Search

Existing work on visualizing multivariate graphs is primarily concerned with representing the attributes of nodes. Even though edges are the constitutive elements of networks, there have been only few attempts to visualize attributes of edges. In this work, we focus on the critical importance of edge attributes for interpreting network visualizations and building trust in the underlying data. We propose 'unfolding of edges' as an interactive approach to integrate multivariate edge attributes dynamically into existing node‐link diagrams. Unfolding edges is an in‐situ approach that gradually transforms basic links into detailed representations of the associated edge attributes. This approach extends focus+context, semantic zoom, and animated transitions for network visualizations to accommodate edge details on‐demand without cluttering the overall graph layout. We explore the design space for the unfolding of edges, which covers aspects of making space for the unfolding, of actually representing the edge context, and of navigating between edges. To demonstrate the utility of our approach, we present two case studies in the context of historical network analysis and computational social science. For these, web‐based prototypes were implemented based on which we conducted interviews with domain experts. The experts' feedback suggests that the proposed unfolding of edges is a useful tool for exploring rich edge information of multivariate graphs. [ABSTRACT FROM AUTHOR]

The elegance of using virtual interactive lenses to provide alternative visual representations for selected regions of interest is highly valued, especially in the realm of visualization. Today, more than 50 lens techniques are known in the closer context of visualization, far more in related fields. In this paper, we extend our previous survey on interactive lenses for visualization. We propose a definition and a conceptual model of lenses as extensions of the classic visualization pipeline. An extensive review of the literature covers lens techniques for different types of data and different user tasks and also includes the technologies employed to display lenses and to interact with them. We introduce a taxonomy of lenses for visualization and illustrate its utility by dissecting in detail a multi-touch lens for exploring large graph layouts. As a conclusion of our review, we identify challenges and unsolved problems to be addressed in future research. [ABSTRACT FROM AUTHOR]

Going beyond established desktop interfaces, researchers have begun re-thinking visualization approaches to make use of alternative display environments and more natural interaction modalities. In this paper, we investigate how spatially-aware mobile displays and a large display wall can be coupled to support graph visualization and interaction. For that purpose, we distribute typical visualization views of classic node-link and matrix representations between displays. The focus of our work lies in novel interaction techniques that enable users to work with personal mobile devices in combination with the wall. We devised and implemented a comprehensive interaction repertoire that supports basic and advanced graph exploration and manipulation tasks, including selection, details-on-demand, focus transitions, interactive lenses, and data editing. A qualitative study has been conducted to identify strengths and weaknesses of our techniques. Feedback showed that combining mobile devices and a wall-sized display is useful for diverse graph-related tasks. We also gained valuable insights regarding the distribution of visualization views and interactive tools among the combined displays. [ABSTRACT FROM AUTHOR]

Guidance can support users during the exploration and analysis of complex data. Previous research focused on characterizing the theoretical aspects of guidance in visual analytics and implementing guidance in different scenarios. However, the evaluation of guidance-enhanced visual analytics solutions remains an open research question. We tackle this question by introducing and validating a practical evaluation methodology for guidance in visual analytics. We identify eight quality criteria to be fulfilled and collect expert feedback on their validity. To facilitate actual evaluation studies, we derive two sets of heuristics. The first set targets heuristic evaluations conducted by expert evaluators. The second set facilitates end-user studies where participants actually use a guidance-enhanced system. By following such a dual approach, the different quality criteria of guidance can be examined from two different perspectives, enhancing the overall value of evaluation studies. To test the practical utility of our methodology, we employ it in two studies to gain insight into the quality of two guidance-enhanced visual analytics solutions, one being a work-in-progress research prototype, and the other being a publicly available visualization recommender system. Based on these two evaluations, we derive good practices for conducting evaluations of guidance in visual analytics and identify pitfalls to be avoided during such studies.

