<p>In the post-genomics era, the sheer volume of data is overwhelming without appropriate tools for data integration and analysis. Studying genomic sequences in the context of other related genomic sequences, i.e. comparative genomics, is a powerful technique enabling the identification of functionally interesting sequence regions based on the principal that similar sequences tend to be either homologous or provide similar functionality.</p> <p>Costs associated with full genome sequencing make it infeasible to sequence every genome of interest. Consequently, simple, smaller genomes are used as model organisms for more complex organisms, for instance, Mouse/Human. An annotated model organism provides a source of annotation for transcribed sequences and other gene regions of the more complex organism based on sequence homology. For example, the gene annotations from the model organism aid interpretation of expression studies in more complex organisms.</p> <p>To assist with comparative genomics research in the Arabidopsis/Brassica (Thale-cress/Canola) model-crop pair, a web-based, graphical genome browser (BioViz) was developed to display short Brassica genomic sequences in the context of the Arabidopsis model organism genome. This involved the development of graphical representations to integrate data from multiple sources and tools, and a novel user interface to provide the user with a more interactive web-based browsing experience. While BioViz was developed for the Arabidopsis/Brassica comparative genomics context, it could be applied to comparative browsing relative to other reference genomes.</p> <p>BioViz proved to be an valuable research support tool for Brassica / Arabidopsis comparative genomics. It provided convenient access to the underlying Arabidopsis annotation, allowed the user to view specific EST sequences in the context of the Arabidopsis genome and other related EST sequences. In addition, the limits to which the project pushed the SVG specification proved influential in the SVG community. The work done for BioViz inspired the definition of an opensource project to define standards for SVG based web applications and a standard framework for SVG based widget sets.</p>

Two-dimensional geometric textures are the geometric analogues of raster (pixel-based) textures and consist of planar distributions of discrete shapes with an inherent structure. These textures have many potential applications in art, computer graphics, and cartography. Synthesizing large textures by hand is generally a tedious task. In raster-based synthesis, many algorithms have been developed to limit the amount of manual effort required. These algorithms take in a small example as a reference and produce larger similar textures using a wide range of approaches. Recently, an increasing number of example-based geometric synthesis algorithms have been proposed. I refer to them in this dissertation as Geometric Texture Synthesis (GTS) algorithms. Analogous to their raster-based counterparts, GTS algorithms synthesize arrangements that ought to be judged by human viewers as “similar” to the example inputs. However, an absence of conventional evaluation procedures in current attempts demands an inquiry into the visual significance of synthesized results. In this dissertation, I present an investigation into GTS and report on my findings from three projects. I start by offering initial steps towards grounding texture synthesis techniques more firmly with our understanding of visual perception through two psychophysical studies. My observations throughout these studies result in important visual cues used by people when generating and/or comparing similarity of geometric arrangements as well a set of strategies adopted by participants when generating arrangements. Based on one of the generation strategies devised in these studies I develop a new geometric synthesis algorithm that uses a tile-based approach to generate arrangements. Textures synthesized by this algorithm are comparable to the state of the art in GTS and provide an additional reference in subsequent evaluations. To conduct effective evaluations of GTS, I start by collecting a set of representative examples, use them to acquire arrangements from multiple sources, and then gather them into a dataset that acts as a standard for the GTS research community. I then utilize this dataset in a second set of psychophysical studies that define an effective methodology for comparing current and future geometric synthesis algorithms.

Two-dimensional geometric textures are the geometric analogues of raster (pixel-based) textures and consist of planar distributions of discrete shapes with an inherent structure. These textures have many potential applications in art, computer graphics, and cartography. Synthesizing large textures by hand is generally a tedious task. In raster-based synthesis, many algorithms have been developed to limit the amount of manual effort required. These algorithms take in a small example as a reference and produce larger similar textures using a wide range of approaches. Recently, an increasing number of example-based geometric synthesis algorithms have been proposed. I refer to them in this dissertation as Geometric Texture Synthesis (GTS) algorithms. Analogous to their raster-based counterparts, GTS algorithms synthesize arrangements that ought to be judged by human viewers as “similar” to the example inputs. However, an absence of conventional evaluation procedures in current attempts demands an inquiry into the visual significance of synthesized results. In this dissertation, I present an investigation into GTS and report on my findings from three projects. I start by offering initial steps towards grounding texture synthesis techniques more firmly with our understanding of visual perception through two psychophysical studies. My observations throughout these studies result in important visual cues used by people when generating and/or comparing similarity of geometric arrangements as well a set of strategies adopted by participants when generating arrangements. Based on one of the generation strategies devised in these studies I develop a new geometric synthesis algorithm that uses a tile-based approach to generate arrangements. Textures synthesized by this algorithm are comparable to the state of the art in GTS and provide an additional reference in subsequent evaluations. To conduct effective evaluations of GTS, I start by collecting a set of representative examples, use them to acquire arrangements from multiple sources, and then gather them into a dataset that acts as a standard for the GTS research community. I then utilize this dataset in a second set of psychophysical studies that define an effective methodology for comparing current and future geometric synthesis algorithms.

