Physics-based subsurface visualization of human tissue.

PubMed

Sharp, Richard; Adams, Jacob; Machiraju, Raghu; Lee, Robert; Crane, Robert

2007-01-01

In this paper, we present a framework for simulating light transport in three-dimensional tissue with inhomogeneous scattering properties. Our approach employs a computational model to simulate light scattering in tissue through the finite element solution of the diffusion equation. Although our model handles both visible and nonvisible wavelengths, we especially focus on the interaction of near infrared (NIR) light with tissue. Since most human tissue is permeable to NIR light, tools to noninvasively image tumors, blood vasculature, and monitor blood oxygenation levels are being constructed. We apply this model to a numerical phantom to visually reproduce the images generated by these real-world tools. Therefore, in addition to enabling inverse design of detector instruments, our computational tools produce physically-accurate visualizations of subsurface structures.

Intelligent Model Management in a Forest Ecosystem Management Decision Support System

Treesearch

Donald Nute; Walter D. Potter; Frederick Maier; Jin Wang; Mark Twery; H. Michael Rauscher; Peter Knopp; Scott Thomasma; Mayukh Dass; Hajime Uchiyama

2002-01-01

Decision making for forest ecosystem management can include the use of a wide variety of modeling tools. These tools include vegetation growth models, wildlife models, silvicultural models, GIS, and visualization tools. NED-2 is a robust, intelligent, goal-driven decision support system that integrates tools in each of these categories. NED-2 uses a blackboard...

Visualizing Terrestrial and Aquatic Systems in 3-D

EPA Science Inventory

The environmental modeling community has a long-standing need for affordable, easy-to-use tools that support 3-D visualization of complex spatial and temporal model output. The Visualization of Terrestrial and Aquatic Systems project (VISTAS) aims to help scientists produce effe...

Stereoscopic applications for design visualization

NASA Astrophysics Data System (ADS)

Gilson, Kevin J.

2007-02-01

Advances in display technology and 3D design visualization applications have made real-time stereoscopic visualization of architectural and engineering projects a reality. Parsons Brinkerhoff (PB) is a transportation consulting firm that has used digital visualization tools from their inception and has helped pioneer the application of those tools to large scale infrastructure projects. PB is one of the first Architecture/Engineering/Construction (AEC) firms to implement a CAVE- an immersive presentation environment that includes stereoscopic rear-projection capability. The firm also employs a portable stereoscopic front-projection system, and shutter-glass systems for smaller groups. PB is using commercial real-time 3D applications in combination with traditional 3D modeling programs to visualize and present large AEC projects to planners, clients and decision makers in stereo. These presentations create more immersive and spatially realistic presentations of the proposed designs. This paper will present the basic display tools and applications, and the 3D modeling techniques PB is using to produce interactive stereoscopic content. The paper will discuss several architectural and engineering design visualizations we have produced.

Evaluation of the 3d Urban Modelling Capabilities in Geographical Information Systems

NASA Astrophysics Data System (ADS)

Dogru, A. O.; Seker, D. Z.

2010-12-01

Geographical Information System (GIS) Technology, which provides successful solutions to basic spatial problems, is currently widely used in 3 dimensional (3D) modeling of physical reality with its developing visualization tools. The modeling of large and complicated phenomenon is a challenging problem in terms of computer graphics currently in use. However, it is possible to visualize that phenomenon in 3D by using computer systems. 3D models are used in developing computer games, military training, urban planning, tourism and etc. The use of 3D models for planning and management of urban areas is very popular issue of city administrations. In this context, 3D City models are produced and used for various purposes. However the requirements of the models vary depending on the type and scope of the application. While a high level visualization, where photorealistic visualization techniques are widely used, is required for touristy and recreational purposes, an abstract visualization of the physical reality is generally sufficient for the communication of the thematic information. The visual variables, which are the principle components of cartographic visualization, such as: color, shape, pattern, orientation, size, position, and saturation are used for communicating the thematic information. These kinds of 3D city models are called as abstract models. Standardization of technologies used for 3D modeling is now available by the use of CityGML. CityGML implements several novel concepts to support interoperability, consistency and functionality. For example it supports different Levels-of-Detail (LoD), which may arise from independent data collection processes and are used for efficient visualization and efficient data analysis. In one CityGML data set, the same object may be represented in different LoD simultaneously, enabling the analysis and visualization of the same object with regard to different degrees of resolution. Furthermore, two CityGML data sets containing the same object in different LoD may be combined and integrated. In this study GIS tools used for 3D modeling issues were examined. In this context, the availability of the GIS tools for obtaining different LoDs of CityGML standard. Additionally a 3D GIS application that covers a small part of the city of Istanbul was implemented for communicating the thematic information rather than photorealistic visualization by using 3D model. An abstract model was created by using a commercial GIS software modeling tools and the results of the implementation were also presented in the study.

Simulation environment and graphical visualization environment: a COPD use-case

PubMed Central

2014-01-01

Background Today, many different tools are developed to execute and visualize physiological models that represent the human physiology. Most of these tools run models written in very specific programming languages which in turn simplify the communication among models. Nevertheless, not all of these tools are able to run models written in different programming languages. In addition, interoperability between such models remains an unresolved issue. Results In this paper we present a simulation environment that allows, first, the execution of models developed in different programming languages and second the communication of parameters to interconnect these models. This simulation environment, developed within the Synergy-COPD project, aims at helping and supporting bio-researchers and medical students understand the internal mechanisms of the human body through the use of physiological models. This tool is composed of a graphical visualization environment, which is a web interface through which the user can interact with the models, and a simulation workflow management system composed of a control module and a data warehouse manager. The control module monitors the correct functioning of the whole system. The data warehouse manager is responsible for managing the stored information and supporting its flow among the different modules. This simulation environment has been validated with the integration of three models: two deterministic, i.e. based on linear and differential equations, and one probabilistic, i.e., based on probability theory. These models have been selected based on the disease under study in this project, i.e., chronic obstructive pulmonary disease. Conclusion It has been proved that the simulation environment presented here allows the user to research and study the internal mechanisms of the human physiology by the use of models via a graphical visualization environment. A new tool for bio-researchers is ready for deployment in various use cases scenarios. PMID:25471327

The nature of the (visualization) game: Challenges and opportunities from computational geophysics

NASA Astrophysics Data System (ADS)

Kellogg, L. H.

2016-12-01

As the geosciences enters the era of big data, modeling and visualization become increasingly vital tools for discovery, understanding, education, and communication. Here, we focus on modeling and visualization of the structure and dynamics of the Earth's surface and interior. The past decade has seen accelerated data acquisition, including higher resolution imaging and modeling of Earth's deep interior, complex models of geodynamics, and high resolution topographic imaging of the changing surface, with an associated acceleration of computational modeling through better scientific software, increased computing capability, and the use of innovative methods of scientific visualization. The role of modeling is to describe a system, answer scientific questions, and test hypotheses; the term "model" encompasses mathematical models, computational models, physical models, conceptual models, statistical models, and visual models of a structure or process. These different uses of the term require thoughtful communication to avoid confusion. Scientific visualization is integral to every aspect of modeling. Not merely a means of communicating results, the best uses of visualization enable scientists to interact with their data, revealing the characteristics of the data and models to enable better interpretation and inform the direction of future investigation. Innovative immersive technologies like virtual reality, augmented reality, and remote collaboration techniques, are being adapted more widely and are a magnet for students. Time-varying or transient phenomena are especially challenging to model and to visualize; researchers and students may need to investigate the role of initial conditions in driving phenomena, while nonlinearities in the governing equations of many Earth systems make the computations and resulting visualization especially challenging. Training students how to use, design, build, and interpret scientific modeling and visualization tools prepares them to better understand the nature of complex, multiscale geoscience data.

Modeling and Visualizing Flow of Chemical Agents Across Complex Terrain

NASA Technical Reports Server (NTRS)

Kao, David; Kramer, Marc; Chaderjian, Neal

2005-01-01

Release of chemical agents across complex terrain presents a real threat to homeland security. Modeling and visualization tools are being developed that capture flow fluid terrain interaction as well as point dispersal downstream flow paths. These analytic tools when coupled with UAV atmospheric observations provide predictive capabilities to allow for rapid emergency response as well as developing a comprehensive preemptive counter-threat evacuation plan. The visualization tools involve high-end computing and massive parallel processing combined with texture mapping. We demonstrate our approach across a mountainous portion of North California under two contrasting meteorological conditions. Animations depicting flow over this geographical location provide immediate assistance in decision support and crisis management.

Accessing and Visualizing scientific spatiotemporal data

NASA Technical Reports Server (NTRS)

Katz, Daniel S.; Bergou, Attila; Berriman, Bruce G.; Block, Gary L.; Collier, Jim; Curkendall, David W.; Good, John; Husman, Laura; Jacob, Joseph C.; Laity, Anastasia;

A standard-enabled workflow for synthetic biology.

PubMed

Myers, Chris J; Beal, Jacob; Gorochowski, Thomas E; Kuwahara, Hiroyuki; Madsen, Curtis; McLaughlin, James Alastair; Mısırlı, Göksel; Nguyen, Tramy; Oberortner, Ernst; Samineni, Meher; Wipat, Anil; Zhang, Michael; Zundel, Zach

2017-06-15

A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

Tools for visually exploring biological networks.

PubMed

Suderman, Matthew; Hallett, Michael

2007-10-15

Many tools exist for visually exploring biological networks including well-known examples such as Cytoscape, VisANT, Pathway Studio and Patika. These systems play a key role in the development of integrative biology, systems biology and integrative bioinformatics. The trend in the development of these tools is to go beyond 'static' representations of cellular state, towards a more dynamic model of cellular processes through the incorporation of gene expression data, subcellular localization information and time-dependent behavior. We provide a comprehensive review of the relative advantages and disadvantages of existing systems with two goals in mind: to aid researchers in efficiently identifying the appropriate existing tools for data visualization; to describe the necessary and realistic goals for the next generation of visualization tools. In view of the first goal, we provide in the Supplementary Material a systematic comparison of more than 35 existing tools in terms of over 25 different features. Supplementary data are available at Bioinformatics online.

Modeling Spatial and Temporal Aspects of Visual Backward Masking

ERIC Educational Resources Information Center

Hermens, Frouke; Luksys, Gediminas; Gerstner, Wulfram; Herzog, Michael H.; Ernst, Udo

2008-01-01

Visual backward masking is a versatile tool for understanding principles and limitations of visual information processing in the human brain. However, the mechanisms underlying masking are still poorly understood. In the current contribution, the authors show that a structurally simple mathematical model can explain many spatial and temporal…

An agent architecture for an integrated forest ecosystem management decision support system

Treesearch

Donald Nute; Walter D. Potter; Mayukh Dass; Astrid Glende; Frederick Maier; Hajime Uchiyama; Jin Wang; Mark Twery; Peter Knopp; Scott Thomasma; H. Michael Rauscher

2003-01-01

A wide variety of software tools are available to support decision in the management of forest ecosystems. These tools include databases, growth and yield models, wildlife models, silvicultural expert systems, financial models, geographical informations systems, and visualization tools. Typically, each of these tools has its own complex interface and data format. To...

Interactive Visual Analysis within Dynamic Ocean Models

NASA Astrophysics Data System (ADS)

Butkiewicz, T.

2012-12-01

The many observation and simulation based ocean models available today can provide crucial insights for all fields of marine research and can serve as valuable references when planning data collection missions. However, the increasing size and complexity of these models makes leveraging their contents difficult for end users. Through a combination of data visualization techniques, interactive analysis tools, and new hardware technologies, the data within these models can be made more accessible to domain scientists. We present an interactive system that supports exploratory visual analysis within large-scale ocean flow models. The currents and eddies within the models are illustrated using effective, particle-based flow visualization techniques. Stereoscopic displays and rendering methods are employed to ensure that the user can correctly perceive the complex 3D structures of depth-dependent flow patterns. Interactive analysis tools are provided which allow the user to experiment through the introduction of their customizable virtual dye particles into the models to explore regions of interest. A multi-touch interface provides natural, efficient interaction, with custom multi-touch gestures simplifying the otherwise challenging tasks of navigating and positioning tools within a 3D environment. We demonstrate the potential applications of our visual analysis environment with two examples of real-world significance: Firstly, an example of using customized particles with physics-based behaviors to simulate pollutant release scenarios, including predicting the oil plume path for the 2010 Deepwater Horizon oil spill disaster. Secondly, an interactive tool for plotting and revising proposed autonomous underwater vehicle mission pathlines with respect to the surrounding flow patterns predicted by the model; as these survey vessels have extremely limited energy budgets, designing more efficient paths allows for greater survey areas.

Visualizing projected Climate Changes - the CMIP5 Multi-Model Ensemble

NASA Astrophysics Data System (ADS)

Böttinger, Michael; Eyring, Veronika; Lauer, Axel; Meier-Fleischer, Karin

2017-04-01

Large ensembles add an additional dimension to climate model simulations. Internal variability of the climate system can be assessed for example by multiple climate model simulations with small variations in the initial conditions or by analyzing the spread in large ensembles made by multiple climate models under common protocols. This spread is often used as a measure of uncertainty in climate projections. In the context of the fifth phase of the WCRP's Coupled Model Intercomparison Project (CMIP5), more than 40 different coupled climate models were employed to carry out a coordinated set of experiments. Time series of the development of integral quantities such as the global mean temperature change for all models visualize the spread in the multi-model ensemble. A similar approach can be applied to 2D-visualizations of projected climate changes such as latitude-longitude maps showing the multi-model mean of the ensemble by adding a graphical representation of the uncertainty information. This has been demonstrated for example with static figures in chapter 12 of the last IPCC report (AR5) using different so-called stippling and hatching techniques. In this work, we focus on animated visualizations of multi-model ensemble climate projections carried out within CMIP5 as a way of communicating climate change results to the scientific community as well as to the public. We take a closer look at measures of robustness or uncertainty used in recent publications suitable for animated visualizations. Specifically, we use the ESMValTool [1] to process and prepare the CMIP5 multi-model data in combination with standard visualization tools such as NCL and the commercial 3D visualization software Avizo to create the animations. We compare different visualization techniques such as height fields or shading with transparency for creating animated visualization of ensemble mean changes in temperature and precipitation including corresponding robustness measures. [1] Eyring, V., Righi, M., Lauer, A., Evaldsson, M., Wenzel, S., Jones, C., Anav, A., Andrews, O., Cionni, I., Davin, E. L., Deser, C., Ehbrecht, C., Friedlingstein, P., Gleckler, P., Gottschaldt, K.-D., Hagemann, S., Juckes, M., Kindermann, S., Krasting, J., Kunert, D., Levine, R., Loew, A., Mäkelä, J., Martin, G., Mason, E., Phillips, A. S., Read, S., Rio, C., Roehrig, R., Senftleben, D., Sterl, A., van Ulft, L. H., Walton, J., Wang, S., and Williams, K. D.: ESMValTool (v1.0) - a community diagnostic and performance metrics tool for routine evaluation of Earth system models in CMIP, Geosci. Model Dev., 9, 1747-1802, doi:10.5194/gmd-9-1747-2016, 2016.

Data Presentation and Visualization (DPV) Interface Control Document

NASA Technical Reports Server (NTRS)

Mazzone, Rebecca A.; Conroy, Michael P.

2015-01-01

Data Presentation and Visualization (DPV) is a subset of the modeling and simulation (M&S) capabilities at Kennedy Space Center (KSC) that endeavors to address the challenges of how to present and share simulation output for analysts, stakeholders, decision makers, and other interested parties. DPV activities focus on the development and provision of visualization tools to meet the objectives identified above, as well as providing supporting tools and capabilities required to make its visualization products available and accessible across NASA.

Visualizing Dataflow Graphs of Deep Learning Models in TensorFlow.

PubMed

Wongsuphasawat, Kanit; Smilkov, Daniel; Wexler, James; Wilson, Jimbo; Mane, Dandelion; Fritz, Doug; Krishnan, Dilip; Viegas, Fernanda B; Wattenberg, Martin

2018-01-01

We present a design study of the TensorFlow Graph Visualizer, part of the TensorFlow machine intelligence platform. This tool helps users understand complex machine learning architectures by visualizing their underlying dataflow graphs. The tool works by applying a series of graph transformations that enable standard layout techniques to produce a legible interactive diagram. To declutter the graph, we decouple non-critical nodes from the layout. To provide an overview, we build a clustered graph using the hierarchical structure annotated in the source code. To support exploration of nested structure on demand, we perform edge bundling to enable stable and responsive cluster expansion. Finally, we detect and highlight repeated structures to emphasize a model's modular composition. To demonstrate the utility of the visualizer, we describe example usage scenarios and report user feedback. Overall, users find the visualizer useful for understanding, debugging, and sharing the structures of their models.

Lifting business process diagrams to 2.5 dimensions

NASA Astrophysics Data System (ADS)

Effinger, Philip; Spielmann, Johannes

2010-01-01

In this work, we describe our visualization approach for business processes using 2.5 dimensional techniques (2.5D). The idea of 2.5D is to add the concept of layering to a two dimensional (2D) visualization. The layers are arranged in a three-dimensional display space. For the modeling of the business processes, we use the Business Process Modeling Notation (BPMN). The benefit of connecting BPMN with a 2.5D visualization is not only to obtain a more abstract view on the business process models but also to develop layering criteria that eventually increase readability of the BPMN model compared to 2D. We present a 2.5D Navigator for BPMN models that offers different perspectives for visualization. Therefore we also develop BPMN specific perspectives. The 2.5D Navigator combines the 2.5D approach with perspectives and allows free navigation in the three dimensional display space. We also demonstrate our tool and libraries used for implementation of the visualizations. The underlying general framework for 2.5D visualizations is explored and presented in a fashion that it can easily be used for different applications. Finally, an evaluation of our navigation tool demonstrates that we can achieve satisfying and aesthetic displays of diagrams stating BPMN models in 2.5D-visualizations.

Energetically optimal travel across terrain: visualizations and a new metric of geographic distance with anthropological applications

NASA Astrophysics Data System (ADS)

Wood, Brian M.; Wood, Zoë J.

2006-01-01

We present a visualization and computation tool for modeling the caloric cost of pedestrian travel across three dimensional terrains. This tool is being used in ongoing archaeological research that analyzes how costs of locomotion affect the spatial distribution of trails and artifacts across archaeological landscapes. Throughout human history, traveling by foot has been the most common form of transportation, and therefore analyses of pedestrian travel costs are important for understanding prehistoric patterns of resource acquisition, migration, trade, and political interaction. Traditionally, archaeologists have measured geographic proximity based on "as the crow flies" distance. We propose new methods for terrain visualization and analysis based on measuring paths of least caloric expense, calculated using well established metabolic equations. Our approach provides a human centered metric of geographic closeness, and overcomes significant limitations of available Geographic Information System (GIS) software. We demonstrate such path computations and visualizations applied to archaeological research questions. Our system includes tools to visualize: energetic cost surfaces, comparisons of the elevation profiles of shortest paths versus least cost paths, and the display of paths of least caloric effort on Digital Elevation Models (DEMs). These analysis tools can be applied to calculate and visualize 1) likely locations of prehistoric trails and 2) expected ratios of raw material types to be recovered at archaeological sites.

Computer-Based Tools for Inquiry in Undergraduate Classrooms: Results from the VGEE

NASA Astrophysics Data System (ADS)

Pandya, R. E.; Bramer, D. J.; Elliott, D.; Hay, K. E.; Mallaiahgari, L.; Marlino, M. R.; Middleton, D.; Ramamurhty, M. K.; Scheitlin, T.; Weingroff, M.; Wilhelmson, R.; Yoder, J.

2002-05-01

The Visual Geophysical Exploration Environment (VGEE) is a suite of computer-based tools designed to help learners connect observable, large-scale geophysical phenomena to underlying physical principles. Technologically, this connection is mediated by java-based interactive tools: a multi-dimensional visualization environment, authentic scientific data-sets, concept models that illustrate fundamental physical principles, and an interactive web-based work management system for archiving and evaluating learners' progress. Our preliminary investigations showed, however, that the tools alone are not sufficient to empower undergraduate learners; learners have trouble in organizing inquiry and using the visualization tools effectively. To address these issues, the VGEE includes an inquiry strategy and scaffolding activities that are similar to strategies used successfully in K-12 classrooms. The strategy is organized around the steps: identify, relate, explain, and integrate. In the first step, students construct visualizations from data to try to identify salient features of a particular phenomenon. They compare their previous conceptions of a phenomenon to the data examine their current knowledge and motivate investigation. Next, students use the multivariable functionality of the visualization environment to relate the different features they identified. Explain moves the learner temporarily outside the visualization to the concept models, where they explore fundamental physical principles. Finally, in integrate, learners use these fundamental principles within the visualization environment by literally placing the concept model within the visualization environment as a probe and watching it respond to larger-scale patterns. This capability, unique to the VGEE, addresses the disconnect that novice learners often experience between fundamental physics and observable phenomena. It also allows learners the opportunity to reflect on and refine their knowledge as well as anchor it within a context for long-term retention. We are implementing the VGEE in one of two otherwise identical entry-level atmospheric courses. In addition to comparing student learning and attitudes in the two courses, we are analyzing student participation with the VGEE to evaluate the effectiveness and usability of the VGEE. In particular, we seek to identify the scaffolding students need to construct physically meaningful multi-dimensional visualizations, and evaluate the effectiveness of the visualization-embedded concept-models in addressing inert knowledge. We will also examine the utility of the inquiry strategy in developing content knowledge, process-of-science knowledge, and discipline-specific investigatory skills. Our presentation will include video examples of student use to illustrate our findings.

Body posture differentially impacts on visual attention towards tool, graspable, and non-graspable objects.

PubMed

Ambrosini, Ettore; Costantini, Marcello

2017-02-01

Viewed objects have been shown to afford suitable actions, even in the absence of any intention to act. However, little is known as to whether gaze behavior (i.e., the way we simply look at objects) is sensitive to action afforded by the seen object and how our actual motor possibilities affect this behavior. We recorded participants' eye movements during the observation of tools, graspable and ungraspable objects, while their hands were either freely resting on the table or tied behind their back. The effects of the observed object and hand posture on gaze behavior were measured by comparing the actual fixation distribution with that predicted by 2 widely supported models of visual attention, namely the Graph-Based Visual Saliency and the Adaptive Whitening Salience models. Results showed that saliency models did not accurately predict participants' fixation distributions for tools. Indeed, participants mostly fixated the action-related, functional part of the tools, regardless of its visual saliency. Critically, the restriction of the participants' action possibility led to a significant reduction of this effect and significantly improved the model prediction of the participants' gaze behavior. We suggest, first, that action-relevant object information at least in part guides gaze behavior. Second, postural information interacts with visual information to the generation of priority maps of fixation behavior. We support the view that the kind of information we access from the environment is constrained by our readiness to act. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Jupiter Environment Tool

NASA Technical Reports Server (NTRS)

Sturm, Erick J.; Monahue, Kenneth M.; Biehl, James P.; Kokorowski, Michael; Ngalande, Cedrick,; Boedeker, Jordan

2012-01-01

The Jupiter Environment Tool (JET) is a custom UI plug-in for STK that provides an interface to Jupiter environment models for visualization and analysis. Users can visualize the different magnetic field models of Jupiter through various rendering methods, which are fully integrated within STK s 3D Window. This allows users to take snapshots and make animations of their scenarios with magnetic field visualizations. Analytical data can be accessed in the form of custom vectors. Given these custom vectors, users have access to magnetic field data in custom reports, graphs, access constraints, coverage analysis, and anywhere else vectors are used within STK.

Early visual analysis tool using magnetoencephalography for treatment and recovery of neuronal dysfunction.

PubMed

Rasheed, Waqas; Neoh, Yee Yik; Bin Hamid, Nor Hisham; Reza, Faruque; Idris, Zamzuri; Tang, Tong Boon

2017-10-01

Functional neuroimaging modalities play an important role in deciding the diagnosis and course of treatment of neuronal dysfunction and degeneration. This article presents an analytical tool with visualization by exploiting the strengths of the MEG (magnetoencephalographic) neuroimaging technique. The tool automates MEG data import (in tSSS format), channel information extraction, time/frequency decomposition, and circular graph visualization (connectogram) for simple result inspection. For advanced users, the tool also provides magnitude squared coherence (MSC) values allowing personalized threshold levels, and the computation of default model from MEG data of control population. Default model obtained from healthy population data serves as a useful benchmark to diagnose and monitor neuronal recovery during treatment. The proposed tool further provides optional labels with international 10-10 system nomenclature in order to facilitate comparison studies with EEG (electroencephalography) sensor space. Potential applications in epilepsy and traumatic brain injury studies are also discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Grohar: Automated Visualization of Genome-Scale Metabolic Models and Their Pathways.

PubMed

Moškon, Miha; Zimic, Nikolaj; Mraz, Miha

2018-05-01

Genome-scale metabolic models (GEMs) have become a powerful tool for the investigation of the entire metabolism of the organism in silico. These models are, however, often extremely hard to reconstruct and also difficult to apply to the selected problem. Visualization of the GEM allows us to easier comprehend the model, to perform its graphical analysis, to find and correct the faulty relations, to identify the parts of the system with a designated function, etc. Even though several approaches for the automatic visualization of GEMs have been proposed, metabolic maps are still manually drawn or at least require large amount of manual curation. We present Grohar, a computational tool for automatic identification and visualization of GEM (sub)networks and their metabolic fluxes. These (sub)networks can be specified directly by listing the metabolites of interest or indirectly by providing reference metabolic pathways from different sources, such as KEGG, SBML, or Matlab file. These pathways are identified within the GEM using three different pathway alignment algorithms. Grohar also supports the visualization of the model adjustments (e.g., activation or inhibition of metabolic reactions) after perturbations are induced.

Modeling human comprehension of data visualizations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matzen, Laura E.; Haass, Michael Joseph; Divis, Kristin Marie

This project was inspired by two needs. The first is a need for tools to help scientists and engineers to design effective data visualizations for communicating information, whether to the user of a system, an analyst who must make decisions based on complex data, or in the context of a technical report or publication. Most scientists and engineers are not trained in visualization design, and they could benefit from simple metrics to assess how well their visualization's design conveys the intended message. In other words, will the most important information draw the viewer's attention? The second is the need formore » cognition-based metrics for evaluating new types of visualizations created by researchers in the information visualization and visual analytics communities. Evaluating visualizations is difficult even for experts. However, all visualization methods and techniques are intended to exploit the properties of the human visual system to convey information efficiently to a viewer. Thus, developing evaluation methods that are rooted in the scientific knowledge of the human visual system could be a useful approach. In this project, we conducted fundamental research on how humans make sense of abstract data visualizations, and how this process is influenced by their goals and prior experience. We then used that research to develop a new model, the Data Visualization Saliency Model, that can make accurate predictions about which features in an abstract visualization will draw a viewer's attention. The model is an evaluation tool that can address both of the needs described above, supporting both visualization research and Sandia mission needs.« less

Creating Visual Materials for Multi-Handicapped Deaf Learners.

ERIC Educational Resources Information Center

Hack, Carole; Brosmith, Susan

1980-01-01

The article describes two groups of visual materials developed for multiply handicapped deaf teenagers. The daily living skills project includes vocabulary lists, visuals, games and a model related to household cleaning, personal grooming, or consumer skills. The occupational information project includes visuals of tools, materials, and clothing…

Scientists' sense making when hypothesizing about disease mechanisms from expression data and their needs for visualization support.

PubMed

Mirel, Barbara; Görg, Carsten

2014-04-26

A common class of biomedical analysis is to explore expression data from high throughput experiments for the purpose of uncovering functional relationships that can lead to a hypothesis about mechanisms of a disease. We call this analysis expression driven, -omics hypothesizing. In it, scientists use interactive data visualizations and read deeply in the research literature. Little is known, however, about the actual flow of reasoning and behaviors (sense making) that scientists enact in this analysis, end-to-end. Understanding this flow is important because if bioinformatics tools are to be truly useful they must support it. Sense making models of visual analytics in other domains have been developed and used to inform the design of useful and usable tools. We believe they would be helpful in bioinformatics. To characterize the sense making involved in expression-driven, -omics hypothesizing, we conducted an in-depth observational study of one scientist as she engaged in this analysis over six months. From findings, we abstracted a preliminary sense making model. Here we describe its stages and suggest guidelines for developing visualization tools that we derived from this case. A single case cannot be generalized. But we offer our findings, sense making model and case-based tool guidelines as a first step toward increasing interest and further research in the bioinformatics field on scientists' analytical workflows and their implications for tool design.

Scientists’ sense making when hypothesizing about disease mechanisms from expression data and their needs for visualization support

PubMed Central

2014-01-01

A common class of biomedical analysis is to explore expression data from high throughput experiments for the purpose of uncovering functional relationships that can lead to a hypothesis about mechanisms of a disease. We call this analysis expression driven, -omics hypothesizing. In it, scientists use interactive data visualizations and read deeply in the research literature. Little is known, however, about the actual flow of reasoning and behaviors (sense making) that scientists enact in this analysis, end-to-end. Understanding this flow is important because if bioinformatics tools are to be truly useful they must support it. Sense making models of visual analytics in other domains have been developed and used to inform the design of useful and usable tools. We believe they would be helpful in bioinformatics. To characterize the sense making involved in expression-driven, -omics hypothesizing, we conducted an in-depth observational study of one scientist as she engaged in this analysis over six months. From findings, we abstracted a preliminary sense making model. Here we describe its stages and suggest guidelines for developing visualization tools that we derived from this case. A single case cannot be generalized. But we offer our findings, sense making model and case-based tool guidelines as a first step toward increasing interest and further research in the bioinformatics field on scientists’ analytical workflows and their implications for tool design. PMID:24766796

A Model-Driven Visualization Tool for Use with Model-Based Systems Engineering Projects

NASA Technical Reports Server (NTRS)

Trase, Kathryn; Fink, Eric

2014-01-01

Model-Based Systems Engineering (MBSE) promotes increased consistency between a system's design and its design documentation through the use of an object-oriented system model. The creation of this system model facilitates data presentation by providing a mechanism from which information can be extracted by automated manipulation of model content. Existing MBSE tools enable model creation, but are often too complex for the unfamiliar model viewer to easily use. These tools do not yet provide many opportunities for easing into the development and use of a system model when system design documentation already exists. This study creates a Systems Modeling Language (SysML) Document Traceability Framework (SDTF) for integrating design documentation with a system model, and develops an Interactive Visualization Engine for SysML Tools (InVEST), that exports consistent, clear, and concise views of SysML model data. These exported views are each meaningful to a variety of project stakeholders with differing subjects of concern and depth of technical involvement. InVEST allows a model user to generate multiple views and reports from a MBSE model, including wiki pages and interactive visualizations of data. System data can also be filtered to present only the information relevant to the particular stakeholder, resulting in a view that is both consistent with the larger system model and other model views. Viewing the relationships between system artifacts and documentation, and filtering through data to see specialized views improves the value of the system as a whole, as data becomes information

Virtual Reality: Visualization in Three Dimensions.

ERIC Educational Resources Information Center

McLellan, Hilary

Virtual reality is a newly emerging tool for scientific visualization that makes possible multisensory, three-dimensional modeling of scientific data. While the emphasis is on visualization, the other senses are added to enhance what the scientist can visualize. Researchers are working to extend the sensory range of what can be perceived in…

SimilarityExplorer: A visual inter-comparison tool for multifaceted climate data

Treesearch

J. Poco; A. Dasgupta; Y. Wei; W. Hargrove; C. Schwalm; R. Cook; E. Bertini; C. Silva

2014-01-01

Inter-comparison and similarity analysis to gauge consensus among multiple simulation models is a critical visualization problem for understanding climate change patterns. Climate models, specifically, Terrestrial Biosphere Models (TBM) represent time and space variable ecosystem processes, for example, simulations of photosynthesis and respiration, using algorithms...

Tool use and the distalization of the end-effector

PubMed Central

Bonaiuto, James B.; Jacobs, Stéphane; Frey, Scott H.

2009-01-01

We review recent neurophysiological data from macaques and humans suggesting that the use of tools extends the internal representation of the actor’s hand, and relate it to our modeling of the visual control of grasping. We introduce the idea that, in addition to extending the body schema to incorporate the tool, tool use involves distalization of the end-effector from hand to tool. Different tools extend the body schema in different ways, with a displaced visual target and a novel, task-specific processing of haptic feedback to the hand. This distalization is critical in order to exploit the unique functional capacities engendered by complex tools. PMID:19347356

RealSurf - A Tool for the Interactive Visualization of Mathematical Models

NASA Astrophysics Data System (ADS)

Stussak, Christian; Schenzel, Peter

For applications in fine art, architecture and engineering it is often important to visualize and to explore complex mathematical models. In former times there were static models of them collected in museums respectively in mathematical institutes. In order to check their properties for esthetical reasons it could be helpful to explore them interactively in 3D in real time. For the class of implicitly given algebraic surfaces we developed the tool RealSurf. Here we give an introduction to the program and some hints for the design of interesting surfaces.

Interactive Visualization of Complex Seismic Data and Models Using Bokeh

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chai, Chengping; Ammon, Charles J.; Maceira, Monica

Visualizing multidimensional data and models becomes more challenging as the volume and resolution of seismic data and models increase. But thanks to the development of powerful and accessible computer systems, a model web browser can be used to visualize complex scientific data and models dynamically. In this paper, we present four examples of seismic model visualization using an open-source Python package Bokeh. One example is a visualization of a surface-wave dispersion data set, another presents a view of three-component seismograms, and two illustrate methods to explore a 3D seismic-velocity model. Unlike other 3D visualization packages, our visualization approach has amore » minimum requirement on users and is relatively easy to develop, provided you have reasonable programming skills. Finally, utilizing familiar web browsing interfaces, the dynamic tools provide us an effective and efficient approach to explore large data sets and models.« less

Interactive Visualization of Complex Seismic Data and Models Using Bokeh

DOE PAGES

Chai, Chengping; Ammon, Charles J.; Maceira, Monica; ...

2018-02-14

Visualizing multidimensional data and models becomes more challenging as the volume and resolution of seismic data and models increase. But thanks to the development of powerful and accessible computer systems, a model web browser can be used to visualize complex scientific data and models dynamically. In this paper, we present four examples of seismic model visualization using an open-source Python package Bokeh. One example is a visualization of a surface-wave dispersion data set, another presents a view of three-component seismograms, and two illustrate methods to explore a 3D seismic-velocity model. Unlike other 3D visualization packages, our visualization approach has amore » minimum requirement on users and is relatively easy to develop, provided you have reasonable programming skills. Finally, utilizing familiar web browsing interfaces, the dynamic tools provide us an effective and efficient approach to explore large data sets and models.« less

DspaceOgre 3D Graphics Visualization Tool

NASA Technical Reports Server (NTRS)

Jain, Abhinandan; Myin, Steven; Pomerantz, Marc I.

2011-01-01

This general-purpose 3D graphics visualization C++ tool is designed for visualization of simulation and analysis data for articulated mechanisms. Examples of such systems are vehicles, robotic arms, biomechanics models, and biomolecular structures. DspaceOgre builds upon the open-source Ogre3D graphics visualization library. It provides additional classes to support the management of complex scenes involving multiple viewpoints and different scene groups, and can be used as a remote graphics server. This software provides improved support for adding programs at the graphics processing unit (GPU) level for improved performance. It also improves upon the messaging interface it exposes for use as a visualization server.

Comparative analysis and visualization of multiple collinear genomes

PubMed Central

2012-01-01

Background Genome browsers are a common tool used by biologists to visualize genomic features including genes, polymorphisms, and many others. However, existing genome browsers and visualization tools are not well-suited to perform meaningful comparative analysis among a large number of genomes. With the increasing quantity and availability of genomic data, there is an increased burden to provide useful visualization and analysis tools for comparison of multiple collinear genomes such as the large panels of model organisms which are the basis for much of the current genetic research. Results We have developed a novel web-based tool for visualizing and analyzing multiple collinear genomes. Our tool illustrates genome-sequence similarity through a mosaic of intervals representing local phylogeny, subspecific origin, and haplotype identity. Comparative analysis is facilitated through reordering and clustering of tracks, which can vary throughout the genome. In addition, we provide local phylogenetic trees as an alternate visualization to assess local variations. Conclusions Unlike previous genome browsers and viewers, ours allows for simultaneous and comparative analysis. Our browser provides intuitive selection and interactive navigation about features of interest. Dynamic visualizations adjust to scale and data content making analysis at variable resolutions and of multiple data sets more informative. We demonstrate our genome browser for an extensive set of genomic data sets composed of almost 200 distinct mouse laboratory strains. PMID:22536897

The Efficacy of a Low-Level Program Visualization Tool for Teaching Programming Concepts to Novice C Programmers.

ERIC Educational Resources Information Center

Smith, Philip A.; Webb, Geoffrey I.

2000-01-01

Describes "Glass-box Interpreter" a low-level program visualization tool called Bradman designed to provide a conceptual model of C program execution for novice programmers and makes visible aspects of the programming process normally hidden from the user. Presents an experiment that tests the efficacy of Bradman, and provides…

Is the Oxygen Atom Static or Dynamic? The Effect of Generating Animations on Students' Mental Models of Atomic Structure

ERIC Educational Resources Information Center

Akaygun, Sevil

2016-01-01

Visualizing the chemical structure and dynamics of particles has been challenging for many students; therefore, various visualizations and tools have been used in chemistry education. For science educators, it has been important to understand how students visualize and represent particular phenomena--i.e., their mental models-- to design more…

An online model composition tool for system biology models

PubMed Central

2013-01-01

Background There are multiple representation formats for Systems Biology computational models, and the Systems Biology Markup Language (SBML) is one of the most widely used. SBML is used to capture, store, and distribute computational models by Systems Biology data sources (e.g., the BioModels Database) and researchers. Therefore, there is a need for all-in-one web-based solutions that support advance SBML functionalities such as uploading, editing, composing, visualizing, simulating, querying, and browsing computational models. Results We present the design and implementation of the Model Composition Tool (Interface) within the PathCase-SB (PathCase Systems Biology) web portal. The tool helps users compose systems biology models to facilitate the complex process of merging systems biology models. We also present three tools that support the model composition tool, namely, (1) Model Simulation Interface that generates a visual plot of the simulation according to user’s input, (2) iModel Tool as a platform for users to upload their own models to compose, and (3) SimCom Tool that provides a side by side comparison of models being composed in the same pathway. Finally, we provide a web site that hosts BioModels Database models and a separate web site that hosts SBML Test Suite models. Conclusions Model composition tool (and the other three tools) can be used with little or no knowledge of the SBML document structure. For this reason, students or anyone who wants to learn about systems biology will benefit from the described functionalities. SBML Test Suite models will be a nice starting point for beginners. And, for more advanced purposes, users will able to access and employ models of the BioModels Database as well. PMID:24006914

Exploratory Climate Data Visualization and Analysis Using DV3D and UVCDAT

NASA Technical Reports Server (NTRS)

Maxwell, Thomas

2012-01-01

Earth system scientists are being inundated by an explosion of data generated by ever-increasing resolution in both global models and remote sensors. Advanced tools for accessing, analyzing, and visualizing very large and complex climate data are required to maintain rapid progress in Earth system research. To meet this need, NASA, in collaboration with the Ultra-scale Visualization Climate Data Analysis Tools (UVCOAT) consortium, is developing exploratory climate data analysis and visualization tools which provide data analysis capabilities for the Earth System Grid (ESG). This paper describes DV3D, a UV-COAT package that enables exploratory analysis of climate simulation and observation datasets. OV3D provides user-friendly interfaces for visualization and analysis of climate data at a level appropriate for scientists. It features workflow inte rfaces, interactive 40 data exploration, hyperwall and stereo visualization, automated provenance generation, and parallel task execution. DV30's integration with CDAT's climate data management system (COMS) and other climate data analysis tools provides a wide range of high performance climate data analysis operations. DV3D expands the scientists' toolbox by incorporating a suite of rich new exploratory visualization and analysis methods for addressing the complexity of climate datasets.

