[pt] Sistemas de software normalmente são descritos por sua arquitetura. Esta descrição fornece uma visão abstrata, demonstrando como o sistema é composto por módulos e interações entre estes módulos. Usando-se a arquitetura como uma especificação executável do sistema, consegue-se maior compromisso entre os requisitos do sistema e sua implementação. Tal compromisso simplifica o desenvolvimento e manutenção de sistemas complexos. Este trabalho define conceitos úteis para a construção, execução e gerenciamento de aplicações distribuídas, usando especificações arquiteturais. A metodologia apresentada distingue a construção de módulos através de programação, da efetiva construção da aplicação, através de configuração (ou especificação da arquitetura). Desta forma, pode-se adotar soluções específicas (e.g. linguagens e metodologias) para módulos particulares, mantendo-se o encapsulamento necessário para seu uso de forma transparente. Para validar os conceitos e permitir sua aplicação em um ambiente de execução real, foi criada uma Linguagem de Configuração chamada BABEL. No decorrer da dissertação, são apresentados os conceitos envolvidos e BABEL. Com o suporte do ambiente RIO, BABEL oferece simplicidade, transparência e flexibilidade para a construção de aplicações distribuídas complexas, possuindo conceitos básicos que viabilizam a elaboração de mecanismos avançados como contratos, herança e polimorfismo. Adicionalmente, são demonstradas experiências decorrentes da implementação de um Interpretador e um Servidor de Nomes para a linguagem. Finalmente, os conhecimentos obtidos com esta pesquisa são apresentados, sugerindo-se trabalhos futuros para continuidade do projeto BABEL. / [en] Software systems are usually described from their architecture. This description provides an abstract vision showing how the system is composed with modules and module interactions. Consistency between the system requirements and implementation may be achieved by using the architecture as a system executable specification. This guarantee of consistency simplifies the development and maintenance of complex systems. This study defines concepts useful to distributed application contructions, execution and management. The presented methodology distinguishes the builiding of modules, throught programming, from the effective application buiding through configuration (or architectural specification). Thus, specific solutions (e.g languages and methodologies) may be adopted for particular modules, preserving the necessary encapsulation for transparent use. A Configuration Language called BABEL was developed to validate these the concepts and apply them in a real execution environment. In the dissertation BABEL ans its related concepts are presented. Along with RIO Environment support, BABEL offers simplicity, transparency and flexibility for complex distributed application construction. It has concepts that allow advanced mechanisms such as contracts, inheritance and polymorphism. Additionally, a language Interpreter and a Name Server implementation for BABEL are presented. Finally, the knowledge gained from this study is presented, along with recommendations for future directions for the BABEL project.

Soient K un corps de nombres d'anneau des entiers O_K et G un groupe fini. Grâce à un résultat de E. Noether, l'anneau des entiers d'une extension galoisienne de K modérément ramifiée, de groupe de Galois G, est un O_K[G]-module localement libre de rang 1. Donc, à chaque extension galoisienne L/K modérément ramifiée, de groupe de Galois G, on peut associer une classe [O_L] dans le groupe des classes des modules localement libres Cl(O_K[G]). L'ensemble des classes de Cl(O_K[G]) qui peuvent être obtenues de cette façon est appelé ensemble des classes réalisables et on le note R(O_K[G]).Dans cette thèse, on étudie différents problèmes liés à R(O_K[G]). Dans la première partie, nous nous focalisons sur la question suivante: R(O_K[G]) est-il un sous-groupe de Cl(O_K[G])? Si G est abélien, L. McCulloh a prouvé que R(O_K[G]) coïncide avec le soi-disant sous-groupe de Stickelberger St(O_K[G]) dans Cl(O_K[G]). Dans le Chapitre 2, nous donnons une présentation détaillée d'un travail non publié de L. McCulloh qui étend la définition de St(O_K[G]) au cas non-abélien et montre que R(O_K[G]) est inclus dans St(O_K[G]) (l'inclusion opposée n'est pas encore connue dans le cas non-abélien). Puis, en utilisant sa définition et le Théorème de