<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>

<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.