Improving Visual Communication.

PubMed

Singh, Gary

2018-01-01

A tool that creates realtime interactive color maps for scientific visualization helped enhance the dynamics of a major research project for the Climate, Ocean, and Sea Ice Modeling team at Los Alamos National Laboratory.

Developing, deploying and reflecting on a web-based geologic simulation tool

NASA Astrophysics Data System (ADS)

Cockett, R.

2015-12-01

Geoscience is visual. It requires geoscientists to think and communicate about processes and events in three spatial dimensions and variations through time. This is hard(!), and students often have difficulty when learning and visualizing the three dimensional and temporal concepts. Visible Geology is an online geologic block modelling tool that is targeted at students in introductory and structural geology. With Visible Geology, students are able to combine geologic events in any order to create their own geologic models and ask 'what-if' questions, as well as interrogate their models using cross sections, boreholes and depth slices. Instructors use it as a simulation and communication tool in demonstrations, and students use it to explore concepts of relative geologic time, structural relationships, as well as visualize abstract geologic representations such as stereonets. The level of interactivity and creativity inherent in Visible Geology often results in a sense of ownership and encourages engagement, leading learners to practice visualization and interpretation skills and discover geologic relationships. Through its development over the last five years, Visible Geology has been used by over 300K students worldwide as well as in multiple targeted studies at the University of Calgary and at the University of British Columbia. The ease of use of the software has made this tool practical for deployment in classrooms of any size as well as for individual use. In this presentation, I will discuss the thoughts behind the implementation and layout of the tool, including a framework used for the development and design of new educational simulations. I will also share some of the surprising and unexpected observations on student interaction with the 3D visualizations, and other insights that are enabled by web-based development and deployment.

AstroBlend: An astrophysical visualization package for Blender

NASA Astrophysics Data System (ADS)

Naiman, J. P.

2016-04-01

The rapid growth in scale and complexity of both computational and observational astrophysics over the past decade necessitates efficient and intuitive methods for examining and visualizing large datasets. Here, I present AstroBlend, an open-source Python library for use within the three dimensional modeling software, Blender. While Blender has been a popular open-source software among animators and visual effects artists, in recent years it has also become a tool for visualizing astrophysical datasets. AstroBlend combines the three dimensional capabilities of Blender with the analysis tools of the widely used astrophysical toolset, yt, to afford both computational and observational astrophysicists the ability to simultaneously analyze their data and create informative and appealing visualizations. The introduction of this package includes a description of features, work flow, and various example visualizations. A website - www.astroblend.com - has been developed which includes tutorials, and a gallery of example images and movies, along with links to downloadable data, three dimensional artistic models, and various other resources.

chromoWIZ: a web tool to query and visualize chromosome-anchored genes from cereal and model genomes.

PubMed

Nussbaumer, Thomas; Kugler, Karl G; Schweiger, Wolfgang; Bader, Kai C; Gundlach, Heidrun; Spannagl, Manuel; Poursarebani, Naser; Pfeifer, Matthias; Mayer, Klaus F X

2014-12-10

Over the last years reference genome sequences of several economically and scientifically important cereals and model plants became available. Despite the agricultural significance of these crops only a small number of tools exist that allow users to inspect and visualize the genomic position of genes of interest in an interactive manner. We present chromoWIZ, a web tool that allows visualizing the genomic positions of relevant genes and comparing these data between different plant genomes. Genes can be queried using gene identifiers, functional annotations, or sequence homology in four grass species (Triticum aestivum, Hordeum vulgare, Brachypodium distachyon, Oryza sativa). The distribution of the anchored genes is visualized along the chromosomes by using heat maps. Custom gene expression measurements, differential expression information, and gene-to-group mappings can be uploaded and can be used for further filtering. This tool is mainly designed for breeders and plant researchers, who are interested in the location and the distribution of candidate genes as well as in the syntenic relationships between different grass species. chromoWIZ is freely available and online accessible at http://mips.helmholtz-muenchen.de/plant/chromoWIZ/index.jsp.

A WebGL Tool for Visualizing the Topology of the Sun's Coronal Magnetic Field

NASA Astrophysics Data System (ADS)

Duffy, A.; Cheung, C.; DeRosa, M. L.

2012-12-01

We present a web-based, topology-viewing tool that allows users to visualize the geometry and topology of the Sun's 3D coronal magnetic field in an interactive manner. The tool is implemented using, open-source, mature, modern web technologies including WebGL, jQuery, HTML 5, and CSS 3, which are compatible with nearly all modern web browsers. As opposed to the traditional method of visualization, which involves the downloading and setup of various software packages-proprietary and otherwise-the tool presents a clean interface that allows the user to easily load and manipulate the model, while also offering great power to choose which topological features are displayed. The tool accepts data encoded in the JSON open format that has libraries available for nearly every major programming language, making it simple to generate the data.

Teaching Science through Pictorial Models during Read-Alouds

ERIC Educational Resources Information Center

Oliveira, Alandeom W.; Rivera, Seema; Glass, Rory; Mastroianni, Michael; Wizner, Francine; Amodeo, Vincent

2013-01-01

This study examines how three elementary teachers refer to pictorial models (photographs, drawings, and cartoons) during science read-alouds. While one teacher used realistic photographs for the purpose of visually verifying facts about crystals, another employed analytical diagrams as heuristic tools to help students visualize complex target…

Single unit approaches to human vision and memory.

PubMed

Kreiman, Gabriel

2007-08-01

Research on the visual system focuses on using electrophysiology, pharmacology and other invasive tools in animal models. Non-invasive tools such as scalp electroencephalography and imaging allow examining humans but show a much lower spatial and/or temporal resolution. Under special clinical conditions, it is possible to monitor single-unit activity in humans when invasive procedures are required due to particular pathological conditions including epilepsy and Parkinson's disease. We review our knowledge about the visual system and visual memories in the human brain at the single neuron level. The properties of the human brain seem to be broadly compatible with the knowledge derived from animal models. The possibility of examining high-resolution brain activity in conscious human subjects allows investigators to ask novel questions that are challenging to address in animal models.

Icarus: visualizer for de novo assembly evaluation.

PubMed

Mikheenko, Alla; Valin, Gleb; Prjibelski, Andrey; Saveliev, Vladislav; Gurevich, Alexey

2016-11-01

: Data visualization plays an increasingly important role in NGS data analysis. With advances in both sequencing and computational technologies, it has become a new bottleneck in genomics studies. Indeed, evaluation of de novo genome assemblies is one of the areas that can benefit from the visualization. However, even though multiple quality assessment methods are now available, existing visualization tools are hardly suitable for this purpose. Here, we present Icarus-a novel genome visualizer for accurate assessment and analysis of genomic draft assemblies, which is based on the tool QUAST. Icarus can be used in studies where a related reference genome is available, as well as for non-model organisms. The tool is available online and as a standalone application. http://cab.spbu.ru/software/icarus CONTACT: aleksey.gurevich@spbu.ruSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Integrating advanced visualization technology into the planetary Geoscience workflow

NASA Astrophysics Data System (ADS)

Huffman, John; Forsberg, Andrew; Loomis, Andrew; Head, James; Dickson, James; Fassett, Caleb

2011-09-01

Recent advances in computer visualization have allowed us to develop new tools for analyzing the data gathered during planetary missions, which is important, since these data sets have grown exponentially in recent years to tens of terabytes in size. As part of the Advanced Visualization in Solar System Exploration and Research (ADVISER) project, we utilize several advanced visualization techniques created specifically with planetary image data in mind. The Geoviewer application allows real-time active stereo display of images, which in aggregate have billions of pixels. The ADVISER desktop application platform allows fast three-dimensional visualization of planetary images overlain on digital terrain models. Both applications include tools for easy data ingest and real-time analysis in a programmatic manner. Incorporation of these tools into our everyday scientific workflow has proved important for scientific analysis, discussion, and publication, and enabled effective and exciting educational activities for students from high school through graduate school.

Visualization of RNA structure models within the Integrative Genomics Viewer.

PubMed

Busan, Steven; Weeks, Kevin M

2017-07-01

Analyses of the interrelationships between RNA structure and function are increasingly important components of genomic studies. The SHAPE-MaP strategy enables accurate RNA structure probing and realistic structure modeling of kilobase-length noncoding RNAs and mRNAs. Existing tools for visualizing RNA structure models are not suitable for efficient analysis of long, structurally heterogeneous RNAs. In addition, structure models are often advantageously interpreted in the context of other experimental data and gene annotation information, for which few tools currently exist. We have developed a module within the widely used and well supported open-source Integrative Genomics Viewer (IGV) that allows visualization of SHAPE and other chemical probing data, including raw reactivities, data-driven structural entropies, and data-constrained base-pair secondary structure models, in context with linear genomic data tracks. We illustrate the usefulness of visualizing RNA structure in the IGV by exploring structure models for a large viral RNA genome, comparing bacterial mRNA structure in cells with its structure under cell- and protein-free conditions, and comparing a noncoding RNA structure modeled using SHAPE data with a base-pairing model inferred through sequence covariation analysis. © 2017 Busan and Weeks; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

An Excel®-based visualization tool of 2-D soil gas concentration profiles in petroleum vapor intrusion

PubMed Central

Verginelli, Iason; Yao, Yijun; Suuberg, Eric M.

2017-01-01

In this study we present a petroleum vapor intrusion tool implemented in Microsoft® Excel® using Visual Basic for Applications (VBA) and integrated within a graphical interface. The latter helps users easily visualize two-dimensional soil gas concentration profiles and indoor concentrations as a function of site-specific conditions such as source strength and depth, biodegradation reaction rate constant, soil characteristics and building features. This tool is based on a two-dimensional explicit analytical model that combines steady-state diffusion-dominated vapor transport in a homogeneous soil with a piecewise first-order aerobic biodegradation model, in which rate is limited by oxygen availability. As recommended in the recently released United States Environmental Protection Agency's final Petroleum Vapor Intrusion guidance, a sensitivity analysis and a simplified Monte Carlo uncertainty analysis are also included in the spreadsheet. PMID:28163564

An Excel®-based visualization tool of 2-D soil gas concentration profiles in petroleum vapor intrusion.

PubMed

Verginelli, Iason; Yao, Yijun; Suuberg, Eric M

2016-01-01

In this study we present a petroleum vapor intrusion tool implemented in Microsoft ® Excel ® using Visual Basic for Applications (VBA) and integrated within a graphical interface. The latter helps users easily visualize two-dimensional soil gas concentration profiles and indoor concentrations as a function of site-specific conditions such as source strength and depth, biodegradation reaction rate constant, soil characteristics and building features. This tool is based on a two-dimensional explicit analytical model that combines steady-state diffusion-dominated vapor transport in a homogeneous soil with a piecewise first-order aerobic biodegradation model, in which rate is limited by oxygen availability. As recommended in the recently released United States Environmental Protection Agency's final Petroleum Vapor Intrusion guidance, a sensitivity analysis and a simplified Monte Carlo uncertainty analysis are also included in the spreadsheet.

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

DOE Office of Scientific and Technical Information (OSTI.GOV)

King, Zachary A.; Drager, Andreas; Ebrahim, Ali

Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way. Second, users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzymes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g. RNA-Seq, proteomics, ChIP)—in conjunction with metabolite- and reaction-oriented data types (e.g. metabolomics, fluxomics).more » Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools.« less

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

PubMed Central

King, Zachary A.; Dräger, Andreas; Ebrahim, Ali; Sonnenschein, Nikolaus; Lewis, Nathan E.; Palsson, Bernhard O.

2015-01-01

Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way. Second, users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzymes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g. RNA-Seq, proteomics, ChIP)—in conjunction with metabolite- and reaction-oriented data types (e.g. metabolomics, fluxomics). Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools. PMID:26313928

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

DOE PAGES

King, Zachary A.; Drager, Andreas; Ebrahim, Ali; ...

2015-08-27

Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way. Second, users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzymes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g. RNA-Seq, proteomics, ChIP)—in conjunction with metabolite- and reaction-oriented data types (e.g. metabolomics, fluxomics).more » Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools.« less

Virtual Manipulatives: Tools for Teaching Mathematics to Students with Learning Disabilities

ERIC Educational Resources Information Center

Shin, Mikyung; Bryant, Diane P.; Bryant, Brian R.; McKenna, John W.; Hou, Fangjuan; Ok, Min Wook

2017-01-01

Many students with learning disabilities demonstrate difficulty in developing a conceptual understanding of mathematical topics. Researchers recommend using visual models to support student learning of the concepts and skills necessary to complete abstract and symbolic mathematical problems. Virtual manipulatives (i.e., interactive visual models)…

Optimal visual-haptic integration with articulated tools.

PubMed

Takahashi, Chie; Watt, Simon J

2017-05-01

When we feel and see an object, the nervous system integrates visual and haptic information optimally, exploiting the redundancy in multiple signals to estimate properties more precisely than is possible from either signal alone. We examined whether optimal integration is similarly achieved when using articulated tools. Such tools (tongs, pliers, etc) are a defining characteristic of human hand function, but complicate the classical sensory 'correspondence problem' underlying multisensory integration. Optimal integration requires establishing the relationship between signals acquired by different sensors (hand and eye) and, therefore, in fundamentally unrelated units. The system must also determine when signals refer to the same property of the world-seeing and feeling the same thing-and only integrate those that do. This could be achieved by comparing the pattern of current visual and haptic input to known statistics of their normal relationship. Articulated tools disrupt this relationship, however, by altering the geometrical relationship between object properties and hand posture (the haptic signal). We examined whether different tool configurations are taken into account in visual-haptic integration. We indexed integration by measuring the precision of size estimates, and compared our results to optimal predictions from a maximum-likelihood integrator. Integration was near optimal, independent of tool configuration/hand posture, provided that visual and haptic signals referred to the same object in the world. Thus, sensory correspondence was determined correctly (trial-by-trial), taking tool configuration into account. This reveals highly flexible multisensory integration underlying tool use, consistent with the brain constructing internal models of tools' properties.

Benchmarking a Visual-Basic based multi-component one-dimensional reactive transport modeling tool

NASA Astrophysics Data System (ADS)

Torlapati, Jagadish; Prabhakar Clement, T.

2013-01-01

We present the details of a comprehensive numerical modeling tool, RT1D, which can be used for simulating biochemical and geochemical reactive transport problems. The code can be run within the standard Microsoft EXCEL Visual Basic platform, and it does not require any additional software tools. The code can be easily adapted by others for simulating different types of laboratory-scale reactive transport experiments. We illustrate the capabilities of the tool by solving five benchmark problems with varying levels of reaction complexity. These literature-derived benchmarks are used to highlight the versatility of the code for solving a variety of practical reactive transport problems. The benchmarks are described in detail to provide a comprehensive database, which can be used by model developers to test other numerical codes. The VBA code presented in the study is a practical tool that can be used by laboratory researchers for analyzing both batch and column datasets within an EXCEL platform.

Application of digital human modeling and simulation for vision analysis of pilots in a jet aircraft: a case study.

PubMed

Karmakar, Sougata; Pal, Madhu Sudan; Majumdar, Deepti; Majumdar, Dhurjati

2012-01-01

Ergonomic evaluation of visual demands becomes crucial for the operators/users when rapid decision making is needed under extreme time constraint like navigation task of jet aircraft. Research reported here comprises ergonomic evaluation of pilot's vision in a jet aircraft in virtual environment to demonstrate how vision analysis tools of digital human modeling software can be used effectively for such study. Three (03) dynamic digital pilot models, representative of smallest, average and largest Indian pilot population were generated from anthropometric database and interfaced with digital prototype of the cockpit in Jack software for analysis of vision within and outside the cockpit. Vision analysis tools like view cones, eye view windows, blind spot area, obscuration zone, reflection zone etc. were employed during evaluation of visual fields. Vision analysis tool was also used for studying kinematic changes of pilot's body joints during simulated gazing activity. From present study, it can be concluded that vision analysis tool of digital human modeling software was found very effective in evaluation of position and alignment of different displays and controls in the workstation based upon their priorities within the visual fields and anthropometry of the targeted users, long before the development of its physical prototype.

Artificial neural network models: A decision support tool for enhancing seedling selection in sugarcane

USDA-ARS?s Scientific Manuscript database

Currently, sugarcane selection begins at the seedling stage with visual selection for cane yield and other yield-related traits. Although subjective and inefficient, visual selection remains the primary method for selection. Visual selection is inefficient because of the confounding effect of genoty...

Visualizing the Heliosphere

NASA Technical Reports Server (NTRS)

Bridgman, William T.; Shirah, Greg W.; Mitchell, Horace G.

2008-01-01

Today, scientific data and models can combine with modern animation tools to produce compelling visualizations to inform and educate. The Scientific Visualization Studio at Goddard Space Flight Center merges these techniques from the very different worlds of entertainment and science to enable scientists and the general public to 'see the unseeable' in new ways.

Revel8or: Model Driven Capacity Planning Tool Suite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Liming; Liu, Yan; Bui, Ngoc B.

2007-05-31

Designing complex multi-tier applications that must meet strict performance requirements is a challenging software engineering problem. Ideally, the application architect could derive accurate performance predictions early in the project life-cycle, leveraging initial application design-level models and a description of the target software and hardware platforms. To this end, we have developed a capacity planning tool suite for component-based applications, called Revel8tor. The tool adheres to the model driven development paradigm and supports benchmarking and performance prediction for J2EE, .Net and Web services platforms. The suite is composed of three different tools: MDAPerf, MDABench and DSLBench. MDAPerf allows annotation of designmore » diagrams and derives performance analysis models. MDABench allows a customized benchmark application to be modeled in the UML 2.0 Testing Profile and automatically generates a deployable application, with measurement automatically conducted. DSLBench allows the same benchmark modeling and generation to be conducted using a simple performance engineering Domain Specific Language (DSL) in Microsoft Visual Studio. DSLBench integrates with Visual Studio and reuses its load testing infrastructure. Together, the tool suite can assist capacity planning across platforms in an automated fashion.« less

Software tool for data mining and its applications

NASA Astrophysics Data System (ADS)

Yang, Jie; Ye, Chenzhou; Chen, Nianyi

2002-03-01

A software tool for data mining is introduced, which integrates pattern recognition (PCA, Fisher, clustering, hyperenvelop, regression), artificial intelligence (knowledge representation, decision trees), statistical learning (rough set, support vector machine), computational intelligence (neural network, genetic algorithm, fuzzy systems). It consists of nine function models: pattern recognition, decision trees, association rule, fuzzy rule, neural network, genetic algorithm, Hyper Envelop, support vector machine, visualization. The principle and knowledge representation of some function models of data mining are described. The software tool of data mining is realized by Visual C++ under Windows 2000. Nonmonotony in data mining is dealt with by concept hierarchy and layered mining. The software tool of data mining has satisfactorily applied in the prediction of regularities of the formation of ternary intermetallic compounds in alloy systems, and diagnosis of brain glioma.

Visualization and modeling of smoke transport over landscape scales

Treesearch

Glenn P. Forney; William Mell

2007-01-01

Computational tools have been developed at the National Institute of Standards and Technology (NIST) for modeling fire spread and smoke transport. These tools have been adapted to address fire scenarios that occur in the wildland urban interface (WUI) over kilometer-scale distances. These models include the smoke plume transport model ALOFT (A Large Open Fire plume...

ADOPT: A tool for automatic detection of tectonic plates at the surface of convection models

NASA Astrophysics Data System (ADS)

Mallard, C.; Jacquet, B.; Coltice, N.

2017-08-01

Mantle convection models with plate-like behavior produce surface structures comparable to Earth's plate boundaries. However, analyzing those structures is a difficult task, since convection models produce, as on Earth, diffuse deformation and elusive plate boundaries. Therefore we present here and share a quantitative tool to identify plate boundaries and produce plate polygon layouts from results of numerical models of convection: Automatic Detection Of Plate Tectonics (ADOPT). This digital tool operates within the free open-source visualization software Paraview. It is based on image segmentation techniques to detect objects. The fundamental algorithm used in ADOPT is the watershed transform. We transform the output of convection models into a topographic map, the crest lines being the regions of deformation (plate boundaries) and the catchment basins being the plate interiors. We propose two generic protocols (the field and the distance methods) that we test against an independent visual detection of plate polygons. We show that ADOPT is effective to identify the smaller plates and to close plate polygons in areas where boundaries are diffuse or elusive. ADOPT allows the export of plate polygons in the standard OGR-GMT format for visualization, modification, and analysis under generic softwares like GMT or GPlates.

Implementing multiresolution models and families of models: from entity-level simulation to desktop stochastic models and "repro" models

NASA Astrophysics Data System (ADS)

McEver, Jimmie; Davis, Paul K.; Bigelow, James H.

2000-06-01

We have developed and used families of multiresolution and multiple-perspective models (MRM and MRMPM), both in our substantive analytic work for the Department of Defense and to learn more about how such models can be designed and implemented. This paper is a brief case history of our experience with a particular family of models addressing the use of precision fires in interdicting and halting an invading army. Our models were implemented as closed-form analytic solutions, in spreadsheets, and in the more sophisticated AnalyticaTM environment. We also drew on an entity-level simulation for data. The paper reviews the importance of certain key attributes of development environments (visual modeling, interactive languages, friendly use of array mathematics, facilities for experimental design and configuration control, statistical analysis tools, graphical visualization tools, interactive post-processing, and relational database tools). These can go a long way towards facilitating MRMPM work, but many of these attributes are not yet widely available (or available at all) in commercial model-development tools--especially for use with personal computers. We conclude with some lessons learned from our experience.

A Comparative Study of Successful Central Nervous System Drugs Using Molecular Modeling

ERIC Educational Resources Information Center

Kim, Hyosub; Sulaimon, Segun; Menezes, Sandra; Son, Anne; Menezes, Warren J. C.

2011-01-01

Molecular modeling is a powerful tool used for three-dimensional visualization and for exploring electrostatic forces involved in drug transport. This tool enhances student understanding of structure-property relationships, as well as actively engaging them in class. Molecular modeling of several central nervous system (CNS) drugs is used to…

Visualising Earth's Mantle based on Global Adjoint Tomography

NASA Astrophysics Data System (ADS)

Bozdag, E.; Pugmire, D.; Lefebvre, M. P.; Hill, J.; Komatitsch, D.; Peter, D. B.; Podhorszki, N.; Tromp, J.

2017-12-01

Recent advances in 3D wave propagation solvers and high-performance computing have enabled regional and global full-waveform inversions. Interpretation of tomographic models is often done on visually. Robust and efficient visualization tools are necessary to thoroughly investigate large model files, particularly at the global scale. In collaboration with Oak Ridge National Laboratory (ORNL), we have developed effective visualization tools and used for visualization of our first-generation global model, GLAD-M15 (Bozdag et al. 2016). VisIt (https://wci.llnl.gov/simulation/computer-codes/visit/) is used for initial exploration of the models and for extraction of seismological features. The broad capability of VisIt, and its demonstrated scalability proved valuable for experimenting with different visualization techniques, and in the creation of timely results. Utilizing VisIt's plugin-architecture, a data reader plugin was developed, which reads the ADIOS (https://www.olcf.ornl.gov/center-projects/adios/) format of our model files. Blender (https://www.blender.org) is used for the setup of lighting, materials, camera paths and rendering of geometry. Python scripting was used to control the orchestration of different geometries, as well as camera animation for 3D movies. While we continue producing 3D contour plots and movies for various seismic parameters to better visualize plume- and slab-like features as well as anisotropy throughout the mantle, our aim is to make visualization an integral part of our global adjoint tomography workflow to routinely produce various 2D cross-sections to facilitate examination of our models after each iteration. This will ultimately form the basis for use of pattern recognition techniques in our investigations. Simulations for global adjoint tomography are performed on ORNL's Titan system and visualization is done in parallel on ORNL's post-processing cluster Rhea.

Navigation Constellation Design Using a Multi-Objective Genetic Algorithm

DTIC Science & Technology

2015-03-26

programs. This specific tool not only offers high fidelity simulations, but it also offers the visual aid provided by STK . The ability to...MATLAB and STK . STK is a program that allows users to model, analyze, and visualize space systems. Users can create objects such as satellites and...position dilution of precision (PDOP) and system cost. This thesis utilized Satellite Tool Kit ( STK ) to calculate PDOP values of navigation

BMDExpress Data Viewer: A Visualization Tool to Analyze ...

EPA Pesticide Factsheets

Regulatory agencies increasingly apply benchmark dose (BMD) modeling to determine points of departure in human risk assessments. BMDExpress applies BMD modeling to transcriptomics datasets and groups genes to biological processes and pathways for rapid assessment of doses at which biological perturbations occur. However, graphing and analytical capabilities within BMDExpress are limited, and the analysis of output files is challenging. We developed a web-based application, BMDExpress Data Viewer, for visualization and graphical analyses of BMDExpress output files. The software application consists of two main components: ‘Summary Visualization Tools’ and ‘Dataset Exploratory Tools’. We demonstrate through two case studies that the ‘Summary Visualization Tools’ can be used to examine and assess the distributions of probe and pathway BMD outputs, as well as derive a potential regulatory BMD through the modes or means of the distributions. The ‘Functional Enrichment Analysis’ tool presents biological processes in a two-dimensional bubble chart view. By applying filters of pathway enrichment p-value and minimum number of significant genes, we showed that the Functional Enrichment Analysis tool can be applied to select pathways that are potentially sensitive to chemical perturbations. The ‘Multiple Dataset Comparison’ tool enables comparison of BMDs across multiple experiments (e.g., across time points, tissues, or organisms, etc.). The ‘BMDL-BM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Minelli, Annalisa, E-mail: Annalisa.Minelli@univ-brest.fr; Marchesini, Ivan, E-mail: Ivan.Marchesini@irpi.cnr.it; Taylor, Faith E., E-mail: Faith.Taylor@kcl.ac.uk

Although there are clear economic and environmental incentives for producing energy from solar and wind power, there can be local opposition to their installation due to their impact upon the landscape. To date, no international guidelines exist to guide quantitative visual impact assessment of these facilities, making the planning process somewhat subjective. In this paper we demonstrate the development of a method and an Open Source GIS tool to quantitatively assess the visual impact of these facilities using line-of-site techniques. The methods here build upon previous studies by (i) more accurately representing the shape of energy producing facilities, (ii) takingmore » into account the distortion of the perceived shape and size of facilities caused by the location of the observer, (iii) calculating the possible obscuring of facilities caused by terrain morphology and (iv) allowing the combination of various facilities to more accurately represent the landscape. The tool has been applied to real and synthetic case studies and compared to recently published results from other models, and demonstrates an improvement in accuracy of the calculated visual impact of facilities. The tool is named r.wind.sun and is freely available from GRASS GIS AddOns. - Highlights: • We develop a tool to quantify wind turbine and photovoltaic panel visual impact. • The tool is freely available to download and edit as a module of GRASS GIS. • The tool takes into account visual distortion of the shape and size of objects. • The accuracy of calculation of visual impact is improved over previous methods.« less

Sandia MEMS Visualization Tools v. 3.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yarberry, Victor; Jorgensen, Craig R.; Young, Andrew I.

This is a revision to the Sandia MEMS Visualization Tools. It replaces all previous versions. New features in this version: Support for AutoCAD 2014 and 2015 . This CD contains an integrated set of electronic files that: a) Provides a 2D Process Visualizer that generates cross-section images of devices constructed using the SUMMiT V fabrication process. b) Provides a 3D Visualizer that generates 3D images of devices constructed using the SUMMiT V fabrication process. c) Provides a MEMS 3D Model generator that creates 3D solid models of devices constructed using the SUMMiT V fabrication process. While there exists some filesmore » on the CD that are used in conjunction with software package AutoCAD , these files are not intended for use independent of the CD. Note that the customer must purchase his/her own copy of AutoCAD to use with these files.« less

Neo: an object model for handling electrophysiology data in multiple formats

PubMed Central

Garcia, Samuel; Guarino, Domenico; Jaillet, Florent; Jennings, Todd; Pröpper, Robert; Rautenberg, Philipp L.; Rodgers, Chris C.; Sobolev, Andrey; Wachtler, Thomas; Yger, Pierre; Davison, Andrew P.

2014-01-01

Neuroscientists use many different software tools to acquire, analyze and visualize electrophysiological signals. However, incompatible data models and file formats make it difficult to exchange data between these tools. This reduces scientific productivity, renders potentially useful analysis methods inaccessible and impedes collaboration between labs. A common representation of the core data would improve interoperability and facilitate data-sharing. To that end, we propose here a language-independent object model, named “Neo,” suitable for representing data acquired from electroencephalographic, intracellular, or extracellular recordings, or generated from simulations. As a concrete instantiation of this object model we have developed an open source implementation in the Python programming language. In addition to representing electrophysiology data in memory for the purposes of analysis and visualization, the Python implementation provides a set of input/output (IO) modules for reading/writing the data from/to a variety of commonly used file formats. Support is included for formats produced by most of the major manufacturers of electrophysiology recording equipment and also for more generic formats such as MATLAB. Data representation and data analysis are conceptually separate: it is easier to write robust analysis code if it is focused on analysis and relies on an underlying package to handle data representation. For that reason, and also to be as lightweight as possible, the Neo object model and the associated Python package are deliberately limited to representation of data, with no functions for data analysis or visualization. Software for neurophysiology data analysis and visualization built on top of Neo automatically gains the benefits of interoperability, easier data sharing and automatic format conversion; there is already a burgeoning ecosystem of such tools. We intend that Neo should become the standard basis for Python tools in neurophysiology. PMID:24600386

Neo: an object model for handling electrophysiology data in multiple formats.

PubMed

Garcia, Samuel; Guarino, Domenico; Jaillet, Florent; Jennings, Todd; Pröpper, Robert; Rautenberg, Philipp L; Rodgers, Chris C; Sobolev, Andrey; Wachtler, Thomas; Yger, Pierre; Davison, Andrew P

2014-01-01

Neuroscientists use many different software tools to acquire, analyze and visualize electrophysiological signals. However, incompatible data models and file formats make it difficult to exchange data between these tools. This reduces scientific productivity, renders potentially useful analysis methods inaccessible and impedes collaboration between labs. A common representation of the core data would improve interoperability and facilitate data-sharing. To that end, we propose here a language-independent object model, named "Neo," suitable for representing data acquired from electroencephalographic, intracellular, or extracellular recordings, or generated from simulations. As a concrete instantiation of this object model we have developed an open source implementation in the Python programming language. In addition to representing electrophysiology data in memory for the purposes of analysis and visualization, the Python implementation provides a set of input/output (IO) modules for reading/writing the data from/to a variety of commonly used file formats. Support is included for formats produced by most of the major manufacturers of electrophysiology recording equipment and also for more generic formats such as MATLAB. Data representation and data analysis are conceptually separate: it is easier to write robust analysis code if it is focused on analysis and relies on an underlying package to handle data representation. For that reason, and also to be as lightweight as possible, the Neo object model and the associated Python package are deliberately limited to representation of data, with no functions for data analysis or visualization. Software for neurophysiology data analysis and visualization built on top of Neo automatically gains the benefits of interoperability, easier data sharing and automatic format conversion; there is already a burgeoning ecosystem of such tools. We intend that Neo should become the standard basis for Python tools in neurophysiology.

Virtual Laboratory as an Element of Visualization When Teaching Chemical Contents in Science Class

ERIC Educational Resources Information Center

Herga, Nataša Rizman; Grmek, Milena Ivanuš; Dinevski, Dejan

2014-01-01

Using a variety of visualization tools for teaching and learning science and chemistry is necessary because pupils better understand chemical phenomena and formulate appropriate mental models. The purpose of the presented study was to determine the importance of a virtual laboratory as a visualization element when addressing chemical contents…

Application of simulation models for the optimization of business processes

NASA Astrophysics Data System (ADS)

Jašek, Roman; Sedláček, Michal; Chramcov, Bronislav; Dvořák, Jiří

2016-06-01

The paper deals with the applications of modeling and simulation tools in the optimization of business processes, especially in solving an optimization of signal flow in security company. As a modeling tool was selected Simul8 software that is used to process modeling based on discrete event simulation and which enables the creation of a visual model of production and distribution processes.

Symbolic modeling of human anatomy for visualization and simulation

NASA Astrophysics Data System (ADS)

Pommert, Andreas; Schubert, Rainer; Riemer, Martin; Schiemann, Thomas; Tiede, Ulf; Hoehne, Karl H.

1994-09-01

Visualization of human anatomy in a 3D atlas requires both spatial and more abstract symbolic knowledge. Within our 'intelligent volume' model which integrates these two levels, we developed and implemented a semantic network model for describing human anatomy. Concepts for structuring (abstraction levels, domains, views, generic and case-specific modeling, inheritance) are introduced. Model, tools for generation and exploration and applications in our 3D anatomical atlas are presented and discussed.

QuakeSim 2.0

NASA Technical Reports Server (NTRS)

Donnellan, Andrea; Parker, Jay W.; Lyzenga, Gregory A.; Granat, Robert A.; Norton, Charles D.; Rundle, John B.; Pierce, Marlon E.; Fox, Geoffrey C.; McLeod, Dennis; Ludwig, Lisa Grant

2012-01-01

QuakeSim 2.0 improves understanding of earthquake processes by providing modeling tools and integrating model applications and various heterogeneous data sources within a Web services environment. QuakeSim is a multisource, synergistic, data-intensive environment for modeling the behavior of earthquake faults individually, and as part of complex interacting systems. Remotely sensed geodetic data products may be explored, compared with faults and landscape features, mined by pattern analysis applications, and integrated with models and pattern analysis applications in a rich Web-based and visualization environment. Integration of heterogeneous data products with pattern informatics tools enables efficient development of models. Federated database components and visualization tools allow rapid exploration of large datasets, while pattern informatics enables identification of subtle, but important, features in large data sets. QuakeSim is valuable for earthquake investigations and modeling in its current state, and also serves as a prototype and nucleus for broader systems under development. The framework provides access to physics-based simulation tools that model the earthquake cycle and related crustal deformation. Spaceborne GPS and Inter ferometric Synthetic Aperture (InSAR) data provide information on near-term crustal deformation, while paleoseismic geologic data provide longerterm information on earthquake fault processes. These data sources are integrated into QuakeSim's QuakeTables database system, and are accessible by users or various model applications. UAVSAR repeat pass interferometry data products are added to the QuakeTables database, and are available through a browseable map interface or Representational State Transfer (REST) interfaces. Model applications can retrieve data from Quake Tables, or from third-party GPS velocity data services; alternatively, users can manually input parameters into the models. Pattern analysis of GPS and seismicity data has proved useful for mid-term forecasting of earthquakes, and for detecting subtle changes in crustal deformation. The GPS time series analysis has also proved useful as a data-quality tool, enabling the discovery of station anomalies and data processing and distribution errors. Improved visualization tools enable more efficient data exploration and understanding. Tools provide flexibility to science users for exploring data in new ways through download links, but also facilitate standard, intuitive, and routine uses for science users and end users such as emergency responders.

CheS-Mapper 2.0 for visual validation of (Q)SAR models

PubMed Central

2014-01-01

Background Sound statistical validation is important to evaluate and compare the overall performance of (Q)SAR models. However, classical validation does not support the user in better understanding the properties of the model or the underlying data. Even though, a number of visualization tools for analyzing (Q)SAR information in small molecule datasets exist, integrated visualization methods that allow the investigation of model validation results are still lacking. Results We propose visual validation, as an approach for the graphical inspection of (Q)SAR model validation results. The approach applies the 3D viewer CheS-Mapper, an open-source application for the exploration of small molecules in virtual 3D space. The present work describes the new functionalities in CheS-Mapper 2.0, that facilitate the analysis of (Q)SAR information and allows the visual validation of (Q)SAR models. The tool enables the comparison of model predictions to the actual activity in feature space. The approach is generic: It is model-independent and can handle physico-chemical and structural input features as well as quantitative and qualitative endpoints. Conclusions Visual validation with CheS-Mapper enables analyzing (Q)SAR information in the data and indicates how this information is employed by the (Q)SAR model. It reveals, if the endpoint is modeled too specific or too generic and highlights common properties of misclassified compounds. Moreover, the researcher can use CheS-Mapper to inspect how the (Q)SAR model predicts activity cliffs. The CheS-Mapper software is freely available at http://ches-mapper.org. Graphical abstract Comparing actual and predicted activity values with CheS-Mapper.

Visual-haptic integration with pliers and tongs: signal “weights” take account of changes in haptic sensitivity caused by different tools

PubMed Central

Takahashi, Chie; Watt, Simon J.

2014-01-01

When we hold an object while looking at it, estimates from visual and haptic cues to size are combined in a statistically optimal fashion, whereby the “weight” given to each signal reflects their relative reliabilities. This allows object properties to be estimated more precisely than would otherwise be possible. Tools such as pliers and tongs systematically perturb the mapping between object size and the hand opening. This could complicate visual-haptic integration because it may alter the reliability of the haptic signal, thereby disrupting the determination of appropriate signal weights. To investigate this we first measured the reliability of haptic size estimates made with virtual pliers-like tools (created using a stereoscopic display and force-feedback robots) with different “gains” between hand opening and object size. Haptic reliability in tool use was straightforwardly determined by a combination of sensitivity to changes in hand opening and the effects of tool geometry. The precise pattern of sensitivity to hand opening, which violated Weber's law, meant that haptic reliability changed with tool gain. We then examined whether the visuo-motor system accounts for these reliability changes. We measured the weight given to visual and haptic stimuli when both were available, again with different tool gains, by measuring the perceived size of stimuli in which visual and haptic sizes were varied independently. The weight given to each sensory cue changed with tool gain in a manner that closely resembled the predictions of optimal sensory integration. The results are consistent with the idea that different tool geometries are modeled by the brain, allowing it to calculate not only the distal properties of objects felt with tools, but also the certainty with which those properties are known. These findings highlight the flexibility of human sensory integration and tool-use, and potentially provide an approach for optimizing the design of visual-haptic devices. PMID:24592245

A Visualization-Based Tutoring Tool for Engineering Education

NASA Astrophysics Data System (ADS)

Nguyen, Tang-Hung; Khoo, I.-Hung

2010-06-01

In engineering disciplines, students usually have hard time to visualize different aspects of engineering analysis and design, which inherently are too complex or abstract to fully understand without the aid of visual explanations or visualizations. As examples, when learning materials and sequences of construction process, students need to visualize how all components of a constructed facility are assembled? Such visualization can not be achieved in a textbook and a traditional lecturing environment. In this paper, the authors present the development of a computer tutoring software, in which different visualization tools including video clips, 3 dimensional models, drawings, pictures/photos together with complementary texts are used to assist students in deeply understanding and effectively mastering materials. The paper will also discuss the implementation and the effectiveness evaluation of the proposed tutoring software, which was used to teach a construction engineering management course offered at California State University, Long Beach.

