La génomique comparée est essentiellement une forme de fouille de données dans des grandes collections de relations n-aires. La croissance du nombre de génomes sequencés créé un stress sur la génomique comparée qui croit, au pire géométriquement, avec la croissance en données de séquence. Aujourd'hui même des laboratoires de taille modeste obtient, de façon routine, plusieurs génomes à la fois - et comme des grands consortia attend de pouvoir réaliser des analyses tout-contre-tout dans le cadre de ses stratégies multi-génomes. Afin d'adresser les besoins à tous niveaux il est nécessaire de repenser les cadres algorithmiques et les technologies de stockage de données utilisés pour la génomique comparée. Pour répondre à ces défis de mise à l'échelle, dans cette thèse nous développons des méthodes originales basées sur les technologies NoSQL et MapReduce. À partir d'une caractérisation des sorts de données utilisés en génomique comparée et d'une étude des utilisations typiques, nous définissons un formalisme pour le Big Data en génomique, l'implémentons dans la plateforme NoSQL Cassandra, et évaluons sa performance. Ensuite, à partir de deux analyses globales très différentes en génomique comparée, nous définissons deux stratégies pour adapter ces applications au paradigme MapReduce et dérivons de nouveaux algorithmes. Pour le premier, l'identification d'événements de fusion et de fission de gènes au sein d'une phylogénie, nous reformulons le problème sous forme d'un parcours en parallèle borné qui évite la latence d'algorithmes de graphe. Pour le second, le clustering consensus utilisé pour identifier des familles de protéines, nous définissons une procédure d'échantillonnage itérative qui converge rapidement vers le résultat global voulu. Pour chacun de ces deux algorithmes, nous l'implémentons dans la plateforme MapReduce Hadoop, et évaluons leurs performances. Cette performance est compétitive et passe à l'échelle beaucoup mieux que les algorithmes existants, mais exige un effort particulier (et futur) pour inventer les algorithmes spécifiques. / Comparative genomics is essentially a form of data mining in large collections of n-ary relations between genomic elements. Increases in the number of sequenced genomes create a stress on comparative genomics that grows, at worse geometrically, for every increase in sequence data. Even modestly-sized labs now routinely obtain several genomes at a time, and like large consortiums expect to be able to perform all-against-all analyses as part of these new multi-genome strategies. In order to address the needs at all levels it is necessary to rethink the algorithmic frameworks and data storage technologies used for comparative genomics.To meet these challenges of scale, in this thesis we develop novel methods based on NoSQL and MapReduce technologies. Using a characterization of the kinds of data used in comparative genomics, and a study of usage patterns for their analysis, we define a practical formalism for genomic Big Data, implement it using the Cassandra NoSQL platform, and evaluate its performance. Furthermore, using two quite different global analyses in comparative genomics, we define two strategies for adapting these applications to the MapReduce paradigm and derive new algorithms. For the first, identifying gene fusion and fission events in phylogenies, we reformulate the problem as a bounded parallel traversal that avoids high-latency graph-based algorithms. For the second, consensus clustering to identify protein families, we define an iterative sampling procedure that quickly converges to the desired global result. For both of these new algorithms, we implement each in the Hadoop MapReduce platform, and evaluate their performance. The performance is competitive and scales much better than existing solutions, but requires particular (and future) effort in devising specific algorithms.

Master of Science / Department of Computing and Information Sciences / Daniel A. Andresen / Recently, the world has been trending toward the use of Smartphone. Today, almost each and every individual is using Smartphone for various purposes benefited by the availability of large number of applications. The memory on the SD (Secure Digital) memory card is going to be a constraint for the usage of the Smartphone for the user. Memory is used for storing large amounts of data, which include various files and important document. Besides having many applications to fill the free space, we hardly have an application that manages the free memory according to the user’s choice. In order to manage the free space on the SD card, we need an application to be developed. All the important files stored on the Android device cannot be retrieved if we lose the Android device. Targeting the problem of handling the memory issues, we developed an application that can be used to provide the security to the important documents and also store unnecessary files on the distributed file servers and retrieve them back on request.

