Interactive, Constraint-based Layout of Engineering Diagrams

Many engineering disciplines require visualisation of networks. Constrained graph layout is a powerful new approach to network layout that allows the user to impose a wide variety application-specific placement constraints—such as downwards pointing directed edges, alignment of nodes, cluster containment and non-overlapping nodes and clusters—on the layout. We have recently developed an efficient algorithm for topology-preserving constrained graph layout. This underpins two dynamic graph layout applications we have developed: a network diagram authoring tool, Dunnart, and a network diagram browser. In this paper we provide an overview of topology-preserving constrained graph layout and illustrate how Dunnart and the network diagram browser can be applied to engineering diagram authoring and visualisation

Integrative visual analysis of protein sequence mutations

BACKGROUND: An important aspect of studying the relationship between protein sequence, structure and function is the molecular characterization of the effect of protein mutations. To understand the functional impact of amino acid changes, the multiple biological properties of protein residues have to be considered together. RESULTS: Here, we present a novel visual approach for analyzing residue mutations. It combines different biological visualizations and integrates them with molecular data derived from external resources. To show various aspects of the biological information on different scales, our approach includes one-dimensional sequence views, three-dimensional protein structure views and two-dimensional views of residue interaction networks as well as aggregated views. The views are linked tightly and synchronized to reduce the cognitive load of the user when switching between them. In particular, the protein mutations are mapped onto the views together with further functional and structural information. We also assess the impact of individual amino acid changes by the detailed analysis and visualization of the involved residue interactions. We demonstrate the effectiveness of our approach and the developed software on the data provided for the BioVis 2013 data contest. CONCLUSIONS: Our visual approach and software greatly facilitate the integrative and interactive analysis of protein mutations based on complementary visualizations. The different data views offered to the user are enriched with information about molecular properties of amino acid residues and further biological knowledge

OntoPlot: A Novel Visualisation for Non-hierarchical Associations in Large Ontologies

Ontologies are formal representations of concepts and complex relationships among them. They have been widely used to capture comprehensive domain knowledge in areas such as biology and medicine, where large and complex ontologies can contain hundreds of thousands of concepts. Especially due to the large size of ontologies, visualisation is useful for authoring, exploring and understanding their underlying data. Existing ontology visualisation tools generally focus on the hierarchical structure, giving much less emphasis to non-hierarchical associations. In this paper we present OntoPlot, a novel visualisation specifically designed to facilitate the exploration of all concept associations whilst still showing an ontology's large hierarchical structure. This hybrid visualisation combines icicle plots, visual compression techniques and interactivity, improving space-efficiency and reducing visual structural complexity. We conducted a user study with domain experts to evaluate the usability of OntoPlot, comparing it with the de facto ontology editor Prot{\'e}g{\'e}. The results confirm that OntoPlot attains our design goals for association-related tasks and is strongly favoured by domain experts.Comment: Accepted at IEEE InfoVis 201

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

Euler diagrams drawn with ellipses area‑proportionally (Edeap)

Background: Area-proportional Euler diagrams are frequently used to visualize data from Microarray experiments, but are also applied to a wide variety of other data from biosciences, social networks and other domains. Results: This paper details Edeap, a new simple, scalable method for drawing areaproportional Euler diagrams with ellipses. We use a search-based technique optimizing a multi-criteria objective function that includes measures for both area accuracy and usability, and which can be extended to further user-defned criteria. The Edeap software is available for use on the web, and the code is open source. In addition to describing our system, we present the frst extensive evaluation of software for producing area-proportional Euler diagrams, comparing Edeap to the current state-of-the-art; circle-based method, venneuler, and an alternative ellipse-based method, eulerr. Conclusions: Our evaluation—using data from the Gene Ontology database via GoMiner, Twitter data from the SNAP database, and randomly generated data sets—shows an ordering for accuracy (from best to worst) of eulerr, followed by Edeap and then venneuler. In terms of runtime, the results are reversed with venneuler being the fastest, followed by Edeap and fnally eulerr. Regarding scalability, eulerr cannot draw non-trivial diagrams beyond 11 sets, whereas no such limitation is present in Edeap or venneuler, both of which draw diagrams up to the tested limit of 20 sets

Crowdsourcing Technology to Support Academic Research

No abstract available

Human-Centred Feasibility Restoration

Decision systems for solving real-world combinatorial problems must be able to report infeasibility in such a way that users can understand the reasons behind it, and understand how to modify the problem to restore feasibility. Current methods mainly focus on reporting one or more subsets of the problem constraints that cause infeasibility. Methods that also show users how to restore feasibility tend to be less flexible and/or problem-dependent. We describe a problem-independent approach to feasibility restoration that combines existing techniques from the literature in novel ways to yield meaningful, useful, practical and flexible user support. We evaluate the resulting framework on two real-world applications

Interaction in the Visualization of Multivariate Networks

International audienceInteraction is a vital component in the visualization of multivariate networks. By allowing people to browse data sets with interactions like panning and zoom- ing, it enables much more information to be seen and explored than would oth- erwise be possible with static visualization. Overview-based interactions afford the user the ability to understand a complete picture of the data or informa- tion landscape and to decide where to direct her attention. Through search and filtering, interaction can reduce cognitive effort on users by allowing them to locate, focus on and understand subsets of the data in isolation. Pivoting and other navigational interactions at both the view- and data-level allow people to identify and then to transition between areas of interest. While there are methods for interacting with graphs and dimensions sep- arately, the combination of both needs special attention. The challenge is to clearly visualize multiple sets of individual dimensions as well as to offer a useful visual overview of data, and allow transitions between these to be easily under- stood. Moreover, we need to find ways to support users in navigating through the complex data space (graphs x dimensions) without "getting lost" without an overburden of interaction actions, as this might me frustrating for the user