Linking Plasma Conditions in the Magnetosphere with Ionospheric Signatures

NASA Technical Reports Server (NTRS)

Rastaetter, Lutz; Kozyra, Janet; Kuznetsova, Maria M.; Berrios, David H.

2012-01-01

Modeling of the full magnetosphere, ring current and ionosphere system has become an indispensable tool in analyzing the series of events that occur during geomagnetic storms. The CCMC has a full model suite available for the magnetosphere, together with visualization tools that allow a user to perform a large variety of analyses. The January, 21, 2005 storm was a moderate-size storm that has been found to feature a large penetration electric field and unusually large polar caps (low-latitude precipitation patterns) that are otherwise found in super storms. Based on simulations runs at CCMC we can outline the likely causes of this behavior. Using visualization tools available to the online user we compare results from different magnetosphere models and present connections found between features in the magnetosphere and the ionosphere that are connected magnetically. The range of magnetic mappings found with different models can be compared with statistical models (Tsyganenko) and the model's fidelity can be verified with observations from low earth orbiting satellites such as DMSP and TIMED.

Applying the metro map to software development management

NASA Astrophysics Data System (ADS)

Aguirregoitia, Amaia; Dolado, J. Javier; Presedo, Concepción

2010-01-01

This paper presents MetroMap, a new graphical representation model for controlling and managing the software development process. Metromap uses metaphors and visual representation techniques to explore several key indicators in order to support problem detection and resolution. The resulting visualization addresses diverse management tasks, such as tracking of deviations from the plan, analysis of patterns of failure detection and correction, overall assessment of change management policies, and estimation of product quality. The proposed visualization uses a metaphor with a metro map along with various interactive techniques to represent information concerning the software development process and to deal efficiently with multivariate visual queries. Finally, the paper shows the implementation of the tool in JavaFX with data of a real project and the results of testing the tool with the aforementioned data and users attempting several information retrieval tasks. The conclusion shows the results of analyzing user response time and efficiency using the MetroMap visualization system. The utility of the tool was positively evaluated.

Real-Time Visualization of Network Behaviors for Situational Awareness

DOE Office of Scientific and Technical Information (OSTI.GOV)

Best, Daniel M.; Bohn, Shawn J.; Love, Douglas V.

Plentiful, complex, and dynamic data make understanding the state of an enterprise network difficult. Although visualization can help analysts understand baseline behaviors in network traffic and identify off-normal events, visual analysis systems often do not scale well to operational data volumes (in the hundreds of millions to billions of transactions per day) nor to analysis of emergent trends in real-time data. We present a system that combines multiple, complementary visualization techniques coupled with in-stream analytics, behavioral modeling of network actors, and a high-throughput processing platform called MeDICi. This system provides situational understanding of real-time network activity to help analysts takemore » proactive response steps. We have developed these techniques using requirements gathered from the government users for which the tools are being developed. By linking multiple visualization tools to a streaming analytic pipeline, and designing each tool to support a particular kind of analysis (from high-level awareness to detailed investigation), analysts can understand the behavior of a network across multiple levels of abstraction.« less

MFV-class: a multi-faceted visualization tool of object classes.

PubMed

Zhang, Zhi-meng; Pan, Yun-he; Zhuang, Yue-ting

2004-11-01

Classes are key software components in an object-oriented software system. In many industrial OO software systems, there are some classes that have complicated structure and relationships. So in the processes of software maintenance, testing, software reengineering, software reuse and software restructure, it is a challenge for software engineers to understand these classes thoroughly. This paper proposes a class comprehension model based on constructivist learning theory, and implements a software visualization tool (MFV-Class) to help in the comprehension of a class. The tool provides multiple views of class to uncover manifold facets of class contents. It enables visualizing three object-oriented metrics of classes to help users focus on the understanding process. A case study was conducted to evaluate our approach and the toolkit.

Freiburg RNA tools: a central online resource for RNA-focused research and teaching.

PubMed

Raden, Martin; Ali, Syed M; Alkhnbashi, Omer S; Busch, Anke; Costa, Fabrizio; Davis, Jason A; Eggenhofer, Florian; Gelhausen, Rick; Georg, Jens; Heyne, Steffen; Hiller, Michael; Kundu, Kousik; Kleinkauf, Robert; Lott, Steffen C; Mohamed, Mostafa M; Mattheis, Alexander; Miladi, Milad; Richter, Andreas S; Will, Sebastian; Wolff, Joachim; Wright, Patrick R; Backofen, Rolf

2018-05-21

The Freiburg RNA tools webserver is a well established online resource for RNA-focused research. It provides a unified user interface and comprehensive result visualization for efficient command line tools. The webserver includes RNA-RNA interaction prediction (IntaRNA, CopraRNA, metaMIR), sRNA homology search (GLASSgo), sequence-structure alignments (LocARNA, MARNA, CARNA, ExpaRNA), CRISPR repeat classification (CRISPRmap), sequence design (antaRNA, INFO-RNA, SECISDesign), structure aberration evaluation of point mutations (RaSE), and RNA/protein-family models visualization (CMV), and other methods. Open education resources offer interactive visualizations of RNA structure and RNA-RNA interaction prediction as well as basic and advanced sequence alignment algorithms. The services are freely available at http://rna.informatik.uni-freiburg.de.

An Intracranial Electroencephalography (iEEG) Brain Function Mapping Tool with an Application to Epilepsy Surgery Evaluation.

PubMed

Wang, Yinghua; Yan, Jiaqing; Wen, Jianbin; Yu, Tao; Li, Xiaoli

2016-01-01

Before epilepsy surgeries, intracranial electroencephalography (iEEG) is often employed in function mapping and epileptogenic foci localization. Although the implanted electrodes provide crucial information for epileptogenic zone resection, a convenient clinical tool for electrode position registration and Brain Function Mapping (BFM) visualization is still lacking. In this study, we developed a BFM Tool, which facilitates electrode position registration and BFM visualization, with an application to epilepsy surgeries. The BFM Tool mainly utilizes electrode location registration and function mapping based on pre-defined brain models from other software. In addition, the electrode node and mapping properties, such as the node size/color, edge color/thickness, mapping method, can be adjusted easily using the setting panel. Moreover, users may manually import/export location and connectivity data to generate figures for further application. The role of this software is demonstrated by a clinical study of language area localization. The BFM Tool helps clinical doctors and researchers visualize implanted electrodes and brain functions in an easy, quick and flexible manner. Our tool provides convenient electrode registration, easy brain function visualization, and has good performance. It is clinical-oriented and is easy to deploy and use. The BFM tool is suitable for epilepsy and other clinical iEEG applications.

An Intracranial Electroencephalography (iEEG) Brain Function Mapping Tool with an Application to Epilepsy Surgery Evaluation

PubMed Central

Wang, Yinghua; Yan, Jiaqing; Wen, Jianbin; Yu, Tao; Li, Xiaoli

2016-01-01

Objects: Before epilepsy surgeries, intracranial electroencephalography (iEEG) is often employed in function mapping and epileptogenic foci localization. Although the implanted electrodes provide crucial information for epileptogenic zone resection, a convenient clinical tool for electrode position registration and Brain Function Mapping (BFM) visualization is still lacking. In this study, we developed a BFM Tool, which facilitates electrode position registration and BFM visualization, with an application to epilepsy surgeries. Methods: The BFM Tool mainly utilizes electrode location registration and function mapping based on pre-defined brain models from other software. In addition, the electrode node and mapping properties, such as the node size/color, edge color/thickness, mapping method, can be adjusted easily using the setting panel. Moreover, users may manually import/export location and connectivity data to generate figures for further application. The role of this software is demonstrated by a clinical study of language area localization. Results: The BFM Tool helps clinical doctors and researchers visualize implanted electrodes and brain functions in an easy, quick and flexible manner. Conclusions: Our tool provides convenient electrode registration, easy brain function visualization, and has good performance. It is clinical-oriented and is easy to deploy and use. The BFM tool is suitable for epilepsy and other clinical iEEG applications. PMID:27199729

Modeling Constellation Virtual Missions Using the Vdot(Trademark) Process Management Tool

NASA Technical Reports Server (NTRS)

Hardy, Roger; ONeil, Daniel; Sturken, Ian; Nix, Michael; Yanez, Damian

2011-01-01

The authors have identified a software tool suite that will support NASA's Virtual Mission (VM) effort. This is accomplished by transforming a spreadsheet database of mission events, task inputs and outputs, timelines, and organizations into process visualization tools and a Vdot process management model that includes embedded analysis software as well as requirements and information related to data manipulation and transfer. This paper describes the progress to date, and the application of the Virtual Mission to not only Constellation but to other architectures, and the pertinence to other aerospace applications. Vdot s intuitive visual interface brings VMs to life by turning static, paper-based processes into active, electronic processes that can be deployed, executed, managed, verified, and continuously improved. A VM can be executed using a computer-based, human-in-the-loop, real-time format, under the direction and control of the NASA VM Manager. Engineers in the various disciplines will not have to be Vdot-proficient but rather can fill out on-line, Excel-type databases with the mission information discussed above. The author s tool suite converts this database into several process visualization tools for review and into Microsoft Project, which can be imported directly into Vdot. Many tools can be embedded directly into Vdot, and when the necessary data/information is received from a preceding task, the analysis can be initiated automatically. Other NASA analysis tools are too complex for this process but Vdot automatically notifies the tool user that the data has been received and analysis can begin. The VM can be simulated from end-to-end using the author s tool suite. The planned approach for the Vdot-based process simulation is to generate the process model from a database; other advantages of this semi-automated approach are the participants can be geographically remote and after refining the process models via the human-in-the-loop simulation, the system can evolve into a process management server for the actual process.

Radio Frequency Ablation Registration, Segmentation, and Fusion Tool

PubMed Central

McCreedy, Evan S.; Cheng, Ruida; Hemler, Paul F.; Viswanathan, Anand; Wood, Bradford J.; McAuliffe, Matthew J.

2008-01-01

The Radio Frequency Ablation Segmentation Tool (RFAST) is a software application developed using NIH's Medical Image Processing Analysis and Visualization (MIPAV) API for the specific purpose of assisting physicians in the planning of radio frequency ablation (RFA) procedures. The RFAST application sequentially leads the physician through the steps necessary to register, fuse, segment, visualize and plan the RFA treatment. Three-dimensional volume visualization of the CT dataset with segmented 3D surface models enables the physician to interactively position the ablation probe to simulate burns and to semi-manually simulate sphere packing in an attempt to optimize probe placement. PMID:16871716

NASA's Lunar and Planetary Mapping and Modeling Program

NASA Astrophysics Data System (ADS)

Law, E.; Day, B. H.; Kim, R. M.; Bui, B.; Malhotra, S.; Chang, G.; Sadaqathullah, S.; Arevalo, E.; Vu, Q. A.

2016-12-01

NASA's Lunar and Planetary Mapping and Modeling Program produces a suite of online visualization and analysis tools. Originally designed for mission planning and science, these portals offer great benefits for education and public outreach (EPO), providing access to data from a wide range of instruments aboard a variety of past and current missions. As a component of NASA's Science EPO Infrastructure, they are available as resources for NASA STEM EPO programs, and to the greater EPO community. As new missions are planned to a variety of planetary bodies, these tools are facilitating the public's understanding of the missions and engaging the public in the process of identifying and selecting where these missions will land. There are currently three web portals in the program: the Lunar Mapping and Modeling Portal or LMMP (http://lmmp.nasa.gov), Vesta Trek (http://vestatrek.jpl.nasa.gov), and Mars Trek (http://marstrek.jpl.nasa.gov). Portals for additional planetary bodies are planned. As web-based toolsets, the portals do not require users to purchase or install any software beyond current web browsers. The portals provide analysis tools for measurement and study of planetary terrain. They allow data to be layered and adjusted to optimize visualization. Visualizations are easily stored and shared. The portals provide 3D visualization and give users the ability to mark terrain for generation of STL files that can be directed to 3D printers. Such 3D prints are valuable tools in museums, public exhibits, and classrooms - especially for the visually impaired. Along with the web portals, the program supports additional clients, web services, and APIs that facilitate dissemination of planetary data to a range of external applications and venues. NASA challenges and hackathons are also providing members of the software development community opportunities to participate in tool development and leverage data from the portals.

A Data-Driven Approach to Interactive Visualization of Power Grids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Jun

Driven by emerging industry standards, electric utilities and grid coordination organizations are eager to seek advanced tools to assist grid operators to perform mission-critical tasks and enable them to make quick and accurate decisions. The emerging field of visual analytics holds tremendous promise for improving the business practices in today’s electric power industry. The conducted investigation, however, has revealed that the existing commercial power grid visualization tools heavily rely on human designers, hindering user’s ability to discover. Additionally, for a large grid, it is very labor-intensive and costly to build and maintain the pre-designed visual displays. This project proposes amore » data-driven approach to overcome the common challenges. The proposed approach relies on developing powerful data manipulation algorithms to create visualizations based on the characteristics of empirically or mathematically derived data. The resulting visual presentations emphasize what the data is rather than how the data should be presented, thus fostering comprehension and discovery. Furthermore, the data-driven approach formulates visualizations on-the-fly. It does not require a visualization design stage, completely eliminating or significantly reducing the cost for building and maintaining visual displays. The research and development (R&D) conducted in this project is mainly divided into two phases. The first phase (Phase I & II) focuses on developing data driven techniques for visualization of power grid and its operation. Various data-driven visualization techniques were investigated, including pattern recognition for auto-generation of one-line diagrams, fuzzy model based rich data visualization for situational awareness, etc. The R&D conducted during the second phase (Phase IIB) focuses on enhancing the prototyped data driven visualization tool based on the gathered requirements and use cases. The goal is to evolve the prototyped tool developed during the first phase into a commercial grade product. We will use one of the identified application areas as an example to demonstrate how research results achieved in this project are successfully utilized to address an emerging industry need. In summary, the data-driven visualization approach developed in this project has proven to be promising for building the next-generation power grid visualization tools. Application of this approach has resulted in a state-of-the-art commercial tool currently being leveraged by more than 60 utility organizations in North America and Europe .« less

Visualization, documentation, analysis, and communication of large scale gene regulatory networks

PubMed Central

Longabaugh, William J.R.; Davidson, Eric H.; Bolouri, Hamid

2009-01-01

Summary Genetic regulatory networks (GRNs) are complex, large-scale, and spatially and temporally distributed. These characteristics impose challenging demands on computational GRN modeling tools, and there is a need for custom modeling tools. In this paper, we report on our ongoing development of BioTapestry, an open source, freely available computational tool designed specifically for GRN modeling. We also outline our future development plans, and give some examples of current applications of BioTapestry. PMID:18757046

Using Interactive Visualization to Analyze Solid Earth Data and Geodynamics Models

NASA Astrophysics Data System (ADS)

Kellogg, L. H.; Kreylos, O.; Billen, M. I.; Hamann, B.; Jadamec, M. A.; Rundle, J. B.; van Aalsburg, J.; Yikilmaz, M. B.

2008-12-01

The geological sciences are challenged to manage and interpret increasing volumes of data as observations and simulations increase in size and complexity. Major projects such as EarthScope and GeoEarthScope are producing the data needed to characterize the structure and kinematics of Earth's surface and interior at unprecedented resolution. At the same time, high-performance computing enables high-precision and fine- detail simulation of geodynamics processes, complementing the observational data. To facilitate interpretation and analysis of these datasets, to evaluate models, and to drive future calculations, we have developed methods of interactive visualization with a special focus on using immersive virtual reality (VR) environments to interact with models of Earth's surface and interior. VR has traditionally been used primarily as a presentation tool allowing active navigation through data. Reaping the full intellectual benefits of immersive VR as a tool for accelerated scientific analysis requires building on the method's strengths, that is, using both 3D perception and interaction with observed or simulated data. Our approach to VR takes advantage of the specialized skills of geoscientists who are trained to interpret geological and geophysical data generated from field observations. Interactive tools allow the scientist to explore and interpret geodynamic models, tomographic models, and topographic observations, while feature extraction tools support quantitative measurement of structures that emerge from numerical simulations or field observations. The use of VR technology enables us to improve our interpretation of crust and mantle structure and of geodynamical processes. Mapping tools based on computer visualization allow virtual "field studies" in inaccessible regions, and an interactive tool allows us to construct digital fault models for use in numerical models. Using the interactive tools on a high-end platform such as an immersive virtual reality room known as a Cave Automatic Virtual Environment (CAVE), enables the scientist to stand in data three-dimensional dataset while taking measurements. The CAVE involves three or more projection surfaces arranged as walls in a room. Stereo projectors combined with a motion tracking system and immersion recreates the experience of carrying out research in the field. This high-end system provides significant advantages for scientists working with complex volumetric data. The interactive tools also work on low-cost platforms that provide stereo views and the potential for interactivity such as a Geowall or a 3D enabled TV. The Geowall is also a well-established tool for education, and in combination with the tools we have developed, enables the rapid transfer of research data and new knowledge to the classroom. The interactive visualization tools can also be used on a desktop or laptop with or without stereo capability. Further information about the Virtual Reality User Interface (VRUI), the 3DVisualizer, the Virtual mapping tools, and the LIDAR viewer, can be found on the KeckCAVES website, www.keckcaves.org.

Toward Rigorous Parameterization of Underconstrained Neural Network Models Through Interactive Visualization and Steering of Connectivity Generation

PubMed Central

Nowke, Christian; Diaz-Pier, Sandra; Weyers, Benjamin; Hentschel, Bernd; Morrison, Abigail; Kuhlen, Torsten W.; Peyser, Alexander

2018-01-01

Simulation models in many scientific fields can have non-unique solutions or unique solutions which can be difficult to find. Moreover, in evolving systems, unique final state solutions can be reached by multiple different trajectories. Neuroscience is no exception. Often, neural network models are subject to parameter fitting to obtain desirable output comparable to experimental data. Parameter fitting without sufficient constraints and a systematic exploration of the possible solution space can lead to conclusions valid only around local minima or around non-minima. To address this issue, we have developed an interactive tool for visualizing and steering parameters in neural network simulation models. In this work, we focus particularly on connectivity generation, since finding suitable connectivity configurations for neural network models constitutes a complex parameter search scenario. The development of the tool has been guided by several use cases—the tool allows researchers to steer the parameters of the connectivity generation during the simulation, thus quickly growing networks composed of multiple populations with a targeted mean activity. The flexibility of the software allows scientists to explore other connectivity and neuron variables apart from the ones presented as use cases. With this tool, we enable an interactive exploration of parameter spaces and a better understanding of neural network models and grapple with the crucial problem of non-unique network solutions and trajectories. In addition, we observe a reduction in turn around times for the assessment of these models, due to interactive visualization while the simulation is computed. PMID:29937723

Open source 3D visualization and interaction dedicated to hydrological models

NASA Astrophysics Data System (ADS)

Richard, Julien; Giangola-Murzyn, Agathe; Gires, Auguste; Tchiguirinskaia, Ioulia; Schertzer, Daniel

2014-05-01

Climate change and surface urbanization strongly modify the hydrological cycle in urban areas, increasing the consequences of extreme events such as floods or draughts. These issues lead to the development of the Multi-Hydro model at the Ecole des Ponts ParisTech (A. Giangola-Murzyn et al., 2012). This fully distributed model allows to compute the hydrological response of urban and peri-urban areas. Unfortunately such models are seldom user friendly. Indeed generating the inputs before launching a new simulation is usually a tricky tasks, and understanding and interpreting the outputs remains specialist tasks not accessible to the wider public. The MH-AssimTool was developed to overcome these issues. To enable an easier and improved understanding of the model outputs, we decided to convert the raw output data (grids file in ascii format) to a 3D display. Some commercial paying models provide a 3D visualization. Because of the cost of their licenses, this kind of tools may not be accessible to the most concerned stakeholders. So, we are developing a new tool based on C++ for the computation, Qt for the graphic user interface, QGIS for the geographical side and OpenGL for the 3D display. All these languages and libraries are open source and multi-platform. We will discuss some preprocessing issues for the data conversion from 2.5D to 3D. Indeed, the GIS data, is considered as a 2.5D (e.i. 2D polygon + one height) and the its transform to 3D display implies a lot of algorithms. For example,to visualize in 3D one building, it is needed to have for each point the coordinates and the elevation according to the topography. Furthermore one have to create new points to represent the walls. Finally the interactions between the model and stakeholders through this new interface and how this helps converting a research tool into a an efficient operational decision tool will be discussed. This ongoing research on the improvement of the visualization methods is supported by the KIC-Climate Blue Green Dream project.

A web platform for integrated surface water - groundwater modeling and data management

NASA Astrophysics Data System (ADS)

Fatkhutdinov, Aybulat; Stefan, Catalin; Junghanns, Ralf

2016-04-01

Model-based decision support systems are considered to be reliable and time-efficient tools for resources management in various hydrology related fields. However, searching and acquisition of the required data, preparation of the data sets for simulations as well as post-processing, visualization and publishing of the simulations results often requires significantly more work and time than performing the modeling itself. The purpose of the developed software is to combine data storage facilities, data processing instruments and modeling tools in a single platform which potentially can reduce time required for performing simulations, hence decision making. The system is developed within the INOWAS (Innovative Web Based Decision Support System for Water Sustainability under a Changing Climate) project. The platform integrates spatially distributed catchment scale rainfall - runoff, infiltration and groundwater flow models with data storage, processing and visualization tools. The concept is implemented in a form of a web-GIS application and is build based on free and open source components, including the PostgreSQL database management system, Python programming language for modeling purposes, Mapserver for visualization and publishing the data, Openlayers for building the user interface and others. Configuration of the system allows performing data input, storage, pre- and post-processing and visualization in a single not disturbed workflow. In addition, realization of the decision support system in the form of a web service provides an opportunity to easily retrieve and share data sets as well as results of simulations over the internet, which gives significant advantages for collaborative work on the projects and is able to significantly increase usability of the decision support system.

A visualization method for teaching the geometric design of highways

DOT National Transportation Integrated Search

2000-04-11

In this project the authors employed state-of-the-art technology for developing visualization tools for teaching highway design. Specifically, the authors used photolog images as the basis for developing dynamic 3-D models of selected geometric eleme...

Algodoo: A Tool for Encouraging Creativity in Physics Teaching and Learning

NASA Astrophysics Data System (ADS)

Gregorcic, Bor; Bodin, Madelen

2017-01-01

Algodoo (http://www.algodoo.com) is a digital sandbox for physics 2D simulations. It allows students and teachers to easily create simulated "scenes" and explore physics through a user-friendly and visually attractive interface. In this paper, we present different ways in which students and teachers can use Algodoo to visualize and solve physics problems, investigate phenomena and processes, and engage in out-of-school activities and projects. Algodoo, with its approachable interface, inhabits a middle ground between computer games and "serious" computer modeling. It is suitable as an entry-level modeling tool for students of all ages and can facilitate discussions about the role of computer modeling in physics.

Haptic over visual information in the distribution of visual attention after tool-use in near and far space.

PubMed

Park, George D; Reed, Catherine L

2015-10-01

Despite attentional prioritization for grasping space near the hands, tool-use appears to transfer attentional bias to the tool's end/functional part. The contributions of haptic and visual inputs to attentional distribution along a tool were investigated as a function of tool-use in near (Experiment 1) and far (Experiment 2) space. Visual attention was assessed with a 50/50, go/no-go, target discrimination task, while a tool was held next to targets appearing near the tool-occupied hand or tool-end. Target response times (RTs) and sensitivity (d-prime) were measured at target locations, before and after functional tool practice for three conditions: (1) open-tool: tool-end visible (visual + haptic inputs), (2) hidden-tool: tool-end visually obscured (haptic input only), and (3) short-tool: stick missing tool's length/end (control condition: hand occupied but no visual/haptic input). In near space, both open- and hidden-tool groups showed a tool-end, attentional bias (faster RTs toward tool-end) before practice; after practice, RTs near the hand improved. In far space, the open-tool group showed no bias before practice; after practice, target RTs near the tool-end improved. However, the hidden-tool group showed a consistent tool-end bias despite practice. Lack of short-tool group results suggested that hidden-tool group results were specific to haptic inputs. In conclusion, (1) allocation of visual attention along a tool due to tool practice differs in near and far space, and (2) visual attention is drawn toward the tool's end even when visually obscured, suggesting haptic input provides sufficient information for directing attention along the tool.

Interactive visualization of numerical simulation results: A tool for mission planning and data analysis

NASA Technical Reports Server (NTRS)

Berchem, J.; Raeder, J.; Walker, R. J.; Ashour-Abdalla, M.

1995-01-01

We report on the development of an interactive system for visualizing and analyzing numerical simulation results. This system is based on visualization modules which use the Application Visualization System (AVS) and the NCAR graphics packages. Examples from recent simulations are presented to illustrate how these modules can be used for displaying and manipulating simulation results to facilitate their comparison with phenomenological model results and observations.

Research on the Intensity Analysis and Result Visualization of Construction Land in Urban Planning

NASA Astrophysics Data System (ADS)

Cui, J.; Dong, B.; Li, J.; Li, L.

2017-09-01

As a fundamental work of urban planning, the intensity analysis of construction land involves many repetitive data processing works that are prone to cause errors or data precision loss, and the lack of efficient methods and tools to visualizing the analysis results in current urban planning. In the research a portable tool is developed by using the Model Builder technique embedded in ArcGIS to provide automatic data processing and rapid result visualization for the works. A series of basic modules provided by ArcGIS are linked together to shape a whole data processing chain in the tool. Once the required data is imported, the analysis results and related maps and graphs including the intensity values and zoning map, the skyline analysis map etc. are produced automatically. Finally the tool is installation-free and can be dispatched quickly between planning teams.

sbml-diff: A Tool for Visually Comparing SBML Models in Synthetic Biology.

PubMed

Scott-Brown, James; Papachristodoulou, Antonis

2017-07-21

We present sbml-diff, a tool that is able to read a model of a biochemical reaction network in SBML format and produce a range of diagrams showing different levels of detail. Each diagram type can be used to visualize a single model or to visually compare two or more models. The default view depicts species as ellipses, reactions as rectangles, rules as parallelograms, and events as diamonds. A cartoon view replaces the symbols used for reactions on the basis of the associated Systems Biology Ontology terms. An abstract view represents species as ellipses and draws edges between them to indicate whether a species increases or decreases the production or degradation of another species. sbml-diff is freely licensed under the three-clause BSD license and can be downloaded from https://github.com/jamesscottbrown/sbml-diff and used as a python package called from other software, as a free-standing command-line application, or online using the form at http://sysos.eng.ox.ac.uk/tebio/upload.

Physically Based Rendering in the Nightshade NG Visualization Platform

NASA Astrophysics Data System (ADS)

Berglund, Karrie; Larey-Williams, Trystan; Spearman, Rob; Bogard, Arthur

2015-01-01

This poster describes our work on creating a physically based rendering model in Nightshade NG planetarium simulation and visualization software (project website: NightshadeSoftware.org). We discuss techniques used for rendering realistic scenes in the universe and dealing with astronomical distances in real time on consumer hardware. We also discuss some of the challenges of rewriting the software from scratch, a project which began in 2011.Nightshade NG can be a powerful tool for sharing data and visualizations. The desktop version of the software is free for anyone to download, use, and modify; it runs on Windows and Linux (and eventually Mac). If you are looking to disseminate your data or models, please stop by to discuss how we can work together.Nightshade software is used in literally hundreds of digital planetarium systems worldwide. Countless teachers and astronomy education groups run the software on flat screens. This wide use makes Nightshade an effective tool for dissemination to educators and the public.Nightshade NG is an especially powerful visualization tool when projected on a dome. We invite everyone to enter our inflatable dome in the exhibit hall to see this software in a 3D environment.

NREL: Renewable Resource Data Center - Solar Resource Models and Tools

Science.gov Websites

Solar Resource Models and Tools The Renewable Resource Data Center (RReDC) features the following -supplied hourly average measured global horizontal data. NSRDB Data Viewer Visualize, explore, and download solar resource data from the National Solar Radiation Database. PVWatts® Calculator PVWattsÂ

Simulation services and analysis tools at the CCMC to study multi-scale structure and dynamics of Earth's magnetopause

NASA Astrophysics Data System (ADS)

Kuznetsova, M. M.; Liu, Y. H.; Rastaetter, L.; Pembroke, A. D.; Chen, L. J.; Hesse, M.; Glocer, A.; Komar, C. M.; Dorelli, J.; Roytershteyn, V.

2016-12-01

The presentation will provide overview of new tools, services and models implemented at the Community Coordinated Modeling Center (CCMC) to facilitate MMS dayside results analysis. We will provide updates on implementation of Particle-in-Cell (PIC) simulations at the CCMC and opportunities for on-line visualization and analysis of results of PIC simulations of asymmetric magnetic reconnection for different guide fields and boundary conditions. Fields, plasma parameters, particle distribution moments as well as particle distribution functions calculated in selected regions of the vicinity of reconnection sites can be analyzed through the web-based interactive visualization system. In addition there are options to request distribution functions in user selected regions of interest and to fly through simulated magnetic reconnection configurations and a map of distributions to facilitate comparisons with observations. A broad collection of global magnetosphere models hosted at the CCMC provide opportunity to put MMS observations and local PIC simulations into global context. We recently implemented the RECON-X post processing tool (Glocer et al, 2016) which allows users to determine the location of separator surface around closed field lines and between open field lines and solar wind field lines. The tool also finds the separatrix line where the two surfaces touch and positions of magnetic nulls. The surfaces and the separatrix line can be visualized relative to satellite positions in the dayside magnetosphere using an interactive HTML-5 visualization for each time step processed. To validate global magnetosphere models' capability to simulate locations of dayside magnetosphere boundaries we will analyze the proximity of MMS to simulated separatrix locations for a set of MMS diffusion region crossing events.

A Visualization Tool for Integrating Research Results at an Underground Mine

NASA Astrophysics Data System (ADS)

Boltz, S.; Macdonald, B. D.; Orr, T.; Johnson, W.; Benton, D. J.

2016-12-01

Researchers with the National Institute for Occupational Safety and Health are conducting research at a deep, underground metal mine in Idaho to develop improvements in ground control technologies that reduce the effects of dynamic loading on mine workings, thereby decreasing the risk to miners. This research is multifaceted and includes: photogrammetry, microseismic monitoring, geotechnical instrumentation, and numerical modeling. When managing research involving such a wide range of data, understanding how the data relate to each other and to the mining activity quickly becomes a daunting task. In an effort to combine this diverse research data into a single, easy-to-use system, a three-dimensional visualization tool was developed. The tool was created using the Unity3d video gaming engine and includes the mine development entries, production stopes, important geologic structures, and user-input research data. The tool provides the user with a first-person, interactive experience where they are able to walk through the mine as well as navigate the rock mass surrounding the mine to view and interpret the imported data in the context of the mine and as a function of time. The tool was developed using data from a single mine; however, it is intended to be a generic tool that can be easily extended to other mines. For example, a similar visualization tool is being developed for an underground coal mine in Colorado. The ultimate goal is for NIOSH researchers and mine personnel to be able to use the visualization tool to identify trends that may not otherwise be apparent when viewing the data separately. This presentation highlights the features and capabilities of the mine visualization tool and explains how it may be used to more effectively interpret data and reduce the risk of ground fall hazards to underground miners.

Dyspraxia in a patient with corticobasal degeneration: the role of visual and tactile inputs to action

PubMed Central

Graham, N.; Zeman, A.; Young, A.; Patterson, K.; Hodges, J.

1999-01-01

OBJECTIVES—To investigate the roles of visual and tactile information in a dyspraxic patient with corticobasal degeneration (CBD) who showed dramatic facilitation in miming the use of a tool or object when he was given a tool to manipulate; and to study the nature of the praxic and neuropsychological deficits in CBD.
METHODS—The subject had clinically diagnosed CBD, and exhibited alien limb behaviour and striking ideomotor dyspraxia. General neuropsychological evaluation focused on constructional and visuospatial abilities, calculation, verbal fluency, episodic and semantic memory, plus spelling and writing because impairments in this domain were presenting complaints. Four experiments assessed the roles of visual and tactile information in the facilitation of motor performance by tools. Experiment 1 evaluated the patient's performance of six limb transitive actions under six conditions: (1) after he described the relevant tool from memory, (2) after he was shown a line drawing of the tool, (3) after he was shown a real exemplar of the tool, (4) after he watched the experimenter perform the action, (5) while he was holding the tool, and (6) immediately after he had performed the action with the tool but with the tool removed from his grasp. Experiment 2 evaluated the use of the same six tools when the patient had tactile but no visual information (while he was blindfolded). Experiments 3 and 4 assessed performance of actions appropriate to the same six tools when the patient had either neutral or inappropriate tactile feedback—that is, while he was holding a non-tool object or a different tool.
RESULTS—Miming of tool use was not facilitated by visual input; moreover, lack of visual information in the blindfolded condition did not reduce performance. The principal positive finding was a dramatic facilitation of the patient's ability to demonstrate object use when he was holding either the appropriate tool or a neutral object. Tools inappropriate to the requested action produced involuntary performance of the stimulus relevant action.
CONCLUSIONS—Tactile stimulation was paramount in the facilitation of motor performance in tool use by this patient with CBD. This outcome suggests that tactile information should be included in models which hypothesise modality specific inputs to the action production system. Significant impairments in spelling and letter production that have not previously been reported in CBD have also been documented.

 PMID:10449556

Data Visualization in Sociology

PubMed Central

Healy, Kieran; Moody, James

2014-01-01

Visualizing data is central to social scientific work. Despite a promising early beginning, sociology has lagged in the use of visual tools. We review the history and current state of visualization in sociology. Using examples throughout, we discuss recent developments in ways of seeing raw data and presenting the results of statistical modeling. We make a general distinction between those methods and tools designed to help explore datasets, and those designed to help present results to others. We argue that recent advances should be seen as part of a broader shift towards easier sharing of the code and data both between researchers and with wider publics, and encourage practitioners and publishers to work toward a higher and more consistent standard for the graphical display of sociological insights. PMID:25342872

Elementary Teachers' Selection and Use of Visual Models

NASA Astrophysics Data System (ADS)

Lee, Tammy D.; Gail Jones, M.

2018-02-01

As science grows in complexity, science teachers face an increasing challenge of helping students interpret models that represent complex science systems. Little is known about how teachers select and use models when planning lessons. This mixed methods study investigated the pedagogical approaches and visual models used by elementary in-service and preservice teachers in the development of a science lesson about a complex system (e.g., water cycle). Sixty-seven elementary in-service and 69 elementary preservice teachers completed a card sort task designed to document the types of visual models (e.g., images) that teachers choose when planning science instruction. Quantitative and qualitative analyses were conducted to analyze the card sort task. Semistructured interviews were conducted with a subsample of teachers to elicit the rationale for image selection. Results from this study showed that both experienced in-service teachers and novice preservice teachers tended to select similar models and use similar rationales for images to be used in lessons. Teachers tended to select models that were aesthetically pleasing and simple in design and illustrated specific elements of the water cycle. The results also showed that teachers were not likely to select images that represented the less obvious dimensions of the water cycle. Furthermore, teachers selected visual models more as a pedagogical tool to illustrate specific elements of the water cycle and less often as a tool to promote student learning related to complex systems.

3D Immersive Visualization: An Educational Tool in Geosciences

NASA Astrophysics Data System (ADS)

Pérez-Campos, N.; Cárdenas-Soto, M.; Juárez-Casas, M.; Castrejón-Pineda, R.

2007-05-01

3D immersive visualization is an innovative tool currently used in various disciplines, such as medicine, architecture, engineering, video games, etc. Recently, the Universidad Nacional Autónoma de México (UNAM) mounted a visualization theater (Ixtli) with leading edge technology, for academic and research purposes that require immersive 3D tools for a better understanding of the concepts involved. The Division of Engineering in Earth Sciences of the School of Engineering, UNAM, is running a project focused on visualization of geoscience data. Its objective is to incoporate educational material in geoscience courses in order to support and to improve the teaching-learning process, especially in well-known difficult topics for students. As part of the project, proffessors and students are trained in visualization techniques, then their data are adapted and visualized in Ixtli as part of a class or a seminar, where all the attendants can interact, not only among each other but also with the object under study. As part of our results, we present specific examples used in basic geophysics courses, such as interpreted seismic cubes, seismic-wave propagation models, and structural models from bathymetric, gravimetric and seismological data; as well as examples from ongoing applied projects, such as a modeled SH upward wave, the occurrence of an earthquake cluster in 1999 in the Popocatepetl volcano, and a risk atlas from Delegación Alvaro Obregón in Mexico City. All these examples, plus those to come, constitute a library for students and professors willing to explore another dimension of the teaching-learning process. Furthermore, this experience can be enhaced by rich discussions and interactions by videoconferences with other universities and researchers.

Automated UAV-based mapping for airborne reconnaissance and video exploitation

NASA Astrophysics Data System (ADS)

Se, Stephen; Firoozfam, Pezhman; Goldstein, Norman; Wu, Linda; Dutkiewicz, Melanie; Pace, Paul; Naud, J. L. Pierre

2009-05-01

Airborne surveillance and reconnaissance are essential for successful military missions. Such capabilities are critical for force protection, situational awareness, mission planning, damage assessment and others. UAVs gather huge amount of video data but it is extremely labour-intensive for operators to analyse hours and hours of received data. At MDA, we have developed a suite of tools towards automated video exploitation including calibration, visualization, change detection and 3D reconstruction. The on-going work is to improve the robustness of these tools and automate the process as much as possible. Our calibration tool extracts and matches tie-points in the video frames incrementally to recover the camera calibration and poses, which are then refined by bundle adjustment. Our visualization tool stabilizes the video, expands its field-of-view and creates a geo-referenced mosaic from the video frames. It is important to identify anomalies in a scene, which may include detecting any improvised explosive devices (IED). However, it is tedious and difficult to compare video clips to look for differences manually. Our change detection tool allows the user to load two video clips taken from two passes at different times and flags any changes between them. 3D models are useful for situational awareness, as it is easier to understand the scene by visualizing it in 3D. Our 3D reconstruction tool creates calibrated photo-realistic 3D models from video clips taken from different viewpoints, using both semi-automated and automated approaches. The resulting 3D models also allow distance measurements and line-of- sight analysis.

