Roberto Therón

BicOverlapper: A tool for bicluster visualization

UNLABELLED BicOverlapper is a tool to visualize biclusters from gene-expression 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

NAPROC-13

MOTIVATION Although natural products represent a reservoir of molecular diversity, the process of isolating and identifying active compounds is a bottleneck in drug discovery programs. The rapid isolation and identification of the bioactive component(s) of natural product mixtures during the bioassay-guided fractionation have become crucial factors in the competition with chemical compound libraries and combinatorial synthetic efforts. In this respect, the use of spectral databases in identification processes is indispensable. RESULTS We have developed a database containing (13)C spectral information of over 6000 natural compounds, which allows for fast identifications of known compounds present in the crude extracts and provides insight into the structural elucidation of unknown compounds. AVAILABILITY http://c13.usal.es

Tap into visual analysis of customization of grouping of activities in eLearning

We have implemented a tool to study relationships and patterns.Temporal correlation of the grouping of activities and students grades was studied.The tool searches for patterns in the frequencies of grouping activities and/or student grades.There is a pattern in the students behavior and performance.The results are consistent across different courses. The use of electronic media in education has a strong impact of on student performance. Prior research has investigated the impact of forum reading and posting, as well as access to reading resources, on academic performance. However, little is known about the relationship between the temporal frequency of these activities and individual students performance. In addition, some studies have proposed different categorizations of student activities, and proved the usefulness of these characterizations for predictive purposes and better understanding of the learning process. One of the biggest concerns when teaching courses in a virtual learning environment is to create and develop instruction in a way that it improves the overall learning experience and results. The present study addresses this concern by drawing upon factors influencing academic performance; more specifically, the study focuses on objective factors related to the interaction between the student and the system (number of resources visited in the learning platform, and number of forum posts and views). On top of that, a visualization tool was designed and implemented to allow for further investigation of the relevance of the study variables. The results from the study show that there is a recurrent pattern in the frequency of behaviors and performance across different courses.

A visual analytics approach for understanding biclustering results from microarray data.

BackgroundMicroarray 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.ResultsWe 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/bicoverlapperConclusionThe 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.

Towards an ontology modeling tool. A validation in software engineering scenarios

Ontology creation and management related processes are very important to define and develop semantic services. Ontology Engineering is the research field that provides the mechanisms to manage the life cycle of the ontologies. However, the process of building ontologies can be tedious and sometimes exhaustive. OWL-VisMod is a tool designed for developing ontological engineering based on visual analytics conceptual modeling for OWL ontologies life cycle management, supporting both creation and understanding tasks. This paper is devoted to evaluate OWL-VisMod through a set of defined tasks. The same tasks also will be done with the most known tool in Ontology Engineering, Protege, in order to compare the obtained results and be able to know how is OWL-VisMod perceived for the expert users. The comparison shows that both tools have similar acceptation scores, but OWL-VisMod presents better feelings regarding users perception tasks due to the visual analytics influence.

TagClusters: Semantic Aggregation of Collaborative Tags beyond TagClouds

TagClouds is a popular visualization for the collaborative tags. However it has some instinct problems such as linguistic issues, high semantic density and poor understanding of hierarchical structure and semantic relation between tags. In this paper we investigate the ways to support semantic understanding of collaborative tags and propose an improved visualization named TagClusters. Based on the semantic analysis of the collaborative tags in Last.fm, the semantic similar tags are clustered into different groups and the visual distance represents the semantic similarity between tags, and thus the visualization offers a better semantic understanding of collaborative tags. A comparative evaluation is conducted with TagClouds and TagClusters based on the same tags collection. The results indicate that TagClusters has advantages in supporting efficient browsing, searching, impression formation and matching. In the future work, we will explore the possibilities of supporting tag recom-mendation and tag-based Music Retrieval based on TagClusters.

Hierarchical-Temporal Data Visualization Using a Tree-Ring Metaphor

This paper describes a novel and efficient visualization technique intended for hierarchical-temporal data using a tree-ring like layout. Temporal hierarchies appear in numerous fields such as genealogy, evolution taxonomies or time lines. In many cases, state-of-the-art static diagrams are produced in these fields. By using several information visualization strategies, such as focus + context, the tree-ring approach has the ability to visualize and navigate these, potentially complex, hierarchies trough time. Thus, a deeper insight into the problem at hand can be gained.

Overlapping Clustered Graphs: Co-authorship Networks Visualization

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, such as quick 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 overlapping groups that makes use of an enhanced variation of force-directed graphs. For a real case study, the tool has been applied to articles in the DBLP database.

A Survey on Ontology Metrics

Ontologies have been widely used in almost any field of application. The use of ontologies should involve the possibility of evaluation of the quality and correctness of them. Some tools and metrics have been proposed to reach this goal. ONTOMETRIC, OntoQA and Protege represent the most important tools to evaluate ontologies. On the other hand, diverse cohesion, coupling and ranking metrics have also been proposed, as well as methodologies such as OntoClean. This paper analyses these tools and metrics, compare them and finally reviews the current state-of-the-art concerning to ontology metrics.

Methods to bicluster validation and comparison in microarray data

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.