Bioinformatics and computational biology (BCB) is a rapidly developing multidisciplinary field which encompasses a wide range of domains, including genomic sequence alignments. It is a fundamental tool in molecular biology in searching for homology between sequences. Sequence alignments are currently gaining close attention due to their great impact on the quality aspects of life such as facilitating early disease diagnosis, identifying the characteristics of a newly discovered sequence, and drug engineering. With the vast growth of genomic data, searching for a sequence homology over huge databases (often measured in gigabytes) is unable to produce results within a realistic time, hence the need for acceleration. Since the exponential increase of biological databases as a result of the human genome project (HGP), supercomputers and other parallel architectures such as the special purpose Very Large Scale Integration (VLSI) chip, Graphic Processing Unit (GPUs) and Field Programmable Gate Arrays (FPGAs) have become popular acceleration platforms. Nevertheless, there are always trade-off between area, speed, power, cost, development time and reusability when selecting an acceleration platform. FPGAs generally offer more flexibility, higher performance and lower overheads. However, they suffer from a relatively low level programming model as compared with off-the-shelf microprocessors such as standard microprocessors and GPUs. Due to the aforementioned limitations, the need has arisen for optimized FPGA core implementations which are crucial for this technology to become viable in high performance computing (HPC). This research proposes the use of state-of-the-art reprogrammable system-on-chip technology on FPGAs to accelerate three widely-used sequence alignment algorithms; the Smith-Waterman with affine gap penalty algorithm, the profile hidden Markov model (HMM) algorithm and the Basic Local Alignment Search Tool (BLAST) algorithm. The three novel aspects of this research are firstly that the algorithms are designed and implemented in hardware, with each core achieving the highest performance compared to the state-of-the-art. Secondly, an efficient scheduling strategy based on the double buffering technique is adopted into the hardware architectures. Here, when the alignment matrix computation task is overlapped with the PE configuration in a folded systolic array, the overall throughput of the core is significantly increased. This is due to the bound PE configuration time and the parallel PE configuration approach irrespective of the number of PEs in a systolic array. In addition, the use of only two configuration elements in the PE optimizes hardware resources and enables the scalability of PE systolic arrays without relying on restricted onboard memory resources. Finally, a new performance metric is devised, which facilitates the effective comparison of design performance between different FPGA devices and families. The normalized performance indicator (speed-up per area per process technology) takes out advantages of the area and lithography technology of any FPGA resulting in fairer comparisons. The cores have been designed using Verilog HDL and prototyped on the Alpha Data ADM-XRC-5LX card with the Virtex-5 XC5VLX110-3FF1153 FPGA. The implementation results show that the proposed architectures achieved giga cell updates per second (GCUPS) performances of 26.8, 29.5 and 24.2 respectively for the acceleration of the Smith-Waterman with affine gap penalty algorithm, the profile HMM algorithm and the BLAST algorithm. In terms of speed-up improvements, comparisons were made on performance of the designed cores against their corresponding software and the reported FPGA implementations. In the case of comparison with equivalent software execution, acceleration of the optimal alignment algorithm in hardware yielded an average speed-up of 269x as compared to the SSEARCH 35 software. For the profile HMM-based sequence alignment, the designed core achieved speed-up of 103x and 8.3x against the HMMER 2.0 and the latest version of HMMER (version 3.0) respectively. On the other hand, the implementation of the gapped BLAST with the two-hit method in hardware achieved a greater than tenfold speed-up compared to the latest NCBI BLAST software. In terms of comparison against other reported FPGA implementations, the proposed normalized performance indicator was used to evaluate the designed architectures fairly. The results showed that the first architecture achieved more than 50 percent improvement, while acceleration of the profile HMM sequence alignment in hardware gained a normalized speed-up of 1.34. In the case of the gapped BLAST with the two-hit method, the designed core achieved 11x speed-up after taking out advantages of the Virtex-5 FPGA. In addition, further analysis was conducted in terms of cost and power performances; it was noted that, the core achieved 0.46 MCUPS per dollar spent and 958.1 MCUPS per watt. This shows that FPGAs can be an attractive platform for high performance computation with advantages of smaller area footprint as well as represent economic ‘green’ solution compared to the other acceleration platforms. Higher throughput can be achieved by redeploying the cores on newer, bigger and faster FPGAs with minimal design effort.