TU-C-17A-03: An Integrated Contour Evaluation Software Tool Using Supervised Pattern Recognition for Radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, H; Tan, J; Kavanaugh, J

Purpose: Radiotherapy (RT) contours delineated either manually or semiautomatically require verification before clinical usage. Manual evaluation is very time consuming. A new integrated software tool using supervised pattern contour recognition was thus developed to facilitate this process. Methods: The contouring tool was developed using an object-oriented programming language C# and application programming interfaces, e.g. visualization toolkit (VTK). The C# language served as the tool design basis. The Accord.Net scientific computing libraries were utilized for the required statistical data processing and pattern recognition, while the VTK was used to build and render 3-D mesh models from critical RT structures in real-timemore » and 360° visualization. Principal component analysis (PCA) was used for system self-updating geometry variations of normal structures based on physician-approved RT contours as a training dataset. The inhouse design of supervised PCA-based contour recognition method was used for automatically evaluating contour normality/abnormality. The function for reporting the contour evaluation results was implemented by using C# and Windows Form Designer. Results: The software input was RT simulation images and RT structures from commercial clinical treatment planning systems. Several abilities were demonstrated: automatic assessment of RT contours, file loading/saving of various modality medical images and RT contours, and generation/visualization of 3-D images and anatomical models. Moreover, it supported the 360° rendering of the RT structures in a multi-slice view, which allows physicians to visually check and edit abnormally contoured structures. Conclusion: This new software integrates the supervised learning framework with image processing and graphical visualization modules for RT contour verification. This tool has great potential for facilitating treatment planning with the assistance of an automatic contour evaluation module in avoiding unnecessary manual verification for physicians/dosimetrists. In addition, its nature as a compact and stand-alone tool allows for future extensibility to include additional functions for physicians’ clinical needs.« less

An Integrated Web-Based 3d Modeling and Visualization Platform to Support Sustainable Cities

NASA Astrophysics Data System (ADS)

Amirebrahimi, S.; Rajabifard, A.

2012-07-01

Sustainable Development is found as the key solution to preserve the sustainability of cities in oppose to ongoing population growth and its negative impacts. This is complex and requires a holistic and multidisciplinary decision making. Variety of stakeholders with different backgrounds also needs to be considered and involved. Numerous web-based modeling and visualization tools have been designed and developed to support this process. There have been some success stories; however, majority failed to bring a comprehensive platform to support different aspects of sustainable development. In this work, in the context of SDI and Land Administration, CSDILA Platform - a 3D visualization and modeling platform -was proposed which can be used to model and visualize different dimensions to facilitate the achievement of sustainability, in particular, in urban context. The methodology involved the design of a generic framework for development of an analytical and visualization tool over the web. CSDILA Platform was then implemented via number of technologies based on the guidelines provided by the framework. The platform has a modular structure and uses Service-Oriented Architecture (SOA). It is capable of managing spatial objects in a 4D data store and can flexibly incorporate a variety of developed models using the platform's API. Development scenarios can be modeled and tested using the analysis and modeling component in the platform and the results are visualized in seamless 3D environment. The platform was further tested using number of scenarios and showed promising results and potentials to serve a wider need. In this paper, the design process of the generic framework, the implementation of CSDILA Platform and technologies used, and also findings and future research directions will be presented and discussed.

Multimodal visualization interface for data management, self-learning and data presentation.

PubMed

Van Sint Jan, S; Demondion, X; Clapworthy, G; Louryan, S; Rooze, M; Cotten, A; Viceconti, M

2006-10-01

A multimodal visualization software, called the Data Manager (DM), has been developed to increase interdisciplinary communication around the topic of visualization and modeling of various aspects of the human anatomy. Numerous tools used in Radiology are integrated in the interface that runs on standard personal computers. The available tools, combined to hierarchical data management and custom layouts, allow analyzing of medical imaging data using advanced features outside radiological premises (for example, for patient review, conference presentation or tutorial preparation). The system is free, and based on an open-source software development architecture, and therefore updates of the system for custom applications are possible.

Performance analysis and optimization of an advanced pharmaceutical wastewater treatment plant through a visual basic software tool (PWWT.VB).

PubMed

Pal, Parimal; Thakura, Ritwik; Chakrabortty, Sankha

2016-05-01

A user-friendly, menu-driven simulation software tool has been developed for the first time to optimize and analyze the system performance of an advanced continuous membrane-integrated pharmaceutical wastewater treatment plant. The software allows pre-analysis and manipulation of input data which helps in optimization and shows the software performance visually on a graphical platform. Moreover, the software helps the user to "visualize" the effects of the operating parameters through its model-predicted output profiles. The software is based on a dynamic mathematical model, developed for a systematically integrated forward osmosis-nanofiltration process for removal of toxic organic compounds from pharmaceutical wastewater. The model-predicted values have been observed to corroborate well with the extensive experimental investigations which were found to be consistent under varying operating conditions like operating pressure, operating flow rate, and draw solute concentration. Low values of the relative error (RE = 0.09) and high values of Willmott-d-index (d will = 0.981) reflected a high degree of accuracy and reliability of the software. This software is likely to be a very efficient tool for system design or simulation of an advanced membrane-integrated treatment plant for hazardous wastewater.

Hierarchical programming for data storage and visualization

USGS Publications Warehouse

Donovan, John M.; Smith, Peter E.; ,

2001-01-01

Graphics software is an essential tool for interpreting, analyzing, and presenting data from multidimensional hydrodynamic models used in estuarine and coastal ocean studies. The post-processing of time-varying three-dimensional model output presents unique requirements for data visualization because of the large volume of data that can be generated and the multitude of time scales that must be examined. Such data can relate to estuarine or coastal ocean environments and come from numerical models or field instruments. One useful software tool for the display, editing, visualization, and printing of graphical data is the Gr application, written by the first author for use in U.S. Geological Survey San Francisco Bay Program. The Gr application has been made available to the public via the Internet since the year 2000. The Gr application is written in the Java (Sun Microsystems, Nov. 29, 2001) programming language and uses the Extensible Markup Language standard for hierarchical data storage. Gr presents a hierarchy of objects to the user that can be edited using a common interface. Java's object-oriented capabilities allow Gr to treat data, graphics, and tools equally and to save them all to a single XML file.

Diy Geospatial Web Service Chains: Geochaining Make it Easy

NASA Astrophysics Data System (ADS)

Wu, H.; You, L.; Gui, Z.

2011-08-01

It is a great challenge for beginners to create, deploy and utilize a Geospatial Web Service Chain (GWSC). People in Computer Science are usually not familiar with geospatial domain knowledge. Geospatial practitioners may lack the knowledge about web services and service chains. The end users may lack both. However, integrated visual editing interfaces, validation tools, and oneclick deployment wizards may help to lower the learning curve and improve modelling skills so beginners will have a better experience. GeoChaining is a GWSC modelling tool designed and developed based on these ideas. GeoChaining integrates visual editing, validation, deployment, execution etc. into a unified platform. By employing a Virtual Globe, users can intuitively visualize raw data and results produced by GeoChaining. All of these features allow users to easily start using GWSC, regardless of their professional background and computer skills. Further, GeoChaining supports GWSC model reuse, meaning that an entire GWSC model created or even a specific part can be directly reused in a new model. This greatly improves the efficiency of creating a new GWSC, and also contributes to the sharing and interoperability of GWSC.

QND – DESIGNING A PARTICIPATORY SCENARIO MODELING TOOL TO INTEGRATE TECHNOLOGY, ECOLOGY, AND SOCIOLOGY IN GUATEMALA’S MAYA BIOSPHERE RESERVE AND BEYOND

EPA Science Inventory

Participatory scenario modeling – an interactive method for visualizing the future – is one of the most promising tools for achieving sustainable land use agreements amongst diverse stakeholder groups. The method has the potential to bridge the gap between the high...

Not Just a Game … When We Play Together, We Learn Together: Interactive Virtual Environments and Gaming Engines for Geospatial Visualization

NASA Astrophysics Data System (ADS)

Shipman, J. S.; Anderson, J. W.

2017-12-01

An ideal tool for ecologists and land managers to investigate the impacts of both projected environmental changes and policy alternatives is the creation of immersive, interactive, virtual landscapes. As a new frontier in visualizing and understanding geospatial data, virtual landscapes require a new toolbox for data visualization that includes traditional GIS tools and uncommon tools such as the Unity3d game engine. Game engines provide capabilities to not only explore data but to build and interact with dynamic models collaboratively. These virtual worlds can be used to display and illustrate data that is often more understandable and plausible to both stakeholders and policy makers than is achieved using traditional maps.Within this context we will present funded research that has been developed utilizing virtual landscapes for geographic visualization and decision support among varied stakeholders. We will highlight the challenges and lessons learned when developing interactive virtual environments that require large multidisciplinary team efforts with varied competences. The results will emphasize the importance of visualization and interactive virtual environments and the link with emerging research disciplines within Visual Analytics.

Interactive visualization of vegetation dynamics

USGS Publications Warehouse

Reed, B.C.; Swets, D.; Bard, L.; Brown, J.; Rowland, James

2001-01-01

Satellite imagery provides a mechanism for observing seasonal dynamics of the landscape that have implications for near real-time monitoring of agriculture, forest, and range resources. This study illustrates a technique for visualizing timely information on key events during the growing season (e.g., onset, peak, duration, and end of growing season), as well as the status of the current growing season with respect to the recent historical average. Using time-series analysis of normalized difference vegetation index (NDVI) data from the advanced very high resolution radiometer (AVHRR) satellite sensor, seasonal dynamics can be derived. We have developed a set of Java-based visualization and analysis tools to make comparisons between the seasonal dynamics of the current year with those from the past twelve years. In addition, the visualization tools allow the user to query underlying databases such as land cover or administrative boundaries to analyze the seasonal dynamics of areas of their own interest. The Java-based tools (data exploration and visualization analysis or DEVA) use a Web-based client-server model for processing the data. The resulting visualization and analysis, available via the Internet, is of value to those responsible for land management decisions, resource allocation, and at-risk population targeting.

Visualizations and Mental Models - The Educational Implications of GEOWALL

NASA Astrophysics Data System (ADS)

Rapp, D.; Kendeou, P.

2003-12-01

Work in the earth sciences has outlined many of the faulty beliefs that students possess concerning particular geological systems and processes. Evidence from educational and cognitive psychology has demonstrated that students often have difficulty overcoming their na‹ve beliefs about science. Prior knowledge is often remarkably resistant to change, particularly when students' existing mental models for geological principles may be faulty or inaccurate. Figuring out how to help students revise their mental models to include appropriate information is a major challenge. Up until this point, research has tended to focus on whether 2-dimensional computer visualizations are useful tools for helping students develop scientifically correct models. Research suggests that when students are given the opportunity to use dynamic computer-based visualizations, they are more likely to recall the learned information, and are more likely to transfer that knowledge to novel settings. Unfortunately, 2-dimensional visualization systems are often inadequate representations of the material that educators would like students to learn. For example, a 2-dimensional image of the Earth's surface does not adequately convey particular features that are critical for visualizing the geological environment. This may limit the models that students can construct following these visualizations. GEOWALL is a stereo projection system that has attempted to address this issue. It can display multidimensional static geologic images and dynamic geologic animations in a 3-dimensional format. Our current research examines whether multidimensional visualization systems such as GEOWALL may facilitate learning by helping students to develop more complex mental models. This talk will address some of the cognitive issues that influence the construction of mental models, and the difficulty of updating existing mental models. We will also discuss our current work that seeks to examine whether GEOWALL is an effective tool for helping students to learn geological information (and potentially restructure their na‹ve conceptions of geologic principles).

Three-Dimensional Soil Landscape Modeling: A Potential Earth Science Teaching Tool

ERIC Educational Resources Information Center

Schmid, Brian M.; Manu, Andrew; Norton, Amy E.

2009-01-01

Three-dimensional visualization is helpful in understanding soils, and three dimensional (3-D) tools are gaining popularity in teaching earth sciences. Those tools are still somewhat underused in soil science, yet soil properties such as texture, color, and organic carbon content vary both vertically and horizontally across the landscape. These…

Power Plant Model Validation Tool

DOE Office of Scientific and Technical Information (OSTI.GOV)

The PPMV is used to validate generator model using disturbance recordings. The PPMV tool contains a collection of power plant models and model validation studies, as well as disturbance recordings from a number of historic grid events. The user can import data from a new disturbance into the database, which converts PMU and SCADA data into GE PSLF format, and then run the tool to validate (or invalidate) the model for a specific power plant against its actual performance. The PNNL PPMV tool enables the automation of the process of power plant model validation using disturbance recordings. The tool usesmore » PMU and SCADA measurements as input information. The tool automatically adjusts all required EPCL scripts and interacts with GE PSLF in the batch mode. The main tool features includes: The tool interacts with GE PSLF; The tool uses GE PSLF Play-In Function for generator model validation; Database of projects (model validation studies); Database of the historic events; Database of the power plant; The tool has advanced visualization capabilities; and The tool automatically generates reports« less

Spatiotemporal data visualisation for homecare monitoring of elderly people.

PubMed

Juarez, Jose M; Ochotorena, Jose M; Campos, Manuel; Combi, Carlo

2015-10-01

Elderly people who live alone can be assisted by home monitoring systems that identify risk scenarios such as falls, fatigue symptoms or burglary. Given that these systems have to manage spatiotemporal data, human intervention is required to validate automatic alarms due to the high number of false positives and the need for context interpretation. The goal of this work was to provide tools to support human action, to identify such potential risk scenarios based on spatiotemporal data visualisation. We propose the MTA (multiple temporal axes) model, a visual representation of temporal information of the activity of a single person at different locations. The main goal of this model is to visualize the behaviour of a person in their home, facilitating the identification of health-risk scenarios and repetitive patterns. We evaluate the model's insight capacity compared with other models using a standard evaluation protocol. We also test its practical suitability of the MTA graphical model in a commercial home monitoring system. In particular, we implemented 8VISU, a visualization tool based on MTA. MTA proved to be more than 90% accurate in identify non-risk scenarios, independently of the length of the record visualised. When the spatial complexity was increased (e.g. number of rooms) the model provided good accuracy form up to 5 rooms. Therefore, user preferences and user performance seem to be balanced. Moreover, it also gave high sensitivity levels (over 90%) for 5-8 rooms. Fall is the most recurrent incident for elderly people. The MTA model outperformed the other models considered in identifying fall scenarios (66% of correctness) and was the second best for burglary and fatigue scenarios (36% of correctness). Our experiments also confirm the hypothesis that cyclic models are the most suitable for fatigue scenarios, the Spiral and MTA models obtaining most positive identifications. In home monitoring systems, spatiotemporal visualization is a useful tool for identifying risk and preventing home accidents in elderly people living alone. The MTA model helps the visualisation in different stages of the temporal data analysis process. In particular, its explicit representation of space and movement is useful for identifying potential scenarios of risk, while the spiral structure can be used for the identification of recurrent patterns. The results of the experiments and the experience using the visualization tool 8VISU proof the potential of the MTA graphical model to mine temporal data and to support caregivers using home monitoring infrastructures. Copyright © 2015 Elsevier B.V. All rights reserved.

From Particles and Point Clouds to Voxel Models: High Resolution Modeling of Dynamic Landscapes in Open Source GIS

NASA Astrophysics Data System (ADS)

Mitasova, H.; Hardin, E. J.; Kratochvilova, A.; Landa, M.

2012-12-01

Multitemporal data acquired by modern mapping technologies provide unique insights into processes driving land surface dynamics. These high resolution data also offer an opportunity to improve the theoretical foundations and accuracy of process-based simulations of evolving landforms. We discuss development of new generation of visualization and analytics tools for GRASS GIS designed for 3D multitemporal data from repeated lidar surveys and from landscape process simulations. We focus on data and simulation methods that are based on point sampling of continuous fields and lead to representation of evolving surfaces as series of raster map layers or voxel models. For multitemporal lidar data we present workflows that combine open source point cloud processing tools with GRASS GIS and custom python scripts to model and analyze dynamics of coastal topography (Figure 1) and we outline development of coastal analysis toolbox. The simulations focus on particle sampling method for solving continuity equations and its application for geospatial modeling of landscape processes. In addition to water and sediment transport models, already implemented in GIS, the new capabilities under development combine OpenFOAM for wind shear stress simulation with a new module for aeolian sand transport and dune evolution simulations. Comparison of observed dynamics with the results of simulations is supported by a new, integrated 2D and 3D visualization interface that provides highly interactive and intuitive access to the redesigned and enhanced visualization tools. Several case studies will be used to illustrate the presented methods and tools and demonstrate the power of workflows built with FOSS and highlight their interoperability.Figure 1. Isosurfaces representing evolution of shoreline and a z=4.5m contour between the years 1997-2011at Cape Hatteras, NC extracted from a voxel model derived from series of lidar-based DEMs.

Modeling and evaluating user behavior in exploratory visual analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reda, Khairi; Johnson, Andrew E.; Papka, Michael E.

Empirical evaluation methods for visualizations have traditionally focused on assessing the outcome of the visual analytic process as opposed to characterizing how that process unfolds. There are only a handful of methods that can be used to systematically study how people use visualizations, making it difficult for researchers to capture and characterize the subtlety of cognitive and interaction behaviors users exhibit during visual analysis. To validate and improve visualization design, however, it is important for researchers to be able to assess and understand how users interact with visualization systems under realistic scenarios. This paper presents a methodology for modeling andmore » evaluating the behavior of users in exploratory visual analysis. We model visual exploration using a Markov chain process comprising transitions between mental, interaction, and computational states. These states and the transitions between them can be deduced from a variety of sources, including verbal transcripts, videos and audio recordings, and log files. This model enables the evaluator to characterize the cognitive and computational processes that are essential to insight acquisition in exploratory visual analysis, and reconstruct the dynamics of interaction between the user and the visualization system. We illustrate this model with two exemplar user studies, and demonstrate the qualitative and quantitative analytical tools it affords.« less

High School Biology Students Use of Visual Molecular Dynamics as an Authentic Tool for Learning about Modeling as a Professional Scientific Practice

ERIC Educational Resources Information Center

Burgin, Stephen R.; Oramous, Jennifer; Kaminski, Michael; Stocker, Linda; Moradi, Mahmoud

2018-01-01

Modeling is a practice of science that is underemphasized in biology classrooms in comparison to its central focus in the physical sciences. Visualizations of the submicroscopic world of molecules are becoming increasingly sophisticated with the evolution of new technologies. With this in mind, we introduced high school biology classrooms to a…

Modeling of Explorative Procedures for Remote Object Identification

DTIC Science & Technology

1991-09-01

haptic sensory system and the simulated foveal component of the visual system. Eventually it will allow multiple applications in remote sensing and...superposition of sensory channels. The use of a force reflecting telemanipulator and computer simulated visual foveal component are the tools which...representation of human search models is achieved by using the proprioceptive component of the haptic sensory system and the simulated foveal component of the

A novel medical image data-based multi-physics simulation platform for computational life sciences.

PubMed

Neufeld, Esra; Szczerba, Dominik; Chavannes, Nicolas; Kuster, Niels

2013-04-06

Simulating and modelling complex biological systems in computational life sciences requires specialized software tools that can perform medical image data-based modelling, jointly visualize the data and computational results, and handle large, complex, realistic and often noisy anatomical models. The required novel solvers must provide the power to model the physics, biology and physiology of living tissue within the full complexity of the human anatomy (e.g. neuronal activity, perfusion and ultrasound propagation). A multi-physics simulation platform satisfying these requirements has been developed for applications including device development and optimization, safety assessment, basic research, and treatment planning. This simulation platform consists of detailed, parametrized anatomical models, a segmentation and meshing tool, a wide range of solvers and optimizers, a framework for the rapid development of specialized and parallelized finite element method solvers, a visualization toolkit-based visualization engine, a Python scripting interface for customized applications, a coupling framework, and more. Core components are cross-platform compatible and use open formats. Several examples of applications are presented: hyperthermia cancer treatment planning, tumour growth modelling, evaluating the magneto-haemodynamic effect as a biomarker and physics-based morphing of anatomical models.

SpacePy - a Python-based library of tools for the space sciences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morley, Steven K; Welling, Daniel T; Koller, Josef

Space science deals with the bodies within the solar system and the interplanetary medium; the primary focus is on atmospheres and above - at Earth the short timescale variation in the the geomagnetic field, the Van Allen radiation belts and the deposition of energy into the upper atmosphere are key areas of investigation. SpacePy is a package for Python, targeted at the space sciences, that aims to make basic data analysis, modeling and visualization easier. It builds on the capabilities of the well-known NumPy and MatPlotLib packages. Publication quality output direct from analyses is emphasized. The SpacePy project seeks tomore » promote accurate and open research standards by providing an open environment for code development. In the space physics community there has long been a significant reliance on proprietary languages that restrict free transfer of data and reproducibility of results. By providing a comprehensive, open-source library of widely used analysis and visualization tools in a free, modern and intuitive language, we hope that this reliance will be diminished. SpacePy includes implementations of widely used empirical models, statistical techniques used frequently in space science (e.g. superposed epoch analysis), and interfaces to advanced tools such as electron drift shell calculations for radiation belt studies. SpacePy also provides analysis and visualization tools for components of the Space Weather Modeling Framework - currently this only includes the BATS-R-US 3-D magnetohydrodynamic model and the RAM ring current model - including streamline tracing in vector fields. Further development is currently underway. External libraries, which include well-known magnetic field models, high-precision time conversions and coordinate transformations are wrapped for access from Python using SWIG and f2py. The rest of the tools have been implemented directly in Python. The provision of open-source tools to perform common tasks will provide openness in the analysis methods employed in scientific studies and will give access to advanced tools to all space scientists regardless of affiliation or circumstance.« less

Web-Based Tools for Data Visualization and Decision Support for South Asia

NASA Astrophysics Data System (ADS)

Jones, N.; Nelson, J.; Pulla, S. T.; Ames, D. P.; Souffront, M.; David, C. H.; Zaitchik, B. F.; Gatlin, P. N.; Matin, M. A.

2017-12-01

The objective of the NASA SERVIR project is to assist developing countries in using information provided by Earth observing satellites to assess and manage climate risks, land use, and water resources. We present a collection of web apps that integrate earth observations and in situ data to facilitate deployment of data and water resources models as decision-making tools in support of this effort. The interactive nature of web apps makes this an excellent medium for creating decision support tools that harness cutting edge modeling techniques. Thin client apps hosted in a cloud portal eliminates the need for the decision makers to procure and maintain the high performance hardware required by the models, deal with issues related to software installation and platform incompatibilities, or monitor and install software updates, a problem that is exacerbated for many of the regional SERVIR hubs where both financial and technical capacity may be limited. All that is needed to use the system is an Internet connection and a web browser. We take advantage of these technologies to develop tools which can be centrally maintained but openly accessible. Advanced mapping and visualization make results intuitive and information derived actionable. We also take advantage of the emerging standards for sharing water information across the web using the OGC and WMO approved WaterML standards. This makes our tools interoperable and extensible via application programming interfaces (APIs) so that tools and data from other projects can both consume and share the tools developed in our project. Our approach enables the integration of multiple types of data and models, thus facilitating collaboration between science teams in SERVIR. The apps developed thus far by our team process time-varying netCDF files from Earth observations and large-scale computer simulations and allow visualization and exploration via raster animation and extraction of time series at selected points and/or regions.

Spectacle and SpecViz: New Spectral Analysis and Visualization Tools

NASA Astrophysics Data System (ADS)

Earl, Nicholas; Peeples, Molly; JDADF Developers

2018-01-01

A new era of spectroscopic exploration of our universe is being ushered in with advances in instrumentation and next-generation space telescopes. The advent of new spectroscopic instruments has highlighted a pressing need for tools scientists can use to analyze and explore these new data. We have developed Spectacle, a software package for analyzing both synthetic spectra from hydrodynamic simulations as well as real COS data with an aim of characterizing the behavior of the circumgalactic medium. It allows easy reduction of spectral data and analytic line generation capabilities. Currently, the package is focused on automatic determination of absorption regions and line identification with custom line list support, simultaneous line fitting using Voigt profiles via least-squares or MCMC methods, and multi-component modeling of blended features. Non-parametric measurements, such as equivalent widths, delta v90, and full-width half-max are available. Spectacle also provides the ability to compose compound models used to generate synthetic spectra allowing the user to define various LSF kernels, uncertainties, and to specify sampling.We also present updates to the visualization tool SpecViz, developed in conjunction with the JWST data analysis tools development team, to aid in the exploration of spectral data. SpecViz is an open source, Python-based spectral 1-D interactive visualization and analysis application built around high-performance interactive plotting. It supports handling general and instrument-specific data and includes advanced tool-sets for filtering and detrending one-dimensional data, along with the ability to isolate absorption regions using slicing and manipulate spectral features via spectral arithmetic. Multi-component modeling is also possible using a flexible model fitting tool-set that supports custom models to be used with various fitting routines. It also features robust user extensions such as custom data loaders and support for user-created plugins that add new functionality.This work was supported in part by HST AR #13919, HST GO #14268, and HST AR #14560.

Visual modeling in an analysis of multidimensional data

NASA Astrophysics Data System (ADS)

Zakharova, A. A.; Vekhter, E. V.; Shklyar, A. V.; Pak, A. J.

2018-01-01

The article proposes an approach to solve visualization problems and the subsequent analysis of multidimensional data. Requirements to the properties of visual models, which were created to solve analysis problems, are described. As a perspective direction for the development of visual analysis tools for multidimensional and voluminous data, there was suggested an active use of factors of subjective perception and dynamic visualization. Practical results of solving the problem of multidimensional data analysis are shown using the example of a visual model of empirical data on the current state of studying processes of obtaining silicon carbide by an electric arc method. There are several results of solving this problem. At first, an idea of possibilities of determining the strategy for the development of the domain, secondly, the reliability of the published data on this subject, and changes in the areas of attention of researchers over time.

Explore the virtual side of earth science

USGS Publications Warehouse

,

1998-01-01

Scientists have always struggled to find an appropriate technology that could represent three-dimensional (3-D) data, facilitate dynamic analysis, and encourage on-the-fly interactivity. In the recent past, scientific visualization has increased the scientist's ability to visualize information, but it has not provided the interactive environment necessary for rapidly changing the model or for viewing the model in ways not predetermined by the visualization specialist. Virtual Reality Modeling Language (VRML 2.0) is a new environment for visualizing 3-D information spaces and is accessible through the Internet with current browser technologies. Researchers from the U.S. Geological Survey (USGS) are using VRML as a scientific visualization tool to help convey complex scientific concepts to various audiences. Kevin W. Laurent, computer scientist, and Maura J. Hogan, technical information specialist, have created a collection of VRML models available through the Internet at Virtual Earth Science (virtual.er.usgs.gov).

ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining.

PubMed

Huan, Tianxiao; Sivachenko, Andrey Y; Harrison, Scott H; Chen, Jake Y

2008-08-12

New systems biology studies require researchers to understand how interplay among myriads of biomolecular entities is orchestrated in order to achieve high-level cellular and physiological functions. Many software tools have been developed in the past decade to help researchers visually navigate large networks of biomolecular interactions with built-in template-based query capabilities. To further advance researchers' ability to interrogate global physiological states of cells through multi-scale visual network explorations, new visualization software tools still need to be developed to empower the analysis. A robust visual data analysis platform driven by database management systems to perform bi-directional data processing-to-visualizations with declarative querying capabilities is needed. We developed ProteoLens as a JAVA-based visual analytic software tool for creating, annotating and exploring multi-scale biological networks. It supports direct database connectivity to either Oracle or PostgreSQL database tables/views, on which SQL statements using both Data Definition Languages (DDL) and Data Manipulation languages (DML) may be specified. The robust query languages embedded directly within the visualization software help users to bring their network data into a visualization context for annotation and exploration. ProteoLens supports graph/network represented data in standard Graph Modeling Language (GML) formats, and this enables interoperation with a wide range of other visual layout tools. The architectural design of ProteoLens enables the de-coupling of complex network data visualization tasks into two distinct phases: 1) creating network data association rules, which are mapping rules between network node IDs or edge IDs and data attributes such as functional annotations, expression levels, scores, synonyms, descriptions etc; 2) applying network data association rules to build the network and perform the visual annotation of graph nodes and edges according to associated data values. We demonstrated the advantages of these new capabilities through three biological network visualization case studies: human disease association network, drug-target interaction network and protein-peptide mapping network. The architectural design of ProteoLens makes it suitable for bioinformatics expert data analysts who are experienced with relational database management to perform large-scale integrated network visual explorations. ProteoLens is a promising visual analytic platform that will facilitate knowledge discoveries in future network and systems biology studies.

Model Evaluation of Continuous Data Pharmacometric Models: Metrics and Graphics

PubMed Central

Nguyen, THT; Mouksassi, M‐S; Holford, N; Al‐Huniti, N; Freedman, I; Hooker, AC; John, J; Karlsson, MO; Mould, DR; Pérez Ruixo, JJ; Plan, EL; Savic, R; van Hasselt, JGC; Weber, B; Zhou, C; Comets, E

2017-01-01

This article represents the first in a series of tutorials on model evaluation in nonlinear mixed effect models (NLMEMs), from the International Society of Pharmacometrics (ISoP) Model Evaluation Group. Numerous tools are available for evaluation of NLMEM, with a particular emphasis on visual assessment. This first basic tutorial focuses on presenting graphical evaluation tools of NLMEM for continuous data. It illustrates graphs for correct or misspecified models, discusses their pros and cons, and recalls the definition of metrics used. PMID:27884052

VISIBIOweb: visualization and layout services for BioPAX pathway models

PubMed Central

Dilek, Alptug; Belviranli, Mehmet E.; Dogrusoz, Ugur

2010-01-01

With recent advancements in techniques for cellular data acquisition, information on cellular processes has been increasing at a dramatic rate. Visualization is critical to analyzing and interpreting complex information; representing cellular processes or pathways is no exception. VISIBIOweb is a free, open-source, web-based pathway visualization and layout service for pathway models in BioPAX format. With VISIBIOweb, one can obtain well-laid-out views of pathway models using the standard notation of the Systems Biology Graphical Notation (SBGN), and can embed such views within one's web pages as desired. Pathway views may be navigated using zoom and scroll tools; pathway object properties, including any external database references available in the data, may be inspected interactively. The automatic layout component of VISIBIOweb may also be accessed programmatically from other tools using Hypertext Transfer Protocol (HTTP). The web site is free and open to all users and there is no login requirement. It is available at: http://visibioweb.patika.org. PMID:20460470

Visualization of the tire-soil interaction area by means of ObjectARX programming interface

NASA Astrophysics Data System (ADS)

Mueller, W.; Gruszczyński, M.; Raba, B.; Lewicki, A.; Przybył, K.; Zaborowicz, M.; Koszela, K.; Boniecki, P.

2014-04-01

The process of data visualization, important for their analysis, becomes problematic when large data sets generated via computer simulations are available. This problem concerns, among others, the models that describe the geometry of tire-soil interaction. For the purpose of a graphical representation of this area and implementation of various geometric calculations the authors have developed a plug-in application for AutoCAD, based on the latest technologies, including ObjectARX, LINQ and the use of Visual Studio platform. Selected programming tools offer a wide variety of IT structures that enable data visualization and data analysis and are important e.g. in model verification.

Interactive visualization to advance earthquake simulation

USGS Publications Warehouse

Kellogg, L.H.; Bawden, G.W.; Bernardin, T.; Billen, M.; Cowgill, E.; Hamann, B.; Jadamec, M.; Kreylos, O.; Staadt, O.; Sumner, D.

2008-01-01

The geological sciences are challenged to manage and interpret increasing volumes of data as observations and simulations increase in size and complexity. For example, simulations of earthquake-related processes typically generate complex, time-varying data sets in two or more dimensions. To facilitate interpretation and analysis of these data sets, evaluate the underlying models, and to drive future calculations, we have developed methods of interactive visualization with a special focus on using immersive virtual reality (VR) environments to interact with models of Earth's surface and interior. Virtual mapping tools allow virtual "field studies" in inaccessible regions. Interactive tools allow us to manipulate shapes in order to construct models of geological features for geodynamic models, while feature extraction tools support quantitative measurement of structures that emerge from numerical simulation or field observations, thereby enabling us to improve our interpretation of the dynamical processes that drive earthquakes. VR has traditionally been used primarily as a presentation tool, albeit with active navigation through data. Reaping the full intellectual benefits of immersive VR as a tool for scientific analysis requires building on the method's strengths, that is, using both 3D perception and interaction with observed or simulated data. This approach also takes advantage of the specialized skills of geological scientists who are trained to interpret, the often limited, geological and geophysical data available from field observations. ?? Birkhaueser 2008.

Cloud-Based Tools to Support High-Resolution Modeling (Invited)

NASA Astrophysics Data System (ADS)

Jones, N.; Nelson, J.; Swain, N.; Christensen, S.

2013-12-01

The majority of watershed models developed to support decision-making by water management agencies are simple, lumped-parameter models. Maturity in research codes and advances in the computational power from multi-core processors on desktop machines, commercial cloud-computing resources, and supercomputers with thousands of cores have created new opportunities for employing more accurate, high-resolution distributed models for routine use in decision support. The barriers for using such models on a more routine basis include massive amounts of spatial data that must be processed for each new scenario and lack of efficient visualization tools. In this presentation we will review a current NSF-funded project called CI-WATER that is intended to overcome many of these roadblocks associated with high-resolution modeling. We are developing a suite of tools that will make it possible to deploy customized web-based apps for running custom scenarios for high-resolution models with minimal effort. These tools are based on a software stack that includes 52 North, MapServer, PostGIS, HT Condor, CKAN, and Python. This open source stack provides a simple scripting environment for quickly configuring new custom applications for running high-resolution models as geoprocessing workflows. The HT Condor component facilitates simple access to local distributed computers or commercial cloud resources when necessary for stochastic simulations. The CKAN framework provides a powerful suite of tools for hosting such workflows in a web-based environment that includes visualization tools and storage of model simulations in a database to archival, querying, and sharing of model results. Prototype applications including land use change, snow melt, and burned area analysis will be presented. This material is based upon work supported by the National Science Foundation under Grant No. 1135482

Developing Visualization Support System for Teaching/Learning Database Normalization

ERIC Educational Resources Information Center

Folorunso, Olusegun; Akinwale, AdioTaofeek

2010-01-01

Purpose: In tertiary institution, some students find it hard to learn database design theory, in particular, database normalization. The purpose of this paper is to develop a visualization tool to give students an interactive hands-on experience in database normalization process. Design/methodology/approach: The model-view-controller architecture…

Rhodobase, a meta-analytical tool for reconstructing gene regulatory networks in a model photosynthetic bacterium.

PubMed

Moskvin, Oleg V; Bolotin, Dmitry; Wang, Andrew; Ivanov, Pavel S; Gomelsky, Mark

2011-02-01

We present Rhodobase, a web-based meta-analytical tool for analysis of transcriptional regulation in a model anoxygenic photosynthetic bacterium, Rhodobacter sphaeroides. The gene association meta-analysis is based on the pooled data from 100 of R. sphaeroides whole-genome DNA microarrays. Gene-centric regulatory networks were visualized using the StarNet approach (Jupiter, D.C., VanBuren, V., 2008. A visual data mining tool that facilitates reconstruction of transcription regulatory networks. PLoS ONE 3, e1717) with several modifications. We developed a means to identify and visualize operons and superoperons. We designed a framework for the cross-genome search for transcription factor binding sites that takes into account high GC-content and oligonucleotide usage profile characteristic of the R. sphaeroides genome. To facilitate reconstruction of directional relationships between co-regulated genes, we screened upstream sequences (-400 to +20bp from start codons) of all genes for putative binding sites of bacterial transcription factors using a self-optimizing search method developed here. To test performance of the meta-analysis tools and transcription factor site predictions, we reconstructed selected nodes of the R. sphaeroides transcription factor-centric regulatory matrix. The test revealed regulatory relationships that correlate well with the experimentally derived data. The database of transcriptional profile correlations, the network visualization engine and the optimized search engine for transcription factor binding sites analysis are available at http://rhodobase.org. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Real-Time Visualization Tool Integrating STEREO, ACE, SOHO and the SDO

NASA Astrophysics Data System (ADS)

Schroeder, P. C.; Luhmann, J. G.; Marchant, W.

2011-12-01

The STEREO/IMPACT team has developed a new web-based visualization tool for near real-time data from the STEREO instruments, ACE and SOHO as well as relevant models of solar activity. This site integrates images, solar energetic particle, solar wind plasma and magnetic field measurements in an intuitive way using near real-time products from NOAA and other sources to give an overview of recent space weather events. This site enhances the browse tools already available at UC Berkeley, UCLA and Caltech which allow users to visualize similar data from the start of the STEREO mission. Our new near real-time tool utilizes publicly available real-time data products from a number of missions and instruments, including SOHO LASCO C2 images from the SOHO team's NASA site, SDO AIA images from the SDO team's NASA site, STEREO IMPACT SEP data plots and ACE EPAM data plots from the NOAA Space Weather Prediction Center and STEREO spacecraft positions from the STEREO Science Center.

LIBRE Stick Figure Tool: A Graphic Organizer to Foster Self-Regulated Social Cognitive Problem Solving

ERIC Educational Resources Information Center

Guerra, Norma S.

2009-01-01

Graphic organizers are powerful visual tools. The representation provides dimension and relationship to ideas and a framework for organization and elaboration. The LIBRE Stick Figure Tool is a graphic organizer for the problem-solving application of the LIBRE Model counseling approach. It resembles a "stick person" and offers the teacher and…

U.S. Geological Survey: A synopsis of Three-dimensional Modeling

USGS Publications Warehouse

Jacobsen, Linda J.; Glynn, Pierre D.; Phelps, Geoff A.; Orndorff, Randall C.; Bawden, Gerald W.; Grauch, V.J.S.

2011-01-01

The U.S. Geological Survey (USGS) is a multidisciplinary agency that provides assessments of natural resources (geological, hydrological, biological), the disturbances that affect those resources, and the disturbances that affect the built environment, natural landscapes, and human society. Until now, USGS map products have been generated and distributed primarily as 2-D maps, occasionally providing cross sections or overlays, but rarely allowing the ability to characterize and understand 3-D systems, how they change over time (4-D), and how they interact. And yet, technological advances in monitoring natural resources and the environment, the ever-increasing diversity of information needed for holistic assessments, and the intrinsic 3-D/4-D nature of the information obtained increases our need to generate, verify, analyze, interpret, confirm, store, and distribute its scientific information and products using 3-D/4-D visualization, analysis, modeling tools, and information frameworks. Today, USGS scientists use 3-D/4-D tools to (1) visualize and interpret geological information, (2) verify the data, and (3) verify their interpretations and models. 3-D/4-D visualization can be a powerful quality control tool in the analysis of large, multidimensional data sets. USGS scientists use 3-D/4-D technology for 3-D surface (i.e., 2.5-D) visualization as well as for 3-D volumetric analyses. Examples of geological mapping in 3-D include characterization of the subsurface for resource assessments, such as aquifer characterization in the central United States, and for input into process models, such as seismic hazards in the western United States.

