VizBin: An application for reference-independent visualization and human-augmented binning of metagenomic data

Background: Metagenomics is limited in its ability to link distinct microbial populations to genetic potential due to a current lack of representative isolate genome sequences. Reference-independent approaches, which exploit for example inherent genomic signatures for the clustering of metagenomic fragments (binning), offer the prospect to...

Visualization of Variation and Variability

As datasets grow in size and complexity, the importance of comparison as a tool for analysis is growing. We define comparison as the act of analyzing variation or variability based on two or more specific instances of the data. This thesis explores a number of cases spread across the range of comparisons, from variability within one entity...

RCytoscape: Tools for exploratory network analysis

Background: Biomolecular pathways and networks are dynamic and complex, and the perturbations to them which cause disease are often multiple, heterogeneous and contingent. Pathway and network visualizations, rendered on a computer or published on paper, however, tend to be static, lacking in detail, and ill-equipped to explore the variety and...

Analyzing and Visualizing Spreadsheets

Spreadsheets are used extensively in industry: they are the number one tool for financial analysis and are also prevalent in other domains, such as logistics and planning. Their flexibility and immediate feedback make them easy to use for non-programmers. But as easy as spreadsheets are to build, so difficult can they be to analyze and adapt....

Supporting professional spreadsheet users by generating leveled dataflow diagrams

Thanks to their flexibility and intuitive programming model, spreadsheets are widely used in industry, often for businesscritical applications. Similar to software developers, professional spreadsheet users demand support for maintaining and transferring their spreadsheets. In this paper, we first study the problems and information needs of...

Visual Analysis of Multi-Field Data

This thesis investigates methods for the visualization of multi-field medical data. In the medical field, data complexity has been growing consistently over the past years. Not only the size of the data grows, but also the need to visualize beyond traditional boundaries. We present a number of novel facets that encompass a general approach to...

Execution Trace Analysis through Massive Sequence and Circular Bundle Views

Preprint of article published in: Journal of Systems and Software (Elsevier), 81 (12), 2008; doi:10.1016/j.jss.2008.02.068 An important part of many software maintenance tasks is to gain a sufficient level of understanding of the system at hand. The use of dynamic information to aid in this software understanding process is a common practice...

Efficient seeding and defragmentation of curvature streamlines for colonic polyp detection

Many computer aided diagnosis (CAD) schemes have been developed for colon cancer detection using Virtual Colonoscopy (VC). In earlier work, we developed an automatic polyp detection method integrating flow visualization techniques, that forms part of the CAD functionality of an existing Virtual Colonoscopy pipeline. Curvature streamlines were...

Selective visualization on curvilinear grids, Selectieve visualisatie op kromlijnige roosters

Visualization of Turbulent Flow