiental. A adoção de SPS requer a criação ou modificação dos modelos de negócios das empresas. A decisão de criar ou modificar um modelo de negócio ocorre no fuzzy front-end por meio da criação de propostas. Desta forma, acredita-se que criação de propostas para SPS auxilia na adoção de modelos de negócio para SPS. No entanto, empresas requerem auxilio na adoção de modelos de negócio para PSS devido a três principais motivos. Primeiro, a maioria dos estudos sobre modelos de negócio para SPS mencionam sua importância, porém não exploram o conteúdo que deve compor esses modelos. Segundo, pesquisas sobre modelos de negócio para SPS levam em consideração uma visão parcial das dimensões de modelos de negócio. Finalmente, é constatada a carência de métodos e ferramentas que auxiliem na adoção de modelos de negócio para PSS no fuzzy front-end. O objetivo desse trabalho é desenvolver um método, denominado Configurador de Propostas de SPS, que guie empresas na criação de propostas de SPS para negócios novos e existentes. Por meio de revisão sistemática de literatura, consulta com especialistas e um estudo de caso exploratório, o método foi desenvolvido. Ele é composto por oito passos e cada passo aborda uma dimensão do modelo de negócios, como por exemplo, proposição de valor. Ainda, cada passo engloba várias tarefas que devem ser executadas para que a proposta de SPS seja criada. Como suporte para realizar as tarefas, um elemento ajuda foi criado. Este elemento inclui exemplos de empresas que adotaram SPS e dicas de práticas, métodos e ferramentas. Com objetivo de avaliar o método, uma aplicação no contexto de um projeto de pesquisa foi realizada, por meio de um estudo de caso. O objetivo dessa aplicação foi criar uma proposta de SPS para um conceito de uma bicicleta e verificar se o método alcança seu propósito, que é ajudar na criação de propostas de SPS. Considerações finais incluem contribuições e limitações do estudo. Um exemplo de contribuição do método é o fornecimento de um conhecimento compartilhado sobre PSS entre diferentes áreas de conhecimento. A falta de aplicação do método em um caso real é uma das limitações deste trabalho. Adicionalmente, pesquisas futuras são sugeridas, como por exemplo, a inclusão de novas tarefas no método e novas relações entre elas, conforme sugerido pelos participantes do segundo estudo de caso.

Product-service systems (PSS), defined as a system of products, services, infrastructure, and networks that aims to satisfy customer needs, support business innovation and has the potential to lead to improved environmental performance. The adoption of PSS requires modifications in the business model of companies or even the creation of new ones. The decision to modify or create business models occurs in the fuzzy front-end through the development of proposals. In this sense, the creation of PSS proposals might assist the adoption of PSS business models in enterprises. However, companies still need support to adopt PSS business models due to three main reasons. First, most of the studies about PSS business models mention its importance but do not explore which content should compose such models. Second, PSS business models are explored considering a partial view of business model dimensions. Finally, there is a lack of methods and tools that support the adoption of PSS business models in the fuzzy front-end. Thereby, the aim of this study is to develop a method, named Configurator of PSS Proposals, to cope with these challenges and assist the creation of PSS proposals for current or new business models. By means of systematic literature review, consulting with experts and an explorative case study, the method was developed. It is composed by eight steps and each step addresses a business model dimension, e.g. value proposition. The steps encompass a range of tasks that must be performed in order to create a PSS proposal. To support carrying out the tasks, a help element is available. This help contains additional information to support the utilization of the method, such as: examples of companies that adopted PSS and hints of practices, methods and tools. To evaluate the method, it was applied through a case study in the context of a research project. The aim was to create a PSS proposal for a bicycle concept and verify whether the method reach its purpose, i.e. is able to support the creation of a PSS proposal. Final considerations include contributions and limitations of this study. An example of contribution of the method is provision of a shared knowledge about PSS between different areas of expertise. As limitation, the lack of application of the method in a real case is highlighted. Additionally, future research is addressed based mainly on the insights gathered in the second case study, e.g. the inclusion of new tasks and relations between them. / Sistema produto-serviço (SPS), definido como um sistema de produtos e serviços, infraestrutura e networks e que visa aumentar a satisfação de clientes, auxilia na inovação nos negócios e tem o potencial de levar à melhoria de desempenho ambiental. A adoção de SPS requer a criação ou modificação dos modelos de negócios das empresas. A decisão de criar ou modificar um modelo de negócio ocorre no fuzzy front-end por meio da