Set visualization facilitates the exploration and analysis of set-type data. However, how sets should be visualized when the data are uncertain is still an open research challenge. To address the problem of depicting uncertainty in set visualization, we ask 1) which aspects of set type data can be affected by uncertainty and 2) which characteristics of uncertainty influence the visualization design. We answer these research questions by first describing a conceptual framework that brings together 1) the information that is primarily relevant in sets (i.e., set membership, set attributes, and element attributes) and 2) different plausible categories of (un)certainty (i.e., certainty, undefined uncertainty as a binary fact, and defined uncertainty as quantifiable measure). Following the structure of our framework, we systematically discuss basic visualization examples of integrating uncertainty in set visualizations. We draw on existing knowledge about general uncertainty visualization and previous evidence of its effectiveness.

Matrix visualizations are a useful tool to provide a general overview of a graph's structure. For multivariate graphs, a remaining challenge is to cope with the attributes that are associated with nodes and edges. Addressing this challenge, we propose responsive matrix cells as a focus+context approach for embedding additional interactive views into a matrix. Responsive matrix cells are local zoomable regions of interest that provide auxiliary data exploration and editing facilities for multivariate graphs. They behave responsively by adapting their visual contents to the cell location, the available display space, and the user task. Responsive matrix cells enable users to reveal details about the graph, compare node and edge attributes, and edit data values directly in a matrix without resorting to external views or tools. We report the general design considerations for responsive matrix cells covering the visual and interactive means necessary to support a seamless data exploration and editing. Responsive matrix cells have been implemented in a web-based prototype based on which we demonstrate the utility of our approach. We describe a walk-through for the use case of analyzing a graph of soccer players and report on insights from a preliminary user feedback session.

Guidance is an emerging topic in the field of visual analytics. Guidance can support users in pursuing their analytical goals more efficiently and help in making the analysis successful. However, it is not clear how guidance approaches should be designed and what specific factors should be considered for effective support. In this paper, we approach this problem from the perspective of guidance designers. We present a framework comprising requirements and a set of specific phases designers should go through when designing guidance for visual analytics. We relate this process with a set of quality criteria we aim to support with our framework, that are necessary for obtaining a suitable and effective guidance solution. To demonstrate the practical usability of our methodology, we apply our framework to the design of guidance in three analysis scenarios and a design walk-through session. Moreover, we list the emerging challenges and report how the framework can be used to design guidance solutions that mitigate these issues., (© 2020 The Authors. Computer Graphics Forum published by Eurographics ‐ The European Association for Computer Graphics and John Wiley & Sons Ltd.)

The enrichment culture KS is one of the few existing autotrophic, nitrate-reducing, Fe(II)-oxidizing cultures that can be continuously transferred without an organic carbon source. We used a combination of catalyzed amplification reporter deposition fluorescence in situ hybridization (CARD-FISH) and nanoscale secondary ion mass spectrometry (NanoSIMS) to analyze community dynamics, single-cell activities, and interactions among the two most abundant microbial community members (i.e., Gallionellaceae sp. and Bradyrhizobium spp.) under autotrophic and heterotrophic growth conditions. CARD-FISH cell counts showed the dominance of the Fe(II) oxidizer Gallionellaceae sp. under autotrophic conditions as well as of Bradyrhizobium spp. under heterotrophic conditions. We used NanoSIMS to monitor the fate of 13 C-labeled bicarbonate and acetate as well as 15 N-labeled ammonium at the single-cell level for both taxa. Under autotrophic conditions, only the Gallionellaceae sp. was actively incorporating 13 C-labeled bicarbonate and 15 N-labeled ammonium. Interestingly, both Bradyrhizobium spp. and Gallionellaceae sp. became enriched in [ 13 C]acetate and [ 15 N]ammonium under heterotrophic conditions. Our experiments demonstrated that Gallionellaceae sp. was capable of assimilating [ 13 C]acetate while Bradyrhizobium spp. were not able to fix CO 2 , although a metagenomics survey of culture KS recently revealed that Gallionellaceae sp. lacks genes for acetate uptake and that the Bradyrhizobium sp. carries the genetic potential to fix CO 2 The study furthermore extends our understanding of the microbial reactions that interlink the nitrogen and Fe cycles in the environment. IMPORTANCE Microbial mechanisms by which Fe(II) is oxidized with nitrate as the terminal electron acceptor are generally referred to as "nitrate-dependent Fe(II) oxidation" (NDFO). NDFO has been demonstrated in laboratory cultures (such as the one studied in this work) and in a variety of marine and freshwater sediments. Recently, the importance of NDFO for the transport of sediment-derived Fe in aquatic ecosystems has been emphasized in a series of studies discussing the impact of NDFO for sedimentary nutrient cycling and redox dynamics in marine and freshwater environments. In this article, we report results from an isotope labeling study performed with the autotrophic, nitrate-reducing, Fe(II)-oxidizing enrichment culture KS, which was first described by Straub et al. (1) about 20 years ago. Our current study builds on the recently published metagenome of culture KS (2)., (Copyright © 2018 American Society for Microbiology.)