Stickelberger classique, nous montrons dans le Chapitre 3 que St(O_K[G]) est trivial si K=Q et G est soit un groupe cyclique d'ordre p soit un groupe diédral d'ordre 2p, avec p premier impair. Ceci, lié aux résultats de McCulloh, nous donne une nouvelle preuve de la trivialité de R(O_K[G]) dans les cas considérés.Les résultats originaux les plus importants sont contenus dans la deuxième partie de cette thèse. Dans le Chapitre 4 nous montrons la fonctorialité de St(O_K[G]) par rapport au changement du corps de base. Ceci implique que si N/L est une extension galoisienne modérément ramifiée, de groupe de Galois G, et St(O_K[G]) est connu être trivial pour un certain sous-corps K de L, alors O_N est un O_K[G]-module stablement libre.Dans le dernier chapitre, nous montrons un résultat concernant la distribution des classes réalisables parmi les extensions galoisiennes de K modérément ramifiées, de groupe de Galois G, dans lesquelles un idéal premier de K donné est totalement décomposé. / Let K be a number field with ring of integers O_K and let G be a finite group.By a result of E. Noether, the ring of integers of a tame Galois extension of K with Galois group G is a locally free O_K[G]-module of rank 1.Thus, to any tame Galois extension L/K with Galois group G we can associate a class [O_L] in the locally free class group Cl(O_K[G]). The set of all classes in Cl(O_K[G]) which can be obtained in this way is called the set of realizable classes and is denoted by R(O_K[G]).In this dissertation we study different problems related to R(O_K[G]).The first part focuses on the following question: is R(O_K[G]) a subgroup of Cl(O_K[G])? When the group G is abelian, L. McCulloh proved that R(O_K[G]) coincides with the so-called Stickelberger subgroup St(O_K[G]) of Cl(O_K[G]). In Chapter 2, we give a detailed presentation of unpublished work by L. McCulloh that extends the definition of St(O_K[G]) to the non-abelian case and shows that R(O_K[G]) is contained in St(O_K[G]) (the opposite inclusion is still not known in the non-abelian case).Then, just using its definition and Stickelberger's classical theorem, we prove in Chapter 3 that St(O_K[G]) is trivial if K=Q and G is either cyclic of order p or dihedral of order 2p, where p is an odd prime number. This, together with McCulloh's results, allows us to have a new proof of the triviality of R(O_K[G]) in the cases just considered.The main original results are contained in the second part of this thesis. In Chapter 4, we prove that St(O_K[G]) has good functorial behavior under restriction of the base field. This has the interesting consequence that, if N/L is a tame Galois extension with Galois group G, and St(O_K[G]) is known to be trivial for some subfield K of L, then O_N is stably free as an O_K[G]-module.In the last chapter, we prove an equidistribution result for Galois module classes amongst tame Galois extensions of K with Galois group G in which a given prime p of K is totally split.

Les nombres de Tamagawa des courbes elliptiques apparaissent dans la formulation de la conjecture de Birch et Swinnerton-Dyer comme certains facteurs locaux. Bloch et Kato (1990) ont trouvé une vaste généralisation de cette définition classique en termes de la théorie de Hodge p-adique. Ils ont associé un nombre de Tamagawa Tam(T) à tout réseau T de représentations p-adiques de de Rham au sens de J.-M. Fontaine. Ces nombres interviennent dans les conjectures de Bloch et Kato sur les valeurs spéciales des fonctions L des motifs.J.-M. Fontaine et B.Perrin-Riou ont formulé une conjecture reliant Tam(T) et le nombre de Tamagawa Tam(T*}(1)) de la représentation duale. Cette conjecture est connue pour les représentations cristallines ce qui permet de calculer explicitement les nombres de Tamagawa des représentations cristallines dont les poids de Hodge-Tate sont tous positifs. En revanche, dans la plupart des autres cas, nous n'avons pas de méthode de calcul explicite. Cette thèse a pour but de donner un encadrement des nombres de Tamagawa des représentations absolument cristallines le long de la tour cyclotomique sans hypothèses supplémentaires sur les poids de Hodge-Tate. Le premier chapitre de cette thèse est dédié à des rappels sur la théorie de Hodge p-adique, la classification de Fontaine des représentations p-adique de corps locaux via la théorie des (phi, Gamma)-modules, sur la cohomologie galoisienne, sur les modules de Wach ou sur la cohomologie d'Iwasawa. Le second chapitre