criação de propostas. Desta forma, acredita-se que criação de propostas para SPS auxilia na adoção de modelos de negócio para SPS. No entanto, empresas requerem auxilio na adoção de modelos de negócio para PSS devido a três principais motivos. Primeiro, a maioria dos estudos sobre modelos de negócio para SPS mencionam sua importância, porém não exploram o conteúdo que deve compor esses modelos. Segundo, pesquisas sobre modelos de negócio para SPS levam em consideração uma visão parcial das dimensões de modelos de negócio. Finalmente, é constatada a carência de métodos e ferramentas que auxiliem na adoção de modelos de negócio para PSS no fuzzy front-end. O objetivo desse trabalho é desenvolver um método, denominado Configurador de Propostas de SPS, que guie empresas na criação de propostas de SPS para negócios novos e existentes. Por meio de revisão sistemática de literatura, consulta com especialistas e um estudo de caso exploratório, o método foi desenvolvido. Ele é composto por oito passos e cada passo aborda uma dimensão do modelo de negócios, como por exemplo, proposição de valor. Ainda, cada passo engloba várias tarefas que devem ser executadas para que a proposta de SPS seja criada. Como suporte para realizar as tarefas, um elemento ajuda foi criado. Este elemento inclui exemplos de empresas que adotaram SPS e dicas de práticas, métodos e ferramentas. Com objetivo de avaliar o método, uma aplicação no contexto de um projeto de pesquisa foi realizada, por meio de um estudo de caso. O objetivo dessa aplicação foi criar uma proposta de SPS para um conceito de uma bicicleta e verificar se o método alcança seu propósito, que é ajudar na criação de propostas de SPS. Considerações finais incluem contribuições e limitações do estudo. Um exemplo de contribuição do método é o fornecimento de um conhecimento compartilhado sobre PSS entre diferentes áreas de conhecimento. A falta de aplicação do método em um caso real é uma das limitações deste trabalho. Adicionalmente, pesquisas futuras são sugeridas, como por exemplo, a inclusão de novas tarefas no método e novas relações entre elas, conforme sugerido pelos participantes do segundo estudo de caso.

Ce travail porte sur l'étude de faisabilité d'une architecture radio, dédiée aux applications WPANs nomades et faible consommation en utilisant la bande autour de 60 GHz. Des débits de l'ordre de Gbps, une compacité élevée et une consommation de puissance faible sont obtenus en réalisant une conception conjointe front-end antenne. Avant de proposer l'architecture adaptée au cahier de charge, une étude préalable du canal de propagation à 60 GHz est faite. Les deux principales normes de canal IEEE, le 802.15.3c et le 802.11.ad, sont étudiées. L'analyse d'une architecture impulsionnelle mono-bande adaptée aux systèmes à faible consommation montre une limitation du débit quand des antennes non directives sont utilisées dans la norme de canal 802.11.ad. Afin de remédier à ce problème, une architecture multi-bande impulsionnelle MBOOK à récepteur non-cohérent est proposée. Cette architecture autorise un haut débit avec l'utilisation de quatre sous bandes. Elle conduit également à une consommation faible grâce à l'utilisation d'un récepteur non-cohérent et d'une topologie différentielle de l'émetteur évitant l'intégration de combineurs. Pour valider le concept d'architecture proposée, des antennes différentielles dédiées à l'architecture différentielle sont conçues. Les premières antennes sont de type patch différentiel excité par des lignes microrubans. Ces dernières présentent des caractéristiques de rayonnement adaptées aux besoins du cahier de charge. Néanmoins elles occupent une surface importante. Afin d'avoir une meilleure compacité, un patch alimenté par couplage à fente est développé. Il exploite deux polarisations linéaires orthogonales excitées par une paire d'entrées différentielles. Afin d'obtenir la directivité élevée nécessaire pour les scénarios LOS à 60 GHz sans utiliser de réseaux d'antennes ou de lentilles diélectriques, des métamatériaux sont utilisés. La mesure des antennes est basée sur la réalisation d'une transition guide d'onde WR-15 ligne microruban pour connecter l'antenne à l'analyseur de réseau. La mesure de l'antenne patch différentielle présente une bonne concordance avec les résultats de simulations. La technologie TQP15 de TriQuint est utilisée pour concevoir les différents éléments de la partie front-end. L'évaluation de la consommation globale d'émetteur valide l'architecture proposée en termes de faible consommation. Ce travail se termine par une évaluation du débit du système en tenant en compte de l'influence de l'antenne et du canal de propagation. Cette évaluation prouve la potentialité de l'architecture en termes de haut débit. On propose finalement une technique basée sur la technologie LTCC pour l'assemblage antenne/front-end / This work deals with the feasibility study of a radio architecture dedicated to mobile WPAN applications at 60 GHz and characterized by a low power consumption. Data rates of the order of Gbps, high compactness and low power consumption are obtained by co-designing the antenna and the front-end. Before proposing the architecture matching the specification needs, a preliminary study of the propagation