Submitted by Ricardo Cedraz Duque Moliterno (ricardo.moliterno@uefs.br) on 2017-10-09T22:34:41Z No. of bitstreams: 1 MATHUES BRITO DE OLIVEIRA Disserta??ov.pdf: 5287293 bytes, checksum: 8d3e3b854b5799f16c0b61b6a5d33f1c (MD5) / Made available in DSpace on 2017-10-09T22:34:41Z (GMT). No. of bitstreams: 1 MATHUES BRITO DE OLIVEIRA Disserta??ov.pdf: 5287293 bytes, checksum: 8d3e3b854b5799f16c0b61b6a5d33f1c (MD5) Previous issue date: 2017-06-12 / The assembly of bacterial genomes consists of a process of reordering fragments so that the original genome can be represented. However, to maximize the results of genome assembly, some steps are required, for instance, read quality analysis and preprocessing, repetition identification and quality check. The process of assembly of genomes is a complex step that involves the type of sequencing that was used, there are several types of sequencers which imply different characteristics for each one for example: fragments size, throughput, among others. Analyzing these characteristics requires the use of several computational tools, to assist in all the processes mentioned above, and since the range of software available is quite broad and distinct, it is necessary for the user to learn to work with this computational diversity, dominating often knowledge that is not of the biological area, implying in less time for a deepening in biological questions. Based on this context, we developed a pipeline to perform an automated fragment analysis, read preprocessing, genome assembly and orientation of contigs, having as the assembly the main objective of the pipeline and that it will be managed by a Web application called GATOOL (Genome Assembly Tool). Aiming to evaluate the performance of the application, tests were carried out with two samples of prokaryotic organisms, which are: Bacillus amyloliquefaciens and Serratia marcescens. Also perform a test with seven SRA samples. Both organisms are sequenced on the Ion PGMTM platform. The tools used to perform the assembly were SPAdes and Velvet, both assemblers use de Bruijn graph algorithm as a paradigm for the assembly of the genome, after this stage the resulting set of contigs was ordered through the CONTIGuator, which is a reference ordering. We observed that the interface GATOOL allowed a quick and easy execution of several steps and processes in the field of genome assembly, including the assembly of two prokaryotic species in an automated way, thus facilitating the use and accomplishment of such processes by any user. / A montagem de genomas bacterianos ? um processo de reordena??o de fragmentos, de forma que se possa representar o genoma original. Entretanto, para que a montagem de um genoma seja realizada visando maximizar os resultados, ? preciso que algumas etapas sejam cumpridas, por exemplo: a an?lise dos fragmentos, o pr?-processamento destes fragmentos e novamente uma repeti??o do processo de an?lise, para verificar a efic?cia do pr?-processamento realizado. O processo de montagem de genomas ? uma etapa complexa, que envolve o tipo de sequenciamento que foi utilizado. Existem diversos tipos de sequenciadores, o que implica caracter?sticas distintas em cada um, como por exemplo: tamanho dos fragmentos, quantidade de fragmentos gerados por corrida, dentre outros. Analisando essas caracter?sticas, faz-se necess?ria a utiliza??o de diversas ferramentas computacionais para auxiliar a todos os processos citados anteriormente e, como a gama de softwares dispon?veis ? bem ampla e distinta, ? importante que o usu?rio domine essa diversidade computacional, contendo muitas vezes conhecimentos que n?o s?o da ?rea biol?gica, implicando menos tempo para um aprofundamento das quest?es biol?gicas. Com base neste contexto, prop?em-se um pipeline para a realiza??o da an?lise de fragmentos, pr?-processamento dos fragmentos, montagem de genomas e orienta??o de contigs, tendo como a montagem o objetivo principal do pipeline e este ser? gerenciado por uma aplica??o web chamada GATOOL (Genome Assembly Tool). Visando avaliar o desempenho da aplica??o, foram feitos testes com duas amostras de organismos procariontes, que s?o: Bacillus amyloliquefaciens e Serratia marcescens. Tamb?m foram realizados testes com sete amostras SRA. Ambos os organismos est?o sequenciados na plataforma Ion PGMTM. Os montadores usados foram o SPAdes e o Velvet, ambos montadores, utilizam o algor?tmo grafo de Bruijn como paradigma para a montagem do genoma; ap?s esta etapa, o conjunto de contigs resultante foi ordenado atrav?s do CONTIGuator, que ? uma ordena??o por refer?ncia. Observamos que a interface GATOOL permitiu uma execu??o r?pida e f?cil de diversas etapas e processos no campo da montagem de genomas, inclusive realizando a montagem de duas esp?cies procariontes de maneira automatizada, facilitando assim a utiliza??o e realiza??o de tais processos por qualquer usu?rio.