Most isolated nitrate-reducing Fe(II)-oxidizing microorganisms are mixotrophic, meaning that Fe(II) is chemically oxidized by nitrite that forms during heterotrophic denitrification, and it is debated to which extent Fe(II) is enzymatically oxidized. One exception is the chemolithoautotrophic enrichment culture KS, a consortium consisting of a dominant Fe(II) oxidizer, Gallionellaceae sp., and less abundant heterotrophic strains (e.g., Bradyrhizobium sp., Nocardioides sp.). Currently, this is the only nitrate-reducing Fe(II)-oxidizing culture for which autotrophic growth has been demonstrated convincingly for many transfers over more than 2 decades. We used 16S rRNA gene amplicon sequencing and physiological growth experiments to analyze the community composition and dynamics of culture KS with various electron donors and acceptors. Under autotrophic conditions, an operational taxonomic unit (OTU) related to known microaerophilic Fe(II) oxidizers within the family Gallionellaceae dominated culture KS. With acetate as an electron donor, most 16S rRNA gene sequences were affiliated with Bradyrhizobium sp. Gallionellaceae sp. not only was able to oxidize Fe(II) under autotrophic and mixotrophic conditions but also survived over several transfers of the culture on only acetate, although it then lost the ability to oxidize Fe(II). Bradyrhizobium spp. became and remained dominant when culture KS was cultivated for only one transfer under heterotrophic conditions, even when conditions were reverted back to autotrophic in the next transfer. This study showed a dynamic microbial community in culture KS that responded to changing substrate conditions, opening up questions regarding carbon cross-feeding, metabolic flexibility of the individual strains in KS, and the mechanism of Fe(II) oxidation by a microaerophile in the absence of O 2 IMPORTANCE Nitrate-reducing Fe(II)-oxidizing microorganisms are present in aquifers, soils, and marine and freshwater sediments. Most nitrate-reducing Fe(II) oxidizers known are mixotrophic, meaning that they need organic carbon to continuously oxidize Fe(II) and grow. In these microbes, Fe(II) was suggested to be chemically oxidized by nitrite that forms during heterotrophic denitrification, and it remains unclear whether or to what extent Fe(II) is enzymatically oxidized. In contrast, the enrichment culture KS was shown to oxidize Fe(II) autotrophically coupled to nitrate reduction. This culture contains the designated Fe(II) oxidizer Gallionellaceae sp. and several heterotrophic strains (e.g., Bradyrhizobium sp.). We showed that culture KS is able to metabolize Fe(II) and a variety of organic substrates and is able to adapt to dynamic environmental conditions. When the community composition changed and Bradyrhizobium became the dominant community member, Fe(II) was still oxidized by Gallionellaceae sp., even when culture KS was cultivated with acetate/nitrate [Fe(II) free] before being switched back to Fe(II)/nitrate., (Copyright © 2018 American Society for Microbiology.)