est dédié à l'exponentielle de Bloch and Kato. Seront rappelées sa définition et sa construction de l'exponentielle de Bloch and Kato en termes de (phi, Gamma)-modules faite par D.Benois. Cette dernière construction permet de généraliser deux résultats de D.Benois et L.Berger qui relient l'exponentielle aux modules de Wach et qui permet de décrire des objets qui apparaissent naturellement dans l'étude des nombres de Tamagawa. Le dernier chapitre est le cœur de cette thèse. Nous commencerons en définissant les nombres de Tamagawa Tam(T) et en donnant certaines propriétés et résultats déjà connus. Nous énonçons ensuite le théorème final qui donne un encadrement des nombres de Tamagawa d'une représentation absolument cristalline V. Y sont également donnés certains cas d'égalité qui permettent de retrouver des formules connues --- lorsque V est positive ou lorsqu'elle provient d'une courbe elliptique et plus généralement d'un groupe formel de dimension 1 et de hauteur 2. Pour prouver ces résultats, nous écrivons les nombres de Tamagawa sous forme d'un indice généralisé dans lequel apparaissent les objets étudiés dans le chapitre précédent. La thèse se termine avec l'étude de plusieurs cas particuliers qui permettent de retrouver des résultats déjà connus. / Tamagawa numbers of elliptic curves appear in the Birch and Swinnerton-Dyer conjecture as local factors. Bloch and Kato generalized the definition using p-adic Hodge theory in 1990. Indeed they associated a number Tam(T) to each lattice T of de Rham representation in the sense of J-M\,Fontaine. This Tamagawa numbers are used in the conjectures of Bloch and Kato on the special values of L-functions of motives.J-M\,Fontaine and B.\,Perrin-Riou expressed a conjecture linking Tam(T) to the Tamagawa number Tam(T*(1)) of the dual representation. This conjecture is now well known for crystalline representations. This yields an explicit formula for Tamagawa number of crystalline p-adic representations having positive Hodge-Tate weights.On the other hand, we have no explicit formula for Tamagawa numbers of most of the crystalline representations. The purpose of the thesis is to give bounds of Tamagawa numbers of crystalline p-adic representations of unramified local field along the cyclotomic tower without further conditions on the Hodge-Tate weights.The first chapter of this thesis is dedicated to reminders on p-adic Hodge-Tate theory, Fontaine's classification of p-adic representations of local fields via (phi, Gamma)-modules, Galois and Iwasawa cohomology, Wach modules etc.The second chapter is dedicated to the Bloch and Kato's exponential map. We will recall its definition and its construction in terms of (phi, Gamma)-modules due to D.Benois. This construction will lead to the generalization of two results of D.\,Benois and L.\,Berger which link the exponential map and Wach modules and give a good description of the objects which naturally appear in the study of Tamagawa numbers.The last chapter is the heart of the thesis. We will begin by giving a definition of Tamagawa number Tam(T) and some first properties and results on theses numbers.We will next express the main theorems which give bounds of Tamagawa numbers of crystalline p-adic representations of unramified local field along the cyclotomic tower. We will also give equality conditions. This allows us to recover already known results such as Tamagawa numbers of positive crystalline representations or of representations coming from elliptic curves.To prove these results, we will write Tamagawa numbers as a generalized index of the modules defined in terms of Wach modules. Theses modules have been deeply studied in the second chapter of this thesis.

This thesis investigates some of the properties of R-modules. The material is presented in three chapters. Definitions and theorems which are assumed are stated in Chapter I. Proofs of these theorems may be found in Zariski and Samuel, Commutative Algebra, Vol. I, 1958. It is assumed that the reader is familiar with the basic properties of commutative rings and ideals in rings. Properties of R-modules are developed in Chapter II. The most important results presented in this chapter include existence theorems for R-modules and properties of submodules in R-modules. The third and final chapter presents an example which illustrates how a ring R, may be regarded as an R-module and speaks of the direct sum of ideals of a ring as a direct sum of submodules.

