Dynamic Interactive Visualization Research Articles

FishGET: A fish gene expression and transcriptome database with improved accuracy and visualization

With the rapid expansion of transcriptome studies in many fishes, a great number of RNA-seq data have been published, allowing for a more systematic understanding of the general profiles and details of gene expression in fish. FishGET is dedicated to gathering and curating fish RNA-seq data to discover more new RNAs, including mRNA and lncRNA, thereby getting a more complete reference transcriptome and providing more comprehensive and accurate transcriptome annotations. We obtained a total of 1362 RNA-seq paired-end data of 8 fishes from 97 different studies, and then we performed transcript assembly, meta-assembly, weighted gene co-expression network analysis (WGCNA), functional annotations, neighbor location annotation, lncRNA type annotation, homology annotation. To promote research into fish genes at the transcriptional level, we developed a user-friendly web interface that allows users to view all information and makes use of multiple types of dynamic interactive visualization services.

Visualizing public transit system operation with GTFS data: A case study of Calgary, Canada

Public transportation agencies are one of the industries that generate a large volume of data on a high frequency and velocity basis. The General Transit Feed Specification (GTFS) is one of the datasets these agencies generate and share openly with the public. GTFS feeds contain data for scheduled transit service including stop and route locations, and schedules information. This paper aims to demonstrate the potential of GTFS data, specifically, the paper describes the development of a GTFS data visualization tool that displays spatial and temporal patterns of transit services from which qualitative information and insights can be gained. In this paper, GTFS data from Calgary Transit was used as a case study. Previous studies focused on the development of visualization tools that display transit movement, or static graphical representation of transit operation. However, there is still a need for a dynamic interactive visualization tool that can also measures and displays transit system operation geographically and statistically. This study builds on the previous investigations and further develops a new public transit system operation visualization tool (called PubtraVis) with six visualization modules that reflect on different transit system operational characteristics; mobility, speed, flow, density, headway, and analysis. The user can evaluate two modules side by side for comparative analysis. The analysis module provides an insightful statistical summary and similarity measure and clustering results based on the transit operation characteristics. PubtraVis was tested with real-world users through a user experience study from which it was found to be useful and easy to start using. PubtraVis can be a useful tool to demonstrate the dynamism of transit vehicles from the entire transit network at a glance, and can be used to facilitate communication between transit operators, city authorities, and the general public regarding the public transit planning and operation.

MODERNIZATION OF GEOGRAPHIC EDUCATION AT HIGH SCHOOL: GEOINFORMATION TRAINING MODELS

The paper deals with contemporary trends of modernization of higher education in the countries of Europe, emphasizes relation between the quality of education and the level of development of the countries' economy, confirms the importance of digital education and provision of new forms of educational services. The problem of mastering new technologies using geoinformation systems and technologies in the process of training future specialists-geographers and geography teachers is analyzed. It is proved that one of the ways of addressing the outlined problem is the implementation of geoinformation training models, and the place of such models among other types of geography training tools is determined. The paper explains the concepts "training model", "geoinformation training model" and outlines their didactic peculiarities. The system of graphic-sign geographic training models is presented, with geoinformation training models being their subtype. The trends of applying geoinformation systems and technologies in the process of teaching geographic disciplines at higher education institutions are characterized. Based on the experience of application of geoinformation training models, the paper emphasizes that they are tools of students’ independent cognitive activities. The paper distinguishes three groups of these models (general, special, combined) and characterizes their varieties. Considerable attention is paid to characterizing special geoinformation models, viz. rendering models, first of all digital elevation models, "draping" models, as well as models of kinematic animation or dynamic interactive visualization of 3D images, routing optimization and self-training models. A considerable didactic potential of electronic maps and atlases is emphasized, which make it possible to study geographic objects, processes and phenomena in the spatial aspect. The conclusion is made that the application of geoinformation training models, on the one hand, allows students to explore independently certain natural or socio-economic objects of the environment. On the other hand, tutors can plan students’ efficient training activities at a high level of complexity and in accordance with their interests.