channel at 60 GHz is made. The two main standards IEEE 802.15.3c and 802.11.ad the channel are studied. The analysis of a single-band architecture suitable for low-power systems shows a data rate limitation when directional antennas are used in the standard channel 802.11.ad. To address this problem, a multi-band impulse architecture MBOOK using a non-coherent receiver is proposed. This architecture allows high throughput with the use of four sub-bands. It also leads to a low power consumption through the use of a non-coherent receiver and a differential transmitter topology avoiding combiners. To validate the concept of the proposed architecture, differential antennas dedicated to the differential architecture are designed. Patch antennas excited by differential microstrip lines fulfil the needs of the specifications but occupy a large area. In order to miniaturize the antenna, slot-fed patch antennas are designed using two orthogonal linear polarizations excited by a pair of differential inputs. To achieve the high directivity required in LOS scenarios without using antenna arrays or dielectric lenses, metamaterials are used. The antenna measurement is based on the realization of a WR-15 waveguide-to-microstrip line transition to connect the antenna to the network analyzer. The differential measurement of the antenna patch exhibits a good agreement with the simulated results. The TriQuint's TQP15 technology is used to design the various circuits of the front-end. The emitter architecture is validated once the overall consumption has been evaluated. This work ends with an evaluation of the throughput of the system taking into account the influence of the antenna and the propagation channel. This evaluation shows the potential of the architecture in terms of high throughput. We finally propose an approach based on the LTCC technology for the antenna / front-end assembly

Ce travail représente une contribution originale à la méthodologie pour le développement de modèles écosystémiques ainsi qu'une première tentative d'une modélisation end-to-end (E2E) de l'écosystème du Courant de Humboldt Nord (ECHN). L'objectif principal du modèle développé dans cette thèse est de construire un outil de gestion écosystémique et d'aide à la décision; raison pour laquelle la crédibilité du modèle est essentielle, laquelle peut-être établie par confrontation aux données. En outre, le ECHN présente une grande variabilité climatique et océanographique à différentes échelles, la source principale de variation inter-annuelle étant l'interruption du cycle d'upwelling saisonnier par l'Oscillation Australe du phénomène El Niño qui a un effet direct sur la survie larvaire et le succès de recrutement des poissons. La pêche peut aussi être fortement variable, en fonction de l'abondance et de l'accessibilité des principales ressources halieutiques. Ce contexte amène deux questions méthodologiques principales que nous explorons dans cette thèse à travers le développement d'un modèle E2E qui couple le modèle OSMOSE, pour la partie haut niveau trophique, au modèle ROMS-PISCES, pour les parties hydrodynamique et biogéochimie:(i) Comment calibrer un modèle écosystémique à partir de séries temporelles de données? (ii) Comment inclure l'impact de la variabilité inter-annuelle de l'environnement et de la pêche? En premier lieu, cette thèse met en évidence plusieurs problèmes liés à la confrontation de modèles écosystémiques complexes aux données et propose une méthodologie pour une calibration séquentielle en plusieurs phases des modèles écosystémiques. Nous proposons deux critères pour classer les paramètres d'un modèle: la dépendance au modèle et la variabilité temporelle des paramètres. A partir de ces critères, et en tenant compte de l'existence d'estimations initiales, on énonce des règles qui permettent de déterminer quels paramètres doivent être estimés, et dans quel ordre, dans le processus de calibration séquentiel. De plus, un nouvel Algorithme Évolutionnaire, conçu pour la calibration de modèles stochastiques et optimisé pour l'estimation du maximum de vraisemblance, a été développé et utilisé pour la calibration du modèle OSMOSE avec des séries temporelles de données.La variabilité environnementale est explicite dans le modèle: le modèle ROMS-PISCES force le modèle OSMOSE et propage les effets bottom-up potentiels dans le réseau trophique à travers les interactions trophiques entre plancton et poisson d'une part, et les changements dans la distribution spatiale du poisson d'autre part. Cette dynamique spatiale des poissons est prise en compte par l'utilisation de modèles de distribution des espèces de type présence/absence, qui sont en général évalués grâce à une matrice de confusion et les indicateurs statistiques qui lui sont associés. Toutefois, quand on considère la prédiction d'un habitat au cours du temps, la variabilité de la distribution spatiale des habitats peut être résumée de manière complémentaire et validée en utilisant les patrons émergents de la forme des distributions spatiales. Nous avons modélisé l'habitat potentiel des principales espèces du ECHN en utilisant plusieurs sources d'information (pêches commerciales, campagnes scientifiques et suivi satellite des navires de pêche) conjointement aux