Abstract: Hypergraphs drawn in the subset standard are useful to represent group relationships using topographic characteristics such as intersection, exclusion and enclosing. However, they present cluttering when dealing with a moderately high number of nodes (more than 20) and large hyperedges (connecting more than 10 nodes, with three or more overlapping nodes). At this complexity level, a study of the visual encoding of hypergraphs is required in order to reduce cluttering and increase the understanding of larger sets. Here we present a graph model and a visual design that help in the visualization of group relationships represented by hypergraphs. This is done by the use of superimposed visualization layers with different abstraction levels and the help of interaction and navigation through the display.
Abstract: Summary: Treevolution is a tool for the representation and exploration of phylogenetic trees that facilitates visual analysis. There are several useful tools to visualize phylogenetic trees, but their level of interaction is usually low, especially in the case of radial representations. Highly interactive visualizations can improve the exploration and understanding of phylogenetic trees. Treevolution implements strategies to interact with phylogenetic trees in order to allow a more thorough analysis by users.
Availability: Treevolution is available at http://vis.usal.es/treevolution
Supplementary material: Additional figures, a user's guide, a video demo and some examples are available at http://vis.usal.es/treevolution
Contact: rodri@usal.es
Abstract: Summary: BicOverlapper is a tool to visualize biclusters from geneexpression matrices in a way that helps to compare biclustering methods, to unravel trends and to highlight relevant genes and conditions. A visual approach can complement biological and statistical analysis and reduce the time spent by specialists interpreting the results of biclustering algorithms. The technique is based on a force-directed graph where biclusters are represented as flexible overlapped groups of genes and conditions. Availability: The BicOverlapper software and supplementary material are available at http://vis.usal.es/bicoverlapper Contact: rodri@usal.es
Abstract: Background
Microarray analysis is an important area of bioinformatics. In the last few years, biclustering has become one of the most popular methods for classifying data from microarrays. Although biclustering can be used in any kind of classification problem, nowadays it is mostly used for microarray data classification. A large number of biclustering algorithms have been developed over the years, however little effort has been devoted to the representation of the results.
Results
We present an interactive framework that helps to infer differences or similarities between biclustering results, to unravel trends and to highlight robust groupings of genes and conditions. These linked representations of biclusters can complement biological analysis and reduce the time spent by specialists on interpreting the results. Within the framework, besides other standard representations, a visualization technique is presented which is based on a force-directed graph where biclusters are represented as flexible overlapped groups of genes and conditions. This microarray analysis framework (BicOverlapper), is available at http://vis.usal.es/bicoverlapper
Conclusions
The main visualization technique, tested with different biclustering results on a real dataset, allows researchers to extract interesting features of the biclustering results, especially the highlighting of overlapping zones that usually represent robust groups of genes and/or conditions. The visual analytics methodology will permit biology experts to study biclustering results without inspecting an overwhelming number of biclusters individually.
Abstract: The analysis of scientific articles produced by different groups of authors helps to identify and characterize research groups and collaborations among them. Although this is a quite studied area, some issues, as quick (almost preattentive) understanding of groups and visualization of large social networks still pose some interesting challenges. In order to contribute to this study, we present a solution based in Overlapper, a tool for the visualization of overlapped groups that makes use of an enhanced variation of force-directed graphs. As a real case study, the tool has been applied to articles in DBLP database.
Abstract: There are lots of validation indexes and techniques to study clustering results. Biclustering algorithms have been applied in Systems Biology, principally in DNA Microarray analysis, for the last years, with great success. Nowadays, there is a big set of biclustering algorithms each one based in different concepts, but there are few intercomparisons that measure their performance. We review and present here some numerical measures, new and evolved from traditional clustering validation techniques, to allow comparisons and validation of biclustering algorithms.
Abstract: Microarray technology produces large amounts of information to be manipulated by analysis methods, such as biclustering algorithms, to extract new knowledge. All-purpose multivariate data visualization tools are usually not enough for studying microarray experiments. Additionally, clustering tools do not provide means of simultaneous visualization of all the biclusters obtained. We present an interactive tool that integrates traditional visualization techniques with others related to bioinformatics, such as transcription regulatory networks and microarray heatmaps, to provide enhanced understanding of the biclustering results. Our aim is to gain insight about the structure of biological data and the behavior of different biclustering algorithms
Abstract: A gamma spectrometer with HPGe detector of 50% relative efficiency and 1 cps total background has been dedicated to the measurement of an intertidal sediment core from a coastal environment at the RÃa de Vigo (Spain). The area is affected by lead pollution and the source identification needs of a precise dating of the sediment core. Such a precise dating requires the measurement not only of the radionuclides directly involved in time calculation, as 210Pb and 226Ra, but also of ancillary radionuclides which inform about the dating model to apply and about the validity of its time estimation. Gamma spectrometry with Ge detectors performs a simultaneous measurement of the full content in gamma-emitters of the sample. However, its use is limited by its high spectral background. We present the characteristics of our lowlevel background gamma spectrometer and also of Galea, the computing tool for the expert analysis of natural radionuclides. Both make possible to get the proper experimental results to reach a suitable dating. The results allowed us to detect a change in the sedimentation dynamics in the area under study, to verify the impact of lead pollution in the 210Pb level, to obtain a sedimentation rate by using the CF:CS model with a suitable correction factor and, finally, to validate the sediment dating.
Abstract: The presented work aims to identify interesting relationships between persons involved in the movie world. The tool integrates different visualization techniques: parallel coordinates, scatterplots, treemaps, word clouds and graph networks, along with textual information and searchs. The visualizations are interconnected and allow overlapping through different data selections to quickly extract data analysis. Though all our visualizations reveals interesting overall information, the analysis converge to our visualization of social networks where detailed interactions are revealed. To prove the analysis power of the tool and obtain more interesting conclussions we have extended proposed data with additional information such as producers, composers, editors and writers, distribution companies, film budgets, etc.
Abstract: This report describes the 14th Annual Graph Drawing Contest, held in conjunction with the 2007 Graph Drawing Symposium in Sydney, Australia. The purpose of the contest is to monitor and challenge the current state of graph-drawing technology.