Automation for System Safety Analysis

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Fleming, Land; Throop, David; Thronesbery, Carroll; Flores, Joshua; Bennett, Ted; Wennberg, Paul

2009-01-01

This presentation describes work to integrate a set of tools to support early model-based analysis of failures and hazards due to system-software interactions. The tools perform and assist analysts in the following tasks: 1) extract model parts from text for architecture and safety/hazard models; 2) combine the parts with library information to develop the models for visualization and analysis; 3) perform graph analysis and simulation to identify and evaluate possible paths from hazard sources to vulnerable entities and functions, in nominal and anomalous system-software configurations and scenarios; and 4) identify resulting candidate scenarios for software integration testing. There has been significant technical progress in model extraction from Orion program text sources, architecture model derivation (components and connections) and documentation of extraction sources. Models have been derived from Internal Interface Requirements Documents (IIRDs) and FMEA documents. Linguistic text processing is used to extract model parts and relationships, and the Aerospace Ontology also aids automated model development from the extracted information. Visualizations of these models assist analysts in requirements overview and in checking consistency and completeness.

From Visual Exploration to Storytelling and Back Again.

PubMed

Gratzl, S; Lex, A; Gehlenborg, N; Cosgrove, N; Streit, M

2016-06-01

The primary goal of visual data exploration tools is to enable the discovery of new insights. To justify and reproduce insights, the discovery process needs to be documented and communicated. A common approach to documenting and presenting findings is to capture visualizations as images or videos. Images, however, are insufficient for telling the story of a visual discovery, as they lack full provenance information and context. Videos are difficult to produce and edit, particularly due to the non-linear nature of the exploratory process. Most importantly, however, neither approach provides the opportunity to return to any point in the exploration in order to review the state of the visualization in detail or to conduct additional analyses. In this paper we present CLUE (Capture, Label, Understand, Explain), a model that tightly integrates data exploration and presentation of discoveries. Based on provenance data captured during the exploration process, users can extract key steps, add annotations, and author "Vistories", visual stories based on the history of the exploration. These Vistories can be shared for others to view, but also to retrace and extend the original analysis. We discuss how the CLUE approach can be integrated into visualization tools and provide a prototype implementation. Finally, we demonstrate the general applicability of the model in two usage scenarios: a Gapminder-inspired visualization to explore public health data and an example from molecular biology that illustrates how Vistories could be used in scientific journals. (see Figure 1 for visual abstract).

From Visual Exploration to Storytelling and Back Again

PubMed Central

Gratzl, S.; Lex, A.; Gehlenborg, N.; Cosgrove, N.; Streit, M.

2016-01-01

The primary goal of visual data exploration tools is to enable the discovery of new insights. To justify and reproduce insights, the discovery process needs to be documented and communicated. A common approach to documenting and presenting findings is to capture visualizations as images or videos. Images, however, are insufficient for telling the story of a visual discovery, as they lack full provenance information and context. Videos are difficult to produce and edit, particularly due to the non-linear nature of the exploratory process. Most importantly, however, neither approach provides the opportunity to return to any point in the exploration in order to review the state of the visualization in detail or to conduct additional analyses. In this paper we present CLUE (Capture, Label, Understand, Explain), a model that tightly integrates data exploration and presentation of discoveries. Based on provenance data captured during the exploration process, users can extract key steps, add annotations, and author “Vistories”, visual stories based on the history of the exploration. These Vistories can be shared for others to view, but also to retrace and extend the original analysis. We discuss how the CLUE approach can be integrated into visualization tools and provide a prototype implementation. Finally, we demonstrate the general applicability of the model in two usage scenarios: a Gapminder-inspired visualization to explore public health data and an example from molecular biology that illustrates how Vistories could be used in scientific journals. (see Figure 1 for visual abstract) PMID:27942091

Performance Measurement, Visualization and Modeling of Parallel and Distributed Programs

NASA Technical Reports Server (NTRS)

Yan, Jerry C.; Sarukkai, Sekhar R.; Mehra, Pankaj; Lum, Henry, Jr. (Technical Monitor)

1994-01-01

This paper presents a methodology for debugging the performance of message-passing programs on both tightly coupled and loosely coupled distributed-memory machines. The AIMS (Automated Instrumentation and Monitoring System) toolkit, a suite of software tools for measurement and analysis of performance, is introduced and its application illustrated using several benchmark programs drawn from the field of computational fluid dynamics. AIMS includes (i) Xinstrument, a powerful source-code instrumentor, which supports both Fortran77 and C as well as a number of different message-passing libraries including Intel's NX Thinking Machines' CMMD, and PVM; (ii) Monitor, a library of timestamping and trace -collection routines that run on supercomputers (such as Intel's iPSC/860, Delta, and Paragon and Thinking Machines' CM5) as well as on networks of workstations (including Convex Cluster and SparcStations connected by a LAN); (iii) Visualization Kernel, a trace-animation facility that supports source-code clickback, simultaneous visualization of computation and communication patterns, as well as analysis of data movements; (iv) Statistics Kernel, an advanced profiling facility, that associates a variety of performance data with various syntactic components of a parallel program; (v) Index Kernel, a diagnostic tool that helps pinpoint performance bottlenecks through the use of abstract indices; (vi) Modeling Kernel, a facility for automated modeling of message-passing programs that supports both simulation -based and analytical approaches to performance prediction and scalability analysis; (vii) Intrusion Compensator, a utility for recovering true performance from observed performance by removing the overheads of monitoring and their effects on the communication pattern of the program; and (viii) Compatibility Tools, that convert AIMS-generated traces into formats used by other performance-visualization tools, such as ParaGraph, Pablo, and certain AVS/Explorer modules.

War and peace: morphemes and full forms in a noninteractive activation parallel dual-route model.

PubMed

Baayen, H; Schreuder, R

This article introduces a computational tool for modeling the process of morphological segmentation in visual and auditory word recognition in the framework of a parallel dual-route model. Copyright 1999 Academic Press.

The Role of Motor Learning in Spatial Adaptation near a Tool

PubMed Central

Brown, Liana E.; Doole, Robert; Malfait, Nicole

2011-01-01

Some visual-tactile (bimodal) cells have visual receptive fields (vRFs) that overlap and extend moderately beyond the skin of the hand. Neurophysiological evidence suggests, however, that a vRF will grow to encompass a hand-held tool following active tool use but not after passive holding. Why does active tool use, and not passive holding, lead to spatial adaptation near a tool? We asked whether spatial adaptation could be the result of motor or visual experience with the tool, and we distinguished between these alternatives by isolating motor from visual experience with the tool. Participants learned to use a novel, weighted tool. The active training group received both motor and visual experience with the tool, the passive training group received visual experience with the tool, but no motor experience, and finally, a no-training control group received neither visual nor motor experience using the tool. After training, we used a cueing paradigm to measure how quickly participants detected targets, varying whether the tool was placed near or far from the target display. Only the active training group detected targets more quickly when the tool was placed near, rather than far, from the target display. This effect of tool location was not present for either the passive-training or control groups. These results suggest that motor learning influences how visual space around the tool is represented. PMID:22174944

Holmes: a graphical tool for development, simulation and analysis of Petri net based models of complex biological systems.

PubMed

Radom, Marcin; Rybarczyk, Agnieszka; Szawulak, Bartlomiej; Andrzejewski, Hubert; Chabelski, Piotr; Kozak, Adam; Formanowicz, Piotr

2017-12-01

Model development and its analysis is a fundamental step in systems biology. The theory of Petri nets offers a tool for such a task. Since the rapid development of computer science, a variety of tools for Petri nets emerged, offering various analytical algorithms. From this follows a problem of using different programs to analyse a single model. Many file formats and different representations of results make the analysis much harder. Especially for larger nets the ability to visualize the results in a proper form provides a huge help in the understanding of their significance. We present a new tool for Petri nets development and analysis called Holmes. Our program contains algorithms for model analysis based on different types of Petri nets, e.g. invariant generator, Maximum Common Transitions (MCT) sets and cluster modules, simulation algorithms or knockout analysis tools. A very important feature is the ability to visualize the results of almost all analytical modules. The integration of such modules into one graphical environment allows a researcher to fully devote his or her time to the model building and analysis. Available at http://www.cs.put.poznan.pl/mradom/Holmes/holmes.html. piotr@cs.put.poznan.pl. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

R-SWAT-FME user's guide

USGS Publications Warehouse

Wu, Yiping; Liu, Shu-Guang

2012-01-01

R program language-Soil and Water Assessment Tool-Flexible Modeling Environment (R-SWAT-FME) (Wu and Liu, 2012) is a comprehensive modeling framework that adopts an R package, Flexible Modeling Environment (FME) (Soetaert and Petzoldt, 2010), for the Soil and Water Assessment Tool (SWAT) model (Arnold and others, 1998; Neitsch and others, 2005). This framework provides the functionalities of parameter identifiability, model calibration, and sensitivity and uncertainty analysis with instant visualization. This user's guide shows how to apply this framework for a customized SWAT project.

Towards a C2 Poly-Visualization Tool: Leveraging the Power of Social-Network Analysis and GIS

DTIC Science & Technology

2011-06-01

from Magsino.14 AutoMap, a product of CASOS at Carnegie Mellon University, is a text-mining tool that enables the extraction of network data from...enables community leaders to prepare for biological attacks using computational models. BioWar is a CASOS package that combines many factors into a...models, demographically accurate agent modes, wind dispersion models, and an error-diagnostic model. Construct, also developed by CASOS , is a

Interactive Visualization of Large-Scale Hydrological Data using Emerging Technologies in Web Systems and Parallel Programming

NASA Astrophysics Data System (ADS)

Demir, I.; Krajewski, W. F.

2013-12-01

As geoscientists are confronted with increasingly massive datasets from environmental observations to simulations, one of the biggest challenges is having the right tools to gain scientific insight from the data and communicate the understanding to stakeholders. Recent developments in web technologies make it easy to manage, visualize and share large data sets with general public. Novel visualization techniques and dynamic user interfaces allow users to interact with data, and modify the parameters to create custom views of the data to gain insight from simulations and environmental observations. This requires developing new data models and intelligent knowledge discovery techniques to explore and extract information from complex computational simulations or large data repositories. Scientific visualization will be an increasingly important component to build comprehensive environmental information platforms. This presentation provides an overview of the trends and challenges in the field of scientific visualization, and demonstrates information visualization and communication tools developed within the light of these challenges.

Design and implementation of visualization methods for the CHANGES Spatial Decision Support System

NASA Astrophysics Data System (ADS)

Cristal, Irina; van Westen, Cees; Bakker, Wim; Greiving, Stefan

2014-05-01

The CHANGES Spatial Decision Support System (SDSS) is a web-based system aimed for risk assessment and the evaluation of optimal risk reduction alternatives at local level as a decision support tool in long-term natural risk management. The SDSS use multidimensional information, integrating thematic, spatial, temporal and documentary data. The role of visualization in this context becomes of vital importance for efficiently representing each dimension. This multidimensional aspect of the required for the system risk information, combined with the diversity of the end-users imposes the use of sophisticated visualization methods and tools. The key goal of the present work is to exploit efficiently the large amount of data in relation to the needs of the end-user, utilizing proper visualization techniques. Three main tasks have been accomplished for this purpose: categorization of the end-users, the definition of system's modules and the data definition. The graphical representation of the data and the visualization tools were designed to be relevant to the data type and the purpose of the analysis. Depending on the end-users category, each user should have access to different modules of the system and thus, to the proper visualization environment. The technologies used for the development of the visualization component combine the latest and most innovative open source JavaScript frameworks, such as OpenLayers 2.13.1, ExtJS 4 and GeoExt 2. Moreover, the model-view-controller (MVC) pattern is used in order to ensure flexibility of the system at the implementation level. Using the above technologies, the visualization techniques implemented so far offer interactive map navigation, querying and comparison tools. The map comparison tools are of great importance within the SDSS and include the following: swiping tool for comparison of different data of the same location; raster subtraction for comparison of the same phenomena varying in time; linked views for comparison of data from different locations and a time slider tool for monitoring changes in spatio-temporal data. All these techniques are part of the interactive interface of the system and make use of spatial and spatio-temporal data. Further significant aspects of the visualization component include conventional cartographic techniques and visualization of non-spatial data. The main expectation from the present work is to offer efficient visualization of risk-related data in order to facilitate the decision making process, which is the final purpose of the CHANGES SDSS. This work is part of the "CHANGES" project, funded by the European Community's 7th Framework Programme.

Pelagic habitat visualization: the need for a third (and fourth) dimension: HabitatSpace

USGS Publications Warehouse

Beegle-Krause, C; Vance, Tiffany; Reusser, Debbie; Stuebe, David; Howlett, Eoin

2009-01-01

Habitat in open water is not simply a 2-D to 2.5-D surface such as the ocean bottom or the air-water interface. Rather, pelagic habitat is a 3-D volume of water that can change over time, leading us to the term habitat space. Visualization and analysis in 2-D is well supported with GIS tools, but a new tool was needed for visualization and analysis in four dimensions. Observational data (cruise profiles (x_o, y_o, z, t_o)), numerical circulation model fields (x,y,z,t), and trajectories (larval fish, 4-D line) need to be merged together in a meaningful way for visualization and analysis. As a first step toward this new framework, UNIDATA’s Integrated Data Viewer (IDV) has been used to create a set of tools for habitat analysis in 4-D. IDV was designed for 3-D+time geospatial data in the meteorological community. NetCDF Java^TM libraries allow the tool to read many file formats including remotely located data (e.g. data available via OPeNDAP ). With this project, IDV has been adapted for use in delineating habitat space for multiple fish species in the ocean. The ability to define and visualize boundaries of a water mass, which meets specific biologically relevant criteria (e.g., volume, connectedness, and inter-annual variability) based on model results and observational data, will allow managers to investigate the survival of individual year classes of commercially important fisheries. Better understanding of the survival of these year classes will lead to improved forecasting of fisheries recruitment.

MATISSE a web-based tool to access, visualize and analyze high resolution minor bodies observation

NASA Astrophysics Data System (ADS)

Zinzi, Angelo; Capria, Maria Teresa; Palomba, Ernesto; Antonelli, Lucio Angelo; Giommi, Paolo

2016-07-01

In the recent years planetary exploration missions acquired data from minor bodies (i.e., dwarf planets, asteroid and comets) at a detail level never reached before. Since these objects often present very irregular shapes (as in the case of the comet 67P Churyumov-Gerasimenko target of the ESA Rosetta mission) "classical" bidimensional projections of observations are difficult to understand. With the aim of providing the scientific community a tool to access, visualize and analyze data in a new way, ASI Science Data Center started to develop MATISSE (Multi-purposed Advanced Tool for the Instruments for the Solar System Exploration - http://tools.asdc.asi.it/matisse.jsp) in late 2012. This tool allows 3D web-based visualization of data acquired by planetary exploration missions: the output could either be the straightforward projection of the selected observation over the shape model of the target body or the visualization of a high-order product (average/mosaic, difference, ratio, RGB) computed directly online with MATISSE. Standard outputs of the tool also comprise downloadable files to be used with GIS software (GeoTIFF and ENVI format) and 3D very high-resolution files to be viewed by means of the free software Paraview. During this period the first and most frequent exploitation of the tool has been related to visualization of data acquired by VIRTIS-M instruments onboard Rosetta observing the comet 67P. The success of this task, well represented by the good number of published works that used images made with MATISSE confirmed the need of a different approach to correctly visualize data coming from irregular shaped bodies. In the next future the datasets available to MATISSE are planned to be extended, starting from the addition of VIR-Dawn observations of both Vesta and Ceres and also using standard protocols to access data stored in external repositories, such as NASA ODE and Planetary VO.

Mixed Initiative Visual Analytics Using Task-Driven Recommendations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cook, Kristin A.; Cramer, Nicholas O.; Israel, David

2015-12-07

Visual data analysis is composed of a collection of cognitive actions and tasks to decompose, internalize, and recombine data to produce knowledge and insight. Visual analytic tools provide interactive visual interfaces to data to support tasks involved in discovery and sensemaking, including forming hypotheses, asking questions, and evaluating and organizing evidence. Myriad analytic models can be incorporated into visual analytic systems, at the cost of increasing complexity in the analytic discourse between user and system. Techniques exist to increase the usability of interacting with such analytic models, such as inferring data models from user interactions to steer the underlying modelsmore » of the system via semantic interaction, shielding users from having to do so explicitly. Such approaches are often also referred to as mixed-initiative systems. Researchers studying the sensemaking process have called for development of tools that facilitate analytic sensemaking through a combination of human and automated activities. However, design guidelines do not exist for mixed-initiative visual analytic systems to support iterative sensemaking. In this paper, we present a candidate set of design guidelines and introduce the Active Data Environment (ADE) prototype, a spatial workspace supporting the analytic process via task recommendations invoked by inferences on user interactions within the workspace. ADE recommends data and relationships based on a task model, enabling users to co-reason with the system about their data in a single, spatial workspace. This paper provides an illustrative use case, a technical description of ADE, and a discussion of the strengths and limitations of the approach.« less

Trans3D: a free tool for dynamical visualization of EEG activity transmission in the brain.

PubMed

Blinowski, Grzegorz; Kamiński, Maciej; Wawer, Dariusz

2014-08-01

The problem of functional connectivity in the brain is in the focus of attention nowadays, since it is crucial for understanding information processing in the brain. A large repertoire of measures of connectivity have been devised, some of them being capable of estimating time-varying directed connectivity. Hence, there is a need for a dedicated software tool for visualizing the propagation of electrical activity in the brain. To this aim, the Trans3D application was developed. It is an open access tool based on widely available libraries and supporting both Windows XP/Vista/7(™), Linux and Mac environments. Trans3D can create animations of activity propagation between electrodes/sensors, which can be placed by the user on the scalp/cortex of a 3D model of the head. Various interactive graphic functions for manipulating and visualizing components of the 3D model and input data are available. An application of the Trans3D tool has helped to elucidate the dynamics of the phenomena of information processing in motor and cognitive tasks, which otherwise would have been very difficult to observe. Trans3D is available at: http://www.eeg.pl/. Copyright © 2014 Elsevier Ltd. All rights reserved.

RHydro - Hydrological models and tools to represent and analyze hydrological data in R

NASA Astrophysics Data System (ADS)

Reusser, Dominik; Buytaert, Wouter

2010-05-01

In hydrology, basic equations and procedures keep being implemented from scratch by scientist, with the potential for errors and inefficiency. The use of libraries can overcome these problems. Other scientific disciplines such as mathematics and physics have benefited significantly from such an approach with freely available implementations for many routines. As an example, hydrological libraries could contain: Major representations of hydrological processes such as infiltration, sub-surface runoff and routing algorithms. Scaling functions, for instance to combine remote sensing precipitation fields with rain gauge data Data consistency checks Performance measures. Here we present a beginning for such a library implemented in the high level data programming language R. Currently, Top-model, data import routines for WaSiM-ETH as well basic visualization and evaluation tools are implemented. The design is such, that a definition of import scripts for additional models is sufficient to have access to the full set of evaluation and visualization tools.

Human visual performance model for crewstation design

NASA Technical Reports Server (NTRS)

Larimer, James; Prevost, Michael; Arditi, Aries; Azueta, Steven; Bergen, James; Lubin, Jeffrey

1991-01-01

An account is given of a Visibility Modeling Tool (VMT) which furnishes a crew-station designer with the means to assess configurational tradeoffs, with a view to the impact of various options on the unambiguous access of information to the pilot. The interactive interface of the VMT allows the manipulation of cockpit geometry, ambient lighting, pilot ergonomics, and the displayed symbology. Performance data can be displayed in the form of 3D contours into the crewstation graphic model, thereby yielding an indication of the operator's visual capabilities.

Ionospheric Simulation System for Satellite Observations and Global Assimilative Modeling Experiments (ISOGAME)

NASA Technical Reports Server (NTRS)

Pi, Xiaoqing; Mannucci, Anthony J.; Verkhoglyadova, Olga P.; Stephens, Philip; Wilson, Brian D.; Akopian, Vardan; Komjathy, Attila; Lijima, Byron A.

2013-01-01

ISOGAME is designed and developed to assess quantitatively the impact of new observation systems on the capability of imaging and modeling the ionosphere. With ISOGAME, one can perform observation system simulation experiments (OSSEs). A typical OSSE using ISOGAME would involve: (1) simulating various ionospheric conditions on global scales; (2) simulating ionospheric measurements made from a constellation of low-Earth-orbiters (LEOs), particularly Global Navigation Satellite System (GNSS) radio occultation data, and from ground-based global GNSS networks; (3) conducting ionospheric data assimilation experiments with the Global Assimilative Ionospheric Model (GAIM); and (4) analyzing modeling results with visualization tools. ISOGAME can provide quantitative assessment of the accuracy of assimilative modeling with the interested observation system. Other observation systems besides those based on GNSS are also possible to analyze. The system is composed of a suite of software that combines the GAIM, including a 4D first-principles ionospheric model and data assimilation modules, an Internal Reference Ionosphere (IRI) model that has been developed by international ionospheric research communities, observation simulator, visualization software, and orbit design, simulation, and optimization software. The core GAIM model used in ISOGAME is based on the GAIM++ code (written in C++) that includes a new high-fidelity geomagnetic field representation (multi-dipole). New visualization tools and analysis algorithms for the OSSEs are now part of ISOGAME.

The visualization of spatial uncertainty

DOE Office of Scientific and Technical Information (OSTI.GOV)

Srivastava, R.M.

1994-12-31

Geostatistical conditions simulation is gaining acceptance as a numerical modeling tool in the petroleum industry. Unfortunately, many of the new users of conditional simulation work with only one outcome or ``realization`` and ignore the many other outcomes that could be produced by their conditional simulation tools. 3-D visualization tools allow them to create very realistic images of this single outcome as reality. There are many methods currently available for presenting the uncertainty information from a family of possible outcomes; most of these, however, use static displays and many present uncertainty in a format that is not intuitive. This paper exploresmore » the visualization of uncertainty through dynamic displays that exploit the intuitive link between uncertainty and change by presenting the use with a constantly evolving model. The key technical challenge to such a dynamic presentation is the ability to create numerical models that honor the available well data and geophysical information and yet are incrementally different so that successive frames can be viewed rapidly as an animated cartoon. An example of volumetric uncertainty from a Gulf Coast reservoir will be used to demonstrate that such a dynamic presentation is the ability to create numerical models that honor the available well data and geophysical information and yet are incrementally different so that successive frames can be viewed rapidly as an animated cartoon. An example of volumetric uncertainty from a Gulf Coast reservoir will be used to demonstrate that such animation is possible and to show that such dynamic displays can be an effective tool in risk analysis for the petroleum industry.« less

NASA Enterprise Visual Analysis

NASA Technical Reports Server (NTRS)

Lopez-Tellado, Maria; DiSanto, Brenda; Humeniuk, Robert; Bard, Richard, Jr.; Little, Mia; Edwards, Robert; Ma, Tien-Chi; Hollifield, Kenneith; White, Chuck

2007-01-01

NASA Enterprise Visual Analysis (NEVA) is a computer program undergoing development as a successor to Launch Services Analysis Tool (LSAT), formerly known as Payload Carrier Analysis Tool (PCAT). NEVA facilitates analyses of proposed configurations of payloads and packing fixtures (e.g. pallets) in a space shuttle payload bay for transport to the International Space Station. NEVA reduces the need to use physical models, mockups, and full-scale ground support equipment in performing such analyses. Using NEVA, one can take account of such diverse considerations as those of weight distribution, geometry, collision avoidance, power requirements, thermal loads, and mechanical loads.

Tools for 3D scientific visualization in computational aerodynamics at NASA Ames Research Center

NASA Technical Reports Server (NTRS)

Bancroft, Gordon; Plessel, Todd; Merritt, Fergus; Watson, Val

1989-01-01

Hardware, software, and techniques used by the Fluid Dynamics Division (NASA) for performing visualization of computational aerodynamics, which can be applied to the visualization of flow fields from computer simulations of fluid dynamics about the Space Shuttle, are discussed. Three visualization techniques applied, post-processing, tracking, and steering, are described, as well as the post-processing software packages used, PLOT3D, SURF (Surface Modeller), GAS (Graphical Animation System), and FAST (Flow Analysis software Toolkit). Using post-processing methods a flow simulation was executed on a supercomputer and, after the simulation was complete, the results were processed for viewing. It is shown that the high-resolution, high-performance three-dimensional workstation combined with specially developed display and animation software provides a good tool for analyzing flow field solutions obtained from supercomputers.

DspaceOgreTerrain 3D Terrain Visualization Tool

NASA Technical Reports Server (NTRS)

Myint, Steven; Jain, Abhinandan; Pomerantz, Marc I.

2012-01-01

DspaceOgreTerrain is an extension to the DspaceOgre 3D visualization tool that supports real-time visualization of various terrain types, including digital elevation maps, planets, and meshes. DspaceOgreTerrain supports creating 3D representations of terrains and placing them in a scene graph. The 3D representations allow for a continuous level of detail, GPU-based rendering, and overlaying graphics like wheel tracks and shadows. It supports reading data from the SimScape terrain- modeling library. DspaceOgreTerrain solves the problem of displaying the results of simulations that involve very large terrains. In the past, it has been used to visualize simulations of vehicle traverses on Lunar and Martian terrains. These terrains were made up of billions of vertices and would not have been renderable in real-time without using a continuous level of detail rendering technique.

AUTOMATED GEOSPATIAL WATERSHED ASSESSMENT ...

EPA Pesticide Factsheets

The Automated Geospatial Watershed Assessment tool (AGWA) is a GIS interface jointly developed by the USDA Agricultural Research Service, the U.S. Environmental Protection Agency, the University of Arizona, and the University of Wyoming to automate the parameterization and execution of the Soil Water Assessment Tool (SWAT) and KINEmatic Runoff and EROSion (KINEROS2) hydrologic models. The application of these two models allows AGWA to conduct hydrologic modeling and watershed assessments at multiple temporal and spatial scales. AGWA’s current outputs are runoff (volumes and peaks) and sediment yield, plus nitrogen and phosphorus with the SWAT model. AGWA uses commonly available GIS data layers to fully parameterize, execute, and visualize results from both models. Through an intuitive interface the user selects an outlet from which AGWA delineates and discretizes the watershed using a Digital Elevation Model (DEM) based on the individual model requirements. The watershed model elements are then intersected with soils and land cover data layers to derive the requisite model input parameters. The chosen model is then executed, and the results are imported back into AGWA for visualization. This allows managers to identify potential problem areas where additional monitoring can be undertaken or mitigation activities can be focused. AGWA also has tools to apply an array of best management practices. There are currently two versions of AGWA available; AGWA 1.5 for

A software platform for continuum modeling of ion channels based on unstructured mesh

NASA Astrophysics Data System (ADS)

Tu, B.; Bai, S. Y.; Chen, M. X.; Xie, Y.; Zhang, L. B.; Lu, B. Z.

2014-01-01

Most traditional continuum molecular modeling adopted finite difference or finite volume methods which were based on a structured mesh (grid). Unstructured meshes were only occasionally used, but an increased number of applications emerge in molecular simulations. To facilitate the continuum modeling of biomolecular systems based on unstructured meshes, we are developing a software platform with tools which are particularly beneficial to those approaches. This work describes the software system specifically for the simulation of a typical, complex molecular procedure: ion transport through a three-dimensional channel system that consists of a protein and a membrane. The platform contains three parts: a meshing tool chain for ion channel systems, a parallel finite element solver for the Poisson-Nernst-Planck equations describing the electrodiffusion process of ion transport, and a visualization program for continuum molecular modeling. The meshing tool chain in the platform, which consists of a set of mesh generation tools, is able to generate high-quality surface and volume meshes for ion channel systems. The parallel finite element solver in our platform is based on the parallel adaptive finite element package PHG which wass developed by one of the authors [1]. As a featured component of the platform, a new visualization program, VCMM, has specifically been developed for continuum molecular modeling with an emphasis on providing useful facilities for unstructured mesh-based methods and for their output analysis and visualization. VCMM provides a graphic user interface and consists of three modules: a molecular module, a meshing module and a numerical module. A demonstration of the platform is provided with a study of two real proteins, the connexin 26 and hemolysin ion channels.

Web-based Visual Analytics for Extreme Scale Climate Science

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steed, Chad A; Evans, Katherine J; Harney, John F

In this paper, we introduce a Web-based visual analytics framework for democratizing advanced visualization and analysis capabilities pertinent to large-scale earth system simulations. We address significant limitations of present climate data analysis tools such as tightly coupled dependencies, ineffi- cient data movements, complex user interfaces, and static visualizations. Our Web-based visual analytics framework removes critical barriers to the widespread accessibility and adoption of advanced scientific techniques. Using distributed connections to back-end diagnostics, we minimize data movements and leverage HPC platforms. We also mitigate system dependency issues by employing a RESTful interface. Our framework embraces the visual analytics paradigm via newmore » visual navigation techniques for hierarchical parameter spaces, multi-scale representations, and interactive spatio-temporal data mining methods that retain details. Although generalizable to other science domains, the current work focuses on improving exploratory analysis of large-scale Community Land Model (CLM) and Community Atmosphere Model (CAM) simulations.« less

Compositing Visualization Tools for Improving Design Decisions

ERIC Educational Resources Information Center

Chung, Wayne C.

2005-01-01

Today's designers deal with a range of communication modes. These modes vary from hand gestures to sketches, physical models, and computer-generated images. It has been the norm to use these mediums throughout the process to visualize the intended design so that the potential users, designers, team members, and clients can understand the end…

Visualizing Compound Rotations with Virtual Reality

ERIC Educational Resources Information Center

Flanders, Megan; Kavanagh, Richard C.

2013-01-01

Mental rotations are among the most difficult of all spatial tasks to perform, and even those with high levels of spatial ability can struggle to visualize the result of compound rotations. This pilot study investigates the use of the virtual reality-based Rotation Tool, created using the Virtual Reality Modeling Language (VRML) together with…

Bridging the Educational Research-Teaching Practice Gap: Foundations for Assessing and Developing Biochemistry Students' Visual Literacy

ERIC Educational Resources Information Center

Schonborn, Konrad J.; Anderson, Trevor R.

2010-01-01

External representations (ERs), such as diagrams, animations, and dynamic models are vital tools for communicating and constructing knowledge in biochemistry. To build a meaningful understanding of structure, function, and process, it is essential that students become visually literate by mastering key cognitive skills that are essential for…

Predicting Learners Styles Based on Fuzzy Model

ERIC Educational Resources Information Center

Alian, Marwah; Shaout, Adnan

2017-01-01

Learners style is grouped into four types mainly; Visual, auditory, kinesthetic and Read/Write. Each type of learners learns primarily through one of the main receiving senses, visual, listening, or by doing. Learner style has an effect on the learning process and learner's achievement. It is better to select suitable learning tool for the learner…

Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB.

PubMed

Hendrickx, Pieter M S; Gutmanas, Aleksandras; Kleywegt, Gerard J

2013-04-01

We describe Vivaldi (VIsualization and VALidation DIsplay; http://pdbe.org/vivaldi), a web-based service for the analysis, visualization, and validation of NMR structures in the Protein Data Bank (PDB). Vivaldi provides access to model coordinates and several types of experimental NMR data using interactive visualization tools, augmented with structural annotations and model-validation information. The service presents information about the modeled NMR ensemble, validation of experimental chemical shifts, residual dipolar couplings, distance and dihedral angle constraints, as well as validation scores based on empirical knowledge and databases. Vivaldi was designed for both expert NMR spectroscopists and casual non-expert users who wish to obtain a better grasp of the information content and quality of NMR structures in the public archive. Copyright © 2013 Wiley Periodicals, Inc.

A Neuro-Oncology Workstation for Structuring, Modeling, and Visualizing Patient Records

PubMed Central

Hsu, William; Arnold, Corey W.; Taira, Ricky K.

2016-01-01

The patient medical record contains a wealth of information consisting of prior observations, interpretations, and interventions that need to be interpreted and applied towards decisions regarding current patient care. Given the time constraints and the large—often extraneous—amount of data available, clinicians are tasked with the challenge of performing a comprehensive review of how a disease progresses in individual patients. To facilitate this process, we demonstrate a neuro-oncology workstation that assists in structuring and visualizing medical data to promote an evidence-based approach for understanding a patient’s record. The workstation consists of three components: 1) a structuring tool that incorporates natural language processing to assist with the extraction of problems, findings, and attributes for structuring observations, events, and inferences stated within medical reports; 2) a data modeling tool that provides a comprehensive and consistent representation of concepts for the disease-specific domain; and 3) a visual workbench for visualizing, navigating, and querying the structured data to enable retrieval of relevant portions of the patient record. We discuss this workstation in the context of reviewing cases of glioblastoma multiforme patients. PMID:27583308

A Neuro-Oncology Workstation for Structuring, Modeling, and Visualizing Patient Records.

PubMed

Hsu, William; Arnold, Corey W; Taira, Ricky K

2010-11-01

The patient medical record contains a wealth of information consisting of prior observations, interpretations, and interventions that need to be interpreted and applied towards decisions regarding current patient care. Given the time constraints and the large-often extraneous-amount of data available, clinicians are tasked with the challenge of performing a comprehensive review of how a disease progresses in individual patients. To facilitate this process, we demonstrate a neuro-oncology workstation that assists in structuring and visualizing medical data to promote an evidence-based approach for understanding a patient's record. The workstation consists of three components: 1) a structuring tool that incorporates natural language processing to assist with the extraction of problems, findings, and attributes for structuring observations, events, and inferences stated within medical reports; 2) a data modeling tool that provides a comprehensive and consistent representation of concepts for the disease-specific domain; and 3) a visual workbench for visualizing, navigating, and querying the structured data to enable retrieval of relevant portions of the patient record. We discuss this workstation in the context of reviewing cases of glioblastoma multiforme patients.

EasyModeller: A graphical interface to MODELLER

PubMed Central

2010-01-01

Background MODELLER is a program for automated protein Homology Modeling. It is one of the most widely used tool for homology or comparative modeling of protein three-dimensional structures, but most users find it a bit difficult to start with MODELLER as it is command line based and requires knowledge of basic Python scripting to use it efficiently. Findings The study was designed with an aim to develop of "EasyModeller" tool as a frontend graphical interface to MODELLER using Perl/Tk, which can be used as a standalone tool in windows platform with MODELLER and Python preinstalled. It helps inexperienced users to perform modeling, assessment, visualization, and optimization of protein models in a simple and straightforward way. Conclusion EasyModeller provides a graphical straight forward interface and functions as a stand-alone tool which can be used in a standard personal computer with Microsoft Windows as the operating system. PMID:20712861

Map Learning with a 3D Printed Interactive Small-Scale Model: Improvement of Space and Text Memorization in Visually Impaired Students.

PubMed

Giraud, Stéphanie; Brock, Anke M; Macé, Marc J-M; Jouffrais, Christophe

2017-01-01

Special education teachers for visually impaired students rely on tools such as raised-line maps (RLMs) to teach spatial knowledge. These tools do not fully and adequately meet the needs of the teachers because they are long to produce, expensive, and not versatile enough to provide rapid updating of the content. For instance, the same RLM can barely be used during different lessons. In addition, those maps do not provide any interactivity, which reduces students' autonomy. With the emergence of 3D printing and low-cost microcontrollers, it is now easy to design affordable interactive small-scale models (SSMs) which are adapted to the needs of special education teachers. However, no study has previously been conducted to evaluate non-visual learning using interactive SSMs. In collaboration with a specialized teacher, we designed a SSM and a RLM representing the evolution of the geography and history of a fictitious kingdom. The two conditions were compared in a study with 24 visually impaired students regarding the memorization of the spatial layout and historical contents. The study showed that the interactive SSM improved both space and text memorization as compared to the RLM with braille legend. In conclusion, we argue that affordable home-made interactive small scale models can improve learning for visually impaired students. Interestingly, they are adaptable to any teaching situation including students with specific needs.

MONGKIE: an integrated tool for network analysis and visualization for multi-omics data.

PubMed

Jang, Yeongjun; Yu, Namhee; Seo, Jihae; Kim, Sun; Lee, Sanghyuk

2016-03-18

Network-based integrative analysis is a powerful technique for extracting biological insights from multilayered omics data such as somatic mutations, copy number variations, and gene expression data. However, integrated analysis of multi-omics data is quite complicated and can hardly be done in an automated way. Thus, a powerful interactive visual mining tool supporting diverse analysis algorithms for identification of driver genes and regulatory modules is much needed. Here, we present a software platform that integrates network visualization with omics data analysis tools seamlessly. The visualization unit supports various options for displaying multi-omics data as well as unique network models for describing sophisticated biological networks such as complex biomolecular reactions. In addition, we implemented diverse in-house algorithms for network analysis including network clustering and over-representation analysis. Novel functions include facile definition and optimized visualization of subgroups, comparison of a series of data sets in an identical network by data-to-visual mapping and subsequent overlaying function, and management of custom interaction networks. Utility of MONGKIE for network-based visual data mining of multi-omics data was demonstrated by analysis of the TCGA glioblastoma data. MONGKIE was developed in Java based on the NetBeans plugin architecture, thus being OS-independent with intrinsic support of module extension by third-party developers. We believe that MONGKIE would be a valuable addition to network analysis software by supporting many unique features and visualization options, especially for analysing multi-omics data sets in cancer and other diseases. .

Human-scale interaction for virtual model displays: a clear case for real tools

NASA Astrophysics Data System (ADS)

Williams, George C.; McDowall, Ian E.; Bolas, Mark T.

1998-04-01

We describe a hand-held user interface for interacting with virtual environments displayed on a Virtual Model Display. The tool, constructed entirely of transparent materials, is see-through. We render a graphical counterpart of the tool on the display and map it one-to-one with the real tool. This feature, combined with a capability for touch- sensitive, discrete input, results in a useful spatial input device that is visually versatile. We discuss the tool's design and interaction techniques it supports. Briefly, we look at the human factors issues and engineering challenges presented by this tool and, in general, by the class of hand-held user interfaces that are see-through.