Le présent travail comporte une analyse du comportement sismique des sols renforcés par des inclusions rigides. L’étude est effectuée à l’aide d’une modélisation numérique tridimensionnelle par différences finies de l’interaction sol-matelas-inclusions-structure. Le comportement du sol est supposé de type élastoplastique avec un amortissement de type Rayleigh. Le travail est présenté en trois chapitres.Le premier chapitre comporte une synthèse des travaux réalisés sur les inclusions rigides et sur l’analyse de leur comportement en zone sismique. Il présente d’abord la technologie de renforcement par inclusions rigides ainsi que son utilisation et les méthodes de calcul sous chargement statique. Ensuite, il donne une synthèse des approches utilisées pour l’analyse de l’interaction sol-structure sous chargement sismique, et plus particulièrement pour les groupes de pieux et les inclusions rigides.Le second chapitre est consacré à l’analyse de l’interaction cinématique du système sol-matelas-inclusions-structure. L’analyse est effectuée à l’aide d’une approche globale qui consiste à calculer la réponse de l’ensemble des éléments du système à un chargement sismique. Elle est réalisée à l’aide d’une modélisation tridimensionnelle et non linéaire du système de renforcement. Le chapitre est composé de trois parties. La première expose le modèle numérique utilisé, la seconde présente une analyse d’un sol renforcé par un groupe de 2x2 inclusions rigides, la dernière est consacrée à une étude de l’influence de principaux paramètres sur la réponse sismique du groupe d’inclusions rigides.Le dernier chapitre est consacré à l’étude de l’influence de la présence de la structure sur l’interaction sol-matelas-inclusions-structure. L'accent est mis sur l’influence des paramètres majeurs tels que les caractéristiques géométriques et mécaniques du matelas, la rigidité des inclusions, les conditions de liaison inclusions-matelas et l’amplitude du chargement. Ce chapitre donne aussi une comparaison entre le comportement sismique des inclusions rigides avec celui d’un groupe de colonnes de module mixte (CMM) et d’un groupe de pieux. / This work includes an analysis of seismic behaviour of soft soil improved by vertical rigid inclusions. The study is conducted by using a three-dimensional finite-difference numerical modelling of soil-gravel layer-inclusions-structure interaction. Soil media is assumed to be elastoplastic with Rayleigh damping. The work is presented in three chapters. The first chapter deals with a review of the literature on research previously conducted on rigid inclusions and their behaviour in seismic areas. Firstly, the technology of soft soil improvement by vertical rigid inclusions, its domains of applications and methods of calculation under static loading are presented. Then, a synthesis of approaches used to evaluate soil-structure interaction under seismic loading is reviewed; we focus more precisely on methods concerned the grouped piles and rigid inclusions.The second chapter is devoted to the analysis of kinematic interaction of soil_gravel layer-inclusions-structure system. The analysis is performed using a global approach which consists of calculating the response of all elements composing the latter system under seismic loading. The analysis is carried out by a nonlinear three-dimensional numerical modelling of the soil reinforcement system. The chapter is divided into three parts. The first one outlines the used numerical model; the second presents an analysis of a soil reinforces by a group of four rigid inclusions. In the third part, we present a parametric study which covers the influence of main parameters on the seismic response of the rigid inclusions group.The last chapter is devoted to the study of the influence of the presence of structure on the soil-gravel layer-inclusion-structure interaction. The influence of major parameters is highlightened by a parametric study concerns the effect of geometric and mechanical characteristics of the gravel layer, inclusion rigidity, the inclusions-gravel layer connection conditions and the amplitude of the seismic loading. The chapter gives a comparison between the seismic behaviour of rigid inclusion (IR) to both column with mixed module (CMM) and a group of classical piles.

No description available.