[pt] Infra-estruturas de suporte a sistemas baseados em componentes de software tipicamente incluem facilidades para instalação, execução e configuração dinâmica das dependências dos componentes de um sistema. Tais facilidades são especialmente importantes quando os componentes do sistema executam em um ambiente distribuído. Neste trabalho, investigamos alguns dos problemas que precisam ser tratados por infra-estruturas de execução de sistemas distribuídos baseados em componentes de software. Para realizar tal investigação, desenvolvemos um conjunto de servi¸cos para o middleware OpenBus, com o intuito de prover facilidades para a execução de aplicações distribuídas. Para ilustrar e avaliar o uso dos serviços desenvolvidos, apresentamos alguns exemplos onde a infra-estrutura é utilizada para executar cenários de teste de uma aplicação distribuída. / [en] Support infrastructures for component-based software systems usually include facilities for installation, execution and dynamic configuration of the system component`s dependencies. Such facilities are specially important when those system components execute in a distributed environment. In this work, we investigate some of the problems that must be handled by runtime infrastructures for distributed systems based on software components. To perform such investigation, we developed a set of services for the OpenBus middleware, aiming to provide facilities for execution of distributed applications. To illustrate and evaluate the use of the developed services, we present some examples where the infrastructure is used for executing test scenarios of a distributed application.

This dissertation considers three related problems in distributed transmission and reception networks. Generally speaking, these types of networks have a transmit cluster with one or more transmit nodes and a receive cluster with one or more receive nodes. Nodes within a given cluster can communicate with each other using a wired or wireless local area network (LAN/WLAN). The overarching goal in this setting is typically to increase the efficiency of communication between the transmit and receive clusters through techniques such as distributed transmit beamforming, distributed reception, or other distributed versions of multi-input multi-output (MIMO) communication. More recently, the problem of wireless power transfer has also been considered in this setting. The first problem considered by this dissertation relates to distributed reception in a setting with a single transmit node and multiple receive nodes. Since exchanging lightly quantized versions of in-phase and quadrature samples results in high throughput requirements on the receive LAN/WLAN, previous work has considered an approach where nodes exchange hard decisions, along with channel magnitudes, to facilitate combining similar to an ideal receive beamformer. It has been shown that this approach leads to a small loss in SNR performance, with large reductions in required LAN/WLAN throughput. A shortcoming of this work, however, is that all of the prior work has assumed that each receive node has a perfect estimation of its channel to the transmitter. To address this shortcoming, the first part of this dissertation investigates the effect of channel estimation error on the SNR performance of distributed reception. Analytical expressions for these effects are obtained for two different modulation schemes, M-PSK and M2-QAM. The analysis shows the somewhat surprising result that channel estimation error causes the same amount of performance degradation in ideal beamforming and pseudo-beamforming systems despite the fact that the channel estimation errors manifests themselves quite differently in both systems. The second problem considered in this dissertation is related to oscillator stability and phase noise modeling. In distributed transmission systems with multiple transmitters in the transmit cluster, synchronization requirements are typically very strict, e.g., on the order of one picosecond, to maintain radio frequency phase alignment across transmitters. Therefore, being able to accurately model the behavior of the oscillators and their phase noise responses is of high importance. Previous approaches have typically relied on a two-state model, but this model is often not sufficiently rich to model low-cost oscillators. This dissertation develops a new three-state oscillator model and a method for estimating the parameters of this model from experimental data. Experimental results show that the proposed model provides up to 3 dB improvement in mean squared error (MSE) performance with respect to a two-state model. The last part of this work is dedicated to the problem of wireless power transfer in a setting with multiple nodes in the transmit cluster and multiple nodes in the receive cluster. The problem is to align the phases of the transmitters to achieve a certain power distribution across the nodes in the receive cluster. To find optimum transmit phases, we consider a iterative approach, similar to the prior work on one-bit feedback for distributed beamforming, in which each receive node sends a one-bit feedback to the transmit cluster indicating if the received power in that time slot for that node is increased. The transmitters then update their phases based on the feedback. What makes this problem particularly interesting is that, unlike the prior work on one-bit feedback for distributed beamforming, this is a multi-objective optimization problem where not every receive node can receive maximum power from the transmit array. Three different phase update decision rules, each based on the one-bit feedback signals, are analyzed. The effect of array sparsity is also investigated in this setting.