Monitoring Areal Snow Cover Using NASA Satellite Imagery

NASA Technical Reports Server (NTRS)

Harshburger, Brian J.; Blandford, Troy; Moore, Brandon

2011-01-01

The objective of this project is to develop products and tools to assist in the hydrologic modeling process, including tools to help prepare inputs for hydrologic models and improved methods for the visualization of streamflow forecasts. In addition, this project will facilitate the use of NASA satellite imagery (primarily snow cover imagery) by other federal and state agencies with operational streamflow forecasting responsibilities. A GIS software toolkit for monitoring areal snow cover extent and producing streamflow forecasts is being developed. This toolkit will be packaged as multiple extensions for ArcGIS 9.x and an opensource GIS software package. The toolkit will provide users with a means for ingesting NASA EOS satellite imagery (snow cover analysis), preparing hydrologic model inputs, and visualizing streamflow forecasts. Primary products include a software tool for predicting the presence of snow under clouds in satellite images; a software tool for producing gridded temperature and precipitation forecasts; and a suite of tools for visualizing hydrologic model forecasting results. The toolkit will be an expert system designed for operational users that need to generate accurate streamflow forecasts in a timely manner. The Remote Sensing of Snow Cover Toolbar will ingest snow cover imagery from multiple sources, including the MODIS Operational Snowcover Data and convert them to gridded datasets that can be readily used. Statistical techniques will then be applied to the gridded snow cover data to predict the presence of snow under cloud cover. The toolbar has the ability to ingest both binary and fractional snow cover data. Binary mapping techniques use a set of thresholds to determine whether a pixel contains snow or no snow. Fractional mapping techniques provide information regarding the percentage of each pixel that is covered with snow. After the imagery has been ingested, physiographic data is attached to each cell in the snow cover image. This data can be obtained from a digital elevation model (DEM) for the area of interest.

The development and discussion of computerized visual perception assessment tool for Chinese characters structures - Concurrent estimation of the overall ability and the domain ability in item response theory approach.

PubMed

Wu, Huey-Min; Lin, Chin-Kai; Yang, Yu-Mao; Kuo, Bor-Chen

2014-11-12

Visual perception is the fundamental skill required for a child to recognize words, and to read and write. There was no visual perception assessment tool developed for preschool children based on Chinese characters in Taiwan. The purposes were to develop the computerized visual perception assessment tool for Chinese Characters Structures and to explore the psychometrical characteristic of assessment tool. This study adopted purposive sampling. The study evaluated 551 kindergarten-age children (293 boys, 258 girls) ranging from 46 to 81 months of age. The test instrument used in this study consisted of three subtests and 58 items, including tests of basic strokes, single-component characters, and compound characters. Based on the results of model fit analysis, the higher-order item response theory was used to estimate the performance in visual perception, basic strokes, single-component characters, and compound characters simultaneously. Analyses of variance were used to detect significant difference in age groups and gender groups. The difficulty of identifying items in a visual perception test ranged from -2 to 1. The visual perception ability of 4- to 6-year-old children ranged from -1.66 to 2.19. Gender did not have significant effects on performance. However, there were significant differences among the different age groups. The performance of 6-year-olds was better than that of 5-year-olds, which was better than that of 4-year-olds. This study obtained detailed diagnostic scores by using a higher-order item response theory model to understand the visual perception of basic strokes, single-component characters, and compound characters. Further statistical analysis showed that, for basic strokes and compound characters, girls performed better than did boys; there also were differences within each age group. For single-component characters, there was no difference in performance between boys and girls. However, again the performance of 6-year-olds was better than that of 4-year-olds, but there were no statistical differences between the performance of 5-year-olds and 6-year-olds. Results of tests with basic strokes, single-component characters and compound characters tests had good reliability and validity. Therefore, it can be apply to diagnose the problem of visual perception at preschool. Copyright © 2014 Elsevier Ltd. All rights reserved.

Web-Based Model Visualization Tools to Aid in Model Optimization and Uncertainty Analysis

NASA Astrophysics Data System (ADS)

Alder, J.; van Griensven, A.; Meixner, T.

2003-12-01

Individuals applying hydrologic models have a need for a quick easy to use visualization tools to permit them to assess and understand model performance. We present here the Interactive Hydrologic Modeling (IHM) visualization toolbox. The IHM utilizes high-speed Internet access, the portability of the web and the increasing power of modern computers to provide an online toolbox for quick and easy model result visualization. This visualization interface allows for the interpretation and analysis of Monte-Carlo and batch model simulation results. Often times a given project will generate several thousands or even hundreds of thousands simulations. This large number of simulations creates a challenge for post-simulation analysis. IHM's goal is to try to solve this problem by loading all of the data into a database with a web interface that can dynamically generate graphs for the user according to their needs. IHM currently supports: a global samples statistics table (e.g. sum of squares error, sum of absolute differences etc.), top ten simulations table and graphs, graphs of an individual simulation using time step data, objective based dotty plots, threshold based parameter cumulative density function graphs (as used in the regional sensitivity analysis of Spear and Hornberger) and 2D error surface graphs of the parameter space. IHM is ideal for the simplest bucket model to the largest set of Monte-Carlo model simulations with a multi-dimensional parameter and model output space. By using a web interface, IHM offers the user complete flexibility in the sense that they can be anywhere in the world using any operating system. IHM can be a time saving and money saving alternative to spending time producing graphs or conducting analysis that may not be informative or being forced to purchase or use expensive and proprietary software. IHM is a simple, free, method of interpreting and analyzing batch model results, and is suitable for novice to expert hydrologic modelers.

Integrated workflows for spiking neuronal network simulations

PubMed Central

Antolík, Ján; Davison, Andrew P.

2013-01-01

The increasing availability of computational resources is enabling more detailed, realistic modeling in computational neuroscience, resulting in a shift toward more heterogeneous models of neuronal circuits, and employment of complex experimental protocols. This poses a challenge for existing tool chains, as the set of tools involved in a typical modeler's workflow is expanding concomitantly, with growing complexity in the metadata flowing between them. For many parts of the workflow, a range of tools is available; however, numerous areas lack dedicated tools, while integration of existing tools is limited. This forces modelers to either handle the workflow manually, leading to errors, or to write substantial amounts of code to automate parts of the workflow, in both cases reducing their productivity. To address these issues, we have developed Mozaik: a workflow system for spiking neuronal network simulations written in Python. Mozaik integrates model, experiment and stimulation specification, simulation execution, data storage, data analysis and visualization into a single automated workflow, ensuring that all relevant metadata are available to all workflow components. It is based on several existing tools, including PyNN, Neo, and Matplotlib. It offers a declarative way to specify models and recording configurations using hierarchically organized configuration files. Mozaik automatically records all data together with all relevant metadata about the experimental context, allowing automation of the analysis and visualization stages. Mozaik has a modular architecture, and the existing modules are designed to be extensible with minimal programming effort. Mozaik increases the productivity of running virtual experiments on highly structured neuronal networks by automating the entire experimental cycle, while increasing the reliability of modeling studies by relieving the user from manual handling of the flow of metadata between the individual workflow stages. PMID:24368902

Integrated workflows for spiking neuronal network simulations.

PubMed

Antolík, Ján; Davison, Andrew P

2013-01-01

The increasing availability of computational resources is enabling more detailed, realistic modeling in computational neuroscience, resulting in a shift toward more heterogeneous models of neuronal circuits, and employment of complex experimental protocols. This poses a challenge for existing tool chains, as the set of tools involved in a typical modeler's workflow is expanding concomitantly, with growing complexity in the metadata flowing between them. For many parts of the workflow, a range of tools is available; however, numerous areas lack dedicated tools, while integration of existing tools is limited. This forces modelers to either handle the workflow manually, leading to errors, or to write substantial amounts of code to automate parts of the workflow, in both cases reducing their productivity. To address these issues, we have developed Mozaik: a workflow system for spiking neuronal network simulations written in Python. Mozaik integrates model, experiment and stimulation specification, simulation execution, data storage, data analysis and visualization into a single automated workflow, ensuring that all relevant metadata are available to all workflow components. It is based on several existing tools, including PyNN, Neo, and Matplotlib. It offers a declarative way to specify models and recording configurations using hierarchically organized configuration files. Mozaik automatically records all data together with all relevant metadata about the experimental context, allowing automation of the analysis and visualization stages. Mozaik has a modular architecture, and the existing modules are designed to be extensible with minimal programming effort. Mozaik increases the productivity of running virtual experiments on highly structured neuronal networks by automating the entire experimental cycle, while increasing the reliability of modeling studies by relieving the user from manual handling of the flow of metadata between the individual workflow stages.

Design strategies and functionality of the Visual Interface for Virtual Interaction Development (VIVID) tool

NASA Technical Reports Server (NTRS)

Nguyen, Lac; Kenney, Patrick J.

1993-01-01

Development of interactive virtual environments (VE) has typically consisted of three primary activities: model (object) development, model relationship tree development, and environment behavior definition and coding. The model and relationship tree development activities are accomplished with a variety of well-established graphic library (GL) based programs - most utilizing graphical user interfaces (GUI) with point-and-click interactions. Because of this GUI format, little programming expertise on the part of the developer is necessary to create the 3D graphical models or to establish interrelationships between the models. However, the third VE development activity, environment behavior definition and coding, has generally required the greatest amount of time and programmer expertise. Behaviors, characteristics, and interactions between objects and the user within a VE must be defined via command line C coding prior to rendering the environment scenes. In an effort to simplify this environment behavior definition phase for non-programmers, and to provide easy access to model and tree tools, a graphical interface and development tool has been created. The principal thrust of this research is to effect rapid development and prototyping of virtual environments. This presentation will discuss the 'Visual Interface for Virtual Interaction Development' (VIVID) tool; an X-Windows based system employing drop-down menus for user selection of program access, models, and trees, behavior editing, and code generation. Examples of these selection will be highlighted in this presentation, as will the currently available program interfaces. The functionality of this tool allows non-programming users access to all facets of VE development while providing experienced programmers with a collection of pre-coded behaviors. In conjunction with its existing, interfaces and predefined suite of behaviors, future development plans for VIVID will be described. These include incorporation of dual user virtual environment enhancements, tool expansion, and additional behaviors.

Interactive Visualization to Advance Earthquake Simulation

NASA Astrophysics Data System (ADS)

Kellogg, Louise H.; Bawden, Gerald W.; Bernardin, Tony; Billen, Magali; Cowgill, Eric; Hamann, Bernd; Jadamec, Margarete; Kreylos, Oliver; Staadt, Oliver; Sumner, Dawn

2008-04-01

The geological sciences are challenged to manage and interpret increasing volumes of data as observations and simulations increase in size and complexity. For example, simulations of earthquake-related processes typically generate complex, time-varying data sets in two or more dimensions. To facilitate interpretation and analysis of these data sets, evaluate the underlying models, and to drive future calculations, we have developed methods of interactive visualization with a special focus on using immersive virtual reality (VR) environments to interact with models of Earth’s surface and interior. Virtual mapping tools allow virtual “field studies” in inaccessible regions. Interactive tools allow us to manipulate shapes in order to construct models of geological features for geodynamic models, while feature extraction tools support quantitative measurement of structures that emerge from numerical simulation or field observations, thereby enabling us to improve our interpretation of the dynamical processes that drive earthquakes. VR has traditionally been used primarily as a presentation tool, albeit with active navigation through data. Reaping the full intellectual benefits of immersive VR as a tool for scientific analysis requires building on the method’s strengths, that is, using both 3D perception and interaction with observed or simulated data. This approach also takes advantage of the specialized skills of geological scientists who are trained to interpret, the often limited, geological and geophysical data available from field observations.

LitPathExplorer: a confidence-based visual text analytics tool for exploring literature-enriched pathway models.

PubMed

Soto, Axel J; Zerva, Chrysoula; Batista-Navarro, Riza; Ananiadou, Sophia

2018-04-15

Pathway models are valuable resources that help us understand the various mechanisms underpinning complex biological processes. Their curation is typically carried out through manual inspection of published scientific literature to find information relevant to a model, which is a laborious and knowledge-intensive task. Furthermore, models curated manually cannot be easily updated and maintained with new evidence extracted from the literature without automated support. We have developed LitPathExplorer, a visual text analytics tool that integrates advanced text mining, semi-supervised learning and interactive visualization, to facilitate the exploration and analysis of pathway models using statements (i.e. events) extracted automatically from the literature and organized according to levels of confidence. LitPathExplorer supports pathway modellers and curators alike by: (i) extracting events from the literature that corroborate existing models with evidence; (ii) discovering new events which can update models; and (iii) providing a confidence value for each event that is automatically computed based on linguistic features and article metadata. Our evaluation of event extraction showed a precision of 89% and a recall of 71%. Evaluation of our confidence measure, when used for ranking sampled events, showed an average precision ranging between 61 and 73%, which can be improved to 95% when the user is involved in the semi-supervised learning process. Qualitative evaluation using pair analytics based on the feedback of three domain experts confirmed the utility of our tool within the context of pathway model exploration. LitPathExplorer is available at http://nactem.ac.uk/LitPathExplorer_BI/. sophia.ananiadou@manchester.ac.uk. Supplementary data are available at Bioinformatics online.

Dependency visualization for complex system understanding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smart, J. Allison Cory

1994-09-01

With the volume of software in production use dramatically increasing, the importance of software maintenance has become strikingly apparent. Techniques now sought and developed for reverse engineering and design extraction and recovery. At present, numerous commercial products and research tools exist which are capable of visualizing a variety of programming languages and software constructs. The list of new tools and services continues to grow rapidly. Although the scope of the existing commercial and academic product set is quite broad, these tools still share a common underlying problem. The ability of each tool to visually organize object representations is increasingly impairedmore » as the number of components and component dependencies within systems increases. Regardless of how objects are defined, complex ``spaghetti`` networks result in nearly all large system cases. While this problem is immediately apparent in modem systems analysis involving large software implementations, it is not new. As will be discussed in Chapter 2, related problems involving the theory of graphs were identified long ago. This important theoretical foundation provides a useful vehicle for representing and analyzing complex system structures. While the utility of directed graph based concepts in software tool design has been demonstrated in literature, these tools still lack the capabilities necessary for large system comprehension. This foundation must therefore be expanded with new organizational and visualization constructs necessary to meet this challenge. This dissertation addresses this need by constructing a conceptual model and a set of methods for interactively exploring, organizing, and understanding the structure of complex software systems.« less

PSSMSearch: a server for modeling, visualization, proteome-wide discovery and annotation of protein motif specificity determinants.

PubMed

Krystkowiak, Izabella; Manguy, Jean; Davey, Norman E

2018-06-05

There is a pressing need for in silico tools that can aid in the identification of the complete repertoire of protein binding (SLiMs, MoRFs, miniMotifs) and modification (moiety attachment/removal, isomerization, cleavage) motifs. We have created PSSMSearch, an interactive web-based tool for rapid statistical modeling, visualization, discovery and annotation of protein motif specificity determinants to discover novel motifs in a proteome-wide manner. PSSMSearch analyses proteomes for regions with significant similarity to a motif specificity determinant model built from a set of aligned motif-containing peptides. Multiple scoring methods are available to build a position-specific scoring matrix (PSSM) describing the motif specificity determinant model. This model can then be modified by a user to add prior knowledge of specificity determinants through an interactive PSSM heatmap. PSSMSearch includes a statistical framework to calculate the significance of specificity determinant model matches against a proteome of interest. PSSMSearch also includes the SLiMSearch framework's annotation, motif functional analysis and filtering tools to highlight relevant discriminatory information. Additional tools to annotate statistically significant shared keywords and GO terms, or experimental evidence of interaction with a motif-recognizing protein have been added. Finally, PSSM-based conservation metrics have been created for taxonomic range analyses. The PSSMSearch web server is available at http://slim.ucd.ie/pssmsearch/.

Spectrum simulation in DTSA-II.

PubMed

Ritchie, Nicholas W M

2009-10-01

Spectrum simulation is a useful practical and pedagogical tool. Particularly with complex samples or trace constituents, a simulation can help to understand the limits of the technique and the instrument parameters for the optimal measurement. DTSA-II, software for electron probe microanalysis, provides both easy to use and flexible tools for simulating common and less common sample geometries and materials. Analytical models based on (rhoz) curves provide quick simulations of simple samples. Monte Carlo models based on electron and X-ray transport provide more sophisticated models of arbitrarily complex samples. DTSA-II provides a broad range of simulation tools in a framework with many different interchangeable physical models. In addition, DTSA-II provides tools for visualizing, comparing, manipulating, and quantifying simulated and measured spectra.

Software For Graphical Representation Of A Network

NASA Technical Reports Server (NTRS)

Mcallister, R. William; Mclellan, James P.

1993-01-01

System Visualization Tool (SVT) computer program developed to provide systems engineers with means of graphically representing networks. Generates diagrams illustrating structures and states of networks defined by users. Provides systems engineers powerful tool simplifing analysis of requirements and testing and maintenance of complex software-controlled systems. Employs visual models supporting analysis of chronological sequences of requirements, simulation data, and related software functions. Applied to pneumatic, hydraulic, and propellant-distribution networks. Used to define and view arbitrary configurations of such major hardware components of system as propellant tanks, valves, propellant lines, and engines. Also graphically displays status of each component. Advantage of SVT: utilizes visual cues to represent configuration of each component within network. Written in Turbo Pascal(R), version 5.0.

Visualizing Without Vision at the Microscale: Students With Visual Impairments Explore Cells With Touch

NASA Astrophysics Data System (ADS)

Jones, M. Gail; Minogue, James; Oppewal, Tom; Cook, Michelle P.; Broadwell, Bethany

2006-12-01

Science instruction is typically highly dependent on visual representations of scientific concepts that are communicated through textbooks, teacher presentations, and computer-based multimedia materials. Little is known about how students with visual impairments access and interpret these types of visually-dependent instructional materials. This study explored the efficacy of new haptic (simulated tactile feedback and kinesthetics) instructional technology for teaching cell morphology and function to middle and high school students with visual impairments. The study examined students' prior experiences learning about the cell and cell functions in classroom instruction, as well as how haptic feedback technology impacted students' awareness of the 3-D nature of an animal cell, the morphology and function of cell organelles, and students' interest in the haptic technology as an instructional tool. Twenty-one students with visual impairment participated in the study. Students explored a tactile model of the cell with a haptic point probe that allowed them to feel the cell and its organelles. Results showed that students made significant gains in their ability to identify cell organelles and found the technology to be highly interesting as an instructional tool. The need for additional adaptive technology for students with visual impairments is discussed.

The role of 3-D interactive visualization in blind surveys of H I in galaxies

NASA Astrophysics Data System (ADS)

Punzo, D.; van der Hulst, J. M.; Roerdink, J. B. T. M.; Oosterloo, T. A.; Ramatsoku, M.; Verheijen, M. A. W.

2015-09-01

Upcoming H I surveys will deliver large datasets, and automated processing using the full 3-D information (two positional dimensions and one spectral dimension) to find and characterize H I objects is imperative. In this context, visualization is an essential tool for enabling qualitative and quantitative human control on an automated source finding and analysis pipeline. We discuss how Visual Analytics, the combination of automated data processing and human reasoning, creativity and intuition, supported by interactive visualization, enables flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities helping the discovery and analysis of subtle structures in the 3-D domain. The requirements for a fully interactive visualization tool are: coupled 1-D/2-D/3-D visualization, quantitative and comparative capabilities, combined with supervised semi-automated analysis. Moreover, the source code must have the following characteristics for enabling collaborative work: open, modular, well documented, and well maintained. We review four state of-the-art, 3-D visualization packages assessing their capabilities and feasibility for use in the case of 3-D astronomical data.

AF-GEOSpace Version 2.0: Space Environment Software Products for 2002

NASA Astrophysics Data System (ADS)

Hilmer, R. V.; Ginet, G. P.; Hall, T.; Holeman, E.; Tautz, M.

2002-05-01

AF-GEOSpace Version 2.0 (release 2002 on WindowsNT/2000/XP) is a graphics-intensive software program developed by AFRL with space environment models and applications. It has grown steadily to become a development tool for automated space weather visualization products and helps with a variety of tasks: orbit specification for radiation hazard avoidance; satellite design assessment and post-event analysis; solar disturbance effects forecasting; frequency and antenna management for radar and HF communications; determination of link outage regions for active ionospheric conditions; and physics research and education. The object-oriented C++ code is divided into five module classes. Science Modules control science models to give output data on user-specified grids. Application Modules manipulate these data and provide orbit generation and magnetic field line tracing capabilities. Data Modules read and assist with the analysis of user-generated data sets. Graphics Modules enable the display of features such as plane slices, magnetic field lines, line plots, axes, the Earth, stars, and satellites. Worksheet Modules provide commonly requested coordinate transformations and calendar conversion tools. Common input data archive sets, application modules, and 1-, 2-, and 3-D visualization tools are provided to all models. The code documentation includes detailed examples with click-by-click instructions for investigating phenomena that have well known effects on communications and spacecraft systems. AF-GEOSpace Version 2.0 builds on the success of its predecessors. The first release (Version 1.21, 1996/IRIX on SGI) contained radiation belt particle flux and dose models derived from CRRES satellite data, an aurora model, an ionosphere model, and ionospheric HF ray tracing capabilities. Next (Version 1.4, 1999/IRIX on SGI) science modules were added related to cosmic rays and solar protons, low-Earth orbit radiation dosages, single event effects probability maps, ionospheric scintillation, and shock propagation models. New application modules for estimating linear energy transfer (LET) and single event upset (SEU) rates in solid-state devices, and graphic modules for visualizing radar fans, communication domes, and satellite detector cones and links were added. Automated FTP scripts permitted users to update their global input parameter set directly from NOAA/SEC. What?s New? Version 2.0 includes the first true dynamic run capabilities and offers new and enhanced graphical and data visualization tools such as 3-D volume rendering and eclipse umbra and penumbra determination. Animations of all model results can now be displayed together in all dimensions. There is a new realistic day-to-day ionospheric scintillation simulation generator (IONSCINT), an upgrade to the WBMOD scintillation code, a simplified HF ionospheric ray tracing module, and applications built on the NASA AE-8 and AP-8 radiation belt models. User-generated satellite data sets can now be visualized along with their orbital ephemeris. A prototype tool for visualizing MHD model results stored in structured grids provides a hint of where future space weather model development efforts are headed. A new graphical user interface (GUI) with improved module tracking and renaming features greatly simplifies software operation. AF-GEOSpace is distributed by the Space Weather Center of Excellence in the Space Vehicles Directorate of AFRL. Recently released for WindowsNT/2000/XP, versions for UNIX and LINUX operating systems will follow shortly. To obtain AF-GEOSpace Version 2.0, please send an e-mail request to the first author.

Visual analytics in cheminformatics: user-supervised descriptor selection for QSAR methods.

PubMed

Martínez, María Jimena; Ponzoni, Ignacio; Díaz, Mónica F; Vazquez, Gustavo E; Soto, Axel J

2015-01-01

The design of QSAR/QSPR models is a challenging problem, where the selection of the most relevant descriptors constitutes a key step of the process. Several feature selection methods that address this step are concentrated on statistical associations among descriptors and target properties, whereas the chemical knowledge is left out of the analysis. For this reason, the interpretability and generality of the QSAR/QSPR models obtained by these feature selection methods are drastically affected. Therefore, an approach for integrating domain expert's knowledge in the selection process is needed for increase the confidence in the final set of descriptors. In this paper a software tool, which we named Visual and Interactive DEscriptor ANalysis (VIDEAN), that combines statistical methods with interactive visualizations for choosing a set of descriptors for predicting a target property is proposed. Domain expertise can be added to the feature selection process by means of an interactive visual exploration of data, and aided by statistical tools and metrics based on information theory. Coordinated visual representations are presented for capturing different relationships and interactions among descriptors, target properties and candidate subsets of descriptors. The competencies of the proposed software were assessed through different scenarios. These scenarios reveal how an expert can use this tool to choose one subset of descriptors from a group of candidate subsets or how to modify existing descriptor subsets and even incorporate new descriptors according to his or her own knowledge of the target property. The reported experiences showed the suitability of our software for selecting sets of descriptors with low cardinality, high interpretability, low redundancy and high statistical performance in a visual exploratory way. Therefore, it is possible to conclude that the resulting tool allows the integration of a chemist's expertise in the descriptor selection process with a low cognitive effort in contrast with the alternative of using an ad-hoc manual analysis of the selected descriptors. Graphical abstractVIDEAN allows the visual analysis of candidate subsets of descriptors for QSAR/QSPR. In the two panels on the top, users can interactively explore numerical correlations as well as co-occurrences in the candidate subsets through two interactive graphs.

Concept of Operations Visualization for Ares I Production

NASA Technical Reports Server (NTRS)

Chilton, Jim; Smith, David Alan

2008-01-01

Establishing Computer Aided Design models of the Ares I production facility, tooling and vehicle components and integrating them into manufacturing visualizations/simulations allows Boeing and NASA to collaborate real time early in the design/development cycle. This collaboration identifies cost effective and lean solutions that can be easily shared with Ares stakeholders (e.g., other NASA Centers and potential science users). These Ares I production visualizations and analyses by their nature serve as early manufacturing improvement precursors for other Constellation elements to be built at the Michoud Assembly Facility such as Ares V and the Altair Lander. Key to this Boeing and Marshall Space Flight Center collaboration has been the use of advanced virtual manufacturing tools to understand the existing Shuttle era infrastructure and trade potential modifications to support Ares I production. These approaches are then used to determine an optimal manufacturing configuration in terms of labor efficiency, safety and facility enhancements. These same models and tools can be used in an interactive simulation of Ares I and V flight to the Space Station or moon to educate the human space constituency (e.g., government, academia, media and the public) in order to increase national and international understanding of Constellation goals and benefits.

Scientific Visualization to Study Flux Transfer Events at the Community Coordinated Modeling Center

NASA Technical Reports Server (NTRS)

Rastatter, Lutz; Kuznetsova, Maria M.; Sibeck, David G.; Berrios, David H.

2011-01-01

In this paper we present results of modeling of reconnection at the dayside magnetopause with subsequent development of flux transfer event signatures. The tools used include new methods that have been added to the suite of visualization methods that are used at the Community Coordinated Modeling Center (CCMC). Flux transfer events result from localized reconnection that connect magnetosheath magnetic field and plasma with magnetospheric fields and plasma and results in flux rope structures that span the dayside magnetopause. The onset of flux rope formation and the three-dimensional structure of flux ropes are studied as they have been modeled by high-resolution magnetohydrodynamic simulations of the dayside magnetosphere of the Earth. We show that flux transfer events are complex three-dimensional structures that require modern visualization and analysis techniques. Two suites of visualization methods are presented and we demonstrate the usefulness of those methods through the CCMC web site to the general science user.

Hyperspectral Reflectance Imaging Technique for Visualization of Moisture Distribution in Cooked Chicken Breast

PubMed Central

Kandpal, Lalit Mohan; Lee, Hoonsoo; Kim, Moon S.; Mo, Changyeun; Cho, Byoung-Kwan

2013-01-01

Spectroscopy has proven to be an efficient tool for measuring the properties of meat. In this article, hyperspectral imaging (HSI) techniques are used to determine the moisture content in cooked chicken breast over the VIS/NIR (400–1,000 nm) spectral range. Moisture measurements were performed using an oven drying method. A partial least squares regression (PLSR) model was developed to extract a relationship between the HSI spectra and the moisture content. In the full wavelength range, the PLSR model possessed a maximum R2p of 0.90 and an SEP of 0.74%. For the NIR range, the PLSR model yielded an R2p of 0.94 and an SEP of 0.71%. The majority of the absorption peaks occurred around 760 and 970 nm, representing the water content in the samples. Finally, PLSR images were constructed to visualize the dehydration and water distribution within different sample regions. The high correlation coefficient and low prediction error from the PLSR analysis validates that HSI is an effective tool for visualizing the chemical properties of meat. PMID:24084119

PetriScape - A plugin for discrete Petri net simulations in Cytoscape.

PubMed

Almeida, Diogo; Azevedo, Vasco; Silva, Artur; Baumbach, Jan

2016-06-04

Systems biology plays a central role for biological network analysis in the post-genomic era. Cytoscape is the standard bioinformatics tool offering the community an extensible platform for computational analysis of the emerging cellular network together with experimental omics data sets. However, only few apps/plugins/tools are available for simulating network dynamics in Cytoscape 3. Many approaches of varying complexity exist but none of them have been integrated into Cytoscape as app/plugin yet. Here, we introduce PetriScape, the first Petri net simulator for Cytoscape. Although discrete Petri nets are quite simplistic models, they are capable of modeling global network properties and simulating their behaviour. In addition, they are easily understood and well visualizable. PetriScape comes with the following main functionalities: (1) import of biological networks in SBML format, (2) conversion into a Petri net, (3) visualization as Petri net, and (4) simulation and visualization of the token flow in Cytoscape. PetriScape is the first Cytoscape plugin for Petri nets. It allows a straightforward Petri net model creation, simulation and visualization with Cytoscape, providing clues about the activity of key components in biological networks.

PetriScape - A plugin for discrete Petri net simulations in Cytoscape.

PubMed

Almeida, Diogo; Azevedo, Vasco; Silva, Artur; Baumbach, Jan

2016-03-01

Systems biology plays a central role for biological network analysis in the post-genomic era. Cytoscape is the standard bioinformatics tool offering the community an extensible platform for computational analysis of the emerging cellular network together with experimental omics data sets. However, only few apps/plugins/tools are available for simulating network dynamics in Cytoscape 3. Many approaches of varying complexity exist but none of them have been integrated into Cytoscape as app/plugin yet. Here, we introduce PetriScape, the first Petri net simulator for Cytoscape. Although discrete Petri nets are quite simplistic models, they are capable of modeling global network properties and simulating their behaviour. In addition, they are easily understood and well visualizable. PetriScape comes with the following main functionalities: (1) import of biological networks in SBML format, (2) conversion into a Petri net, (3) visualization as Petri net, and (4) simulation and visualization of the token flow in Cytoscape. PetriScape is the first Cytoscape plugin for Petri nets. It allows a straightforward Petri net model creation, simulation and visualization with Cytoscape, providing clues about the activity of key components in biological networks.

ePlant and the 3D data display initiative: integrative systems biology on the world wide web.

PubMed

Fucile, Geoffrey; Di Biase, David; Nahal, Hardeep; La, Garon; Khodabandeh, Shokoufeh; Chen, Yani; Easley, Kante; Christendat, Dinesh; Kelley, Lawrence; Provart, Nicholas J

2011-01-10

Visualization tools for biological data are often limited in their ability to interactively integrate data at multiple scales. These computational tools are also typically limited by two-dimensional displays and programmatic implementations that require separate configurations for each of the user's computing devices and recompilation for functional expansion. Towards overcoming these limitations we have developed "ePlant" (http://bar.utoronto.ca/eplant) - a suite of open-source world wide web-based tools for the visualization of large-scale data sets from the model organism Arabidopsis thaliana. These tools display data spanning multiple biological scales on interactive three-dimensional models. Currently, ePlant consists of the following modules: a sequence conservation explorer that includes homology relationships and single nucleotide polymorphism data, a protein structure model explorer, a molecular interaction network explorer, a gene product subcellular localization explorer, and a gene expression pattern explorer. The ePlant's protein structure explorer module represents experimentally determined and theoretical structures covering >70% of the Arabidopsis proteome. The ePlant framework is accessed entirely through a web browser, and is therefore platform-independent. It can be applied to any model organism. To facilitate the development of three-dimensional displays of biological data on the world wide web we have established the "3D Data Display Initiative" (http://3ddi.org).

ESTEEM: A Novel Framework for Qualitatively Evaluating and Visualizing Spatiotemporal Embeddings in Social Media

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arendt, Dustin L.; Volkova, Svitlana

Analyzing and visualizing large amounts of social media communications and contrasting short-term conversation changes over time and geo-locations is extremely important for commercial and government applications. Earlier approaches for large-scale text stream summarization used dynamic topic models and trending words. Instead, we rely on text embeddings – low-dimensional word representations in a continuous vector space where similar words are embedded nearby each other. This paper presents ESTEEM,1 a novel tool for visualizing and evaluating spatiotemporal embeddings learned from streaming social media texts. Our tool allows users to monitor and analyze query words and their closest neighbors with an interactive interface.more » We used state-of- the-art techniques to learn embeddings and developed a visualization to represent dynamically changing relations between words in social media over time and other dimensions. This is the first interactive visualization of streaming text representations learned from social media texts that also allows users to contrast differences across multiple dimensions of the data.« less

Visual Reasoning Tools in Action: Double Number Lines, Area Models, and Other Diagrams Power Up Students' Ability to Solve and Make Sense of Various Problems

ERIC Educational Resources Information Center

Watanabe, Tad

2015-01-01

The Common Core State Standards for Mathematics (CCSSM) (CCSSI 2010) identifies the strategic use of appropriate tools as one of the mathematical practices and emphasizes the use of pictures and diagrams as reasoning tools. Starting with the early elementary grades, CCSSM discusses students' solving of problems "by drawing." In later…

Lunar and Vesta Web Portals

NASA Astrophysics Data System (ADS)

Law, E.; JPL Luna Mapping; Modeling Project Team

2015-06-01

The Lunar Mapping and Modeling Project offers Lunar Mapping and Modeling Portal (http://lmmp.nasa.gov) and Vesta Trek Portal (http://vestatrek.jpl.nasa.gov) providing interactive visualization and analysis tools to enable users to access mapped Lunar and Vesta data products.

Tactile Sun: Bringing an Invisible Universe to the Visually Impaired

NASA Astrophysics Data System (ADS)

Isidro, G. M.; Pantoja, C. A.

2014-07-01

A tactile model of the Sun has been created as a strategy for communicating astronomy to the blind or visually impaired, and as a useful outreach tool for general audiences. The model design was a collaboration between an education specialist, an astronomy specialist and a sculptor. The tactile Sun has been used at astronomy outreach events in Puerto Rico to make activities more inclusive and to increase public awareness of the needs of those with disabilities.

Validity of the growth model of the 'computerized visual perception assessment tool for Chinese characters structures'.

PubMed

Wu, Huey-Min; Li, Cheng-Hsaun; Kuo, Bor-Chen; Yang, Yu-Mao; Lin, Chin-Kai; Wan, Wei-Hsiang

2017-08-01

Morphological awareness is the foundation for the important developmental skills involved with vocabulary, as well as understanding the meaning of words, orthographic knowledge, reading, and writing. Visual perception of space and radicals in two-dimensional positions of Chinese characters' morphology is very important in identifying Chinese characters. The important predictive variables of special and visual perception in Chinese characters identification were investigated in the growth model in this research. The assessment tool is the "Computerized Visual Perception Assessment Tool for Chinese Characters Structures" developed by this study. There are two constructs, basic stroke and character structure. In the basic stroke, there are three subtests of one, two, and more than three strokes. In the character structure, there are three subtests of single-component character, horizontal-compound character, and vertical-compound character. This study used purposive sampling. In the first year, 551 children 4-6 years old participated in the study and were monitored for one year. In the second year, 388 children remained in the study and the successful follow-up rate was 70.4%. This study used a two-wave cross-lagged panel design to validate the growth model of the basic stroke and the character structure. There was significant correlation of the basic stroke and the character structure at different time points. The abilities in the basic stroke and in the character structure steadily developed over time for preschool children. Children's knowledge of the basic stroke effectively predicted their knowledge of the basic stroke and the character structure. Copyright © 2017 Elsevier Ltd. All rights reserved.

New Visual Methods for Teaching Intersectionality from a Spatial Perspective in a Geography and Gender Course

ERIC Educational Resources Information Center

Baylina Ferré, Mireia; Rodó de Zárate, Maria

2016-01-01

Intersectionality is a complex concept to deal with when doing research but also when teaching the interrelationships between space and social relations. Here we present "Relief Maps" as a visual tool for teaching intersectionality and its spatial dimension in higher education courses. "Relief Maps" are a model developed for…

Using Molecular Visualization to Explore Protein Structure and Function and Enhance Student Facility with Computational Tools

ERIC Educational Resources Information Center

Terrell, Cassidy R.; Listenberger, Laura L.

2017-01-01

Recognizing that undergraduate students can benefit from analysis of 3D protein structure and function, we have developed a multiweek, inquiry-based molecular visualization project for Biochemistry I students. This project uses a virtual model of cyclooxygenase-1 (COX-1) to guide students through multiple levels of protein structure analysis. The…

Integration of visual and motion cues for simulator requirements and ride quality investigation

NASA Technical Reports Server (NTRS)

Young, L. R.

1976-01-01

Practical tools which can extend the state of the art of moving base flight simulation for research and training are developed. Main approaches to this research effort include: (1) application of the vestibular model for perception of orientation based on motion cues: optimum simulator motion controls; and (2) visual cues in landing.

The pyPHaz software, an interactive tool to analyze and visualize results from probabilistic hazard assessments

NASA Astrophysics Data System (ADS)

Tonini, Roberto; Selva, Jacopo; Costa, Antonio; Sandri, Laura

2014-05-01

Probabilistic Hazard Assessment (PHA) is becoming an essential tool for risk mitigation policies, since it allows to quantify the hazard due to hazardous phenomena and, differently from the deterministic approach, it accounts for both aleatory and epistemic uncertainties. On the other hand, one of the main disadvantages of PHA methods is that their results are not easy to understand and interpret by people who are not specialist in probabilistic tools. For scientists, this leads to the issue of providing tools that can be easily used and understood by decision makers (i.e., risk managers or local authorities). The work here presented fits into the problem of simplifying the transfer between scientific knowledge and land protection policies, by providing an interface between scientists, who produce PHA's results, and decision makers, who use PHA's results for risk analyses. In this framework we present pyPHaz, an open tool developed and designed to visualize and analyze PHA results due to one or more phenomena affecting a specific area of interest. The software implementation has been fully developed with the free and open-source Python programming language and some featured Python-based libraries and modules. The pyPHaz tool allows to visualize the Hazard Curves (HC) calculated in a selected target area together with different levels of uncertainty (mean and percentiles) on maps that can be interactively created and modified by the user, thanks to a dedicated Graphical User Interface (GUI). Moreover, the tool can be used to compare the results of different PHA models and to merge them, by creating ensemble models. The pyPHaz software has been designed with the features of storing and accessing all the data through a MySQL database and of being able to read as input the XML-based standard file formats defined in the frame of GEM (Global Earthquake Model). This format model is easy to extend also to any other kind of hazard, as it will be shown in the applications here used as examples of the pyPHaz potentialities, that are focused on a Probabilistic Volcanic Hazard Assessment (PVHA) for tephra dispersal and fallout applied to the municipality of Naples.

MARs Tools for Interactive ANalysis (MARTIAN): Google Maps Tools for Visual Exploration of Geophysical Modeling on Mars

NASA Astrophysics Data System (ADS)

Dimitrova, L. L.; Haines, M.; Holt, W. E.; Schultz, R. A.; Richard, G.; Haines, A. J.