Visual analytics (VA) is typically applied in scenarios where complex data has to be analyzed. Unfortunately, there is a natural correlation between the complexity of the data and the complexity of the tools to study them. An adverse effect of complicated tools is that analytical goals are more difficult to reach. Therefore, it makes sense to consider methods that guide or assist users in the visual analysis process. Several such methods already exist in the literature, yet we are lacking a general model that facilitates in-depth reasoning about guidance. We establish such a model by extending van Wijk's model of visualization with the fundamental components of guidance. Guidance is defined as a process that gradually narrows the gap that hinders effective continuation of the data analysis. We describe diverse inputs based on which guidance can be generated and discuss different degrees of guidance and means to incorporate guidance into VA tools. We use existing guidance approaches from the literature to illustrate the various aspects of our model. As a conclusion, we identify research challenges and suggest directions for future studies. With our work we take a necessary step to pave the way to a systematic development of guidance techniques that effectively support users in the context of VA.

Nitrate-dependent ferrous iron [Fe(II)] oxidation (NDFO) is a well-recognized chemolithotrophic pathway in anoxic sediments. The neutrophilic chemolithoautotrophic enrichment culture KS originally obtained from a freshwater sediment (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl Environ Microbiol 62:1458-1460, 1996) has been used as a model system to study NDFO. However, the primary Fe(II) oxidizer in this culture has not been isolated, despite extensive efforts to do so. Here, we present a metagenomic analysis of this enrichment culture in order to gain insight into electron transfer pathways and the roles of different bacteria in the culture. We obtained a near-complete genome of the primary Fe(II) oxidizer, a species in the family Gallionellaceae, and draft genomes from its flanking community members. A search of the putative extracellular electron transfer pathways in these genomes led to the identification of a homolog of the MtoAB complex [a porin-multiheme cytochromec system identified in neutrophilic microaerobic Fe(II)-oxidizing Sideroxydans lithotrophicus ES-1] in a Gallionellaceae sp., and findings of other putative genes involving cytochromecand multicopper oxidases, such as Cyc2 and OmpB. Genome-enabled metabolic reconstruction revealed that this Gallionellaceae sp. lacks nitric oxide and nitrous oxide reductase genes and may partner with flanking populations capable of complete denitrification to avoid toxic metabolite accumulation, which may explain its resistance to growth in pure culture. This and other revealed interspecies interactions and metabolic interdependencies in nitrogen and carbon metabolisms may allow these organisms to cooperate effectively to achieve robust chemolithoautotrophic NDFO. Overall, the results significantly expand our knowledge of NDFO and suggest a range of genetic targets for further exploration., (Copyright © 2016, American Society for Microbiology. All Rights Reserved.)

Visualizing trajectory attribute data is challenging because it involves showing the trajectories in their spatio-temporal context as well as the attribute values associated with the individual points of trajectories. Previous work on trajectory visualization addresses selected aspects of this problem, but not all of them. We present a novel approach to visualizing trajectory attribute data. Our solution covers space, time, and attribute values. Based on an analysis of relevant visualization tasks, we designed the visualization solution around the principle of stacking trajectory bands. The core of our approach is a hybrid 2D/3D display. A 2D map serves as a reference for the spatial context, and the trajectories are visualized as stacked 3D trajectory bands along which attribute values are encoded by color. Time is integrated through appropriate ordering of bands and through a dynamic query mechanism that feeds temporally aggregated information to a circular time display. An additional 2D time graph shows temporal information in full detail by stacking 2D trajectory bands. Our solution is equipped with analytical and interactive mechanisms for selecting and ordering of trajectories, and adjusting the color mapping, as well as coordinated highlighting and dedicated 3D navigation. We demonstrate the usefulness of our novel visualization by three examples related to radiation surveillance, traffic analysis, and maritime navigation. User feedback obtained in a small experiment indicates that our hybrid 2D/3D solution can be operated quite well.