O Licenciamento Ambiental é instrumento que se mostra com estreita ligação com processos de avaliação de impacto ambiental, e somente deve ser concedido após a certeza da conciliação entre a atividade e a qualidade ambiental. No Estado de São Paulo é usado o Relatório Ambiental Preliminar (RAP) como forma de se analisar a viabilidade ambiental de empreendimentos. Concluiu-se que o mesmo não serve como elemento no processo de licenciamento de gasodutos, pois não exige a necessidade de estudo de alternativas locacionais, e em sendo assim, seu uso não garante que a atividade analisada demonstre viabilidade ambiental, função fundamental de qualquer Estudo de Impacto Ambiental. O estudo de viabilidade ambiental necessita instrumentos que atribuam confiabilidade ao processo decisório e a Avaliação de Risco Ambiental (ARA) é uma ferramenta importantíssima, pois complementa a avaliação sobre a viabilidade ambiental do empreendimento, e se mostra útil para o Licenciamento Ambiental de atividades. Dessa forma, o principal motivo de escolha desta ferramenta decorre do fato de seu uso servir como instrumento para tomadas de decisões mais racionais e efetivas onde exista possibilidade de danos, o que a torna de suma importância na verificação da viabilidade ambiental de um empreendimento. A ARA foi aplicada ao transporte de gás natural por gasodutos, porque este combustível tem ganhado maior espaço na matriz energética do Brasil, com crescente tendência de expansão. Concluiu-se que a ARA deve ser usada desde o início do processo de licenciamento, já para a obtenção da primeira das licenças que é a LP. Com isso, os riscos são avaliados e usados como critério fundamental para o estudo de localização do traçado do gasoduto. Dessa maneira, os riscos de fatalidades associados a acidentes com gasodutos são reduzidos, garantindo mínimos riscos à população / Environmental Licensing is a tool showing great connection with the environmental impact assessment process, and should only be granted after the conciliation between activity and environmental quality is verified. The State of Sao Paulo has implemented the Preliminary Environmental Report (PER), which is used to evaluate the environmental suitability of activities. As it does not require consideration of all location (siting) and technology alternatives, the use of PER for licensing purposes does not assure under any circumstance that the analyzed activity presents environmental suitability, which is a fundamental role of any environmental impact study. Environmental suitability evaluation needs instruments to increase reliability to decision making, and Risk Assessment (RA) is a very important tool because it complements the analysis about the activity's environmental suitability, making it essential for the Environmental Licensing process. RA was applied to the conveying of natural gas through pipes because the Brazilian natural gas network has been expanding for the last few years. It was concluded that RA should be used from the beginning of the environmental licensing process, adopting associated risks as fundamental criteria for location study of the gas pipe route, which is an essential condition to define the environmental suitability of the proposed activity. This way, fatality risks posed by the gas lines are reduced, assuring minimal risks to the population/environment

O gás natural é uma fonte alternativa ao petróleo. É uma fonte de energia considerada mais limpa e segura dentre as fontes de energias não renováveis e, por isso, vem aumentando sua participação na matriz energética. Deste modo, impulsionou a criação e ampliação de diversas malhas de gasodutos. O objetivo do presente trabalho é simular redes de gasodutos utilizando ferramentas computacionais disponíveis no mercado. O HYSYS® foi adequado para simular longos gasodutos lineares. Portanto, a estratégia sequencial modular foi adequada para estas configurações. Contudo, não apresentaram bons resultados para redes. O software gratuito iiSE apresenta bons resultados para redes complexas, comprovando que os softwares orientados a equações são mais apropriados para sistemas com paralelismo. / Natural gas is an alternative source for oil. It is an energy source considered more clean and safe among the non-renewable energy sources and, therefore, its participation is increasing in the energy matrix. In this way, spurred the creation and expansion of several meshes of pipelines. The objective of this study is to simulate gas pipeline networks using computational tools available on the market. The HYSYS ® was suitable to simulate long linear gas pipelines. Therefore, the sequential modular strategy was appropriate for these settings. However, did not provide good results for networks. The free software iiSE presents good results for complex networks, proving that the software orixented to equations are more suitable for systems with parallelism.