De nos jours, les objets virtuels sont devenus omniprésents. On les trouve dans de nombreux domaines comme le divertissement (cinéma, jeux vidéo, etc.), la conception assistée par ordinateur ou encore la réalité virtuelle. Nous nous intéressons en particulier à la modélisation d'objets 3D dans le domaine de la création artistique. Ici, la création d'images riches nécessite de faire appel à des modèles très détaillés et donc extrêmement complexes. Les surfaces de subdivision, traditionnellement utilisées dans ces domaines, voient leur complexité croître rapidement lorsqu'on ajoute des détails, et la gestion de la connectivité du maillage de contrôle devient trop contraignante. Une approche standard pour gérer la complexité de tels modèles est d'utiliser des représentations différentes pour la forme générale de la surface et les détails. Cependant, ces détails sont représentés par des cartes matricielles qui ne possèdent pas la plupart des avantages des représentations vectorielles, et cela complexifie certaines tâches, comme par exemple l'animation. Dans cette thèse, nous proposons deux nouvelles représentations vectorielles, la première pour les surfaces de base, la deuxième pour les détails. Nous utilisons pour cette dernière une représentation vectorielle appelée images de diffusion permettant de créer des variations lisses à l'aide d'un ensemble réduit de contraintes. Cela nous permet de représenter aussi bien la géométrie que la couleur ou d'autres paramètres nécessaires au rendu de façon purement vectoriel, en conservant des contrôles de haut niveau.Notre première contribution est une représentation de surfaces, baptisée LS3, issue de la combinaison entre surfaces de subdivision et -point set surfaces. Cette approche réduit notablement les artefacts des surfaces de subdivision aux alentours de sommets dits extraordinaires, qui sont connus pour poser problème. Nous présentons une analyse numérique des propriétés de ces surfaces, qui tend à montrer que du point de vue de la continuité elles se comportent au moins aussi bien que les schémas de subdivision linéaires traditionnels. Notre deuxième contribution est un solveur pour les images de diffusion dont le principal avantage est de produire en sortie une autre représentation vectorielle légère et très rapide à évaluer. Nous illustrons la force de note solveur sur de nombreux exemples difficiles ou impossibles à réaliser avec les méthodes précédentes. Pour conclure, nous montrons comment combiner nos deux contributions pour obtenir une représentation de surface entièrement vectorielle capable de représenter des détails sans avoir à manipuler la connectivité d'un maillage. / Nowadays, virtual objects have become omnipresent. We can find them in various domains such as entertainment (movies, video games, etc.), computer-aided design or virtual reality. Our main focus in this document is the modeling of 3D objects in the domain of artistic creation, where rich images creation requires highly detailed and complex models.Subdivision surfaces, the most used surface representation in this domain, quickly become very dense as the user add details, and manual handling of the connectivity becomes too cumbersome. A standard approach to handle the complexity of such models is to separate the overall shape of the surface and the details. Although, these detail maps are often stored in bitmap images that does not provide the advantages of vectorial representation, which complicate some tasks, like animation.In this document, we present two new vectorial representations: the first one for the base surface, the second one for the detail maps. For the later, we use a vectorial representation called diffusion images that allow to create smooth or sharp variations from a small set of constraints. This enables us to represent geometry as well as color or any other parameter required for rendering, while keeping high-level controls.Our first contribution is a surface representation, called LS3, based on the combination of subdivision surfaces and point set surfaces. This approach reduces notably artifacts that subdivision surfaces produce around so called extraordinary vertices. We also present a numerical analysis of the mathematical properties of these surfaces, that show that they behave at least as well as classical subdivision schemes.Our second contribution is a solver for diffusion images that has the particularity to produce as output a denser vectorial representation which is light and fast to evaluate. We show the advantages of this approach on several examples that would be hard or impossible to produce with former methods.To conclude, we show how these two contributions can be used together to obtain a fully vectorial surface representation able to produce detailed surfaces without needing to deal with complex connectivity.