O principal objetivo desta tese consiste em propor, desenvolver e implementar uma infra-estrutura para gerenciamento de um Banco de Dados baseado em Grid. O armazenamento de objetos complexos como áudio, vídeo, softwares etc., em Sistemas de Banco de Dados, sempre se dá de maneira integral, ou seja, o documento, independente do seu tamanho, não é fragmentado pelo Sistema de Gerência de Banco de Dados (SGBD) ao ser armazenado. Metodologias de modelagem de dados utilizadas também não especificam a fragmentação ou segmentação de um documento complexo quando do seu armazenamento, pois só contemplam a fragmentação das estruturas de armazenamento, no caso relações ou classes, e não os objetos que serão armazenados. Ao avaliarmos o desempenho de sistemas que armazenam objetos complexos, verificamos que o tamanho dos objetos armazenados influencia consideravelmente o desempenho destes sistemas. Como objetos multimídia, softwares, etc., necessitam de grandes volumes em disco para seu armazenamento, métodos de replicação ou distribuição de cópias tradicionais tornam-se muito dispendiosos e por vezes ineficientes. Com a infra-estrutura desenvolvida neste trabalho foi possível segmentar e distribuir atributos complexos de linhas de uma tabela, instaladas em Bancos de Dados baseado em Grid. Nossa solução melhorou o desempenho do sistema que tinha a necessidade de armazenar documentos de tamanho elevado, acima de um tamanho limite. Também foi testada com sucesso a possível utilização dos códigos LDPC nesta infra-estrutura. Entretanto, não observamos ganhos que justificassem sua utilização em aplicações semelhantes a nossa. / This Thesis presents a proposal of an infrastructure to allow the distribution of data in a Database Grid. The storage of complex objects, such as audio, video and software etc. in Databases is always done in an integral way. This means that the object, regardless of its size, it is not fragmented by the Database Management System (DBMS). Methodologies used for data modeling also do not allow fragmentation or segmentation of complex objects. This happens because only the fragmentation of storage structures such as tables or classes are taken into account, not the embedded objects. When we evaluate the performance of systems that store complex objects, we can verify that the size of the stored objects has considerable impact. Since multimedia objects or software distribution package require significant disk space for storage, traditional methods for replication or distribution of copies become very costly and many times inefficient. With the infrastructure developed in this work it was possible to segment and to distribute complex attributes of lines of a table in Database Grids. In this way, our solution improves the performance of the system that had the necessity to store documents of raised size, above of a specified boundary-value. Also the possible use of codes LDPC in this infrastructure was tested successfully. However, does not observe profits that justified its use in same ours applications.

O principal objetivo desta tese consiste em propor, desenvolver e implementar uma infra-estrutura para gerenciamento de um Banco de Dados baseado em Grid. O armazenamento de objetos complexos como áudio, vídeo, softwares etc., em Sistemas de Banco de Dados, sempre se dá de maneira integral, ou seja, o documento, independente do seu tamanho, não é fragmentado pelo Sistema de Gerência de Banco de Dados (SGBD) ao ser armazenado. Metodologias de modelagem de dados utilizadas também não especificam a fragmentação ou segmentação de um documento complexo quando do seu armazenamento, pois só contemplam a fragmentação das estruturas de armazenamento, no caso relações ou classes, e não os objetos que serão armazenados. Ao avaliarmos o desempenho de sistemas que armazenam objetos complexos, verificamos que o tamanho dos objetos armazenados influencia consideravelmente o desempenho destes sistemas. Como objetos multimídia, softwares, etc., necessitam de grandes volumes em disco para seu armazenamento, métodos de replicação ou distribuição de cópias tradicionais tornam-se muito dispendiosos e por vezes ineficientes. Com a infra-estrutura desenvolvida neste trabalho foi possível segmentar e distribuir atributos complexos de linhas de uma tabela, instaladas em Bancos de Dados baseado em Grid. Nossa solução melhorou o desempenho do sistema que tinha a necessidade de armazenar documentos de tamanho elevado, acima de um tamanho limite. Também foi testada com sucesso a possível utilização dos códigos LDPC nesta infra-estrutura. Entretanto, não observamos ganhos que justificassem sua utilização em aplicações semelhantes a nossa. / This Thesis presents a proposal of an infrastructure to allow the distribution of data in a Database Grid. The storage of complex objects, such as audio, video and software etc. in Databases is always done in an integral way. This means that the object, regardless of its size, it is not fragmented by the Database Management System (DBMS). Methodologies used for data modeling also do not allow fragmentation or segmentation of complex objects. This happens because only the fragmentation of storage structures such as tables or classes are taken into account, not the embedded objects. When we evaluate the performance of systems that store complex objects, we can verify that the size of the stored objects has considerable impact. Since multimedia objects or software distribution package require significant disk space for storage, traditional methods for replication or distribution of copies become very costly and many times inefficient. With the infrastructure developed in this work it was possible to segment and to distribute complex attributes of lines of a table in Database Grids. In this way, our solution improves the performance of the system that had the necessity to store documents of raised size, above of a specified boundary-value. Also the possible use of codes LDPC in this infrastructure was tested successfully. However, does not observe profits that justified its use in same ours applications.