O etanol, produto proveniente da indústria sucroalcooleira, um dos setores mais importantes da economia brasileira, atrai a atenção dos países desenvolvidos. O aumento de sua demanda em todo o mundo, motivado por razões econômicas e ambientais, impulsiona sua exportação. O volume exportado passou de 750 milhões de litros em 2003 para 3,5 bilhões de litros em 2006 e os produtores estimam que em cinco anos este volume alcance 6,5 bilhões de litros. Diante da perspectiva de acréscimo nas exportações, e do fato de quase 90% da produção brasileira concentra-se no Centro-Sul, esta dissertação tem por objetivo analisar as alternativas de transporte de etanol para exportação no médio prazo, baseado no plano de investimentos proposto pelo projeto do corredor de exportação de etanol da Transpetro, um dos investimentos propostos para melhorar a eficiência logística do transporte de etanol. Tais investimentos pretendem atender a demanda instalada pelo mercado internacional de forma satisfatória, garantindo o suprimento do combustível e prevenindo o surgimento de gargalos logísticos motivados por falta de infra-estrutura suficiente para o escoamento da produção. Foram avaliadas três alternativas de transporte que representam a movimentação de etanol das unidades produtoras aos portos: alternativa rodoviária, alternativa rodo-dutoviária, e alternativa rodo-hidro-dutoviária. Definidas as alternativas, foram identificadas as trinta principais zonas produtoras de etanol e analisadas as alternativas específicas para cada uma. Assim, foi possível identificar as principais vantagens competitivas das alternativas de transporte por região produtora e verificar os ganhos derivados do transporte por dutos e pela hidrovia no escoamento da produção de etanol até os principais portos. / Ethanol, a product originated from the sugarcane and ethanol industry, one of the most important sectors in the brazilian economy is attracting the interest of the developed countries. The exportation of ethanol is stimulated by the increasing worldwide demand driven by economic and environmental reasons. The exported volume increased from more than 750 million liters in 2003 to 3.5 billion liters in 2006 and, in the next five years, the brazilian producers expect that this volume will reach 6.5 billion liters. Because of this expectation in increasing exportations of ethanol, and being aware that the center-south region of Brazil produces almost 90% of the brazilian ethanol, the objective of this dissertation is to analyze the alternatives of transportation of ethanol for exportation in the medium term. This study is based in the Transpetro´s corridor of ethanol exportation investment plan, which is one of the proposed investments to increase the logistic efficiency of the transportation of ethanol. These investments intend to satisfactorily fulfill the demand of the international market, guaranteeing the supply of ethanol and preventing the appearance of logistic gaps due to lacks of infra-structure for transporting the product. Three alternatives of transportation were evaluated, representing the transportation of ethanol from the manufacturing units to the ports: roadway alternative, road-pipeline alternative and road-waterway-pipeline alternative. After the definition of these alternatives, the thirty major manufacturing zones of ethanol were defined and each zone had these alternatives analyzed. As a result, the major competitive advantages of the transportation alternatives by zone were identified. Also, the potential gains of transporting ethanol to the major seaports by pipelines and waterways were evaluated.

