<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>

<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>

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

In this thesis context refers to information about the environment (the user or entity's surroundings) that can influence and determine the behavior of a computing system. Context-awareness means that the computer can adapt to the situation in which it is working. Context is a key issue in mobile computing, especially with handheld devices (such as PDAs and mobile phones), due to the fact that they can be used while on the move; hence the environment around them can change. The environment of a static device may also change and require the device to adapt. Applications and systems that exploit context by both sensing and reacting to their environment are called context-aware applications. Devices that are context-aware are able to perceive stimuli and react accordingly, with minimal interaction with the user. Providing context-aware services to users of mobile devices via context-aware applications is becoming an important and significant factor in the market and is a developing industry. In this thesis we analyze and develop an application that exploits context to provide a service that improves the interaction between humans and a computer. The thesis begins with a study of what types of sensors are available to provide information about the device's context. This is followed by the design of an appropriate way of using the selected sensor (ecompass) to provide a means of adapting a service to the user's and device's context. The focus is every day activities of a student at a university - specifically finding the location of a meeting room for a seminar; however, similar scenarios exist for other types of users. After determining that it was feasible to add a e-compass as a sensor to an existing personal digital assistant and to provide a map to the mobile user, the focus of the thesis shifted to an examination of the performance of the adaptation of the map as the user moved the device. Initially it required excessive time to render the map on the device, thus as the user moved the device the map was not updated quickly enough for the user to know their correct orientation with respect to the map. Therefore the thesis project examined how this performance could be improved sufficiently that the rendering would keep up with the change in orientation of the device. This investigation lead to a shift from server based rendering of the map as an image, followed by the transfer of the image to the device for display; to a sending a scalable vector graphics version of the map to the device for local rendering. While initially this was expected to be much faster than transferring an image for an actual map of the building where this work was taking place the local rendering was actually slower. This subsequently lead to server based pruning of the irrelevant details from the map, then a transfer of the relevant portion of the map to the device, followed by local rendering. / I den här avhandlingen hänvisar 'context' till information om miljön (i användarens eller enhetens omgivning) som kan bestämma och påverka beteendet hos ett datorsystem. Contex-awareness innebär att datorn kan anpassa sig till den situation där den arbetar. Context är en central fråga för mobila enheter, speciellt för handhållna enheter (t.ex. handdatorer och mobiltelefoner), på grund av att de kan användas på resande fot där omgivningen hela tiden förändras. Omgivningen för en statisk enhet kan också förändras och kräver att enheten kan anpassa sig. Applikationer och system som utnyttjar context genom att både känna av och reagera på sin omgivning kallas context-aware applications. Enheter som är kontextmedvetna kan uppfatta stimuli och reagera på den med minimal användarinteraktion. Att tillhandahålla kontextmedvetna tjänster till användare av mobila enheter via kontextmedvetna applikationer blir en allt viktigare och betydelsefullare faktor på marknaden och är en växande industri. I den här avhandlingen analyserar och utvecklar vi ett program som utnyttjar kontext för att tillhandahålla en tjänst som förbättrar samspelet mellan människa och dator. Avhandlingen inleds med en undersökning av vilka typer av sensorer som finns tillgängliga för att tillhandahålla information om enhetens kontext. Detta följs av en design för att på lämpligaste sätt använda den valda sensorn (e-kompass) för att tillhandahålla ett sätt att anpassa en tjänst till användaren och enhetens kontext. Fokus är vardagsaktivitieter för en student vid ett universitet - särskilt att hitta till ett konferensrum för ett seminarium, liknande scenarier finns även för andra typer av användare. Efter att ha fastställt att det var möjligt att koppla en sensor, i form av en e-kompass, till en befintlig personal digital assistant samt att visa en karta för användaren, flyttades fokus för avhandlingen till en undersökning om tjänstens prestanda när användaren flyttade enheten. Initialt krävde enheten väldigt lång tid att rendera kartan och när enheten flyttades uppdaterades kartan inte tillräckligt snabbt för att användaren skulle veta sin riktning i relation till kartan. Därför undersöktes hur prestandan kunde förbättras så att enheten skulle kunna hänga med bättre när enhetens riktning förändrades. Undersökningen ledde till att istället för att rendera en bild på servern och sedan skicka till enheten, skapa en vektorbaserad bild på servern, skicka till enheten och rendera lokalt. Även om detta initialt förväntades vara mycket snabbare än att överföra en bild av en verklig karta var den lokala renderingen faktiskt ännu långsammare. Detta ledde till en serverbaserad gallring av ovidkommande kartdetaljer samt beskärning innan kartan fördes över till enheten och renderades lokalt.