3D Interactive Visualization Method of Urban Waterlogging Based on Cesium

Abstract. Urban waterlogging, as a common natural disaster in China, seriously restricted the development of society. Nowadays, while the computer technology is developing continuously, the urban waterlogging model is also constantly improved. These models can simulate the process of urban waterlogging, but the simulation results are not intuitive. So it is difficult for users to understand how the model works. Therefore, it is important to find a way to show the simulation results so that people can see the waterlogging simulation intuitively. Cesium, as a three-dimensional visualization platform, can reproduce the process of the urban waterlogging. It will make sense if we could show the simulation results on the Cesium platform. Nowadays, many studies focus on both urban waterlogging and visualization methods. However, there are fewer studies on the combination of the two, especially the interactive visualization of urban waterlogging under parameter adjustment. Therefore, this paper mainly focuses on urban three-dimensional interactive visualization method based on Cesium.On the one hand, the three-dimensional visualization of the urban waterlogging simulation facilitates the intuitive expression of the simulation results. Without visualization, the results of the simulation are only some complicated and unintuitive figures for most non-experts. On the other hand, visualization based on the Cesium platform can better adapt to the cross-platform application. It can better meet the needs of different terminal devices of different users for the visualization platform, so that users can obtain the disaster information more accurately, consistently and intuitively. It is conducive for management departments to respond to sudden disasters more quickly and efficiently.This research aims to propose a three-dimensional dynamic interactive visualization method for urban waterlogging. Particularly, we hope to find out how to integrate urban waterlogging model and 3D visualization platform. With this 3D visualization platform, we can combine the advantages of the SWMM (Storm Water Management Model) and Cesium platform. Using this platform, it will be easier and more effective to respond to disasters for the masses and management departments.The following two issues are resolved in this study: i) How do model parameters affect the urban waterlogging simulation and visualization results? ii) How to integrate SWMM and Cesium 3D visualization platform?In order to address the above research objectives, we will apply the following methodologies: i) We will analyse the parameters of the SWMM for the urban waterlogging visualization. Under the premise of understanding the development process of the urban waterlogging, we will analyse the modelling principle of the urban waterlogging, the mechanism of each part of the model separately. Then, we will find out the method of determining the model parameters of urban waterlogging and its influence on the simulation visualization results. ii) We will study integration methods of urban waterlogging model and 3D visualization platform. We will analyse the mechanism and process of urban waterlogging. We will also calculate the urban waterlogging process data by the SWMM, and establish a three-dimensional visualization platform by the node.js and Cesium, which can dynamically show the process of urban waterlogging. iii) We will complete the design and implementation of the interactive visualization platform of urban waterlogging. According to the above research, taking the Xianlin Campus of Nanjing Normal University as an example, we will build a dynamic interactive visualization system of urban waterlogging simulation based on Cesium. We will also verify the effectiveness of the system by comparing it with actual flood situation.With this study, we expect to answer how model parameters affect the urban waterlogging simulation and visualization results. As expected results, we plan to build an interactive visualization system of urban waterlogging simulation based on Cesium, publish the flood calculation results into the 3D scene. This will make urban waterlogging process shown in the 3D scene. This visualization system is designed for different users, including specialists, government and individual. It means that you can use the system easily even if you are non-cartographers or non-IT-specialists.

Study on multi-source data integrating standard and 3D cartographic visualization of urban flooding based on CityGML