The rapidly increasing number of cores available in multicore processors does not necessarily lead directly to a commensurate increase in performance: programs written in conventional languages, such as C, need careful restructuring, preferably automatically, before the benefits can be observed in improved run-times. Even then, much depends upon the intrinsic capacity of the original program for concurrent execution. Using software techniques to parallelize the sequential application can raise the level of gain from multicore systems. Parallel programming is not an easy job for the user, who has to deal with many issues such as dependencies, synchronization, load balancing, and race conditions. For this reason the role of automatically parallelizing compilers and techniques for the extraction of several threads from single-threaded programs, without programmer intervention, is becoming more important and may help to deliver better utilization of modern hardware. One parallelizing technique that has been shown to be an effective for the parallelization of applications that have irregular control flow and complex memory access patterns is Decoupled Software Pipeline (DSWP). This transformation partitions the loop body into a set of stages, ensuring that critical path dependencies are kept local to a stage. Each stage becomes a thread and data is passed between threads using inter-core communication. The success of DSWP depends on being able to extract the relatively fine-grain parallelism that is present in many applications. Another technique which offers potential gains in parallelizing general purpose applications is slicing. Program slicing transforms large programs into several smaller ones that execute independently, each consisting of only statements relevant to the computation of certain, socalled, (program) points. This dissertation explores the possibility of performance benefits arising from a secondary transformation of DSWP stages by slicing. To that end a new combination method called DSWP/Slice is presented. Our observation is that individual DSWP stages can be parallelized by slicing, leading to an improvement in performance of the longest duration DSWP stages. In particular, this approach can be applicable in cases where DOALL is not. In consequence better load balancing can be achieved between the DSWP stages. Moreover, we introduce an automatic implementation of the combination method using Low Level Virtual Machine (LLVM) compiler framework. This combination is particularly effective when the whole long stage comprises a function body. More than one slice extracted from a function body can speed up its execution time and also increases the scalability of DSWP. An evaluation of this technique on six programs with a range of dependence patterns leads to considerable performance gains on a core-i7 870 machine with 4-cores/8-threads. The results are obtained from an automatic implementation that shows the proposed method can give a factor of up to 1.8 speed up compared with the original sequential code.

Stop-motion animation is a traditional form of animation that has been practised for over 100 years. While the unique look and feel of stop-motion animation has been retained in modern productions, the production process has been modernised to take advantage of technological advancements. Modern stop-frame animation production integrates digital imaging technology and computational methods with traditional hand-crafted skills. This portfolio documents three projects undertaken at Aardman Animations, each investigated with the aim of improving efficiency in the stop-motion production process: - Rig removal is the removal of equipment, or ‘rigging’, used on set during stop-motion animation to hold characters or objects in unstable positions. All rigging captured in frames must be removed in post-production and currently manual methods are used which can be very time-consuming. The key task is to separate the character from the rig. In Chapter 2, I present a novel spatio-temporal segmentation algorithm for segmenting characters from stop-motion footage. The algorithm has been designed to work with stop-motion animated content, in contrast to other state of the art algorithms which struggled when tested on stop-motion footage. - Set shift is a problem which occurs when background items on set move subtly over the time taken to shoot a scene. For example, temperature and humidity changes can cause wood to warp during a weekend, changing the position of a background object the following week. These small ‘shifts’ are recorded in the footage and must be corrected in post-production. Chapter 3 describes the problem in detail, investigates potential solutions and explains why solving set shift automatically is a significant challenge. - Plasticine shading is required when a plasticine model has to be generated computationally. One motivation for producing footage computationally is that problems such as rig removal and set shift do not arise. In order to simulate plasticine accurately, the distinct reflectance model of this material must be known and reproduced. By collecting experimental data from plasticine samples and fitting parametric models, I have developed a bespoke surface shading model for plasticine (Chapter 4). This new model provides the best fit to the measured data when compared to existing state of the art surface shaders. It has been implemented into commercially used production systems, for use with existing rendering software. Advancing state of the art research is only one of the challenges when working in a production studio such as Aardman Animations. Additionally, findings must be integrated into the production pipeline. Chapter 5 discusses the challenges and constraints faced when conducting research in this environment. In order for stop-motion animation to remain competitive it is vital that production companies stay up-to-date with technological advancements in research areas that can contribute to their production processes. I conclude by discussing whether technological advancements can help Aardman Animations in improving the efficiency of their stop-motion production pipeline.