O presente trabalho propõe uma arquitetura de utilização de Data Warehouses em computadores móveis, descreve os componentes desta arquitetura (dados e processos) que permite o sincronismo dos dados baseado em metadados e limitado ao escopo de acesso de cada usuário. As estruturas de dados e os processos que compõem a arquitetura proposta são reduzidos a problemas conhecidos e já solucionados, justificando sua viabilidade. Além disso, o presente trabalho também fornece diretrizes para avaliar a complexidade e o impacto causados por alterações de esquema no Data Warehouse central que devem ser refletidas nos data marts localizados nas plataformas móveis. A avaliação da complexidade e impacto das alterações nos esquemas do Data Warehouse pode auxiliar os administradores do ambiente a planejar a implementação destas alterações, propondo melhores alternativas no caso de alterações de esquema mais complexas e que causem um impacto maior no ambiente. A importância do trabalho está relacionada a casos reais de necessidade de evolução nas bases de dados analíticas (Data Warehouse) em computadores móveis, nos quais os usuários mantêm seu próprio subconjunto de dados do Data Warehouse para apoiar os processos de negócios. / This work presents an architecture for using Data Warehouses in mobile computers and describes the architecture components (data and processes) that allow the data synchronism based on metadata and restricted to the scope of access for each user. The data structures and the processes composing the architecture are reduced to already known and solved problems, justifying its feasibility. Besides, this work also provides the guidelines to evaluate the complexity and impact caused by changes of schema in the central Data Warehouse that must be reflected in the data marts located in the mobile platforms. The analysis of the complexity and impact of the changes made to the schemas may help environment administrators to plan these changes and propose better alternatives when dealing with more complex schema changes causing a greater impact on the environment. The relevance of this work is related to real cases that require evolution of analytical databases (Data Warehouse) in mobile computers in which the users keep their own subset of Data Warehouse information to support their business processes.

Este trabalho apresenta um modelo de dinâmica de desenvolvimento distribuído de software, cujo objetivo é representar a realidade e os aspectos de ambientes de DDS (Desenvolvimento distribuído de software), a fim de torná-los observáveis e descritíveis qualitativa e quantitativamente. Um modelo preliminar foi elaborado a partir da revisão bibliográfica e de um caso de experimentação desenvolvido por LErario et al (2004). Para a construção e validação deste modelo, a metodologia de estudo de múltiplos casos foi aplicada em diversas organizações que desenvolvem software de maneira distribuída. Ao modelo preliminar foram adicionados estados e transições significantes para a dinâmica do desenvolvimento distribuído de software, originando então o M3DS (Modelo de Dinâmica de Desenvolvimento Distribuído de Software). Duas versões do M3DS são apresentadas. Uma versão construída sobre uma máquina de estados, cujo objetivo é representar apenas a transições entre os estados. Outra versão equivalente, porém mais formal, é apresentada no formato de redes de Petri, na qual é possível visualizar a dependência entre transições e mudanças de estado. Com este modelo, é possível compreender o funcionamento de um projeto distribuído e auxiliar na eficácia da gestão da rede de produção, além de auxiliar as demais entidades e pessoas envolvidas a obterem um posicionamento na rede mais preciso. O M3DS pode, também, auxiliar a detecção proativa de problemas originados a partir do desenvolvimento a distância. Os resultados apresentados neste trabalho respondem a questão de como as organizações desenvolvedoras de software produzem software de maneira distribuída. A riginalidade da pesquisa centra-se na construção de um modelo de dinâmica do desenvolvimento distribuído elaborado com os dados levantados a partir de seis estudos de casos. / This work presents a dynamic model of distributed development of software, whose objective is to represent the reality and the aspects of DDS environments, in order to turn them qualitatively and quantitatively observable. A preliminary model was elaborated from the bibliographical revision and an experimentation case developed by L\'Erario et al (2004). The construction and validation of this model used the methodology multiple cases study in several organizations that develop software in a distributed way. After this, states and transitions were added in the dynamics model of the distributed development of software creating the M3DS. (Dynamics Model of Distributed Development of Software). Two versions of M3DS are presented. A version built on a state machine whose objective is demonstrating the transitions among the states. Another version equivalent, however more formal, it is presented in the format of Petri nets. The second version makes possible to visualize the dependence between transitions and state changes. With this model it is possible to understand the operation of a distributed project, aiding in the effectiveness of the manager of the network production and people can obtain a precise positioning in network. Besides, M3DS can also aid the proactive detection of problems originated from the development at the distance. The results presented in this work answer the question: how the development software organizations produce software in a distributed way. The originality of the research is the construction of a model of dynamics of the distributed development elaborated from data of six cases studies.