données environnementales issues d'observations satellites et in-situ, de 1992 à 2008. L'habitat potentiel est estimé sur cette période d'étude avec une résolution mensuelle, et le modèle est validé à partir d'informations du système, en utilisant une approche pattern-oriented.Le modèle écosystémique E2E ROMS-PISCES-OSMOSE pour le ECHN est calibré en une approche par maximum de vraisemblance pour ajuster des séries temporelles mensuelles de 1992 à 2008. En conclusion,quelques applications potentielles du modèle pour la gestion des pêches sont présentées et nous discutons leurs limitations et les perspectives. / This work represents an original contribution to the methodology for ecosystem models' development as well as the first attempt of an end-to-end (E2E) model for the Northern Humboldt Current Ecosystem (NHCE). The main purpose of the developed model is to build a tool for ecosystem-based management and decision making, reason why the credibility of the model is essential, and this can be assessed through confrontation to data. Additionally, the NHCE exhibits a high climatic and oceanographic variability at several scales, the major source of interannual variability being the interruption of the upwelling seasonality by the El Nino Southern Oscillation, which has direct effects on larval survival and fish recruitment success. Fishing activity can also be highly variable, depending on the abundance and accessibility of the main fishery resources. This context brings the two main methodological questions addressed in this thesis, through the development of an end-to-end model coupling the high trophic level model OSMOSE to the hydrodynamics and biogeochemical model ROMS-PISCES: i) how to calibrate ecosystem models using time series data and ii) how to incorporate the impact of the interannual variability of the environment and fishing.First, this thesis highlights some issues related to the confrontation of complex ecosystem models to data and proposes a methodology for a sequential multi-phases calibration of ecosystem models. We propose two criteria to classify the parameters of a model: the model dependency and the time variability of the parameters. Then, these criteria along with the availability of approximate initial estimates are used as decision rules to determine which parameters need to be estimated, and their precedence order in the sequential calibration process. Additionally, a new Evolutionary Algorithm designed for the calibration of stochastic models (e.g Individual Based Model) and optimized for maximum likelihood estimation has been developed and applied to the calibration of the OSMOSE model to data time series.The environmental variability is explicit in the model: the ROMS-PISCES model forces the OSMOSE model and drives potential bottom-up effects up the foodweb through plankton and fish trophic interactions, as well as through changes in the spatial distribution of fish. The latter effect was taken into account using presence/absence species distribution models which are traditionally assessed through a confusion matrix and the statistical metrics associated to it. However, when considering the prediction of the habitat against time, the variability in the spatial distribution of the habitat can be summarized and validated using the emerging patterns from the shape of the spatial distributions. We modeled the potential habitat of the main species of the Humboldt Current Ecosystem using several sources of information (fisheries, scientific surveys and satellite monitoring of vessels) jointly with environmental data from remote sensing and in situ observations, from 1992 to 2008. The potential habitat was predicted over the study period with monthly resolution, and the model was validated using quantitative and qualitative information of the system using a pattern oriented approach.The final ROMS-PISCES-OSMOSE E2E ecosystem model for the NHCE was calibrated using our evolutionary algorithm and a likelihood approach to fit monthly time series data of landings, abundance indices and catch at length distributions from 1992 to 2008. To conclude, some applications of the model for fishery management are presented and their limitations and perspectives discussed.

This dissertation research attempts to explore efficient algorithms and engineering methodologies of analyzing the overall reliability and availability of networks integrated with software failures and hardware failures. Node failures, link failures, and software failures are concurrently and dynamically considered in networks with complex topologies. MORIN (MOdeling Reliability for Integrated Networks) method is proposed and discussed as an approach for analyzing reliability of integrated networks. A Simplified Availability Modeling Tool (SAMOT) is developed and introduced to evaluate and analyze the availability of networks consisting of software and hardware component systems with architectural redundancy. In this dissertation, relevant research efforts in analyzing network reliability and availability are reviewed and discussed, experimental data results of proposed MORIN methodology and SAMOT application are provided, and recommendations for future researches in the network reliability study are summarized as well.