Ce travail porte sur la mise en forme des matériaux composites à matrice polymère renforcée par des fibres courtes dont les performances physiques et mécaniques sont directement reliées à la distribution spatiale et à l’orientation des renforts employés. Il se focalise sur l’étude des mécanismes de déformation se produisant au cours de l’écoulement de ces systèmes qui se comportent comme des suspensions de fibres non-newtoniennes. Le problème est abordé par une procédure originale combinant images 3D acquises en temps réel et simulations numériques avancées, réalisées à l’échelle des fibres. Dans le premier cas, des suspensions modèles avec fluide suspensif non-newtonien ont été déformées en compression dans des conditions confinées dans un microtomographe à rayons X synchrotron. Cette technique a permis l’acquisition en temps réel de clichés 3D à forte résolution spatiale de l’écoulement des suspensions. Dans le deuxième cas, un code de calculs éléments finis 3D a été utilisé, celui-ci étant capable de décrire finement des objets immergés dans des fluides non-newtoniens, par des level-sets et des techniques de remaillage anisotrope. La pertinence des simulations numériques dans les régimes de concentration dilués à semi-dilués a été jaugée par une comparaison expériences-simulations avancée.De là, dans le régime de concentration dilué, nous montrons que le confinement de l’écoulement et le comportement rhéofluidifiant du fluide suspensif ont une influence mineure sur la cinématique des fibres, si ces dernières sont suffisamment éloignées des plateaux de compression. Si ce prérequis n’est pas respecté, l’effet du confinement devient important. Des modifications au modèle heuristique d’haltère de la littérature ont été proposées pour corriger la cinématique de fibres. Dans le régime semi-dilué, des déviations de la cinématique de fibres sont également observées au cœur des suspensions. Ces déviations sont principalement liées aux interactions hydrodynamiques entre fibres suffisamment voisines. La cinématique des fibres prédite par le modèle de Jeffery et les approximations de champ affine sont mises en défaut. Dans le régime concentré, si l’évolution de l’orientation globale de la suspension est étonnamment bien décrite par l’équation de Jeffery, de très importantes fluctuations des champs de translation et de rotation des fibres sont observées à l’échelle des fibres. Celles-ci sont induites par les nombreux contacts entre fibres qui peuvent par ailleurs être correctement prédits par le modèle de tube. / This study focuses on the processing of short fibre-reinforced polymer composites. The physical and mechanical properties of these materials are mainly affected by the position and orientation distribution of fibres induced during their forming. Thus, we analysed the flow-induced micro-mechanisms that arose at the fibre scale during the forming stage of these complex systems which behave as non-Newtonian fibre suspensions. For that purpose, an original approach was developed by combining 3D imaging technique and direct numerical simulation, both performed at the fibre scale. Hence, several model fibre suspensions with a non-Newtonian suspending fluid and with a concentration regime that ranged from dilute to concentrated were prepared . They were subjected to confined lubricated compression loadings using a rheometer mounted on a synchrotron X-ray microtomograph. Thanks to very short scanning times, 3D images of the evolving fibrous microstructures at high spatial resolution were recorded in real-time. These experiments were also simulated using a dedicated Finite Element library enabling an accurate description of fibre kinematics in complex suspending fluids thanks to high performance computation, level sets and adaptive anisotropic meshing. The efficiency of the numerical simulation from the dilute to semi-dilute concentration regimes was assessed through experimental and numerical comparisons.Then, we showed that the confinement effect and the non-Newtonian rheology of the suspending fluid had a weak effect on the fibre kinematics, if the fibres were sufficiently far from the compression platens, typically the fibre-platen distance should be larger than twice the fibre diameter. Otherwise, confinement effects occurred. Some extensions of the dumbbell model were proposed to correct the fibre kinematics in this flow conditions. In semi-dilute concentration, deviations of the fibre kinematics compared to the Jeffery’s predictions were also observed and related to hydrodynamic interactions between fibres. In this case, the predictions of Jeffery’s model and the related assumption of affine fibre motions are less relevant. In the concentrated regime, even if the overall orientation of fibre suspension could be astonishingly well described by using the Jeffery’s model, strong fluctuations on each fibre motion and rotation were observed. These deviations were induced by the numerous fibre-fibre contacts, which could be correctly predicted by the tube model.