2006-12-01

Interactive maps of surface-breaking faults and stress models on Mars provide important tools to engage undergraduate students, educators, and scientists with current geological and geophysical research. We have developed a map based on the Google Maps API -- an Internet based tool combining DHTML and AJAX, -- which allows very large maps to be viewed over the World Wide Web. Typically, small portions of the maps are downloaded as needed, rather than the entire image at once. This set-up enables relatively fast access for users with low bandwidth. Furthermore, Google Maps provides an extensible interactive interface making it ideal for visualizing multiple data sets at the user's choice. The Google Maps API works primarily with data referenced to latitudes and longitudes, which is then mapped in Mercator projection only. We have developed utilities for general cylindrical coordinate systems by converting these coordinates into equivalent Mercator projection before including them on the map. The MARTIAN project is available at http://rock.geo.sunysb.edu/~holt/Mars/MARTIAN/. We begin with an introduction to the Martian surface using a topography model. Faults from several datasets are classified by type (extension vs. compression) and by time epoch. Deviatoric stresses due to gravitational potential energy differences, calculated from the topography and crustal thickness, can be overlain. Several quantitative measures for the fit of the stress field to the faults are also included. We provide introductory text and exercises spanning a range of topics: how are faults identified, what stress is and how it relates to faults, what gravitational potential energy is and how variations in it produce stress, how the models are created, and how these models can be evaluated and interpreted. The MARTIAN tool is used at Stony Brook University in GEO 310: Introduction to Geophysics, a class geared towards junior and senior geosciences majors. Although this project is in its early stages, high school and college teachers, as well as researchers have expressed interest in using and extending these tools for visualizing and interacting with data on Earth and other planetary bodies.

Interactive 3D visualization tools for stereotactic atlas-based functional neurosurgery

NASA Astrophysics Data System (ADS)

St. Jean, Philippe; Kasrai, Reza; Clonda, Diego; Sadikot, Abbas F.; Evans, Alan C.; Peters, Terence M.

1998-06-01

Many of the critical basal ganglia structures are not distinguishable on anatomical magnetic resonance imaging (MRI) scans, even though they differ in functionality. In order to provide the neurosurgeon with this missing information, a deformable volumetric atlas of the basal ganglia has been created from the Shaltenbrand and Wahren atlas of cryogenic slices. The volumetric atlas can be non-linearly deformed to an individual patient's MRI. To facilitate the clinical use of the atlas, a visualization platform has been developed for pre- and intra-operative use which permits manipulation of the merged atlas and MRI data sets in two- and three-dimensional views. The platform includes graphical tools which allow the visualization of projections of the leukotome and other surgical tools with respect to the atlas data, as well as pre- registered images from any other imaging modality. In addition, a graphical interface has been designed to create custom virtual lesions using computer models of neurosurgical tools for intra-operative planning. To date 17 clinical cases have been successfully performed using the described system.

Information Extraction for System-Software Safety Analysis: Calendar Year 2008 Year-End Report

NASA Technical Reports Server (NTRS)

Malin, Jane T.

2009-01-01

This annual report describes work to integrate a set of tools to support early model-based analysis of failures and hazards due to system-software interactions. The tools perform and assist analysts in the following tasks: 1) extract model parts from text for architecture and safety/hazard models; 2) combine the parts with library information to develop the models for visualization and analysis; 3) perform graph analysis and simulation to identify and evaluate possible paths from hazard sources to vulnerable entities and functions, in nominal and anomalous system-software configurations and scenarios; and 4) identify resulting candidate scenarios for software integration testing. There has been significant technical progress in model extraction from Orion program text sources, architecture model derivation (components and connections) and documentation of extraction sources. Models have been derived from Internal Interface Requirements Documents (IIRDs) and FMEA documents. Linguistic text processing is used to extract model parts and relationships, and the Aerospace Ontology also aids automated model development from the extracted information. Visualizations of these models assist analysts in requirements overview and in checking consistency and completeness.

Survey of visualization and analysis tools

NASA Technical Reports Server (NTRS)

Meyer, P. J.

1994-01-01

A large number of commercially available visualization and analysis tools are available to the researcher. Some of the strengths and limitations of some of these tools, from the viewpoint of the earth sciences discipline, are discussed. Visualization and analysis tools fall into one of two categories: those that are designed to a specific purpose and are non-extensive and those that are generic visual programming tools that are extensible. Most of the extensible packages examined incorporate a data flow paradigm.

The geospatial modeling interface (GMI) framework for deploying and assessing environmental models

USDA-ARS?s Scientific Manuscript database

Geographical information systems (GIS) software packages have been used for close to three decades as analytical tools in environmental management for geospatial data assembly, processing, storage, and visualization of input data and model output. However, with increasing availability and use of ful...

An open-source Java-based Toolbox for environmental model evaluation: The MOUSE Software Application

USDA-ARS?s Scientific Manuscript database

A consequence of environmental model complexity is that the task of understanding how environmental models work and identifying their sensitivities/uncertainties, etc. becomes progressively more difficult. Comprehensive numerical and visual evaluation tools have been developed such as the Monte Carl...

Visible Earthquakes: a web-based tool for visualizing and modeling InSAR earthquake data

NASA Astrophysics Data System (ADS)

Funning, G. J.; Cockett, R.

2012-12-01

InSAR (Interferometric Synthetic Aperture Radar) is a technique for measuring the deformation of the ground using satellite radar data. One of the principal applications of this method is in the study of earthquakes; in the past 20 years over 70 earthquakes have been studied in this way, and forthcoming satellite missions promise to enable the routine and timely study of events in the future. Despite the utility of the technique and its widespread adoption by the research community, InSAR does not feature in the teaching curricula of most university geoscience departments. This is, we believe, due to a lack of accessibility to software and data. Existing tools for the visualization and modeling of interferograms are often research-oriented, command line-based and/or prohibitively expensive. Here we present a new web-based interactive tool for comparing real InSAR data with simple elastic models. The overall design of this tool was focused on ease of access and use. This tool should allow interested nonspecialists to gain a feel for the use of such data and greatly facilitate integration of InSAR into upper division geoscience courses, giving students practice in comparing actual data to modeled results. The tool, provisionally named 'Visible Earthquakes', uses web-based technologies to instantly render the displacement field that would be observable using InSAR for a given fault location, geometry, orientation, and slip. The user can adjust these 'source parameters' using a simple, clickable interface, and see how these affect the resulting model interferogram. By visually matching the model interferogram to a real earthquake interferogram (processed separately and included in the web tool) a user can produce their own estimates of the earthquake's source parameters. Once satisfied with the fit of their models, users can submit their results and see how they compare with the distribution of all other contributed earthquake models, as well as the mean and median models. We envisage that the ensemble of contributed models will be useful both as a research resource and in the classroom. Locations of earthquakes derived from InSAR data have already been demonstrated to differ significantly from those obtained from global seismic networks (Weston et al., 2011), and the locations obtained by our users will enable us to identify systematic mislocations that are likely due to errors in Earth velocity models used to locate earthquakes. If the tool is incorporated into geophysics, tectonics and/or structural geology classes, in addition to familiarizing students with InSAR and elastic deformation modeling, the spread of different results for each individual earthquake will allow the teaching of concepts such as model uncertainty and non-uniqueness when modeling real scientific data. Additionally, the process students go through to optimize their estimates of fault parameters can easily be tied into teaching about the concepts of forward and inverse problems, which are common in geophysics.

Automated Geospatial Watershed Assessment (AGWA) Tool for hydrologic modeling and watershed assessment

EPA Pesticide Factsheets

Using basic, easily attainable GIS data, AGWA provides a simple, direct, and repeatable methodology for hydrologic model setup, execution, and visualization. AGWA experiences activity from over 170 countries. It l has been downloaded over 11,000 times.

BMDExpress Data Viewer: A Visualization Tool to Analyze BMDExpress Datasets

EPA Science Inventory

Regulatory agencies increasingly apply benchmark dose (BMD) modeling to determine points of departure in human risk assessments. BMDExpress applies BMD modeling to transcriptomics datasets and groups genes to biological processes and pathways for rapid assessment of doses at whic...

Alexander Meets Michotte: A Simulation Tool Based on Pattern Programming and Phenomenology

ERIC Educational Resources Information Center

Basawapatna, Ashok

2016-01-01

Simulation and modeling activities, a key point of computational thinking, are currently not being integrated into the science classroom. This paper describes a new visual programming tool entitled the Simulation Creation Toolkit. The Simulation Creation Toolkit is a high level pattern-based phenomenological approach to bringing rapid simulation…

Comprehensive Modeling and Visualization of Cardiac Anatomy and Physiology from CT Imaging and Computer Simulations

PubMed Central

Sun, Peng; Zhou, Haoyin; Ha, Seongmin; Hartaigh, Bríain ó; Truong, Quynh A.; Min, James K.

2016-01-01

In clinical cardiology, both anatomy and physiology are needed to diagnose cardiac pathologies. CT imaging and computer simulations provide valuable and complementary data for this purpose. However, it remains challenging to gain useful information from the large amount of high-dimensional diverse data. The current tools are not adequately integrated to visualize anatomic and physiologic data from a complete yet focused perspective. We introduce a new computer-aided diagnosis framework, which allows for comprehensive modeling and visualization of cardiac anatomy and physiology from CT imaging data and computer simulations, with a primary focus on ischemic heart disease. The following visual information is presented: (1) Anatomy from CT imaging: geometric modeling and visualization of cardiac anatomy, including four heart chambers, left and right ventricular outflow tracts, and coronary arteries; (2) Function from CT imaging: motion modeling, strain calculation, and visualization of four heart chambers; (3) Physiology from CT imaging: quantification and visualization of myocardial perfusion and contextual integration with coronary artery anatomy; (4) Physiology from computer simulation: computation and visualization of hemodynamics (e.g., coronary blood velocity, pressure, shear stress, and fluid forces on the vessel wall). Substantially, feedback from cardiologists have confirmed the practical utility of integrating these features for the purpose of computer-aided diagnosis of ischemic heart disease. PMID:26863663

ARC integration into the NEAMS Workbench

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stauff, N.; Gaughan, N.; Kim, T.

2017-01-01

One of the objectives of the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Integration Product Line (IPL) is to facilitate the deployment of the high-fidelity codes developed within the program. The Workbench initiative was launched in FY-2017 by the IPL to facilitate the transition from conventional tools to high fidelity tools. The Workbench provides a common user interface for model creation, real-time validation, execution, output processing, and visualization for integrated codes.

Business intelligence tools for radiology: creating a prototype model using open-source tools.

PubMed

Prevedello, Luciano M; Andriole, Katherine P; Hanson, Richard; Kelly, Pauline; Khorasani, Ramin

2010-04-01

Digital radiology departments could benefit from the ability to integrate and visualize data (e.g. information reflecting complex workflow states) from all of their imaging and information management systems in one composite presentation view. Leveraging data warehousing tools developed in the business world may be one way to achieve this capability. In total, the concept of managing the information available in this data repository is known as Business Intelligence or BI. This paper describes the concepts used in Business Intelligence, their importance to modern Radiology, and the steps used in the creation of a prototype model of a data warehouse for BI using open-source tools.

Enabling Rapid Naval Architecture Design Space Exploration

NASA Technical Reports Server (NTRS)

Mueller, Michael A.; Dufresne, Stephane; Balestrini-Robinson, Santiago; Mavris, Dimitri

2011-01-01

Well accepted conceptual ship design tools can be used to explore a design space, but more precise results can be found using detailed models in full-feature computer aided design programs. However, defining a detailed model can be a time intensive task and hence there is an incentive for time sensitive projects to use conceptual design tools to explore the design space. In this project, the combination of advanced aerospace systems design methods and an accepted conceptual design tool facilitates the creation of a tool that enables the user to not only visualize ship geometry but also determine design feasibility and estimate the performance of a design.

GIS-MODFLOW: Ein kleines OpenSource-Werkzeug zur Anbindung von GIS-Daten an MODFLOW

NASA Astrophysics Data System (ADS)

Gossel, Wolfgang

2013-06-01

The numerical model MODFLOW (Harbaugh 2005) is an efficient and up-to-date tool for groundwater flow modelling. On the other hand, Geo-Information-Systems (GIS) provide useful tools for data preparation and visualization that can also be incorporated in numerical groundwater modelling. An interface between both would therefore be useful for many hydrogeological investigations. To date, several integrated stand-alone tools have been developed that rely on MODFLOW, MODPATH and transport modelling tools. Simultaneously, several open source-GIS codes were developed to improve functionality and ease of use. These GIS tools can be used as pre- and post-processors of the numerical model MODFLOW via a suitable interface. Here we present GIS-MODFLOW as an open-source tool that provides a new universal interface by using the ESRI ASCII GRID data format that can be converted into MODFLOW input data. This tool can also treat MODFLOW results. Such a combination of MODFLOW and open-source GIS opens new possibilities to render groundwater flow modelling, and simulation results, available to larger circles of hydrogeologists.

An Interdisciplinary Guided Inquiry on Estuarine Transport Using a Computer Model in High School Classrooms

ERIC Educational Resources Information Center

Chan, Kit Yu Karen; Yang, Sylvia; Maliska, Max E.; Grunbaum, Daniel

2012-01-01

The National Science Education Standards have highlighted the importance of active learning and reflection for contemporary scientific methods in K-12 classrooms, including the use of models. Computer modeling and visualization are tools that researchers employ in their scientific inquiry process, and often computer models are used in…

An Excel[TM] Model of a Radioactive Series

ERIC Educational Resources Information Center

Andrews, D. G. H.

2009-01-01

A computer model of the decay of a radioactive series, written in Visual Basic in Excel[TM], is presented. The model is based on the random selection of cells in an array. The results compare well with the theoretical equations. The model is a useful tool in teaching this aspect of radioactivity. (Contains 4 figures.)

Map Learning with a 3D Printed Interactive Small-Scale Model: Improvement of Space and Text Memorization in Visually Impaired Students

PubMed Central

Giraud, Stéphanie; Brock, Anke M.; Macé, Marc J.-M.; Jouffrais, Christophe

2017-01-01

Special education teachers for visually impaired students rely on tools such as raised-line maps (RLMs) to teach spatial knowledge. These tools do not fully and adequately meet the needs of the teachers because they are long to produce, expensive, and not versatile enough to provide rapid updating of the content. For instance, the same RLM can barely be used during different lessons. In addition, those maps do not provide any interactivity, which reduces students’ autonomy. With the emergence of 3D printing and low-cost microcontrollers, it is now easy to design affordable interactive small-scale models (SSMs) which are adapted to the needs of special education teachers. However, no study has previously been conducted to evaluate non-visual learning using interactive SSMs. In collaboration with a specialized teacher, we designed a SSM and a RLM representing the evolution of the geography and history of a fictitious kingdom. The two conditions were compared in a study with 24 visually impaired students regarding the memorization of the spatial layout and historical contents. The study showed that the interactive SSM improved both space and text memorization as compared to the RLM with braille legend. In conclusion, we argue that affordable home-made interactive small scale models can improve learning for visually impaired students. Interestingly, they are adaptable to any teaching situation including students with specific needs. PMID:28649209

Evaluating an immersive virtual environment prototyping and simulation system

NASA Astrophysics Data System (ADS)

Nemire, Kenneth

1997-05-01

An immersive virtual environment (IVE) modeling and simulation tool is being developed for designing advanced weapon and training systems. One unique feature of the tool is that the design, and not just visualization of the design is accomplished with the IVE tool. Acceptance of IVE tools requires comparisons with current commercial applications. In this pilot study, expert users of a popular desktop 3D graphics application performed identical modeling and simulation tasks using both the desktop and IVE applications. The IVE tool consisted of a head-mounted display, 3D spatialized sound, spatial trackers on head and hands, instrumented gloves, and a simulated speech recognition system. The results are preliminary because performance from only four users has been examined. When using the IVE system, users completed the tasks to criteria in less time than when using the desktop application. Subjective ratings of the visual displays in each system were similar. Ratings for the desktop controls were higher than for the IVE controls. Ratings of immersion and user enjoyment were higher for the IVE than for the desktop application. These results are particular remarkable because participants had used the desktop application regularly for three to five years and the prototype IVE tool for only three to six hours.

An Instructional Method for the AutoCAD Modeling Environment.

ERIC Educational Resources Information Center

Mohler, James L.

1997-01-01

Presents a command organizer for AutoCAD to aid new uses in operating within the 3-D modeling environment. Addresses analyzing the problem, visualization skills, nonlinear tools, a static view of a dynamic model, the AutoCAD organizer, environment attributes, and control of the environment. Contains 11 references. (JRH)

A robust and flexible Geospatial Modeling Interface (GMI) for deploying and evaluating natural resource models

USDA-ARS?s Scientific Manuscript database

Geographical information systems (GIS) software packages have been used for nearly three decades as analytical tools in natural resource management for geospatial data assembly, processing, storage, and visualization of input data and model output. However, with increasing availability and use of fu...

ACORNS: A Tool for the Visualisation and Modelling of Atypical Development

ERIC Educational Resources Information Center

Moore, D. G.; George, R.

2011-01-01

Across many academic disciplines visualisation and notation systems are used for modelling data and developing theory, but in child development visual models are not widely used; yet researchers and students of developmental difficulties may benefit from a visualisation and notation system which can clearly map developmental outcomes and…

Visual Basic, Excel-based fish population modeling tool - The pallid sturgeon example

USGS Publications Warehouse

Moran, Edward H.; Wildhaber, Mark L.; Green, Nicholas S.; Albers, Janice L.

2016-02-10

The model presented in this report is a spreadsheet-based model using Visual Basic for Applications within Microsoft Excel (http://dx.doi.org/10.5066/F7057D0Z) prepared in cooperation with the U.S. Army Corps of Engineers and U.S. Fish and Wildlife Service. It uses the same model structure and, initially, parameters as used by Wildhaber and others (2015) for pallid sturgeon. The difference between the model structure used for this report and that used by Wildhaber and others (2015) is that variance is not partitioned. For the model of this report, all variance is applied at the iteration and time-step levels of the model. Wildhaber and others (2015) partition variance into parameter variance (uncertainty about the value of a parameter itself) applied at the iteration level and temporal variance (uncertainty caused by random environmental fluctuations with time) applied at the time-step level. They included implicit individual variance (uncertainty caused by differences between individuals) within the time-step level.The interface developed for the model of this report is designed to allow the user the flexibility to change population model structure and parameter values and uncertainty separately for every component of the model. This flexibility makes the modeling tool potentially applicable to any fish species; however, the flexibility inherent in this modeling tool makes it possible for the user to obtain spurious outputs. The value and reliability of the model outputs are only as good as the model inputs. Using this modeling tool with improper or inaccurate parameter values, or for species for which the structure of the model is inappropriate, could lead to untenable management decisions. By facilitating fish population modeling, this modeling tool allows the user to evaluate a range of management options and implications. The goal of this modeling tool is to be a user-friendly modeling tool for developing fish population models useful to natural resource managers to inform their decision-making processes; however, as with all population models, caution is needed, and a full understanding of the limitations of a model and the veracity of user-supplied parameters should always be considered when using such model output in the management of any species.

Combined Hydrologic (AGWA-KINEROS2) and Hydraulic (HEC2) Modeling for Post-Fire Runoff and Inundation Risk Assessment through a Set of Python Tools

NASA Astrophysics Data System (ADS)

Barlow, J. E.; Goodrich, D. C.; Guertin, D. P.; Burns, I. S.

2016-12-01

Wildfires in the Western United States can alter landscapes by removing vegetation and changing soil properties. These altered landscapes produce more runoff than pre-fire landscapes which can lead to post-fire flooding that can damage infrastructure and impair natural resources. Resources, structures, historical artifacts and others that could be impacted by increased runoff are considered values at risk. .The Automated Geospatial Watershed Assessment tool (AGWA) allows users to quickly set up and execute the Kinematic Runoff and Erosion model (KINEROS2 or K2) in the ESRI ArcMap environment. The AGWA-K2 workflow leverages the visualization capabilities of GIS to facilitate evaluation of rapid watershed assessments for post-fire planning efforts. High relative change in peak discharge, as simulated by K2, provides a visual and numeric indicator to investigate those channels in the watershed that should be evaluated for more detailed analysis, especially if values at risk are within or near that channel. Modeling inundation extent along a channel would provide more specific guidance about risk along a channel. HEC-2 and HEC-RAS can be used for hydraulic modeling efforts at the reach and river system scale. These models have been used to address flood boundaries and, accordingly, flood risk. However, data collection and organization for hydraulic models can be time consuming and therefore a combined hydrologic-hydraulic modeling approach is not often employed for rapid assessments. A simplified approach could streamline this process and provide managers with a simple workflow and tool to perform a quick risk assessment for a single reach. By focusing on a single reach highlighted by large relative change in peak discharge, data collection efforts can be minimized and the hydraulic computations can be performed to supplement risk analysis. The incorporation of hydraulic analysis through a suite of Python tools (as outlined by HEC-2) with AGWA-K2 will allow more rapid applications of combined hydrologic-hydraulic modeling. This combined modeling approach is built in the ESRI ArcGIS application to enable rapid model preparation, execution and result visualization for risk assessment in post-fire environments.

'spup' - an R package for uncertainty propagation in spatial environmental modelling

NASA Astrophysics Data System (ADS)

Sawicka, Kasia; Heuvelink, Gerard

2016-04-01

Computer models have become a crucial tool in engineering and environmental sciences for simulating the behaviour of complex static and dynamic systems. However, while many models are deterministic, the uncertainty in their predictions needs to be estimated before they are used for decision support. Currently, advances in uncertainty propagation and assessment have been paralleled by a growing number of software tools for uncertainty analysis, but none has gained recognition for a universal applicability, including case studies with spatial models and spatial model inputs. Due to the growing popularity and applicability of the open source R programming language we undertook a project to develop an R package that facilitates uncertainty propagation analysis in spatial environmental modelling. In particular, the 'spup' package provides functions for examining the uncertainty propagation starting from input data and model parameters, via the environmental model onto model predictions. The functions include uncertainty model specification, stochastic simulation and propagation of uncertainty using Monte Carlo (MC) techniques, as well as several uncertainty visualization functions. Uncertain environmental variables are represented in the package as objects whose attribute values may be uncertain and described by probability distributions. Both numerical and categorical data types are handled. Spatial auto-correlation within an attribute and cross-correlation between attributes is also accommodated for. For uncertainty propagation the package has implemented the MC approach with efficient sampling algorithms, i.e. stratified random sampling and Latin hypercube sampling. The design includes facilitation of parallel computing to speed up MC computation. The MC realizations may be used as an input to the environmental models called from R, or externally. Selected static and interactive visualization methods that are understandable by non-experts with limited background in statistics can be used to summarize and visualize uncertainty about the measured input, model parameters and output of the uncertainty propagation. We demonstrate that the 'spup' package is an effective and easy tool to apply and can be used in multi-disciplinary research and model-based decision support.

'spup' - an R package for uncertainty propagation analysis in spatial environmental modelling

NASA Astrophysics Data System (ADS)

Sawicka, Kasia; Heuvelink, Gerard

2017-04-01

Computer models have become a crucial tool in engineering and environmental sciences for simulating the behaviour of complex static and dynamic systems. However, while many models are deterministic, the uncertainty in their predictions needs to be estimated before they are used for decision support. Currently, advances in uncertainty propagation and assessment have been paralleled by a growing number of software tools for uncertainty analysis, but none has gained recognition for a universal applicability and being able to deal with case studies with spatial models and spatial model inputs. Due to the growing popularity and applicability of the open source R programming language we undertook a project to develop an R package that facilitates uncertainty propagation analysis in spatial environmental modelling. In particular, the 'spup' package provides functions for examining the uncertainty propagation starting from input data and model parameters, via the environmental model onto model predictions. The functions include uncertainty model specification, stochastic simulation and propagation of uncertainty using Monte Carlo (MC) techniques, as well as several uncertainty visualization functions. Uncertain environmental variables are represented in the package as objects whose attribute values may be uncertain and described by probability distributions. Both numerical and categorical data types are handled. Spatial auto-correlation within an attribute and cross-correlation between attributes is also accommodated for. For uncertainty propagation the package has implemented the MC approach with efficient sampling algorithms, i.e. stratified random sampling and Latin hypercube sampling. The design includes facilitation of parallel computing to speed up MC computation. The MC realizations may be used as an input to the environmental models called from R, or externally. Selected visualization methods that are understandable by non-experts with limited background in statistics can be used to summarize and visualize uncertainty about the measured input, model parameters and output of the uncertainty propagation. We demonstrate that the 'spup' package is an effective and easy tool to apply and can be used in multi-disciplinary research and model-based decision support.

Web3DMol: interactive protein structure visualization based on WebGL.

PubMed

Shi, Maoxiang; Gao, Juntao; Zhang, Michael Q

2017-07-03

A growing number of web-based databases and tools for protein research are being developed. There is now a widespread need for visualization tools to present the three-dimensional (3D) structure of proteins in web browsers. Here, we introduce our 3D modeling program-Web3DMol-a web application focusing on protein structure visualization in modern web browsers. Users submit a PDB identification code or select a PDB archive from their local disk, and Web3DMol will display and allow interactive manipulation of the 3D structure. Featured functions, such as sequence plot, fragment segmentation, measure tool and meta-information display, are offered for users to gain a better understanding of protein structure. Easy-to-use APIs are available for developers to reuse and extend Web3DMol. Web3DMol can be freely accessed at http://web3dmol.duapp.com/, and the source code is distributed under the MIT license. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Data visualization and analysis tools for the MAVEN mission

NASA Astrophysics Data System (ADS)

Harter, B.; De Wolfe, A. W.; Putnam, B.; Brain, D.; Chaffin, M.

2016-12-01

The Mars Atmospheric and Volatile Evolution (MAVEN) mission has been collecting data at Mars since September 2014. We have developed new software tools for exploring and analyzing the science data. Our open-source Python toolkit for working with data from MAVEN and other missions is based on the widely-used "tplot" IDL toolkit. We have replicated all of the basic tplot functionality in Python, and use the bokeh and matplotlib libraries to generate interactive line plots and spectrograms, providing additional functionality beyond the capabilities of IDL graphics. These Python tools are generalized to work with missions beyond MAVEN, and our software is available on Github. We have also been exploring 3D graphics as a way to better visualize the MAVEN science data and models. We have constructed a 3D visualization of MAVEN's orbit using the CesiumJS library, which not only allows viewing of MAVEN's orientation and position, but also allows the display of selected science data sets and their variation over time.

Using Participatory System Dynamics Modeling to Examine the Local HIV Test and Treatment Care Continuum in Order to Reduce Community Viral Load.

PubMed

Weeks, Margaret R; Li, Jianghong; Lounsbury, David; Green, Helena Danielle; Abbott, Maryann; Berman, Marcie; Rohena, Lucy; Gonzalez, Rosely; Lang, Shawn; Mosher, Heather

2017-12-01

Achieving community-level goals to eliminate the HIV epidemic requires coordinated efforts through community consortia with a common purpose to examine and critique their own HIV testing and treatment (T&T) care system and build effective tools to guide their efforts to improve it. Participatory system dynamics (SD) modeling offers conceptual, methodological, and analytical tools to engage diverse stakeholders in systems conceptualization and visual mapping of dynamics that undermine community-level health outcomes and identify those that can be leveraged for systems improvement. We recruited and engaged a 25-member multi-stakeholder Task Force, whose members provide or utilize HIV-related services, to participate in SD modeling to examine and address problems of their local HIV T&T service system. Findings from the iterative model building sessions indicated Task Force members' increasingly complex understanding of the local HIV care system and demonstrated their improved capacity to visualize and critique multiple models of the HIV T&T service system and identify areas of potential leverage. Findings also showed members' enhanced communication and consensus in seeking deeper systems understanding and options for solutions. We discuss implications of using these visual SD models for subsequent simulation modeling of the T&T system and for other community applications to improve system effectiveness. © Society for Community Research and Action 2017.

Examining the Conceptual Understandings of Geoscience Concepts of Students with Visual Impairments: Implications of 3-D Printing

ERIC Educational Resources Information Center

Koehler, Karen E.

2017-01-01

The purpose of this qualitative study was to explore the use of 3-D printed models as an instructional tool in a middle school science classroom for students with visual impairments and compare their use to traditional tactile graphics for aiding conceptual understanding of geoscience concepts. Specifically, this study examined if the students'…

Integration of Audio Visual Multimedia for Special Education Pre-Service Teachers' Self Reflections in Developing Teaching Competencies

ERIC Educational Resources Information Center

Sediyani, Tri; Yufiarti; Hadi, Eko

2017-01-01

This study aims to develop a model of learning by integrating multimedia and audio-visual self-reflective learners. This multimedia was developed as a tool for prospective teachers as learners in the education of children with special needs to reflect on their teaching competencies before entering the world of education. Research methods to…

Integrated Data Visualization and Virtual Reality Tool

NASA Technical Reports Server (NTRS)

Dryer, David A.

1998-01-01

The Integrated Data Visualization and Virtual Reality Tool (IDVVRT) Phase II effort was for the design and development of an innovative Data Visualization Environment Tool (DVET) for NASA engineers and scientists, enabling them to visualize complex multidimensional and multivariate data in a virtual environment. The objectives of the project were to: (1) demonstrate the transfer and manipulation of standard engineering data in a virtual world; (2) demonstrate the effects of design and changes using finite element analysis tools; and (3) determine the training and engineering design and analysis effectiveness of the visualization system.

The Development of a Visual-Perceptual Chemistry Specific (VPCS) Assessment Tool

ERIC Educational Resources Information Center

Oliver-Hoyo, Maria; Sloan, Caroline

2014-01-01

The development of the Visual-Perceptual Chemistry Specific (VPCS) assessment tool is based on items that align to eight visual-perceptual skills considered as needed by chemistry students. This tool includes a comprehensive range of visual operations and presents items within a chemistry context without requiring content knowledge to solve…

A Global System for Transportation Simulation and Visualization in Emergency Evacuation Scenarios

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Wei; Liu, Cheng; Thomas, Neil

2015-01-01

Simulation-based studies are frequently used for evacuation planning and decision making processes. Given the transportation systems complexity and data availability, most evacuation simulation models focus on certain geographic areas. With routine improvement of OpenStreetMap road networks and LandScanTM global population distribution data, we present WWEE, a uniform system for world-wide emergency evacuation simulations. WWEE uses unified data structure for simulation inputs. It also integrates a super-node trip distribution model as the default simulation parameter to improve the system computational performance. Two levels of visualization tools are implemented for evacuation performance analysis, including link-based macroscopic visualization and vehicle-based microscopic visualization. Formore » left-hand and right-hand traffic patterns in different countries, the authors propose a mirror technique to experiment with both scenarios without significantly changing traffic simulation models. Ten cities in US, Europe, Middle East, and Asia are modeled for demonstration. With default traffic simulation models for fast and easy-to-use evacuation estimation and visualization, WWEE also retains the capability of interactive operation for users to adopt customized traffic simulation models. For the first time, WWEE provides a unified platform for global evacuation researchers to estimate and visualize their strategies performance of transportation systems under evacuation scenarios.« less

Wyoming greater sage-grouse habitat prioritization: A collection of multi-scale seasonal models and geographic information systems land management tools

USGS Publications Warehouse

O'Donnell, Michael S.; Aldridge, Cameron L.; Doherty, Kevin E.; Fedy, Bradley C.

2015-01-01

We deliver all products described herein as online geographic information system data for visualization and downloading. We outline the data properties for each model and their data inputs, describe the process of selecting appropriate data products for multifarious applications, describe all data products and software, provide newly derived model composites, and discuss how land managers may use the models to inform future sage-grouse studies and potentially refine conservation efforts. The models, software tools, and associated opportunities for novel applications of these products should provide a suite of additional, but not exclusive, tools for assessing Wyoming Greater Sage-grouse habitats, which land managers, conservationists, and scientists can apply to myriad applications.

Integrated Modeling Environment

NASA Technical Reports Server (NTRS)

Mosier, Gary; Stone, Paul; Holtery, Christopher

2006-01-01

The Integrated Modeling Environment (IME) is a software system that establishes a centralized Web-based interface for integrating people (who may be geographically dispersed), processes, and data involved in a common engineering project. The IME includes software tools for life-cycle management, configuration management, visualization, and collaboration.

Benefits of using a Social-Ecological Systems Approach to Conceptualize and Model Wetlands Restoration

EPA Science Inventory

Using a social-ecological systems (SES) perspective to examine wetland restoration helps decision-makers recognize interdependencies and relations between ecological and social components of coupled systems. Conceptual models are an invaluable tool to capture, visualize, and orga...

Web-based decision support and visualization tools for water quality management in the Chesapeake Bay watershed

USGS Publications Warehouse

Mullinix, C.; Hearn, P.; Zhang, H.; Aguinaldo, J.

2009-01-01

Federal, State, and local water quality managers charged with restoring the Chesapeake Bay ecosystem require tools to maximize the impact of their limited resources. To address this need, the U.S. Geological Survey (USGS) and the Environmental Protection Agency's Chesapeake Bay Program (CBP) are developing a suite of Web-based tools called the Chesapeake Online Assessment Support Toolkit (COAST). The goal of COAST is to help CBP partners identify geographic areas where restoration activities would have the greatest effect, select the appropriate management strategies, and improve coordination and prioritization among partners. As part of the COAST suite of tools focused on environmental restoration, a water quality management visualization component called the Nutrient Yields Mapper (NYM) tool is being developed by USGS. The NYM tool is a web application that uses watershed yield estimates from USGS SPAtially Referenced Regressions On Watershed (SPARROW) attributes model (Schwarz et al., 2006) [6] to allow water quality managers to identify important sources of nitrogen and phosphorous within the Chesapeake Bay watershed. The NYM tool utilizes new open source technologies that have become popular in geospatial web development, including components such as OpenLayers and GeoServer. This paper presents examples of water quality data analysis based on nutrient type, source, yield, and area of interest using the NYM tool for the Chesapeake Bay watershed. In addition, we describe examples of map-based techniques for identifying high and low nutrient yield areas; web map engines; and data visualization and data management techniques.

Visual Predictive Check in Models with Time-Varying Input Function.

PubMed

Largajolli, Anna; Bertoldo, Alessandra; Campioni, Marco; Cobelli, Claudio

2015-11-01

The nonlinear mixed effects models are commonly used modeling techniques in the pharmaceutical research as they enable the characterization of the individual profiles together with the population to which the individuals belong. To ensure a correct use of them is fundamental to provide powerful diagnostic tools that are able to evaluate the predictive performance of the models. The visual predictive check (VPC) is a commonly used tool that helps the user to check by visual inspection if the model is able to reproduce the variability and the main trend of the observed data. However, the simulation from the model is not always trivial, for example, when using models with time-varying input function (IF). In this class of models, there is a potential mismatch between each set of simulated parameters and the associated individual IF which can cause an incorrect profile simulation. We introduce a refinement of the VPC by taking in consideration a correlation term (the Mahalanobis or normalized Euclidean distance) that helps the association of the correct IF with the individual set of simulated parameters. We investigate and compare its performance with the standard VPC in models of the glucose and insulin system applied on real and simulated data and in a simulated pharmacokinetic/pharmacodynamic (PK/PD) example. The newly proposed VPC performance appears to be better with respect to the standard VPC especially for the models with big variability in the IF where the probability of simulating incorrect profiles is higher.

Drawing-to-Learn: A Framework for Using Drawings to Promote Model-Based Reasoning in Biology

PubMed Central

Quillin, Kim; Thomas, Stephen

2015-01-01

The drawing of visual representations is important for learners and scientists alike, such as the drawing of models to enable visual model-based reasoning. Yet few biology instructors recognize drawing as a teachable science process skill, as reflected by its absence in the Vision and Change report’s Modeling and Simulation core competency. Further, the diffuse research on drawing can be difficult to access, synthesize, and apply to classroom practice. We have created a framework of drawing-to-learn that defines drawing, categorizes the reasons for using drawing in the biology classroom, and outlines a number of interventions that can help instructors create an environment conducive to student drawing in general and visual model-based reasoning in particular. The suggested interventions are organized to address elements of affect, visual literacy, and visual model-based reasoning, with specific examples cited for each. Further, a Blooming tool for drawing exercises is provided, as are suggestions to help instructors address possible barriers to implementing and assessing drawing-to-learn in the classroom. Overall, the goal of the framework is to increase the visibility of drawing as a skill in biology and to promote the research and implementation of best practices. PMID:25713094

Integration of Dynamic Models in Range Operations

NASA Technical Reports Server (NTRS)

Bardina, Jorge; Thirumalainambi, Rajkumar

2004-01-01

This work addresses the various model interactions in real-time to make an efficient internet based decision making tool for Shuttle launch. The decision making tool depends on the launch commit criteria coupled with physical models. Dynamic interaction between a wide variety of simulation applications and techniques, embedded algorithms, and data visualizations are needed to exploit the full potential of modeling and simulation. This paper also discusses in depth details of web based 3-D graphics and applications to range safety. The advantages of this dynamic model integration are secure accessibility and distribution of real time information to other NASA centers.

A web-based screening tool for near-port air quality assessments

PubMed Central

Isakov, Vlad; Barzyk, Timothy M.; Smith, Elizabeth R.; Arunachalam, Saravanan; Naess, Brian; Venkatram, Akula

2018-01-01

The Community model for near-PORT applications (C-PORT) is a screening tool with an intended purpose of calculating differences in annual averaged concentration patterns and relative contributions of various source categories over the spatial domain within about 10 km of the port. C-PORT can inform decision-makers and concerned citizens about local air quality due to mobile source emissions related to commercial port activities. It allows users to visualize and evaluate different planning scenarios, helping them identify the best alternatives for making long-term decisions that protect community health and sustainability. The web-based, easy-to-use interface currently includes data from 21 seaports primarily in the Southeastern U.S., and has a map-based interface based on Google Maps. The tool was developed to visualize and assess changes in air quality due to changes in emissions and/or meteorology in order to analyze development scenarios, and is not intended to support or replace any regulatory models or programs. PMID:29681760

π Scope: python based scientific workbench with visualization tool for MDSplus data

NASA Astrophysics Data System (ADS)

Shiraiwa, S.

2014-10-01

π Scope is a python based scientific data analysis and visualization tool constructed on wxPython and Matplotlib. Although it is designed to be a generic tool, the primary motivation for developing the new software is 1) to provide an updated tool to browse MDSplus data, with functionalities beyond dwscope and jScope, and 2) to provide a universal foundation to construct interface tools to perform computer simulation and modeling for Alcator C-Mod. It provides many features to visualize MDSplus data during tokamak experiments including overplotting different signals and discharges, various plot types (line, contour, image, etc.), in-panel data analysis using python scripts, and publication quality graphics generation. Additionally, the logic to produce multi-panel plots is designed to be backward compatible with dwscope, enabling smooth migration for dwscope users. πScope uses multi-threading to reduce data transfer latency, and its object-oriented design makes it easy to modify and expand while the open source nature allows portability. A built-in tree data browser allows a user to approach the data structure both from a GUI and a script, enabling relatively complex data analysis workflow to be built quickly. As an example, an IDL-based interface to perform GENRAY/CQL3D simulations was ported on πScope, thus allowing LHCD simulation to be run between-shot using C-Mod experimental profiles. This workflow is being used to generate a large database to develop a LHCD actuator model for the plasma control system. Supported by USDoE Award DE-FC02-99ER54512.