by Zhao Lei. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2002. / Includes bibliographical references (leaves 78-85). / Abstracts in English and Chinese. / Abstract --- p.ii / Acknowledgments --- p.iv / Chapter 1 --- Introduction --- p.1 / Chapter 2 --- Background --- p.5 / Chapter 2.1 --- Agents --- p.5 / Chapter 2.1.1 --- Deliberative Agents --- p.7 / Chapter 2.1.2 --- Reactive Agents --- p.8 / Chapter 2.1.3 --- Interacting Agents --- p.9 / Chapter 2.1.4 --- Hybrid Architectures --- p.10 / Chapter 2.2 --- Real-time Artificial Intelligence --- p.10 / Chapter 2.3 --- Real-Time Agents --- p.12 / Chapter 2.3.1 --- The Subsumption Architecture --- p.13 / Chapter 2.3.2 --- The InterRAP Architecture --- p.15 / Chapter 2.3.3 --- The 3T Architecture --- p.16 / Chapter 2.4 --- On-line Scheduling in Real-Time Agents --- p.18 / Chapter 3 --- A Real-Time Agent Architecture --- p.20 / Chapter 3.1 --- Human Cognition Model --- p.20 / Chapter 3.1.1 --- Perception --- p.22 / Chapter 3.1.2 --- Cognition --- p.22 / Chapter 3.1.3 --- Action --- p.23 / Chapter 3.2 --- Real-Time Message Passing Primitives and Process Structuring --- p.24 / Chapter 3.2.1 --- Message Passing as IPC --- p.25 / Chapter 3.2.2 --- Administrator and Worker Processes --- p.28 / Chapter 3.3 --- Agent Architecture --- p.29 / Chapter 3.3.1 --- Sensor Workers and the Sensor Administrator --- p.30 / Chapter 3.3.2 --- The Cognition Workers --- p.32 / Chapter 3.3.3 --- "The Task Administrator, the Scheduler Worker and Ex- ecutor Workers" --- p.32 / Chapter 3.4 --- An Agent-Based Real-time Arcade Game --- p.34 / Chapter 4 --- A Multiple Method Approach to Task Scheduling --- p.37 / Chapter 4.1 --- Task Scheduling Mechanism --- p.37 / Chapter 4.1.1 --- Task and Action --- p.38 / Chapter 4.1.2 --- Task Administrator --- p.40 / Chapter 4.1.3 --- Task Scheduler --- p.43 / Chapter 4.2 --- A Task Scheduling Model --- p.44 / Chapter 4.3 --- Combination Rules and Special Cases --- p.46 / Chapter 4.4 --- Scheduling Algorithms --- p.49 / Chapter 5 --- Task Scheduling Model: Analysis and Experiments --- p.53 / Chapter 5.1 --- Goodness Measure --- p.53 / Chapter 5.2 --- Theoretical Analysis --- p.54 / Chapter 5.3 --- Implementation --- p.59 / Chapter 5.3.1 --- Task Generator Implementation --- p.59 / Chapter 5.3.2 --- Executor Workers Implementation --- p.61 / Chapter 5.4 --- Experimental Results --- p.62 / Chapter 5.4.1 --- Hybrid Mechanism and Individual Algorithms --- p.63 / Chapter 5.4.2 --- Effect of Average Execution Time --- p.65 / Chapter 5.4.3 --- Effect of the Greedy Algorithm --- p.65 / Chapter 5.4.4 --- Effect of the Advanced Algorithm --- p.67 / Chapter 5.4.5 --- Effect of Actions and Relations Among Them --- p.68 / Chapter 5.4.6 --- Effect of Deadline --- p.71 / Chapter 6 --- Conclusions --- p.73 / Chapter 6.1 --- Summary of Contributions --- p.73 / Chapter 6.2 --- Future Work --- p.75

Zhang, Yupeng. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references (leaves 45-48). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts also in Chinese.