In the past decade, fast advancements have been made in the sequencing, digitalization and collection of the biological data. However the bottleneck remains at the point of analysis and extraction of patterns from the data. We have developed a method that is aimed at widening this bottleneck by automating the knowledge extraction from the biological data. Our approach is aimed at discovering patterns in a set of DNA sequences based on the location of transcription factor binding sites or any other biological markers with the emphasis of discovering relationships. A variety of statistical and computational methods exists to analyze such data. However, they either require an initial hypothesis, which is later tested, or classify the data based on its attributes. Our approach does not require an initial hypothesis and the classification it produces is based on the relationships between attributes. The value of such approach is that is is able to uncover new knowledge about the data by inducing a general theory based on basic known rules. The core of our approach lies in an inductive logic programming engine, which, based on positive and negative examples as well as background knowledge, is able to induce a descriptive, human-readable theory, describing the data. An application provides an end-to-end analysis of DNA sequences. A simple to use Web interface accepts a set of related sequences to be analyzed, set of negative example sequences to contrast the main set (optional), and a set of possible genetic markers as position-specific scoring matrices. A Java-based backend formats the sequences, determines the location of the genetic markers inside them and passes the information to the ILP engine, which induces the theory. The model, assumed in our background knowledge, is a set of basic interactions between biological markers in any DNA sequence. This makes our approach applicable to analyze a wide variety of biological problems, including detection of cis-regulatory modules and analysis of ChIP-Sequencing experiments. We have evaluated our method in the context of such applications on two real world datasets as well as a number of specially designed synthetic datasets. The approach has shown to have merit even in situations when no significant classification could be determined.

L'objet de cette thèse est d'étudier la géométrie des immeubles à angles droits. Ces espaces, définis par J. Tits sont des espaces singuliers qui peuvent être vus comme des généralisations des arbres en dimension supérieure. La thèse est divisée en deux parties. Dans la première partie, nous décrivons comment la notion de résidus parallèles permet de comprendre l'action d'un groupe sur un immeuble. En corollaire nous retrouvons que dans un groupe de Coxeter et dans un produit graphé les intersections de sous-groupes paraboliques sont paraboliques. Dans la seconde partie, nous abordons la structure quasi-conforme du bord des immeubles hyperboliques à angles droits. En particulier, nous trouvons des exemples d'immeubles de dimension 3 et 4 dont le bord vérifie la propriété combinatoire de Loewner. Cette propriété est une version faible de la propriété de Loewner. Cette partie est motivée par le fait que, depuis G.D. Mostow, la structure quasi-conforme au bord a mené à plusieurs résultats de rigidités dans les espaces hyperboliques. Dans le cas des immeubles de dimension 2, M. Bourdon et H. Pajot ont prouvé la rigidité des quasi-isométries en utilisant la propriété de Loewner au bord. / The object of this thesis is to study the geometry of right-angled buildings. These spaces, defined by J. Tits, are singular spaces that can be seen as trees of higher dimension. The thesis is divided in two parts. In the first part, we describe how the notion of parallel residues allows to understand the action of a group on the building. As a corollary we recover that in Coxeter groups and in graph products intersections of parabolic subgroups are parabolic. In the second part, we discuss the quasiconformal structure of boundaries of right-angled hyperbolic buildings thanks to combinatorial tools. In particular, we exhibit some examples of buildings of dimension 3 and 4 whose boundary satisfy the combinatorial Loewner property. This property is a weak version of the Loewner property. This part is motivated by the fact that the quasiconformal structure of the boundary led to many results of rigidity in hyperbolic spaces since G.D. Mostow. In the case of buildings of dimension 2, many works have been done by M. Bourdon and H. Pajot. In particular, the Loewner property on the boundary permitted them to prove the quasi-isometry rigidity for some buildings of dimension 2.