This thesis proposes a novel image primitive - the <b>diffusion curve</b>. This primitive relies on the principle that images can be defined via their discontinuities, and concentrates image features along contours. The diffusion curve can be defined in vector graphics, as well as in raster graphics, to increase user control during the process of art creation. The <i>vectorial diffusion curve</i> primitive augments the expressive powers of vector images by capturing complex spatial appearance behaviors. Diffusion curves represent a simple and easy-to-manipulate support for complex content representation and edition. In <i>raster</i> images, diffusion curves define a higher level structural organization of the pixel image. This structure is used to create simplified or exaggerated representations of photographs in a way consistent with the original image content. Finally, a fully automatic vectorization method is presented, that converts raster diffusion curve to vector diffusion curve.

A set top box is an embedded device, much like a computer with limited capabilities. Its main purpose is to decode a video signal and output it to a TV. The set top box market is constantly growing and to be competitive in it, a set top box has to be able to do more than only TV. One way to make an attractive product is to give it an appealing user interface. This thesis is a part of a larger work at the company to find new ways to create graphical user interfaces. Its goal is to investigate what SVG implementations that exits, which one that is most suitable for an integration attempt and then perform the integration. Several SVG engines were investigated and one provided by the company was selected for integration. Three ways to integrate the SVG engine were identified. One of these alternatives was to extend the callback interface be- tween the engine and the underlying platform. Because of the good fit with the current architecture this alternative was chosen and implemented. As a part of this investigation a demo application suite of SVG content was also constructed. This investigation resulted in a working integration of the chosen SVG engine on the platform. It has also showed that SVG is a suitable language to build graphical user interfaces on set top boxes.

<p>A set top box is an embedded device, much like a computer with limited capabilities. Its main purpose is to decode a video signal and output it to a TV. The set top box market is constantly growing and to be competitive in it, a set top box has to be able to do more than only TV. One way to make an attractive product is to give it an appealing user interface. This thesis is a part of a larger work at the company to find new ways to create graphical user interfaces. Its goal is to investigate what SVG implementations that exits, which one that is most suitable for an integration attempt and then perform the integration.</p><p>Several SVG engines were investigated and one provided by the company was selected for integration. Three ways to integrate the SVG engine were identified. One of these alternatives was to extend the callback interface be- tween the engine and the underlying platform. Because of the good fit with the current architecture this alternative was chosen and implemented. As a part of this investigation a demo application suite of SVG content was also constructed.</p><p>This investigation resulted in a working integration of the chosen SVG engine on the platform. It has also showed that SVG is a suitable language to build graphical user interfaces on set top boxes.</p>

The microstructure of the brain at the cellular level provides crucial information for the understanding of the function of the brain. A large volume of high-resolution brain image data from 3D microscopy is an essential resource to study detailed microstructures of the brain. Accordingly, we have worked on obtaining high-resolution image data of entire mouse brains using the Knife-Edge Scanning Microscope (KESM). Furthermore, to disseminate these high-resolution whole mouse brain data sets to the neuroscience research community, we developed a web-based brain atlas, the KESM Brain Atlas (KESMBA). To visualize the data sets in 3D while using only a standard web browser, we employed distance attenuation and Google Maps API. The KESMBA is a powerful tool to analyze and share the KESM mouse brain data sets, but the image loading was slow because of the number of raster image (PNG) tiles and the file size. Moreover, since Google Maps API is governed by a commercial license, it does not provide enough flexibility for customization, extension, and mirroring. To solve these issues, we designed and developed a new KESM mouse brain atlas that uses a vector graphics format called Scalable Vector Graphics (SVG) instead of PNG, and OpenLayers API instead of Google Maps API. The SVG-based KESMBA using OpenLayers allows faster navigation and exploration of the KESM data, and more overlay of layers with the 4 times reduced file size compared to PNG tiles. Due to the reduced file size, the SVG-based KESMBA using OpenLayers is 2.45 times faster than the original atlas. By enhancing the performance, the users can more easily access the KESM data. We expect the SVG-based KESMBA to accelerate new discoveries in neuroscience.