O reparo em dutos defeituosos é previsto por normas e literatura, porém existe grande espaço para definição dos parâmetros ideais para aplicação prática e avaliação do desempenho destes reparos em fadiga. O presente trabalho tem por objetivo a definição dos parâmetros ideais para aplicação de reparos eficientes do tipo dupla calha sem solda circunferencial e com carregamento externo em escala real em dutos com defeitos de mossa com cava. O reparo é baseado na instalação de duas calhas concêntricas ao duto a ser reparado, preenchendo-se o defeito com resina e aplicando carga de compressão através de atuadores hidráulicos com correntes a fim de induzir tensões compressivas na região do defeito e, por fim, as calhas são unidas longitudinalmente pelo processo de soldagem. Para este trabalho, foi realizada uma modelagem numérica utilizando o método de elementos finitos de modo a simular a reprodução do defeito, ensaios de fadiga sem reparo, parâmetros para aplicação do reparo, ensaios de fadiga com reparo e, por fim, ensaio hidrostático. O procedimento proposto foi a reprodução do defeito, primeiramente o duto foi deformado com uma esfera metálica, de modo a formar uma mossa de profundidade igual a 6 % do diâmetro externo e, em seguida, a cava foi usinada com a utilização de um disco abrasivo. Após a produção do defeito, três amostras foram ensaiadas em fadiga, de modo a produzir uma amostra de referência sem reparo a ser comparada com os corpos de prova com reparo. O reparo dupla calha foi aplicado em duas amostras com defeito, sendo essas então submetidas a ensaios de fadiga. Esses ensaios indicaram que ambas as amostras resistiram a um número de ciclos correspondentes a 100 anos de vida em serviço. Por fim, as amostras reparadas após o ensaio de fadiga foram submetidas a ensaios hidrostáticos até a ruptura, a fim de avaliar a vida remanescente. Ambos os dutos romperam fora da região reparada, com uma pressão 2,1 %, menor que a pressão calculada analiticamente. Como principal resultado, foram obtidos parâmetros ideais para aplicação do reparo dupla calha em dutos com defeito tipo mossa com cava. Os resultados experimentais mostram convergência em relação aos dados do modelo numérico, provando que a modelagem por elementos finitos pode ser uma ferramenta útil no desenvolvimento deste tipo de trabalho. / Defective duct repairs are envisaged by norms and by the literature, yet there is enough space left to define ideal parameters for practical application and performance evaluation of these fatigue repairs. This work’s objective is to define the ideal parameters for the application of efficient repairs in double spouts without circumferential welding and real scale external loading in ducts with dent and gouge defects. The repair is based on the installation of two concentric spouts in the duct, filling the defect with resin and applying compression loading through hydraulic actuators with currents to induce compressive stresses in the defective area. Afterwards, the spouts are united lengthwise through the process of welding. To develop this work, we conducted a numerical modelling by using the finite element method to simulate the reproduction of the defect, as well as fatigue tests with no repairs, parameters for the application of repairs, fatigue tests with repairs, and finally a hydrostatic test. The proposed procedure was the reproduction of the defect. At first the duct was deformed with a metallic sphere, to form a dent whose depth was equal to 6 % of the external diameter and, subsequently, the gouge was machined with the help of an abrasive disk. Following the production of a defect, three samples were tested in fatigue to produce a reference sample without repair which would be compared to the samples with repairs. The double spout repair was applied in two samples with defects, which were then subjected to fatigue tests. These tests showed that both samples resisted to a number of cycles corresponding to a 100-year use lifespan. At last, the samples repaired after fatigue tests were subjected to hydrostatic tests until rupture, in order to evaluate their remaining lifespan. Both ducts ruptured outside of the repaired region, with a stress rate of 2.1 %, lower than the stress calculated analytically. The main result of this study was obtaining ideal parameters for the application of double spout repair in ducts with dents and gouge defects. The experimental results show convergence in relation to the numerical model data, proving that finite element modelling can be a useful tool when conducting this kind of work.