Made available in DSpace on 2014-06-11T19:32:18Z (GMT). No. of bitstreams: 0 Previous issue date: 2008-10-17Bitstream added on 2014-06-13T20:43:12Z : No. of bitstreams: 1 moreira_mr_dr_rcla.pdf: 2967010 bytes, checksum: a3a8fd8d971c6b62113182b986e3ed84 (MD5) / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / 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. / 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.

<p>An IPTV Set-top box enables the possibility of doing much more than decodingtelevision content. Its Ethernet interface gives it the same possibilities to communicatewith the outside world as any network device. This enables a wide rangeof services from internet radio to acting as a digital media receiver in your homenetwork. These highly interactive services increase the demands for responsiveand visually attractive user interfaces.Due to the cost-sensitive market of IPTV STBs the preferred platform to developthe user interface is the HTML browser as it allows for fast developmenttimes and low costs. As a W3C standard it also offers high portability and hardwareabstraction making it easy to use more than one STB vendor. The cons ofHTML based GUIs are low performance and lacklustre graphics.This thesis aims to find out if SVG can be used to achieve rich, scalable and animatedgraphics with high performance and still keep the attractive characteristicsof HTML.To do this much effort was put into identifying the strenghts and weaknesses ofSVG. The lessons learned resulted in an SVG AJAX framework called TOIXSVGmaking it possible to develop SVG GUIs in the same manner as modern Rich InternetApplications, enabling component reuse to make sure development time scalespreferably with the scope and complexity of the user interface. Along with theframework several new widgets had to be developed to achieve the targeted functionality.As a proof of concept a mock-up GUI was created with the frameworkand widgets.</p>

An IPTV Set-top box enables the possibility of doing much more than decodingtelevision content. Its Ethernet interface gives it the same possibilities to communicatewith the outside world as any network device. This enables a wide rangeof services from internet radio to acting as a digital media receiver in your homenetwork. These highly interactive services increase the demands for responsiveand visually attractive user interfaces.Due to the cost-sensitive market of IPTV STBs the preferred platform to developthe user interface is the HTML browser as it allows for fast developmenttimes and low costs. As a W3C standard it also offers high portability and hardwareabstraction making it easy to use more than one STB vendor. The cons ofHTML based GUIs are low performance and lacklustre graphics.This thesis aims to find out if SVG can be used to achieve rich, scalable and animatedgraphics with high performance and still keep the attractive characteristicsof HTML.To do this much effort was put into identifying the strenghts and weaknesses ofSVG. The lessons learned resulted in an SVG AJAX framework called TOIXSVGmaking it possible to develop SVG GUIs in the same manner as modern Rich InternetApplications, enabling component reuse to make sure development time scalespreferably with the scope and complexity of the user interface. Along with theframework several new widgets had to be developed to achieve the targeted functionality.As a proof of concept a mock-up GUI was created with the frameworkand widgets.

The aim of this thesis is to develop an educational methodology for the following languages: Markdown, HyperText Markup Language (HTML), eXtensible Markup Language (XML) and Scalable Vector Graphics (SVG); and to verify the methodology at Czech elementary schools on the lower secondary level. An integral part of the methodology is also an introduction to the history and development, as well as the theory of syntax of the mentioned markup languages, necessary for teaching according to this methodology. The methodology uses specific examples, on which the students can verify their newly acquired knowledge in practice. The verification of the methodology took place in the form of teaching at two Czech elementary schools. The teaching took place in the seventh grade within the compulsory elective subject of informatics, in the ninth grade within a compulsory subject. The expected differences in understanding the markup languages education in favor of the ninth year have not been confirmed. The motivation of the students proved to play much greater role than their age. The verification of the methodology has shown that it is necessary to pay careful attention to the precise formulation of the task assignments and guidelines to the students, to avoid confusion and substitution of the source code of the...

This diploma thesis focuses on graph database data visualization, where data is stored in RDF format. Standard visualisation of RDF data in tables does not offer sufficiently usable user view. One of the goals of this work is to show RDF data in interactive graph, which is ideal form of viewing data considering lucidity and information value. The graph gives good view of not only the data itself but also relationships between the data. Another goal is to test ability of browsers to visualize large amounts of data.