Resumo: Os movimentos de massa na Serra do Mar são alvos de muito interesse e estudo devido à alta incidência e aos conseqüentes impactos ambientais e econômicos. Portanto, reunir várias informações sobre movimentos de massa, e disponibilizá-los como um produto de fácil aquisição e de navegabilidade para o conhecimento de alunos de graduação, é o desafio desse trabalho. Como área de aplicação, escolheu-se o município de Cubatão, pela significativa incidência de escorregamentos e pela importância da região no contexto nacional, frente a aspectos econômicos e ambientais. Desta forma, o objetivo principal é produzir um Atlas Multimídia sobre os processos de movimentos de massa, como contribuição ao ensino de graduação, nas áreas de Ciências da Terra e Engenharia e avaliar a aplicabilidade da linguagem SVG (Scalable Vectorial Graphics) na produção de mapas interativos. Foi efetuada uma consulta a docentes e alunos da área de Ciências da Terra, sobre o interesse na utilização de material didático multimídia como apoio ao ensino e aprendizado e os resultados obtidos mostraram o claro interesse deste público no desenvolvimento do material .O Atlas interativo elaborado, voltado especificamente a escorregamentos, usando interfaces gráficas na linguagem SVG,mostrou que é possível a publicação de aplicações cartográficas interativas utilizando o SVG. Acredita-se que a utilização deste tipo de material como apoio ao ensino e aprendizado seja uma tendência crescente, impulsionada pelos avanços tecnológicos e pela forte inserção da informática em todos os setores de atividade. Inseridos neste contexto, os atuais alunos, desde muito cedo, vivem a informática nos seus cotidianos e a inserção destes recursos em sala de aula torna os cursos mais atrativos para este público. / Abstract: Mass movements of Serra do Mar are the subject of much interest and study due to high incidence, the consequent environmental and economic impacts. For these reasons, to get some information about mass movements and make them available as a product of easy acquisition and navigability for the knowledge of undergraduate students, it is the challenge of this work. The study area was the Cubatão city by the significant incidence of slip and the importance of the region in the national context, in face of economic and environmental aspects. Thus, the main goal is to produce an Atlas Multimedia about processes of mass movements, to contribute to the education of undergraduate students in Earth Sciences and Engineering areas and evaluate the applicability of the SVG (Scalable Vectorial Graphics) language in the production of interactive maps. It was done a questionnaire for the purpose of gathering information from teachers and students in Earth Sciences area, about the interest in the use of multimedia educational materials to support teaching and learning. The results showed clear interest of the public in developing the material. The Interactive Atlas prepared, specifically to landslide, using graphical interfaces in the SVG language, showed that it is possible to publish interactive mapping applications using SVG. It was believed that the use of such material to support teaching and learning is a growing trend, driven by technological advances and the strong integration of computer science technology in all sectors of this activity. In this context, the current students, from an early age, living in their everyday computing and the integration of these resources in the classroom make the courses more appealing to the public. / Orientador: Paulina Setti Riedel / Coorientador: Cristhiane da Silva Ramos / Banca: Teresa Galloti Florenzano / Banca: Diana Sarita Hamburger / Banca: Rosângela Doin de Almeida / Banca: Paulo Milton Barbosa Landim / Possui anexo 1 CD_ROM com o título: Atlas multimídia sobre movimentos de massa na sera do Mar paulista: município de Cubatão/SP / Doutor

To guarantee the well-functioning of modern societies, it is essential to ensure thatcitizens are aware of their environment as well as the government's actions andperformance. Therefor citizens need to have access to data collected by publicbodies from the activities within their society. However, these data may not easilyand instantly be perceivable by people. To release the potential of these data,which lead to improving the lives of citizen, the data need to analyzed, enhancedand eventually visualized, so the outcome would be usable to all regardless theirage and education. In this project, we propose, design, implement, and evaluate aninteractive analytical visualization framework for open-data. To achieve our purpose,the recent open data-sets from Sundsvall Municipality has been used as bothour case-study and demonstration sample. The solution has been design and builtbased on a set of requirements and principles we suggested for an ideal solution.The offered solution in this project enables users to analyze data by interactingwith the visualization graphics. The solution let the user extract information andfacts from large data-sets, and correlate different property of data by applying filtersand categorizing data, and see the result instantly. Standard web technologieswere used to implement the solution, namely HTML5, JavaScript, and SVGgraphics, which made the system to be cross-platform and high-performing. Tohandle the big-data, we enhance the data-set before-hand by performing aggregateoperations using Map-Reduce and parallel computing algorithms (i.e. Java-8 parallelstreams), and the further computation is implemented in JavaScript, and processedat the client-side.