Linguagens de programação orientadas a objetos possuem diversas características que facilitam sua utilização frente a outras linguagens imperativas. No projeto e desenvolvimento de software, o mecanismo de herança permite a construção de sistemas na forma incremental e evolutiva, possibilitando a reutilização de códigos já escritos. Também a possível atingir aplicações com bons níveis de segurança e confiabilidade, através do encapsulamento de dados e funções sob forma de objetos, que também representam a unidade básica de execução em uma linguagem orientada a objetos. O mesmo recurso que possibilita níveis elevados de segurança permite que linguagens orientadas a objetos sejam inerentemente distribuídas. Objetos possuem tanto área de dados e código de execução independentes dos demais. Acessos aos dados internos de um objeto somente são possíveis através de mensagens explicitas entre objetos. Neste caso um objeto solicita uma ação específica a outro objeto, podendo ser enviados parâmetros e existir retorno de resultados. Este trabalho apresenta um modelo para construção de uma linguagem orientada a objetos distribuída. O ambiente para suportar a execução ao modelo é compostos por vários nodos de processamento com memórias locais individuais e contando com uma rede de comunicação para troca de mensagens entre os nodos. O modelo e discutido em dois níveis distintos: a nível de linguagem e a nível operacional. A nível de linguagem são analisados os recursos de programação normalmente utilizados em linguagens orientadas a objetos quando implementados em ambientes distribuídos. O ambiente de suporte A execução necessário ao suporte do modelo da linguagem a analisado pelo nível operacional. A apresentação do modelo a nível de linguagem discute as características de uma linguagem orientada a objetos distribuída frente as implementações seqüenciais convencionais. E ressaltada a implementado de herança em um ambiente de execução distribuído, que, não podendo ser através de compartilhamento, é efetuada através de copia de código. Também são apresentadas novas diretivas de compilação necessárias exclusivamente a ambientes distribuídos. Tais diretivas visam explorar níveis de concorrência de uma aplicação durante sua execução, diferenciando classes que definem objetos locais ou distribuídos e diferentes tipos de mensagens entre objetos. As formas de extrair o melhor desempenho nas aplicações e o gerenciamento do ambiente de execução são os pontos abordados pelo nível operacional do modelo. Em operação neste nível, um elemento de gerencia de execução permite o controle tanto dos objetos da aplicação quanto dos nodos de processamento disponíveis para execução. A tarefa de controle de objetos viabiliza a criação e remoção de objetos durante a execução da aplicação, bem como a identificação de localização destes. O controle dos nodos de processamento possibilita analisar continuamente a carga computacional dos nodos de processamento. Assim, cada objeto a ser criado pode ser alocado em um nodo onde a carga computacional esteja baixa, propiciando um melhor desempenho no momento de execução da aplicação distribuído a carga entre os nodos. A unido do modelo de execução distribuído proposto a uma linguagem orientada a objetos resulta em uma linguagem eficiente tanto na produção de software como no desempenho de aplicações. A eficiência na produção de sistemas 6 obtida através de dois itens, a utilização do paradigma de orientação a objetos e a transparência do nível operacional para o programador, que não necessita conhecer os mecanismos utilizados para ativação de objetos e envio de mensagens. A eficiência de execução é obtida através da utilização de múltiplos nodos processadores servindo como base a execução. Neste trabalho é também apresentado um protótipo para uma linguagem suportando o modelo distribuído proposto. A linguagem, denominada DPC++ (Processamento Distribuído em C++), é voltada para execução em redes de estações de trabalho, sobre o sistema operacional Unix, utilizando sockets como mecanismo de comunicação. O estilo de programação em DPC++ é baseado em C++. / The objects-oriented programming languages have many features who make simple their use in front of others imperatives languages. In the software project and development, the inheritance mechanism allows an increasing and evaluative way of codes that have been written. It also possible gain applications with goods levels of security and confiability with the encapsulation of both data and functions in the form of object, which represent the basic execution unit in an object-oriented language. The same resource that provides high levels of security also permits that object-oriented languages may be inherently distributed. Objects have their own area of data, their execution codes are independent from the other. Accesses to the internal data of an object are possible only through a specific protocol among objets. When this occurs, an object requests a specific action to other