Afin de construire des systèmes intelligents, où les machines sont capables de raisonner exactement comme les humains, les données avec sémantique sont une exigence majeure. Ce besoin a conduit à l’apparition du Web sémantique, qui propose des technologies standards pour représenter et interroger les données avec sémantique. RDF est le modèle répandu destiné à décrire de façon formelle les ressources Web, et SPARQL est le langage de requête qui permet de rechercher, d’ajouter, de modifier ou de supprimer des données RDF. Être capable de stocker et de rechercher des données avec sémantique a engendré le développement des nombreux systèmes de gestion des données RDF.L’évolution rapide du Web sémantique a provoqué le passage de systèmes de gestion des données centralisées à ceux distribués. Les premiers systèmes étaient fondés sur les architectures pair-à-pair et client-serveur, alors que récemment l’attention se porte sur le cloud computing.Les environnements de cloud computing ont fortement impacté la recherche et développement dans les systèmes distribués. Les fournisseurs de cloud offrent des infrastructures distribuées autonomes pouvant être utilisées pour le stockage et le traitement des données. Les principales caractéristiques du cloud computing impliquent l’évolutivité́, la tolérance aux pannes et l’allocation élastique des ressources informatiques et de stockage en fonction des besoins des utilisateurs.Cette thèse étudie la conception et la mise en œuvre d’algorithmes et de systèmes passant à l’échelle pour la gestion des données du Web sémantique sur des platformes cloud. Plus particulièrement, nous étudions la performance et le coût d’exploitation des services de cloud computing pour construire des entrepôts de données du Web sémantique, ainsi que l’optimisation de requêtes SPARQL pour les cadres massivement parallèles.Tout d’abord, nous introduisons les concepts de base concernant le Web sémantique et les principaux composants des systèmes fondés sur le cloud. En outre, nous présentons un aperçu des systèmes de gestion des données RDF (centralisés et distribués), en mettant l’accent sur les concepts critiques de stockage, d’indexation, d’optimisation des requêtes et d’infrastructure.Ensuite, nous présentons AMADA, une architecture de gestion de données RDF utilisant les infrastructures de cloud public. Nous adoptons le modèle de logiciel en tant que service (software as a service - SaaS), où la plateforme réside dans le cloud et des APIs appropriées sont mises à disposition des utilisateurs, afin qu’ils soient capables de stocker et de récupérer des données RDF. Nous explorons diverses stratégies de stockage et d’interrogation, et nous étudions leurs avantages et inconvénients au regard de la performance et du coût monétaire, qui est une nouvelle dimension importante à considérer dans les services de cloud public.Enfin, nous présentons CliqueSquare, un système distribué de gestion des données RDF basé sur Hadoop. CliqueSquare intègre un nouvel algorithme d’optimisation qui est capable de produire des plans massivement parallèles pour des requêtes SPARQL. Nous présentons une famille d’algorithmes d’optimisation, s’appuyant sur les équijointures n- aires pour générer des plans plats, et nous comparons leur capacité à trouver les plans les plus plats possibles. Inspirés par des techniques de partitionnement et d’indexation existantes, nous présentons une stratégie de stockage générique appropriée au stockage de données RDF dans HDFS (Hadoop Distributed File System). Nos résultats expérimentaux valident l’effectivité et l’efficacité de l’algorithme d’optimisation démontrant également la performance globale du système. / In order to build smart systems, where machines are able to reason exactly like humans, data with semantics is a major requirement. This need led to the advent of the Semantic Web, proposing standard ways for representing and querying data with semantics. RDF is the prevalent data model used to describe web resources, and SPARQL is the query language that allows expressing queries over RDF data. Being able to store and query data with semantics triggered the development of many RDF data management systems. The rapid evolution of the Semantic Web provoked the shift from centralized data management systems to distributed ones. The first systems to appear relied on P2P and client-server architectures, while recently the focus moved to cloud computing.Cloud computing environments have strongly impacted research and development in distributed software platforms. Cloud providers offer distributed, shared-nothing infrastructures that may be used for data storage and processing. The main features of cloud computing involve scalability, fault-tolerance, and elastic allocation of computing and storage resources following the needs of the users.This thesis investigates the design and implementation of scalable algorithms and systems for cloud-based Semantic Web data management. In particular, we study the performance and cost of exploiting commercial cloud infrastructures to build Semantic Web data repositories, and the optimization of SPARQL queries for massively parallel frameworks.First, we introduce the basic concepts around Semantic Web and the main components and frameworks interacting in massively parallel cloud-based systems. In addition, we provide an extended overview of existing RDF data management systems in the centralized and distributed settings, emphasizing on the critical concepts of storage, indexing, query optimization, and infrastructure. Second, we present AMADA, an architecture for RDF data management using public cloud infrastructures. We follow the Software as a Service (SaaS) model, where the complete platform is running in the cloud and appropriate APIs are provided to the end-users for storing and retrieving RDF data. We explore various storage and querying strategies revealing pros and cons with respect to performance and also to monetary cost, which is a important new dimension to consider in public cloud services. Finally, we present CliqueSquare, a distributed RDF data management system built on top of Hadoop, incorporating a novel optimization algorithm that is able to produce massively parallel plans for SPARQL queries. We present a family of optimization algorithms, relying on n-ary (star) equality joins to build flat plans, and compare their ability to find the flattest possibles. Inspired by existing partitioning and indexing techniques we present a generic storage strategy suitable for storing RDF data in HDFS (Hadoop’s Distributed File System). Our experimental results validate the efficiency and effectiveness of the optimization algorithm demonstrating also the overall performance of the system.