Abstract. Urban flooding refers to the phenomenon of water accumulation in cities due to strong precipitation or continuous precipitation exceeding urban drainage capacity. At present, the problem of urban flooding has become another major urban disease after other urban problems such as crowded people, traffic congestion and environmental pollution (Weiwu W, et al. 2015). In order to better cope with the problem of waterlogging, there are many hydrodynamic models that can accurately simulate the process of pipe network drainage and water accumulation. However, there are currently two limitations that limit the practicality of these hydrodynamic models. First, these models often require a large amount of input data as a support. These data exhibit multi-source, heterogeneity, multi-scale, multi-resolution and other characteristics, which bring great difficulty to data acquisition and processing (Dongdong Z, et al. 2014). Second, the analysis results of the model contain a large amount of waterlogging related information. However, this information is usually represented by simple texts and tables, which is not conducive to interpretation, transmission and visualization. Especially for location-related information, such as flooding points, flow information of various parts of the drainage pipe, water depth in the flooded area, etc., non-interactive two-dimensional maps or tables can cause inconvenience to disaster management and decision-making.Therefore, a proper data model, respecting the needs of integration of multisource input and output data of waterlogging simulation and analysis and the needs of 3D visualization in front end, is needed. As a matter of fact, what in the last years has proven to be an emerging and effective approach is the adoption of standard-based, integrated semantic 3D virtual city models, which represent an information hub for most of the above-mentioned needs (Agugiaro et al. 2018). In particular, being based on open standards (e.g. on the CityGML standard proposed by the Open Geospatial Consortium), virtual city models firstly reduce the effort in terms of data preparation and provision. Secondly, they offer clear data structures, ontologies and semantics to facilitate data exchange between different domains and applications, and 3D visualization which is essential for crisis management (Herman L, Řezník T, 2015). However, a standardized and omni-comprehensive urban data model covering also the waterlogging domain is still missing. Even CityGML falls partially short when it comes to the definition of specific entities and attributes for waterlogging-related applications.This study aims to propose an Waterlogging Application Domain Extension (ADE) for CityGML 2.0, which is used to integrate the multi-source input data and the rich waterlogging related information of waterlogging simulation and analysis. In order to achieve the above objectives, the following contents will be investigated:(1) Analysis of urban hydrodynamic models’ function and their data characteristicsAnalyze the function of the hydrodynamic model in the city, and explore the source, precision and organizational structure of the input and output data during the simulation and analysis of waterlogging.(2) Construction of waterlogging data integration model based on CityGMLBased on the CityGML2.0 and its ADE mechanism, we will construct a conceptual model of waterlogging data integration standard, to describe the geometric and spatial structure of urban buildings, vegetation, land-use, underground pipelines, waterlogging related entities, etc. And more information about waterlogging, such as flooding points, drainage network carrying pressure, catchment area, etc., will be integrated into the corresponding fields of the data integration model in a reasonable way to facilitate Internet transmission and visualization.(3) Interactive 3D visualization method based on the proposed waterlogging ADEBased on the rich waterlogging-related information in the waterlogging ADE, combined with 3D visualization technology, the 3D dynamic interactive visualization method is explored, in order to provide more intuitive data support for waterlogging disaster management and decision-making.Through this study, we expect to improve the efficiency and practicability of the current waterlogging simulation and analysis by integrating the waterlogging related data from multi-source based on CityGML. As the result of the research, we intend to develop a prototype system based on the multi-source waterlogging related data integration method proposed in this study. With this standard, we can provide unified and standard data support for the waterlogging model. At the same time, the results of the waterlogging models are automatically integrated into the data set for dynamic 3D visualization.

Dynamics of Inter-Molecular Interactions Between Single Aβ42 Oligomeric and Aggregate Species by High-Speed Atomic Force Microscopy

Within the amyloid hypothesis in Alzheimer's disease, current focus has shifted to earlier stages of amyloid beta (Aβ) peptide assembly, involving soluble oligomers and smaller aggregates, which are more toxic to cells compared to their morphological distinct fibril forms. Critical to the Aβ field is unlocking the molecular-level kinetic pathways of oligomerization, leading to the culprit subset or specific species of Aβ oligomer populations responsible for the disease etiology. Here, we apply high-speed atomic force microscopy to enable direct visualization of dynamic interactions between single Aβ42 oligomers and aggregate forms, with combined nanometre structural and millisecond temporal resolution in liquid. Analysis of dimensions revealed up to three main Aβ42 species distributions, in addition to the appearance of monomers that showed fast surface diffusion compared to the larger Aβ42 species. Significantly, we devised a new single-molecule analysis based on image contrast in high-speed atomic force microscopy movies to quantify rate determining kinetic constants for interactions between the different Aβ42 species. The findings revealed that smaller Aβ42 species show an exponential decay of lifetime distribution, indicating that all molecules undergo the same process with a single well-defined energy barrier. In contrast, larger aggregates show randomized lifetimes, indicating a distribution of interactions energies/barriers that must be overcome in order to dissociate. We interpret the latter as being due to “permissive” binding, arising from different conformation states of the aggregates, along with a variety of accessible interacting groups. Inevitably, this may lead to the formation of different complexes or alloforms, which is known to contribute to difficulties in identifying Aβ oligomer toxicity and has implications for mechanisms underlying neuronal death accompanying Alzheimer's disease.