object with or without parameters or results return. This work presents a model for build a distributed object-oriented language, devoted to environments compounded by several processing nodes with local memory and linked by a communication network. The model is discussed in two different levels: language level and operational level. In the language level are analyzed the programming resources usually used in object-oriented languages when implemented in distributed environments. The executing environments support are analyzed in the operational level. In the language level presentation are made a discussion about distributed object-oriented language features in front of conventional sequential implementations. It is emphasized inheritance in a distributed executing environment, who is done by code copy, due to can not be by memory sharing. Also are presented news compilation directives necessaries to the distributed environment. Those directives aim to explorer concurrence levels in an application during its execution, differing class who defining local or distributed objects and the different messages types among objects. The operational level boards the ways that mean to extract the best performance for the applications and the execution environment management. An execution manager element allows the control as the application objects as the available to execution processor nodes. The task of object control makes possible the objects creation and removal during the application executing as well their network identification. The processor nodes control allows the continuous analyzes of the computational load in the nodes available to processing. In this way, every object to be created can be allocated in a node with low occupation rates, propitiating a better performance in the application executing. The union of the proposed distributed execution model to an objectoriented language results in an efficient language as in the software production as in execution performance. The systems production efficiency is obtained from two items: the utilization of the object-oriented paradigm an the transparency of the operational level to the programmer, that no need know the used mechanisms to object activation and message exchange. The execution efficiency is gained by the utilization of multiples processor nodes supporting the application executing. In this work is presented a prototype that implements the proposed model. The language, called DPC++, Distributed Processing in C++, is turned to execute in workstation network with Unix operational system, using sockets as communication mechanism. The style of DPC++ programming are based in C++.

O presente trabalho propõe uma arquitetura de utilização de Data Warehouses em computadores móveis, descreve os componentes desta arquitetura (dados e processos) que permite o sincronismo dos dados baseado em metadados e limitado ao escopo de acesso de cada usuário. As estruturas de dados e os processos que compõem a arquitetura proposta são reduzidos a problemas conhecidos e já solucionados, justificando sua viabilidade. Além disso, o presente trabalho também fornece diretrizes para avaliar a complexidade e o impacto causados por alterações de esquema no Data Warehouse central que devem ser refletidas nos data marts localizados nas plataformas móveis. A avaliação da complexidade e impacto das alterações nos esquemas do Data Warehouse pode auxiliar os administradores do ambiente a planejar a implementação destas alterações, propondo melhores alternativas no caso de alterações de esquema mais complexas e que causem um impacto maior no ambiente. A importância do trabalho está relacionada a casos reais de necessidade de evolução nas bases de dados analíticas (Data Warehouse) em computadores móveis, nos quais os usuários mantêm seu próprio subconjunto de dados do Data Warehouse para apoiar os processos de negócios. / This work presents an architecture for using Data Warehouses in mobile computers and describes the architecture components (data and processes) that allow the data synchronism based on metadata and restricted to the scope of access for each user. The data structures and the processes composing the architecture are reduced to already known and solved problems, justifying its feasibility. Besides, this work also provides the guidelines to evaluate the complexity and impact caused by changes of schema in the central Data Warehouse that must be reflected in the data marts located in the mobile platforms. The analysis of the complexity and impact of the changes made to the schemas may help environment administrators to plan these changes and propose better alternatives when dealing with more complex schema changes causing a greater impact on the environment. The relevance of this work is related to real cases that require evolution of analytical databases (Data Warehouse) in mobile computers in which the users keep their own subset of Data Warehouse information to support their business processes.