Interactive visualization of metabolic networks using virtual reality

A combination of graph layouts in 3D space, interactive computer graphics, and virtual reality (VR) can increase the size of understandable networks for metabolic network visualization. Two models, the directed graph and the compound graph, were used to represent a metabolic network. The directed graph, or nonhierarchical visualization, considers the adjacency relationships. For the nonhierarchical visualization, the weighted GEM-3D layout was adopted to emphasize the reactions among metabolite nodes. The compound graph, or hierarchical visualization, explicitly takes the hierarchical relationships like the pathway-molecule hierarchy or the compartment-molecule hierarchy into consideration to improve the performance and perception. An algorithm was designed, which combines the hierarchical force model with the simulated annealing method, to efficiently generate an effective layout for the compound graph. A detail-on-demand method improved the rendering performance and perception of the hierarchical visualization. The directed graph was also used to represent a sub-network composed of reactions of interest (ROIs), which reveal reactions involving a specific node. The fan layout was proposed for ROIs focusing on a metabolite node. The radial layout was adopted for ROIs focusing on a gene node. Graphics scenes were constructed for the network. The shapes and material properties of geometric objects, such as colors, transparencies, and textures, can encode biological properties, such as node names, reaction edge types, etc. Graphics animations like color morph, shape morph, and edge vibration were used to superimpose gene expression profiling data to the network. Interactions for an effective visualization were defined and implemented using VR interfaces. A pilot usability study and some qualitative comparisons were conducted to show potential advantages of stereoscopic VR for metabolic network visualization

A New Approach for Visualizing UML Class Diagrams

UML diagrams have become increasingly important in the engineering and reengineering processes for software systems. Of particular interest are UML class diagrams whose purpose is to display class hierarchies (generalizations), associations, aggregations, and compositions in one picture. The combination of hierarchical and non-hierarchical relations poses a special challenge to a graph layout tool. Existing layout tools treat hierarchical and non-hierarchical relations either alike or as separate tasks in a two-phase process as in, e.g., cite{See97}. We suggest a new approach for visualizing UML class diagrams leading to a balanced mixture of the following aesthetic criteria: Crossing minimization, bend minimization, uniform direction within each class hierarchy, no nesting of one class hierarchy within another, orthogonal layout, merging of multiple inheritance edges, and good edge labelling. We have realized our approach within the graph drawing library GoVisual. Experiments show the superiority to state-of-the-art and industrial standard layouts

A New Approach for Visualizing UML Class Diagrams

UML diagrams have become increasingly important in the engineering and reengineering processes for software systems. Of particular interest are UML class diagrams whose purpose is to display class hierarchies (generalizations), associations, aggregations, and compositions in one picture. The combination of hierarchical and non-hierarchical relations poses a special challenge to a graph layout tool. Existing layout tools treat hierarchical and non-hierarchical relations either alike or as separate tasks in a two-phase process as in, e.g., cite{See97}. We suggest a new approach for visualizing UML class diagrams leading to a balanced mixture of the following aesthetic criteria: Crossing minimization, bend minimization, uniform direction within each class hierarchy, no nesting of one class hierarchy within another, orthogonal layout, merging of multiple inheritance edges, and good edge labelling. We have realized our approach within the graph drawing library GoVisual. Experiments show the superiority to state-of-the-art and industrial standard layouts

Large scale network analysis with interactive visualisation

This paper proposes a new interactive visualisation for analysing large hierarchical structures and networks. The technique combines of different graph layout methods with a layout refinement process, an interactive navigation mechanism and clustering algorithms. The integration of these components makes it flexible in dealing with a variety of graph and hierarchical structures. Interactive exploration is enabled with chaincontext view. We aim to provide user with an effective mechanism for understanding of the nature of various networks. This could lead to the discovering and revealing of the hidden structures and relationships among elements as well as relationships associated with the elements. © 2009 IEEE

Extending constrained hierarchical layout for drawing UML activity diagrams

Ankara : The Department of Computer Engineering and Institute Engineering and Science of Bilkent University, 2002.Thesis (Master's) -- Bilkent University, 2002.Includes bibliographical references leaves 48-51.While modeling an object-oriented software, a visual language called Unified Modeling Language (UML) may be used. UML is a language and notation for specification, construction, visualization, and documentation of models of software systems. It consists of a variety of diagrams including class diagrams and activity diagrams. Graph layout has become an important area of research in Computer Science for the last couple of decades. There is a wide range of applications for graph layout including data structures, databases, software engineering, VLSI technology, electrical engineering, production planning, chemistry, and biology. Diagrams are more effective means of expressing relational information and automatic graph layout makes them to be more comprehensible. In other words, with graph layout techniques, the readability and the comprehensibility of the graphs increases and the complexity is reduced. UML diagrams are no exception. In this thesis, we present graph layout algorithms for UML activity diagrams based on constrained hierarchical layout. We use an existing implementation of constrained hierarchical layout to draw UML activity diagrams. We analyze and present the results of these new layout algorithms.Yüksel, H MehmetM.S

Immersive Interaction with Pedigree Graph Visualisations

Immersive reality technologies such as Virtual Reality(VR) and Augmented Reality (AR) offer interesting opportunities in the visualisation of data. However, despite their recent popularity, research in regards to graph data visualisation using these technologies is limited, especially so for hierarchical graphs. Pedigrees, a specific type of hierarchical data that model the breeding of plant varieties within a species are a novel and interesting application area of these visualisations. We present a study on the appropriate way to visualise pedigree graph data within immersive reality. We develop a novel immersive reality application that incorporates innovative interaction techniques, and model six different graph layouts based on a hierarchical application of existing graph layout techniques. These graph layouts include the planar, cylinder, floor, sphere, cone (force directed) and vase. These six layouts were compared with a within-subjects user study measuring task accuracy, task completion time, and qualitative sentiment from the user. The results of the study did not indicate any statistically significant superior graph layout in regards to task accuracy and task completion time. However, we found that the floor layout performed the poorest in all metrics measured. These findings indicate that most 3D layouts achieve very similar performance with not only each other but the 2D baseline planar view in regards to task accuracy or task completion time. However, the sphere layout was the most positively received by the users, even more so than the 2D baseline planar layout based on the qualitative questionnaire. As such, the advantage that is possessed by some 3D layouts (but not all) such as the sphere is how they are more positively perceived