PanoromiX: a time-course network medicine platform integrating molecular assays and pathophenotypic data

BackgroundNetwork medicine aims to map molecular perturbations of any given diseases onto complex networks with functional interdependencies that underlie a pathological phenotype. Furthermore, investigating the time dimension of disease progression from a network perspective is key to gaining key insights to the disease process and to identify diagnostic or therapeutic targets. Existing platforms are ineffective to modularize the large complex systems into subgroups and consolidate heterogeneous data to web-based interactive animation.ResultsWe have developed PanoromiX platform, a data-agnostic dynamic interactive visualization web application, enables the visualization of outputs from genome based molecular assays onto modular and interactive networks that are correlated with any pathophenotypic data (MRI, Xray, behavioral, etc.) over a time course all in one pane. As a result, PanoromiX reveals the complex organizing principles that orchestrate a disease-pathology from a gene regulatory network (nodes, edges, hubs, etc.) perspective instead of snap shots of assays. Without extensive programming experience, users can design, share, and interpret their dynamic networks through the PanoromiX platform with rich built-in functionalities.ConclusionsThis emergent tool of network medicine is the first to visualize the interconnectedness of tailored genome assays to pathological networks and phenotypes for cells or organisms in a data-agnostic manner. As an advanced network medicine tool, PanoromiX allows monitoring of panel of biomarker perturbations over the progression of diseases, disease classification based on changing network modules that corresponds to specific patho-phenotype as opposed to clinical symptoms, systematic exploration of complex molecular interactions and distinct disease states via regulatory network changes, and the discovery of novel diagnostic and therapeutic targets.

An Evaluation Method of Visualization Using Visual Momentum Based on Eye-Tracking Data

A new method based on eye-tracking data — visual momentum (VM) — was introduced to quantitatively evaluate a dynamic interactive visualization interface. We extracted the dimensionless factors from the raw eye-tracking data, including the fixation time factor [Formula: see text], the saccade amplitude factor D and the fixation number factor [Formula: see text]. A predictive regression model of VM was deduced by eye movement factors and the performance response time (RT). In Experiment 1, the experimental visualization materials were designed with six effectiveness levels according to design techniques proposed by Woods to improve VM (total replacement, fixed format data replacement, long shot, perceptual landmark and spatial representation) and were tested in six parallel subject groups. The coefficients of the regression model were calculated from the data of 42 valid subjects in Experiment 1. The mean VM of each group exhibited an increasing trend with an increase in design techniques. The data of the performance and eye tracking among the combined high VM group, middle VM group and low VM group indicated significant differences. The data analysis indicates that the results were consistent with the previous qualitative research of VM. We tested and verified this regression model in Experiment 2 with another dynamic interactive visualization. The results indicated that the VM calculated by the regression model was significantly correlated with the performance data. Therefore, the virtual parameter VM can be a quantitative indicator for evaluating dynamic visualization. It could be a useful evaluation method for the dynamic visualization in general working environments.

Beyond the G-spot: clitourethrovaginal complex anatomy in female orgasm.

The search for the legendary, highly erogenous vaginal region, the Gräfenberg spot (G-spot), has produced important data, substantially improving understanding of the complex anatomy and physiology of sexual responses in women. Modern imaging techniques have enabled visualization of dynamic interactions of female genitals during self-sexual stimulation or coitus. Although no single structure consistent with a distinct G-spot has been identified, the vagina is not a passive organ but a highly dynamic structure with an active role in sexual arousal and intercourse. The anatomical relationships and dynamic interactions between the clitoris, urethra, and anterior vaginal wall have led to the concept of a clitourethrovaginal (CUV) complex, defining a variable, multifaceted morphofunctional area that, when properly stimulated during penetration, could induce orgasmic responses. Knowledge of the anatomy and physiology of the CUV complex might help to avoid damage to its neural, muscular, and vascular components during urological and gynaecological surgical procedures.