Métodos acurados de avaliação de tenacidade à fratura, incluindo curvas de resistência ao rasgamento dúctil de juntas soldadas de dutos e risers rígidos, tornam-se essenciais em procedimentos de avaliação de defeitos em regiões de soldas e zonas termicamente afetadas, nas quais defeitos não detectados podem se propagar devido às grandes tensões e deformações envolvidas na instalação e/ou operação dessa classe de estruturas. Este trabalho apresenta uma investigação experimental da tenacidade à fratura de uma junta soldada de um duto rígido de aço API 5L X80 (curvas J-Ãa). A motivação para este trabalho decorre da demanda crescente na aplicação de dutos de alta resistência na indústria de óleo e gás, em particular dutos submarinos e risers rígidos em catenária. Para tal, foram empregados corpos de prova de tração SE(T) fixados por garras, e flexão três pontos SE(B) contendo entalhe no centro da solda, para determinação das curvas J-R pelo método do corpo de prova único utilizando a técnica da flexibilidade no descarregamento, além das funções de flexibilidade e fatores n referentes aos corpos de prova SE(T) e SE(B) em função do nível de dissimilaridades mecânicas, o que permite obter valores mais assertivos das propriedades de tenacidade à fratura de juntas soldadas. / Accurate measurements of fracture resistance properties, including crack growth resistance curves for pipeline girth welds, become essential in defect assessment procedures of the weldment region and the heat affected zone, where undetected crack-like defects (such as lack of penetration, deep undercuts, root cracks, etc.) may exhibit further crack extension due to high tensile stresses and strains during installation and in-service operation. This work presents an investigation of the ductile tearing properties for a girth weld made of an API 5L X80 pipeline steel using experimentally measured crack growth resistance curves (J-Ãa curves). Use of these materials is motivated by the increasing demand in the number of applications for manufacturing high strength pipes for the oil and gas industry including marine applications and steel catenary risers. Testing of the pipeline girth welds utilized sidegrooved, clamped SE(T) specimens and 3P bend SE(B) specimens with a weld centerline notch to determine the crack growth resistance curves based upon the unloading compliance (UC) method using a single specimen technique. Recently developed compliance functions and n-factors applicable for SE(T) and SE(B) fracture specimens with homogeneous material and overmatch welds are introduced to determine crack growth resistance data from laboratory measurements of load-displacement records. This experimental characterization provides additional toughness data which serve to evaluate crack growth resistance properties of pipeline girth welds using SE(T) and SE(B) specimens with weld centerline cracks.