Microarray technology makes it possible to identify changes in gene expression of an organism, under various conditions. The challenge to researchers that employ microarray expression profiling is that once pre-processing is completed, and a cluster of co-expressed genes obtained, is to derive biological meaning from this data. Data mining is thus essential for deducing significant biological information such as the identification of new biological mechanisms or putative drug targets. While many algorithms and software have been developed for analysing gene expression, the extraction of relevant information from experimental data is still a substantial challenge, requiring significant time and skill. MADIBA (MicroArray Data Interface for Biological Annotation) facilitates the assignment of biological meaning to gene expression clusters by automating the post-processing stage. A relational database has been designed to store the data from gene to pathway for Plasmodium falciparum, Oryza sativa (rice), Arabidopsis thaliana, and Pectobacterium atrosepticum (Pba) As input, the user submits a cluster of genes, either the gene identifiers or the gene sequences. Tools within the web interface allow rapid analyses for the identification of the Gene Ontology terms relevant to each cluster; visualising the metabolic pathways where the gene products are implicated, their genomic localisations, putative common transcriptional regulatory elements in the upstream sequences, and an analysis specific to the organism being studied. The user has the option of outputting selected results of the analyses, either in PDF or plain text formats. MADIBA is an integrated, online tool that will assist researchers in interpreting their results and understand the meaning of the co-expression of a cluster of genes. Functionality of MADIBA was used to analyse a number of gene clusters from several experiments – expression profiling of the Plasmodium falciparum life cycle, a Ralstonia solanacearum infection ofArabidopsis thaliana, a rice treatment with BTH, a millet SA- and MeJ-treatment experiment, and an expI mutant experiment in Pectobacterium atrosepticum. Data from the Plasmodium falciparum and rice were used to illustrate MADIBA’s functionality. For the A. thaliana analyses, the DRASTIC database was implemented to identify how genes respond to various treatments. In addition, a method named PCA Experiment Comparer was developed, which compares the expression values of the numerous experiments in NASCArrays. Using the A. thaliana-R. solanacearum interaction data several related experiments matched in both the susceptible and resistant interactions. In the millet analyses, besides defence related genes being identified, several genes also involved in photosynthesis were found, possibly suggesting a relation between light and defence signalling. The Pba data identified genes involved in quorum sensing, as well as some associated genes with no known function that may also be related to this regulatory process. With the advent of whole genome microarray chips and an increasing number of organisms being sequenced, tools such as MADIBA will become even more significant in understanding the underlying biology. MADIBA provides access to several genomic data sources and analyses, allowing users to quickly annotate and visualise the results. MADIBA is freely available and can be accessed at http://www.bi.up.ac.za/MADIBA/. Copyright / Dissertation (MSc)--University of Pretoria, 2009. / Biochemistry / unrestricted

On construit de nouvelles connexions quantiques intégrables dans fibrés vectoriels au-dessus d'espaces de modules de surfaces de Riemann et de leurs généralisations sauvages, en utilisant deux approches différentes. Premièrement, on utilise la quantification par déformation pour construire de nouvelles connexions intégrables à partir d'Hamiltoniennes d'isomonodromie irrégulières, dans l'esprit de Reshetikhin de la dérivation de la connexion de Knizhnik-Zamolodchikov à partir des Hamiltoniennes de Schlesinger. Deuxièmement, on construit une version complexe de la connexion de Hitchin pour la quantification géométrique de l'espace de modules de Hitchin sur une surface de genre un, par rapport au groupe SL(2,C) et à des polarisations Kähleriennes, en complémentant l'approche par polarisations réelles de Witten. Finalement, on utilise la transformée de Bargmann pour dériver une formule pour la connexion de Hitchin-Witten dans le fibré vectoriel des sections holomorphes, et pour transformer l'action de Hitchin en une transformée sur l'espace de Segal--Bargmann, basée sur les états cohérents. / We construct new flat quantum connections on vector bundles over moduli spaces of Riemann surfaces and their wild generalisations, using two different approaches. Firstly, we use deformation quantisation to construct new flat connections from irregular isomonodromy Hamiltonians, in the spirit of Reshetikhin's derivation of the Knizhnik-Zamolodchikov connection from the Schlesinger Hamiltonians. Secondly, we construct a complex version of the Hitchin connection for the geometric quantisation of the Hitchin moduli space over a surface of genus one, with respect to the group SL(2,C) and to Kähler polarisations, complementing Witten's real polarisation approach. Finally, we use the Bargmann transform to derive a formula for the connection of Hitchin-Witten on the vector bundle of holomorphic sections, and to turn Hitchin's action into a transform on the Segal--Bargmann space, which relies on coherent states.