GenomeViz: visualizing microbial genomes

BACKGROUND: An increasing number of microbial genomes are being sequenced and deposited in public databases. In addition, several closely related strains are also being sequenced in order to understand the genetic basis of diversity and mechanisms that lead to the acquisition of new genetic traits. These exercises have necessitated the requirement for visualizing microbial genomes and performing genome comparisons on a finer scale. We have developed GenomeViz to enable rapid visualization and subsequent comparisons of several microbial genomes in an interactive environment. RESULTS: Here we describe a program that allows visualization of both qualitative and quantitative information from complete and partially sequenced microbial genomes. Using GenomeViz, data deriving from studies on genomic islands, gene/protein classifications, GC content, GC skew, whole genome alignments, microarrays and proteomics may be plotted. Several genomes can be visualized interactively at the same time from a comparative genomic perspective and publication quality circular genome plots can be created. CONCLUSIONS: GenomeViz should allow researchers to perform visualization and comparative analysis of up to eight different microbial genomes simultaneously

VisGenome: visualization of single and comparative genome representations

VisGenome visualizes single and comparative representations for the rat, the mouse and the human chromosomes at different levels of detail. The tool offers smooth zooming and panning which is more flexible than seen in other browsers. It presents information available in Ensembl for single chromosomes, as well as homologies (orthologue predictions including ortholog one2one, apparent ortholog one2one, ortholog many2many) for any two chromosomes from different species. The application can query supporting data from Ensembl by invoking a link in a browser

3-D interactive visualisation tools for HI spectral line imaging

Upcoming HI surveys will deliver such large datasets that automated processing using the full 3-D information to find and characterize HI objects is unavoidable. Full 3-D visualization is an essential tool for enabling qualitative and quantitative inspection and analysis of the 3-D data, which is often complex in nature. Here we present $\tt{SlicerAstro}$, an open-source extension of 3DSlicer, a multi-platform open source software package for visualization and medical image processing, which we developed for the inspection and analysis of HI spectral line data. We describe its initial capabilities, including 3-D filtering, 3-D selection and comparative modelling

Detection mechanism for ferroelectric domain boundaries with lateral force microscopy

The contrast mechanism for the visualization of ferroelectric domain boundaries with lateral force microscopy is generally assumed to be caused by mechanical deformation of the sample due to the converse piezoelectric effect. We show, however, that electrostatic interactions between the charged tip and the electric fields arising from the surface polarization charges dominate the contrast mechanism. This explanation is sustained by quantitative analysis of the measured forces as well as by comparative measurements on different materials

Network of the Day: Aggregating and Visualizing Entity Networks from Online Sources

This software demonstration paper presents a project on the interactive visualization of social media data. The data presentation fuses German Twitter data and a social relation network extracted from German online news. Such fusion allows for comparative analysis of the two types of media. Our system will additionally enable users to explore relationships between named entities, and to investigate events as they develop over time. Cooperative tagging of relationships is enabled through the active involvement of users. The system is available online for a broad user audience