Subsea pipelines are subjected to wave and steady current loads which cause pipeline stability problems. Current knowledge and understanding on the pipeline on-bottom stability is based on the research programmes from the 1980’s such as the Pipeline Stability Design Project (PIPESTAB) and American Gas Association (AGA) in Joint Industry Project. These projects have mainly provided information regarding hydrodynamic loads on pipeline and soil resistance in isolation. In reality, the pipeline stability problem is much more complex involving hydrodynamic loadings, pipeline response, soil resistance, embedment and pipe-soil-fluid interaction. In this thesis Computational Fluid Dynamics (CFD) modelling is used to investigate and establish the interrelationship between fluid (hydrodynamics), pipe (subsea pipeline), and soil (seabed). The effect of soil types, soil resistance, soil porosity and soil unit weight on embedment was examined. The overall pipeline stability alongside pipeline diameter and weight and hydrodynamic effect on both soil (resulting in scouring) and pipeline was also investigated. The use of CFD provided a better understanding of the complex physical processes of fluid-pipe-soil interaction. The results show that the magnitude of passive resistance is on the average eight times that of lateral resistance. Thus passive resistance is of greater significance for subsea pipeline stability design hence the reason why Coulomb’s friction theory is considered as conservative for stability design analysis, as it ignores passive resistance and underestimates lateral resistance. Previous works (such as that carried out by Lyons and DNV) concluded that soil resistance should be determined by considering Coulomb’s friction based on lateral resistance and passive resistance due to pipeline embedment, but the significance of passive resistance in pipeline stability and its variation in sand and clay soils have not be established as shown in this thesis. The results for soil porosity show that increase in pipeline stability with increasing porosity is due to increased soil liquefaction which increases soil resistance. The pipe-soil interaction model by Wagner et al. established the effect of soil porosity on lateral soil resistance but did not attribute it to soil liquefaction. Results showed that the effect of pipeline diameter and weight vary with soil type; for sand, pipeline diameter showed a greater influence on embedment with a 110% increase in embedment (considering combined effect of diameter and weight) and a 65% decrease in embedment when normalised with diameter. While pipeline weight showed a greater influence on embedment in clay with a 410% increase. The work of Gao et al. did not completely establish the combined effect of pipeline diameter and weight and soil type on stability. Results also show that pipeline instability is due to a combination of pipeline displacement due to vortex shedding and scouring effect with increasing velocity. As scoring progresses, maximum embedment is reached at the point of highest velocity. The conclusion of this thesis is that designing for optimum subsea pipeline stability without adopting an overly conservative approach requires taking into consideration the following; combined effect of hydrodynamics of fluid flow on soil type and properties, and the pipeline, and the resultant scour effect leading to pipeline embedment. These results were validated against previous experimental and analytical work of Gao et al, Brennodden et al and Griffiths.

The VISTA Variables in the Vía Láctea survey is a multi-epoch, near-infrared (NIR) search for RR Lyrae stars, which trace the structure and evolutionary history of the Galactic Bulge. To measure accurate light-curves for these and other variable sources in the crowded fields of the Bulge, we have built a pipeline to perform difference imaging analysis (DIA) on VVV data. This is the first time DIA has been carried out with a large-scale NIR survey, which presents certain specific challenges such as the large pixel scales and high variable background. This thesis begins with an investigation into the wider problem of reference image selection for DIA. Through this study, we found that an alternative formulation of traditional DIA - Target Image Convolution - yields better results for VVV. This technique is employed in the core image subtraction engine for the VVV DIA pipeline. This work also details the pipelines for carrying out calibration, period-finding and Fourier modelling on the light-curves of DIA sources, as well as for obtaining their dereddened NIR magnitudes and colours. To validate the pipelines, the magnitude calibration is checked against another NIR survey (in the most challenging Galactic centre field) and analysis results are crosschecked against the OGLE-IV catalogue of RR Lyrae (in a low-extinction region of the Galactic bulge). Both studies are used to determine the efficacy of the existing pipeline and identify areas for improvement. DIA generally shows a significant improvement over existing aperture photometry. Using the NIR properties of VVV DIA counterparts to the OGLE-IV RR Lyrae, we demonstrate that it is possible to identify new variables with this pipeline, including RR Lyrae.