TULIP 4

Tulip is an information visualization framework dedicated to the analysis and visualization of relational data. Based on more than 15 years of research and development, Tulip is built on a suite of tools and techniques , that can be used to address a large variety of domain-specific problems. With Tulip, we aim to provide Python and/or C++ developers a complete library, supporting the design of interactive information visualization applications for relational data, that can be customized to address a wide range of visualization problems. In its current iteration, Tulip enables the development of algorithms, visual encodings, interaction techniques, data models, and domain-specific visualizations. This development pipeline makes the framework efficient for creating research prototypes as well as developing end-user applications. The recent addition of a complete Python programming layer wraps up Tulip as an ideal tool for fast prototyping and treatment automation, allowing to focus on problem solving, and as a great system for teaching purposes at all education levels

3DScape: three dimensional visualization plug-in for Cytoscape

3DScape is the first plug-in which enables three-
dimensional network visualization in Cytoscape. The extra dimension is useful in accommodating, visualizing, and distinguishing larger networks with multiple crossing connections.
Special features in 3DScape include 3D layout algorithms, mapping onto 3D models and animation effects on a series of expression data. 3DScape is available at http://www.rendware.co

Mapping Tasks to Interactions for Graph Exploration and Graph Editing on Interactive Surfaces

Graph exploration and editing are still mostly considered independently and systems to work with are not designed for todays interactive surfaces like smartphones, tablets or tabletops. When developing a system for those modern devices that supports both graph exploration and graph editing, it is necessary to 1) identify what basic tasks need to be supported, 2) what interactions can be used, and 3) how to map these tasks and interactions. This technical report provides a list of basic interaction tasks for graph exploration and editing as a result of an extensive system review. Moreover, different interaction modalities of interactive surfaces are reviewed according to their interaction vocabulary and further degrees of freedom that can be used to make interactions distinguishable are discussed. Beyond the scope of graph exploration and editing, we provide an approach for finding and evaluating a mapping from tasks to interactions, that is generally applicable. Thus, this work acts as a guideline for developing a system for graph exploration and editing that is specifically designed for interactive surfaces.Comment: 21 pages, minor corrections (typos etc.

Obvious: a meta-toolkit to encapsulate information visualization toolkits. One toolkit to bind them all

This article describes “Obvious”: a meta-toolkit that abstracts and encapsulates information visualization toolkits implemented in the Java language. It intends to unify their use and postpone the choice of which concrete toolkit(s) to use later-on in the development of visual analytics applications. We also report on the lessons we have learned when wrapping popular toolkits with Obvious, namely Prefuse, the InfoVis Toolkit, partly Improvise, JUNG and other data management libraries. We show several examples on the uses of Obvious, how the different toolkits can be combined, for instance sharing their data models. We also show how Weka and RapidMiner, two popular machine-learning toolkits, have been wrapped with Obvious and can be used directly with all the other wrapped toolkits. We expect Obvious to start a co-evolution process: Obvious is meant to evolve when more components of Information Visualization systems will become consensual. It is also designed to help information visualization systems adhere to the best practices to provide a higher level of interoperability and leverage the domain of visual analytics

Towards Scalable Visual Exploration of Very Large RDF Graphs

In this paper, we outline our work on developing a disk-based infrastructure for efficient visualization and graph exploration operations over very large graphs. The proposed platform, called graphVizdb, is based on a novel technique for indexing and storing the graph. Particularly, the graph layout is indexed with a spatial data structure, i.e., an R-tree, and stored in a database. In runtime, user operations are translated into efficient spatial operations (i.e., window queries) in the backend.Comment: 12th Extended Semantic Web Conference (ESWC 2015

MetaboCraft: building a Minecraft plugin for metabolomics

Motivation: The rapid advances in metabolomics pose a significant challenge in presentation and interpretation of results. Development of new, engaging visual aids is crucial to advancing our understanding of new findings. Results: We have developed MetaboCraft, a Minecraft plugin which creates immersive visualisations of metabolic networks and pathways in a 3-D environment and allows the results of user experiments to be viewed in this context, presenting a novel approach to exploring the metabolome

Code Flows: Visualizing Structural Evolution of Source Code

Understanding detailed changes done to source code is of great importance in software maintenance. We present Code Flows, a method to visualize the evolution of source code geared to the understanding of fine and mid-level scale changes across several file versions. We enhance an existing visual metaphor to depict software structure changes with techniques that emphasize both following unchanged code as well as detecting and highlighting important events such as code drift, splits, merges, insertions and deletions. The method is illustrated with the analysis of a real-world C++ code system.

Code Flows: Visualizing Structural Evolution of Source Code

Understanding detailed changes done to source code is of great importance in software maintenance. We present Code Flows, a method to visualize the evolution of source code geared to the understanding of fine and mid-level scale changes across several file versions. We enhance an existing visual metaphor to depict software structure changes with techniques that emphasize both following unchanged code as well as detecting and highlighting important events such as code drift, splits, merges, insertions and deletions. The method is illustrated with the analysis of a real-world C++ code system.

rNAV 2.0: a visualization tool for bacterial sRNA-mediated regulatory networks mining

Data description. Data description and availability, and parameter settings used in this study. (PDF 101 kb