Visualization of the Phosphoproteomic Data from AfCS with the Google Motion Chart Gadget

AbstractResults from multivariate molecular biological experiments become increasingly complex. Hence, the challenge of projecting high-dimensional data onto few dimensions for effective data visualization is becoming increasingly important in Systems Biology. Effective data visualization can summarize the activity of many variables over time as well as display relationships between variables. Dynamic interactive visualization tools can provide scientists with ways of visually identifying relationship and patterns, and improve communication of results on the web and in presentations. For this, interactive systems with animation have great potential since they add dimensions to static images limited to two dimensions. Interactivity and animation is particularly useful for showing time-series trends in multi-dimensional data. The Flash-based Motion Chart Google Gadget available through GoogleDocs is a recent advance in multi-dimensional data visualization. The Motion Chart Gadget is a component of the Trendalyzer software, which was developed for web-based animation of statistical results. Here we demonstrate the use of this Gadget to visualize molecular biological data, the phosphoproteomics results published on the Data Center of the Signaling Gateway web-site.

Identification of New Fluorescent Protein Fragments for Bimolecular Fluorescence Complementation Analysis Under Physiological Conditions

Protein-protein interactions play a pivotal role in coordinating many cellular processes. Determination of subcellular localization of interacting proteins and visualization of dynamic interactions in living cells are crucial to elucidate cellular functions of proteins. Using fluorescent proteins, we previously developed a bimolecular fluorescence complementation (BiFC) assay and a multicolor BiFC assay to visualize protein-protein interactions in living cells. However, the sensitivity of chromophore maturation of enhanced yellow fluorescent protein (YFP) to higher temperatures requires preincubation at lower temperatures prior to visualizing the BiFC signal. This could potentially limit their applications for the study of many signaling molecules. Here we report the identification of new fluorescent protein fragments derived from Venus and Cerulean for BiFC and multicolor BiFC assays under physiological culture conditions. More importantly, the newly identified combinations exhibit a 13-fold higher BiFC efficiency than originally identified fragments derived from YFP. Furthermore, the use of new combinations reduces the amount of plasmid required for transfection and shortens the incubation time, leading to a 2-fold increase in specific BiFC signals. These newly identified fluorescent protein fragments will facilitate the study of protein-protein interactions in living cells and whole animals under physiological conditions.

VizCluster and its Application on Classifying Gene Expression Data

Visualization enables us to find structures, features, patterns, and relationships in a dataset by presenting the data in various graphical forms with possible interactions. A visualization can provide a qualitative overview of large and complex datasets, can summarize data, and can assist in identifying regions of interest and appropriate parameters focused on quantitative analysis. Recently, DNA microarray technology provides a broad snapshot of the state of the cell, by measuring the expression levels of thousands of genes simultaneously. Such information can thus be used to analyze different samples by gene expression profiles. It has already had a significant impact on the field of bioinformatics, requiring innovative techniques to efficiently and effectively extract, analyze, and visualize these fast growing data. In this paper, we present a dynamic interactive visualization environment, VizCluster, and its application on classifying gene expression data. VizCluster takes advantage of graphical visualization methods to reveal underlining data patterns. It combines the merits of both high dimensional projection scatter-plot and parallel coordinate plot. In its core lies a nonlinear projection which maps the n-dimensional vectors onto two-dimensional points. To preserve the information at different scales and yet reduce the typical problem of parallel coordinate plots being messy caused by overlapping lines, a zip zooming viewing method is proposed. Integrated with other features, VizCluster is developed to give a simple, fast, intuitive, and yet powerful view of the data set. Its primary applications are on the classification of samples and evaluation of gene clusters for microarray datasets. Three gene expression datasets are used to illustrate the approach. We demonstrate that VizCluster approach is promising to be used for analyzing and visualizing microarray data sets and further development is worthwhile.