This project addresses parallelization of building and testing projects written i Java programming language. It proposes software that uses methods of continual integration, parallelization and distribution of computationally intensive tasks to grid architecture. Suggested software helps to accelerate the development of software product and automation of its parts.

Master thesis is dealing with design and implementation of ray-tracing and path-tracing using IPP library. Theoretical part discusses current trends in acceleration of selected algorithms and also possibilities of parallelization. Design of ray-tracing and path-tracing algorithm and form of parallelization are described in proposal. This part also discusses implementation of adaptive sampling and importance sampling with Monte Carlo method to accelerate path-tracing algorithm. Next part is dealing with particular steps in implementation of selected rendering methods regarding IPP library. Implementation of network interface using Boost library is also discussed. At the end, implemented methods are subjected to performance and quality test. Final product of this thesis is server aplication capable of handling multiple connections which provides visualisation and client application which implements ray-tracing and path-tracing.

The Protein Data Bank (PDB) is the definitive electronic repository for experimentally-derived protein structures, composed mainly of those determined by X-ray crystallography. Approximately 200 new structures are added weekly to the PDB, and at the time of writing, it contains approximately 97,000 structures. This represents an expanding wealth of high-quality information but there seem to be few bioinformatics tools that consider and analyse these data as an ensemble. This thesis explores the development of three efficient, fast algorithms and software implementations to study protein structure using the entire PDB. The first project is a crystal-form matching tool that takes a unit cell and quickly (< 1 second) retrieves the most related matches from the PDB. The unit cell matches are combined with sequence alignments using a novel Family Clustering Algorithm to display the results in a user-friendly way. The software tool, Nearest-cell, has been incorporated into the X-ray data collection pipeline at the Diamond Light Source, and is also available as a public web service. The bulk of the thesis is devoted to the study and prediction of protein disorder. Initially, trying to update and extend an existing predictor, RONN, the limitations of the method were exposed and a novel predictor (called MoreRONN) was developed that incorporates a novel sequence-based clustering approach to disorder data inferred from the PDB and DisProt. MoreRONN is now clearly the best-in-class disorder predictor and will soon be offered as a public web service. The third project explores the development of a clustering algorithm for protein structural fragments that can work on the scale of the whole PDB. While protein structures have long been clustered into loose families, there has to date been no comprehensive analytical clustering of short (~6 residue) fragments. A novel fragment clustering tool was built that is now leading to a public database of fragment families and representative structural fragments that should prove extremely helpful for both basic understanding and experimentation. Together, these three projects exemplify how cutting-edge computational approaches applied to extensive protein structure libraries can provide user-friendly tools that address critical everyday issues for structural biologists.

This master's thesis describes Semantic Enrichment Component (SEC), that searches entities (e.g., persons or places) in the input text document and returns information about them. The goals of this component are to create a single interface for named entity recognition tools, to enable parallel document processing, to save memory while using the knowledge base, and to speed up access to its content. To achieve these goals, the output of the named entity recognition tools in the text was specified, the tool for storing the preprocessed knowledge base into the shared memory was implemented, and the client-server scheme was used to create the component.