Web-based haptic applications for blind people to create virtual graphs

Haptic technology has great potentials in many applications. This paper introduces our work on delivery haptic information via the Web. A multimodal tool has been developed to allow blind people to create virtual graphs independently. Multimodal interactions in the process of graph creation and exploration are provided by using a low-cost haptic device, the Logitech WingMan Force Feedback Mouse, and Web audio. The Web-based tool also provides blind people with the convenience of receiving information at home. In this paper, we present the development of the tool and evaluation results. Discussions on the issues related to the design of similar Web-based haptic applications are also given

A signaling visualization toolkit to support rational design of combination therapies and biomarker discovery: SiViT

Targeted cancer therapy aims to disrupt aberrant cellular signalling pathways. Biomarkers are surrogates of pathway state, but there is limited success in translating candidate biomarkers to clinical practice due to the intrinsic complexity of pathway networks. Systems biology approaches afford better understanding of complex, dynamical interactions in signalling pathways targeted by anticancer drugs. However, adoption of dynamical modelling by clinicians and biologists is impeded by model inaccessibility. Drawing on computer games technology, we present a novel visualisation toolkit, SiViT, that converts systems biology models of cancer cell signalling into interactive simulations that can be used without specialist computational expertise. SiViT allows clinicians and biologists to directly introduce for example loss of function mutations and specific inhibitors. SiViT animates the effects of these introductions on pathway dynamics, suggesting further experiments and assessing candidate biomarker effectiveness. In a systems biology model of Her2 signalling we experimentally validated predictions using SiViT, revealing the dynamics of biomarkers of drug resistance and highlighting the role of pathway crosstalk. No model is ever complete: the iteration of real data and simulation facilitates continued evolution of more accurate, useful models. SiViT will make accessible libraries of models to support preclinical research, combinatorial strategy design and biomarker discovery

A comparative evaluation of dynamic visualisation tools

Despite their potential applications in software comprehension, it appears that dynamic visualisation tools are seldom used outside the research laboratory. This paper presents an empirical evaluation of five dynamic visualisation tools - AVID, Jinsight, jRMTool, Together ControlCenter diagrams and Together ControlCenter debugger. The tools were evaluated on a number of general software comprehension and specific reverse engineering tasks using the HotDraw objectoriented framework. The tasks considered typical comprehension issues, including identification of software structure and behaviour, design pattern extraction, extensibility potential, maintenance issues, functionality location, and runtime load. The results revealed that the level of abstraction employed by a tool affects its success in different tasks, and that tools were more successful in addressing specific reverse engineering tasks than general software comprehension activities. It was found that no one tool performs well in all tasks, and some tasks were beyond the capabilities of all five tools. This paper concludes with suggestions for improving the efficacy of such tools

The Open Graph Archive: A Community-Driven Effort

In order to evaluate, compare, and tune graph algorithms, experiments on well designed benchmark sets have to be performed. Together with the goal of reproducibility of experimental results, this creates a demand for a public archive to gather and store graph instances. Such an archive would ideally allow annotation of instances or sets of graphs with additional information like graph properties and references to the respective experiments and results. Here we examine the requirements, and introduce a new community project with the aim of producing an easily accessible library of graphs. Through successful community involvement, it is expected that the archive will contain a representative selection of both real-world and generated graph instances, covering significant application areas as well as interesting classes of graphs.Comment: 10 page

Fast filtering and animation of large dynamic networks

Detecting and visualizing what are the most relevant changes in an evolving network is an open challenge in several domains. We present a fast algorithm that filters subsets of the strongest nodes and edges representing an evolving weighted graph and visualize it by either creating a movie, or by streaming it to an interactive network visualization tool. The algorithm is an approximation of exponential sliding time-window that scales linearly with the number of interactions. We compare the algorithm against rectangular and exponential sliding time-window methods. Our network filtering algorithm: i) captures persistent trends in the structure of dynamic weighted networks, ii) smoothens transitions between the snapshots of dynamic network, and iii) uses limited memory and processor time. The algorithm is publicly available as open-source software.Comment: 6 figures, 2 table

Evaluation of two interaction techniques for visualization of dynamic graphs

Several techniques for visualization of dynamic graphs are based on different spatial arrangements of a temporal sequence of node-link diagrams. Many studies in the literature have investigated the importance of maintaining the user's mental map across this temporal sequence, but usually each layout is considered as a static graph drawing and the effect of user interaction is disregarded. We conducted a task-based controlled experiment to assess the effectiveness of two basic interaction techniques: the adjustment of the layout stability and the highlighting of adjacent nodes and edges. We found that generally both interaction techniques increase accuracy, sometimes at the cost of longer completion times, and that the highlighting outclasses the stability adjustment for many tasks except the most complex ones.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

Octilinear Force-Directed Layout with Mental Map Preservation for Schematic Diagrams

We present an algorithm for automatically laying out metro map style schematics using a force-directed approach, where we use a localized version of the standard spring embedder forces combined with an octilinear magnetic force. The two types of forces used during layout are naturally conflicting, and the existing method of simply combining these to generate a resultant force does not give satisfactory results. Hence we vary the forces, emphasizing the standard forces in the beginning to produce a well distributed graph, with the octilinear forces becoming prevalent at the end of the layout, to ensure that the key requirement of line angles at intervals of 45? is obtained. Our method is considerably faster than the more commonly used search-based approaches, and we believe the results are superior to the previous force-directed approach. We have further developed this technique to address the issues of dynamic schematic layout. We use a Delaunay triangulation to construct a schematic “frame”, which is used to retain relative node positions and permits full control of the level of mental map preservation. This technique is the first to combine mental map preservation techniques with the additional layout criteria of schematic diagrams. To conclude, we present the results of a study to investigate the relationship between the level of mental map preservation and the user response time and accuracy

Information visualization for DNA microarray data analysis: A critical review

Graphical representation may provide effective means of making sense of the complexity and sheer volume of data produced by DNA microarray experiments that monitor the expression patterns of thousands of genes simultaneously. The ability to use ldquoabstractrdquo graphical representation to draw attention to areas of interest, and more in-depth visualizations to answer focused questions, would enable biologists to move from a large amount of data to particular records they are interested in, and therefore, gain deeper insights in understanding the microarray experiment results. This paper starts by providing some background knowledge of microarray experiments, and then, explains how graphical representation can be applied in general to this problem domain, followed by exploring the role of visualization in gene expression data analysis. Having set the problem scene, the paper then examines various multivariate data visualization techniques that have been applied to microarray data analysis. These techniques are critically reviewed so that the strengths and weaknesses of each technique can be tabulated. Finally, several key problem areas as well as possible solutions to them are discussed as being a source for future work