SAVS: A Space and Atmospheric Visualization Science system

NASA Technical Reports Server (NTRS)

Szuszczewicz, E. P.; Mankofsky, A.; Blanchard, P.; Goodrich, C.; McNabb, D.; Kamins, D.

1995-01-01

The research environment faced by space and atmospheric scientists in the 1990s is characterized by unprecedented volumes of new data, by ever-increasing repositories of unexploited mission files, and by the widespread use of empirical and large-scale computational models needed for the synthesis of understanding across data sets and discipline boundaries. The effective analysis and interpretation of such massive amounts of information have become the subjects of legitimate concern. With SAVS (a Space and Atmospheric Visualization Science System), we address these issues by creating a 'push-button' software environment that mimics the logical scientific processes in data acquisition, reduction, and analysis without requiring a detailed understanding of the methods, networks, and modules that link the tools and effectively execute the functions. SAVS provides (1) a customizable framework for accessing a powerful set of visualization tools based on the popular AVS visualization software with hooks to PV-Wave and access to Khoros modules, (2) a set of mathematical and statistical tools, (3) an extensible library of discipline-specific functions and models (e.g., MSIS, IRI, Feldstein Oval, IGRF, satellite tracking with CADRE-3, etc.), and (4) capabilities for local and remote data base access. The system treats scalar, vector, and image data, and runs on most common Unix workstations. We present a description of SAVS and its components, followed by several applications based on generic research interests in interplanetary and magnetospheric physics (IMP/ISTP), active experiments in space (CRRES), and mission planning focused on the Earth's thermospheric, ionospheric, and mesospheric domains (TIMED).

Planning Tool for Strategic Evaluation of Facility Plans - 13570

DOE Office of Scientific and Technical Information (OSTI.GOV)

Magoulas, Virginia; Cercy, Michael; Hall, Irin

2013-07-01

Savannah River National Laboratory (SRNL) has developed a strategic planning tool for the evaluation of the utilization of its unique resources for processing and research and development of nuclear materials. The Planning Tool is a strategic level tool for assessing multiple missions that could be conducted utilizing the SRNL facilities and showcasing the plan. Traditional approaches using standard scheduling tools and laying out a strategy on paper tended to be labor intensive and offered either a limited or cluttered view for visualizing and communicating results. A tool that can assess the process throughput, duration, and utilization of the facility wasmore » needed. SRNL teamed with Newport News Shipbuilding (NNS), a division of Huntington Ingalls Industries, to create the next generation Planning Tool. The goal of this collaboration was to create a simulation based tool that allows for quick evaluation of strategies with respect to new or changing missions, and clearly communicates results to the decision makers. This tool has been built upon a mature modeling and simulation software previously developed by NNS. The Planning Tool provides a forum for capturing dependencies, constraints, activity flows, and variable factors. It is also a platform for quickly evaluating multiple mission scenarios, dynamically adding/updating scenarios, generating multiple views for evaluating/communicating results, and understanding where there are areas of risks and opportunities with respect to capacity. The Planning Tool that has been developed is useful in that it presents a clear visual plan for the missions at the Savannah River Site (SRS). It not only assists in communicating the plans to SRS corporate management, but also allows the area stakeholders a visual look at the future plans for SRS. The design of this tool makes it easily deployable to other facility and mission planning endeavors. (authors)« less

Generating DEM from LIDAR data - comparison of available software tools

NASA Astrophysics Data System (ADS)

Korzeniowska, K.; Lacka, M.

2011-12-01

In recent years many software tools and applications have appeared that offer procedures, scripts and algorithms to process and visualize ALS data. This variety of software tools and of "point cloud" processing methods contributed to the aim of this study: to assess algorithms available in various software tools that are used to classify LIDAR "point cloud" data, through a careful examination of Digital Elevation Models (DEMs) generated from LIDAR data on a base of these algorithms. The works focused on the most important available software tools: both commercial and open source ones. Two sites in a mountain area were selected for the study. The area of each site is 0.645 sq km. DEMs generated with analysed software tools ware compared with a reference dataset, generated using manual methods to eliminate non ground points. Surfaces were analysed using raster analysis. Minimum, maximum and mean differences between reference DEM and DEMs generated with analysed software tools were calculated, together with Root Mean Square Error. Differences between DEMs were also examined visually using transects along the grid axes in the test sites.

Using Visual Simulation Tools And Learning Outcomes-Based Curriculum To Help Transportation Engineering Students And Practitioners To Better Understand And Design Traffic Signal Control Systems

DOT National Transportation Integrated Search

2012-06-01

The use of visual simulation tools to convey complex concepts has become a useful tool in education as well as in research. : This report describes a project that developed curriculum and visualization tools to train transportation engineering studen...

3D Visualization for Phoenix Mars Lander Science Operations

NASA Technical Reports Server (NTRS)

Edwards, Laurence; Keely, Leslie; Lees, David; Stoker, Carol

2012-01-01

Planetary surface exploration missions present considerable operational challenges in the form of substantial communication delays, limited communication windows, and limited communication bandwidth. A 3D visualization software was developed and delivered to the 2008 Phoenix Mars Lander (PML) mission. The components of the system include an interactive 3D visualization environment called Mercator, terrain reconstruction software called the Ames Stereo Pipeline, and a server providing distributed access to terrain models. The software was successfully utilized during the mission for science analysis, site understanding, and science operations activity planning. A terrain server was implemented that provided distribution of terrain models from a central repository to clients running the Mercator software. The Ames Stereo Pipeline generates accurate, high-resolution, texture-mapped, 3D terrain models from stereo image pairs. These terrain models can then be visualized within the Mercator environment. The central cross-cutting goal for these tools is to provide an easy-to-use, high-quality, full-featured visualization environment that enhances the mission science team s ability to develop low-risk productive science activity plans. In addition, for the Mercator and Viz visualization environments, extensibility and adaptability to different missions and application areas are key design goals.

Parmodel: a web server for automated comparative modeling of proteins.

PubMed

Uchôa, Hugo Brandão; Jorge, Guilherme Eberhart; Freitas Da Silveira, Nelson José; Camera, João Carlos; Canduri, Fernanda; De Azevedo, Walter Filgueira

2004-12-24

Parmodel is a web server for automated comparative modeling and evaluation of protein structures. The aim of this tool is to help inexperienced users to perform modeling, assessment, visualization, and optimization of protein models as well as crystallographers to evaluate structures solved experimentally. It is subdivided in four modules: Parmodel Modeling, Parmodel Assessment, Parmodel Visualization, and Parmodel Optimization. The main module is the Parmodel Modeling that allows the building of several models for a same protein in a reduced time, through the distribution of modeling processes on a Beowulf cluster. Parmodel automates and integrates the main softwares used in comparative modeling as MODELLER, Whatcheck, Procheck, Raster3D, Molscript, and Gromacs. This web server is freely accessible at .

The adenosine triphosphate method as a quality control tool to assess 'cleanliness' of frequently touched hospital surfaces.

PubMed

Knape, L; Hambraeus, A; Lytsy, B

2015-10-01

The adenosine triphosphate (ATP) method is widely accepted as a quality control method to complement visual assessment, in the specifications of requirements, when purchasing cleaning contractors in Swedish hospitals. To examine whether the amount of biological load, as measured by ATP on frequently touched near-patient surfaces, had been reduced after an intervention; to evaluate the correlation between visual assessment and ATP levels on the same surfaces; to identify aspects of the performance of the ATP method as a tool in evaluating hospital cleanliness. A prospective intervention study in three phases was carried out in a medical ward and an intensive care unit (ICU) at a regional hospital in mid-Sweden between 2012 and 2013. Existing cleaning procedures were defined and baseline tests were sampled by visual inspection and ATP measurements of ten frequently touched surfaces in patients' rooms before and after intervention. The intervention consisted of educating nursing staff about the importance of hospital cleaning and direct feedback of ATP levels before and after cleaning. The mixed model showed a significant decrease in ATP levels after the intervention (P < 0.001). Relative light unit values were lower in the ICU. Cleanliness as judged by visual assessments improved. In the logistic regression analysis, there was a significant association between visual assessments and ATP levels. Direct feedback of ATP levels, together with education and introduction of written cleaning protocols, were effective tools to improve cleanliness. Visual assessment correlated with the level of ATP but the correlation was not absolute. The ATP method could serve as an educational tool for staff, but is not enough to assess hospital cleanliness in general as only a limited part of a large area is covered. Copyright © 2015 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Interaction Junk: User Interaction-Based Evaluation of Visual Analytic Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Endert, Alexander; North, Chris

2012-10-14

With the growing need for visualization to aid users in understanding large, complex datasets, the ability for users to interact and explore these datasets is critical. As visual analytic systems have advanced to leverage powerful computational models and data analytics capabilities, the modes by which users engage and interact with the information are limited. Often, users are taxed with directly manipulating parameters of these models through traditional GUIs (e.g., using sliders to directly manipulate the value of a parameter). However, the purpose of user interaction in visual analytic systems is to enable visual data exploration – where users can focusmore » on their task, as opposed to the tool or system. As a result, users can engage freely in data exploration and decision-making, for the purpose of gaining insight. In this position paper, we discuss how evaluating visual analytic systems can be approached through user interaction analysis, where the goal is to minimize the cognitive translation between the visual metaphor and the mode of interaction (i.e., reducing the “Interactionjunk”). We motivate this concept through a discussion of traditional GUIs used in visual analytics for direct manipulation of model parameters, and the importance of designing interactions the support visual data exploration.« less

Water Network Tool for Resilience v. 1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

2015-12-09

WNTR is a python package designed to simulate and analyze resilience of water distribution networks. The software includes: - Pressure driven and demand driven hydraulic simulation - Water quality simulation to track concentration, trace, and water age - Conditional controls to simulate power outages - Models to simulate pipe breaks - A wide range of resilience metrics - Analysis and visualization tools

RIPGIS-NET: a GIS tool for riparian groundwater evapotranspiration in MODFLOW.

PubMed

Ajami, Hoori; Maddock, Thomas; Meixner, Thomas; Hogan, James F; Guertin, D Phillip

2012-01-01

RIPGIS-NET, an Environmental System Research Institute (ESRI's) ArcGIS 9.2/9.3 custom application, was developed to derive parameters and visualize results of spatially explicit riparian groundwater evapotranspiration (ETg), evapotranspiration from saturated zone, in groundwater flow models for ecohydrology, riparian ecosystem management, and stream restoration. Specifically RIPGIS-NET works with riparian evapotranspiration (RIP-ET), a modeling package that works with the MODFLOW groundwater flow model. RIP-ET improves ETg simulations by using a set of eco-physiologically based ETg curves for plant functional subgroups (PFSGs), and separates ground evaporation and plant transpiration processes from the water table. The RIPGIS-NET program was developed in Visual Basic 2005, .NET framework 2.0, and runs in ArcMap 9.2 and 9.3 applications. RIPGIS-NET, a pre- and post-processor for RIP-ET, incorporates spatial variability of riparian vegetation and land surface elevation into ETg estimation in MODFLOW groundwater models. RIPGIS-NET derives RIP-ET input parameters including PFSG evapotranspiration curve parameters, fractional coverage areas of each PFSG in a MODFLOW cell, and average surface elevation per riparian vegetation polygon using a digital elevation model. RIPGIS-NET also provides visualization tools for modelers to create head maps, depth to water table (DTWT) maps, and plot DTWT for a PFSG in a polygon in the Geographic Information System based on MODFLOW simulation results. © 2011, The Author(s). Ground Water © 2011, National Ground Water Association.

Faceted Visualization of Three Dimensional Neuroanatomy By Combining Ontology with Faceted Search

PubMed Central

Veeraraghavan, Harini; Miller, James V.

2013-01-01

In this work, we present a faceted-search based approach for visualization of anatomy by combining a three dimensional digital atlas with an anatomy ontology. Specifically, our approach provides a drill-down search interface that exposes the relevant pieces of information (obtained by searching the ontology) for a user query. Hence, the user can produce visualizations starting with minimally specified queries. Furthermore, by automatically translating the user queries into the controlled terminology our approach eliminates the need for the user to use controlled terminology. We demonstrate the scalability of our approach using an abdominal atlas and the same ontology. We implemented our visualization tool on the opensource 3D Slicer software. We present results of our visualization approach by combining a modified Foundational Model of Anatomy (FMA) ontology with the Surgical Planning Laboratory (SPL) Brain 3D digital atlas, and geometric models specific to patients computed using the SPL brain tumor dataset. PMID:24006207

Faceted visualization of three dimensional neuroanatomy by combining ontology with faceted search.

PubMed

Veeraraghavan, Harini; Miller, James V

2014-04-01

In this work, we present a faceted-search based approach for visualization of anatomy by combining a three dimensional digital atlas with an anatomy ontology. Specifically, our approach provides a drill-down search interface that exposes the relevant pieces of information (obtained by searching the ontology) for a user query. Hence, the user can produce visualizations starting with minimally specified queries. Furthermore, by automatically translating the user queries into the controlled terminology our approach eliminates the need for the user to use controlled terminology. We demonstrate the scalability of our approach using an abdominal atlas and the same ontology. We implemented our visualization tool on the opensource 3D Slicer software. We present results of our visualization approach by combining a modified Foundational Model of Anatomy (FMA) ontology with the Surgical Planning Laboratory (SPL) Brain 3D digital atlas, and geometric models specific to patients computed using the SPL brain tumor dataset.

MATISSE: A novel tool to access, visualize and analyse data from planetary exploration missions

NASA Astrophysics Data System (ADS)

Zinzi, A.; Capria, M. T.; Palomba, E.; Giommi, P.; Antonelli, L. A.

2016-04-01

The increasing number and complexity of planetary exploration space missions require new tools to access, visualize and analyse data to improve their scientific return. ASI Science Data Center (ASDC) addresses this request with the web-tool MATISSE (Multi-purpose Advanced Tool for the Instruments of the Solar System Exploration), allowing the visualization of single observation or real-time computed high-order products, directly projected on the three-dimensional model of the selected target body. Using MATISSE it will be no longer needed to download huge quantity of data or to write down a specific code for every instrument analysed, greatly encouraging studies based on joint analysis of different datasets. In addition the extremely high-resolution output, to be used offline with a Python-based free software, together with the files to be read with specific GIS software, makes it a valuable tool to further process the data at the best spatial accuracy available. MATISSE modular structure permits addition of new missions or tasks and, thanks to dedicated future developments, it would be possible to make it compliant to the Planetary Virtual Observatory standards currently under definition. In this context the recent development of an interface to the NASA ODE REST API by which it is possible to access to public repositories is set.

Introducing GHOST: The Geospace/Heliosphere Observation & Simulation Tool-kit

NASA Astrophysics Data System (ADS)

Murphy, J. J.; Elkington, S. R.; Schmitt, P.; Wiltberger, M. J.; Baker, D. N.

2013-12-01

Simulation models of the heliospheric and geospace environments can provide key insights into the geoeffective potential of solar disturbances such as Coronal Mass Ejections and High Speed Solar Wind Streams. Advanced post processing of the results of these simulations greatly enhances the utility of these models for scientists and other researchers. Currently, no supported centralized tool exists for performing these processing tasks. With GHOST, we introduce a toolkit for the ParaView visualization environment that provides a centralized suite of tools suited for Space Physics post processing. Building on the work from the Center For Integrated Space Weather Modeling (CISM) Knowledge Transfer group, GHOST is an open-source tool suite for ParaView. The tool-kit plugin currently provides tools for reading LFM and Enlil data sets, and provides automated tools for data comparison with NASA's CDAweb database. As work progresses, many additional tools will be added and through open-source collaboration, we hope to add readers for additional model types, as well as any additional tools deemed necessary by the scientific public. The ultimate end goal of this work is to provide a complete Sun-to-Earth model analysis toolset.

Scalable Visual Analytics of Massive Textual Datasets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krishnan, Manoj Kumar; Bohn, Shawn J.; Cowley, Wendy E.

2007-04-01

This paper describes the first scalable implementation of text processing engine used in Visual Analytics tools. These tools aid information analysts in interacting with and understanding large textual information content through visual interfaces. By developing parallel implementation of the text processing engine, we enabled visual analytics tools to exploit cluster architectures and handle massive dataset. The paper describes key elements of our parallelization approach and demonstrates virtually linear scaling when processing multi-gigabyte data sets such as Pubmed. This approach enables interactive analysis of large datasets beyond capabilities of existing state-of-the art visual analytics tools.

A graph algebra for scalable visual analytics.

PubMed

Shaverdian, Anna A; Zhou, Hao; Michailidis, George; Jagadish, Hosagrahar V

2012-01-01

Visual analytics (VA), which combines analytical techniques with advanced visualization features, is fast becoming a standard tool for extracting information from graph data. Researchers have developed many tools for this purpose, suggesting a need for formal methods to guide these tools' creation. Increased data demands on computing requires redesigning VA tools to consider performance and reliability in the context of analysis of exascale datasets. Furthermore, visual analysts need a way to document their analyses for reuse and results justification. A VA graph framework encapsulated in a graph algebra helps address these needs. Its atomic operators include selection and aggregation. The framework employs a visual operator and supports dynamic attributes of data to enable scalable visual exploration of data.

The Multisensory Attentional Consequences of Tool Use: A Functional Magnetic Resonance Imaging Study

PubMed Central

Holmes, Nicholas P.; Spence, Charles; Hansen, Peter C.; Mackay, Clare E.; Calvert, Gemma A.

2008-01-01

Background Tool use in humans requires that multisensory information is integrated across different locations, from objects seen to be distant from the hand, but felt indirectly at the hand via the tool. We tested the hypothesis that using a simple tool to perceive vibrotactile stimuli results in the enhanced processing of visual stimuli presented at the distal, functional part of the tool. Such a finding would be consistent with a shift of spatial attention to the location where the tool is used. Methodology/Principal Findings We tested this hypothesis by scanning healthy human participants' brains using functional magnetic resonance imaging, while they used a simple tool to discriminate between target vibrations, accompanied by congruent or incongruent visual distractors, on the same or opposite side to the tool. The attentional hypothesis was supported: BOLD response in occipital cortex, particularly in the right hemisphere lingual gyrus, varied significantly as a function of tool position, increasing contralaterally, and decreasing ipsilaterally to the tool. Furthermore, these modulations occurred despite the fact that participants were repeatedly instructed to ignore the visual stimuli, to respond only to the vibrotactile stimuli, and to maintain visual fixation centrally. In addition, the magnitude of multisensory (visual-vibrotactile) interactions in participants' behavioural responses significantly predicted the BOLD response in occipital cortical areas that were also modulated as a function of both visual stimulus position and tool position. Conclusions/Significance These results show that using a simple tool to locate and to perceive vibrotactile stimuli is accompanied by a shift of spatial attention to the location where the functional part of the tool is used, resulting in enhanced processing of visual stimuli at that location, and decreased processing at other locations. This was most clearly observed in the right hemisphere lingual gyrus. Such modulations of visual processing may reflect the functional importance of visuospatial information during human tool use. PMID:18958150

Subsurface data visualization in Virtual Reality

NASA Astrophysics Data System (ADS)

Krijnen, Robbert; Smelik, Ruben; Appleton, Rick; van Maanen, Peter-Paul

2017-04-01

Due to their increasing complexity and size, visualization of geological data is becoming more and more important. It enables detailed examining and reviewing of large volumes of geological data and it is often used as a communication tool for reporting and education to demonstrate the importance of the geology to policy makers. In the Netherlands two types of nation-wide geological models are available: 1) Layer-based models in which the subsurface is represented by a series of tops and bases of geological or hydrogeological units, and 2) Voxel models in which the subsurface is subdivided in a regular grid of voxels that can contain different properties per voxel. The Geological Survey of the Netherlands (GSN) provides an interactive web portal that delivers maps and vertical cross-sections of such layer-based and voxel models. From this portal you can download a 3D subsurface viewer that can visualize the voxel model data of an area of 20 × 25 km with 100 × 100 × 5 meter voxel resolution on a desktop computer. Virtual Reality (VR) technology enables us to enhance the visualization of this volumetric data in a more natural way as compared to a standard desktop, keyboard mouse setup. The use of VR for data visualization is not new but recent developments has made expensive hardware and complex setups unnecessary. The availability of consumer of-the-shelf VR hardware enabled us to create an new intuitive and low visualization tool. A VR viewer has been implemented using the HTC Vive head set and allows visualization and analysis of the GSN voxel model data with geological or hydrogeological units. The user can navigate freely around the voxel data (20 × 25 km) which is presented in a virtual room at a scale of 2 × 2 or 3 × 3 meters. To enable analysis, e.g. hydraulic conductivity, the user can select filters to remove specific hydrogeological units. The user can also use slicing to cut-off specific sections of the voxel data to get a closer look. This slicing can be done in any direction using a 'virtual knife'. Future plans are to further improve performance from 30 up to 90 Hz update rate to reduce possible motion sickness, add more advanced filtering capabilities as well as a multi user setup, annotation capabilities and visualizing of historical data.

Models Extracted from Text for System-Software Safety Analyses

NASA Technical Reports Server (NTRS)

Malin, Jane T.

2010-01-01

This presentation describes extraction and integration of requirements information and safety information in visualizations to support early review of completeness, correctness, and consistency of lengthy and diverse system safety analyses. Software tools have been developed and extended to perform the following tasks: 1) extract model parts and safety information from text in interface requirements documents, failure modes and effects analyses and hazard reports; 2) map and integrate the information to develop system architecture models and visualizations for safety analysts; and 3) provide model output to support virtual system integration testing. This presentation illustrates the methods and products with a rocket motor initiation case.

3-D interactive visualisation tools for Hi spectral line imaging

NASA Astrophysics Data System (ADS)

van der Hulst, J. M.; Punzo, D.; Roerdink, J. B. T. M.

2017-06-01

Upcoming HI surveys will deliver such large datasets that automated processing using the full 3-D information to find and characterize HI objects is unavoidable. Full 3-D visualization is an essential tool for enabling qualitative and quantitative inspection and analysis of the 3-D data, which is often complex in nature. Here we present SlicerAstro, an open-source extension of 3DSlicer, a multi-platform open source software package for visualization and medical image processing, which we developed for the inspection and analysis of HI spectral line data. We describe its initial capabilities, including 3-D filtering, 3-D selection and comparative modelling.

A universal Model-R Coupler to facilitate the use of R functions for model calibration and analysis

USGS Publications Warehouse

Wu, Yiping; Liu, Shuguang; Yan, Wende

2014-01-01

Mathematical models are useful in various fields of science and engineering. However, it is a challenge to make a model utilize the open and growing functions (e.g., model inversion) on the R platform due to the requirement of accessing and revising the model's source code. To overcome this barrier, we developed a universal tool that aims to convert a model developed in any computer language to an R function using the template and instruction concept of the Parameter ESTimation program (PEST) and the operational structure of the R-Soil and Water Assessment Tool (R-SWAT). The developed tool (Model-R Coupler) is promising because users of any model can connect an external algorithm (written in R) with their model to implement various model behavior analyses (e.g., parameter optimization, sensitivity and uncertainty analysis, performance evaluation, and visualization) without accessing or modifying the model's source code.

Real-time dose calculation and visualization for the proton therapy of ocular tumours

NASA Astrophysics Data System (ADS)

Pfeiffer, Karsten; Bendl, Rolf

2001-03-01

A new real-time dose calculation and visualization was developed as part of the new 3D treatment planning tool OCTOPUS for proton therapy of ocular tumours within a national research project together with the Hahn-Meitner Institut Berlin. The implementation resolves the common separation between parameter definition, dose calculation and evaluation and allows a direct examination of the expected dose distribution while adjusting the treatment parameters. The new tool allows the therapist to move the desired dose distribution under visual control in 3D to the appropriate place. The visualization of the resulting dose distribution as a 3D surface model, on any 2D slice or on the surface of specified ocular structures is done automatically when adapting parameters during the planning process. In addition, approximate dose volume histograms may be calculated with little extra time. The dose distribution is calculated and visualized in 200 ms with an accuracy of 6% for the 3D isodose surfaces and 8% for other objects. This paper discusses the advantages and limitations of this new approach.

Visualization techniques for computer network defense

NASA Astrophysics Data System (ADS)

Beaver, Justin M.; Steed, Chad A.; Patton, Robert M.; Cui, Xiaohui; Schultz, Matthew

2011-06-01

Effective visual analysis of computer network defense (CND) information is challenging due to the volume and complexity of both the raw and analyzed network data. A typical CND is comprised of multiple niche intrusion detection tools, each of which performs network data analysis and produces a unique alerting output. The state-of-the-practice in the situational awareness of CND data is the prevalent use of custom-developed scripts by Information Technology (IT) professionals to retrieve, organize, and understand potential threat events. We propose a new visual analytics framework, called the Oak Ridge Cyber Analytics (ORCA) system, for CND data that allows an operator to interact with all detection tool outputs simultaneously. Aggregated alert events are presented in multiple coordinated views with timeline, cluster, and swarm model analysis displays. These displays are complemented with both supervised and semi-supervised machine learning classifiers. The intent of the visual analytics framework is to improve CND situational awareness, to enable an analyst to quickly navigate and analyze thousands of detected events, and to combine sophisticated data analysis techniques with interactive visualization such that patterns of anomalous activities may be more easily identified and investigated.

ACTIVIS: Visual Exploration of Industry-Scale Deep Neural Network Models.

PubMed

Kahng, Minsuk; Andrews, Pierre Y; Kalro, Aditya; Polo Chau, Duen Horng

2017-08-30

While deep learning models have achieved state-of-the-art accuracies for many prediction tasks, understanding these models remains a challenge. Despite the recent interest in developing visual tools to help users interpret deep learning models, the complexity and wide variety of models deployed in industry, and the large-scale datasets that they used, pose unique design challenges that are inadequately addressed by existing work. Through participatory design sessions with over 15 researchers and engineers at Facebook, we have developed, deployed, and iteratively improved ACTIVIS, an interactive visualization system for interpreting large-scale deep learning models and results. By tightly integrating multiple coordinated views, such as a computation graph overview of the model architecture, and a neuron activation view for pattern discovery and comparison, users can explore complex deep neural network models at both the instance- and subset-level. ACTIVIS has been deployed on Facebook's machine learning platform. We present case studies with Facebook researchers and engineers, and usage scenarios of how ACTIVIS may work with different models.

Modeling the Round Earth through Diagrams

NASA Astrophysics Data System (ADS)

Padalkar, Shamin; Ramadas, Jayashree

Earlier studies have found that students, including adults, have problems understanding the scientifically accepted model of the Sun-Earth-Moon system and explaining day-to-day astronomical phenomena based on it. We have been examining such problems in the context of recent research on visual-spatial reasoning. Working with middle school students in India, we have developed a pedagogical sequence to build the mental model of the Earth and tried it in three schools for socially and educationally disadvantaged students. This pedagogy was developed on the basis of (1) a reading of current research in imagery and visual-spatial reasoning and (2) students' difficulties identified during the course of pretests and interviews. Visual-spatial tools such as concrete (physical) models, gestures, and diagrams are used extensively in the teaching sequence. The building of a mental model is continually integrated with drawing inferences to understand and explain everyday phenomena. The focus of this article is inferences drawn with diagrams.

CLMSVault: A Software Suite for Protein Cross-Linking Mass-Spectrometry Data Analysis and Visualization.

PubMed

Courcelles, Mathieu; Coulombe-Huntington, Jasmin; Cossette, Émilie; Gingras, Anne-Claude; Thibault, Pierre; Tyers, Mike

2017-07-07

Protein cross-linking mass spectrometry (CL-MS) enables the sensitive detection of protein interactions and the inference of protein complex topology. The detection of chemical cross-links between protein residues can identify intra- and interprotein contact sites or provide physical constraints for molecular modeling of protein structure. Recent innovations in cross-linker design, sample preparation, mass spectrometry, and software tools have significantly improved CL-MS approaches. Although a number of algorithms now exist for the identification of cross-linked peptides from mass spectral data, a dearth of user-friendly analysis tools represent a practical bottleneck to the broad adoption of the approach. To facilitate the analysis of CL-MS data, we developed CLMSVault, a software suite designed to leverage existing CL-MS algorithms and provide intuitive and flexible tools for cross-platform data interpretation. CLMSVault stores and combines complementary information obtained from different cross-linkers and search algorithms. CLMSVault provides filtering, comparison, and visualization tools to support CL-MS analyses and includes a workflow for label-free quantification of cross-linked peptides. An embedded 3D viewer enables the visualization of quantitative data and the mapping of cross-linked sites onto PDB structural models. We demonstrate the application of CLMSVault for the analysis of a noncovalent Cdc34-ubiquitin protein complex cross-linked under different conditions. CLMSVault is open-source software (available at https://gitlab.com/courcelm/clmsvault.git ), and a live demo is available at http://democlmsvault.tyerslab.com/ .

Visualization Tools for Teaching Computer Security

ERIC Educational Resources Information Center

Yuan, Xiaohong; Vega, Percy; Qadah, Yaseen; Archer, Ricky; Yu, Huiming; Xu, Jinsheng

2010-01-01

Using animated visualization tools has been an important teaching approach in computer science education. We have developed three visualization and animation tools that demonstrate various information security concepts and actively engage learners. The information security concepts illustrated include: packet sniffer and related computer network…

Visualization and Analytics Tools for Infectious Disease Epidemiology: A Systematic Review

PubMed Central

Carroll, Lauren N.; Au, Alan P.; Detwiler, Landon Todd; Fu, Tsung-chieh; Painter, Ian S.; Abernethy, Neil F.

2014-01-01

Background A myriad of new tools and algorithms have been developed to help public health professionals analyze and visualize the complex data used in infectious disease control. To better understand approaches to meet these users' information needs, we conducted a systematic literature review focused on the landscape of infectious disease visualization tools for public health professionals, with a special emphasis on geographic information systems (GIS), molecular epidemiology, and social network analysis. The objectives of this review are to: (1) Identify public health user needs and preferences for infectious disease information visualization tools; (2) Identify existing infectious disease information visualization tools and characterize their architecture and features; (3) Identify commonalities among approaches applied to different data types; and (4) Describe tool usability evaluation efforts and barriers to the adoption of such tools. Methods We identified articles published in English from January 1, 1980 to June 30, 2013 from five bibliographic databases. Articles with a primary focus on infectious disease visualization tools, needs of public health users, or usability of information visualizations were included in the review. Results A total of 88 articles met our inclusion criteria. Users were found to have diverse needs, preferences and uses for infectious disease visualization tools, and the existing tools are correspondingly diverse. The architecture of the tools was inconsistently described, and few tools in the review discussed the incorporation of usability studies or plans for dissemination. Many studies identified concerns regarding data sharing, confidentiality and quality. Existing tools offer a range of features and functions that allow users to explore, analyze, and visualize their data, but the tools are often for siloed applications. Commonly cited barriers to widespread adoption included lack of organizational support, access issues, and misconceptions about tool use. Discussion and Conclusion As the volume and complexity of infectious disease data increases, public health professionals must synthesize highly disparate data to facilitate communication with the public and inform decisions regarding measures to protect the public's health. Our review identified several themes: consideration of users' needs, preferences, and computer literacy; integration of tools into routine workflow; complications associated with understanding and use of visualizations; and the role of user trust and organizational support in the adoption of these tools. Interoperability also emerged as a prominent theme, highlighting challenges associated with the increasingly collaborative and interdisciplinary nature of infectious disease control and prevention. Future work should address methods for representing uncertainty and missing data to avoid misleading users as well as strategies to minimize cognitive overload. PMID:24747356

Visualization and analytics tools for infectious disease epidemiology: a systematic review.

PubMed

Carroll, Lauren N; Au, Alan P; Detwiler, Landon Todd; Fu, Tsung-Chieh; Painter, Ian S; Abernethy, Neil F

2014-10-01

A myriad of new tools and algorithms have been developed to help public health professionals analyze and visualize the complex data used in infectious disease control. To better understand approaches to meet these users' information needs, we conducted a systematic literature review focused on the landscape of infectious disease visualization tools for public health professionals, with a special emphasis on geographic information systems (GIS), molecular epidemiology, and social network analysis. The objectives of this review are to: (1) identify public health user needs and preferences for infectious disease information visualization tools; (2) identify existing infectious disease information visualization tools and characterize their architecture and features; (3) identify commonalities among approaches applied to different data types; and (4) describe tool usability evaluation efforts and barriers to the adoption of such tools. We identified articles published in English from January 1, 1980 to June 30, 2013 from five bibliographic databases. Articles with a primary focus on infectious disease visualization tools, needs of public health users, or usability of information visualizations were included in the review. A total of 88 articles met our inclusion criteria. Users were found to have diverse needs, preferences and uses for infectious disease visualization tools, and the existing tools are correspondingly diverse. The architecture of the tools was inconsistently described, and few tools in the review discussed the incorporation of usability studies or plans for dissemination. Many studies identified concerns regarding data sharing, confidentiality and quality. Existing tools offer a range of features and functions that allow users to explore, analyze, and visualize their data, but the tools are often for siloed applications. Commonly cited barriers to widespread adoption included lack of organizational support, access issues, and misconceptions about tool use. As the volume and complexity of infectious disease data increases, public health professionals must synthesize highly disparate data to facilitate communication with the public and inform decisions regarding measures to protect the public's health. Our review identified several themes: consideration of users' needs, preferences, and computer literacy; integration of tools into routine workflow; complications associated with understanding and use of visualizations; and the role of user trust and organizational support in the adoption of these tools. Interoperability also emerged as a prominent theme, highlighting challenges associated with the increasingly collaborative and interdisciplinary nature of infectious disease control and prevention. Future work should address methods for representing uncertainty and missing data to avoid misleading users as well as strategies to minimize cognitive overload. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Simulating Earthquakes for Science and Society: Earthquake Visualizations Ideal for use in Science Communication and Education

NASA Astrophysics Data System (ADS)

de Groot, R.

2008-12-01

The Southern California Earthquake Center (SCEC) has been developing groundbreaking computer modeling capabilities for studying earthquakes. These visualizations were initially shared within the scientific community but have recently gained visibility via television news coverage in Southern California. Computers have opened up a whole new world for scientists working with large data sets, and students can benefit from the same opportunities (Libarkin & Brick, 2002). For example, The Great Southern California ShakeOut was based on a potential magnitude 7.8 earthquake on the southern San Andreas fault. The visualization created for the ShakeOut was a key scientific and communication tool for the earthquake drill. This presentation will also feature SCEC Virtual Display of Objects visualization software developed by SCEC Undergraduate Studies in Earthquake Information Technology interns. According to Gordin and Pea (1995), theoretically visualization should make science accessible, provide means for authentic inquiry, and lay the groundwork to understand and critique scientific issues. This presentation will discuss how the new SCEC visualizations and other earthquake imagery achieve these results, how they fit within the context of major themes and study areas in science communication, and how the efficacy of these tools can be improved.

Visual illusion of tool use recalibrates tactile perception

PubMed Central

Miller, Luke E.; Longo, Matthew R.; Saygin, Ayse P.

2018-01-01

Brief use of a tool recalibrates multisensory representations of the user’s body, a phenomenon called tool embodiment. Despite two decades of research, little is known about its boundary conditions. It has been widely argued that embodiment requires active tool use, suggesting a critical role for somatosensory and motor feedback. The present study used a visual illusion to cast doubt on this view. We used a mirror-based setup to induce a visual experience of tool use with an arm that was in fact stationary. Following illusory tool use, tactile perception was recalibrated on this stationary arm, and with equal magnitude as physical use. Recalibration was not found following illusory passive tool holding, and could not be accounted for by sensory conflict or general interhemispheric plasticity. These results suggest visual tool-use signals play a critical role in driving tool embodiment. PMID:28196765

eLoom and Flatland: specification, simulation and visualization engines for the study of arbitrary hierarchical neural architectures.

PubMed

Caudell, Thomas P; Xiao, Yunhai; Healy, Michael J

2003-01-01

eLoom is an open source graph simulation software tool, developed at the University of New Mexico (UNM), that enables users to specify and simulate neural network models. Its specification language and libraries enables users to construct and simulate arbitrary, potentially hierarchical network structures on serial and parallel processing systems. In addition, eLoom is integrated with UNM's Flatland, an open source virtual environments development tool to provide real-time visualizations of the network structure and activity. Visualization is a useful method for understanding both learning and computation in artificial neural networks. Through 3D animated pictorially representations of the state and flow of information in the network, a better understanding of network functionality is achieved. ART-1, LAPART-II, MLP, and SOM neural networks are presented to illustrate eLoom and Flatland's capabilities.

In silico modeling for tumor growth visualization.

PubMed

Jeanquartier, Fleur; Jean-Quartier, Claire; Cemernek, David; Holzinger, Andreas

2016-08-08

Cancer is a complex disease. Fundamental cellular based studies as well as modeling provides insight into cancer biology and strategies to treatment of the disease. In silico models complement in vivo models. Research on tumor growth involves a plethora of models each emphasizing isolated aspects of benign and malignant neoplasms. Biologists and clinical scientists are often overwhelmed by the mathematical background knowledge necessary to grasp and to apply a model to their own research. We aim to provide a comprehensive and expandable simulation tool to visualizing tumor growth. This novel Web-based application offers the advantage of a user-friendly graphical interface with several manipulable input variables to correlate different aspects of tumor growth. By refining model parameters we highlight the significance of heterogeneous intercellular interactions on tumor progression. Within this paper we present the implementation of the Cellular Potts Model graphically presented through Cytoscape.js within a Web application. The tool is available under the MIT license at https://github.com/davcem/cpm-cytoscape and http://styx.cgv.tugraz.at:8080/cpm-cytoscape/ . In-silico methods overcome the lack of wet experimental possibilities and as dry method succeed in terms of reduction, refinement and replacement of animal experimentation, also known as the 3R principles. Our visualization approach to simulation allows for more flexible usage and easy extension to facilitate understanding and gain novel insight. We believe that biomedical research in general and research on tumor growth in particular will benefit from the systems biology perspective.

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

DOE PAGES

King, Zachary A.; Lu, Justin; Drager, Andreas; ...

2015-10-17

In this study, genome-scale metabolic models are mathematically structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scalemore » metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data.« less

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

PubMed Central

King, Zachary A.; Lu, Justin; Dräger, Andreas; Miller, Philip; Federowicz, Stephen; Lerman, Joshua A.; Ebrahim, Ali; Palsson, Bernhard O.; Lewis, Nathan E.

2016-01-01

Genome-scale metabolic models are mathematically-structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scale metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data. PMID:26476456

Collaboration tools and techniques for large model datasets

USGS Publications Warehouse

Signell, R.P.; Carniel, S.; Chiggiato, J.; Janekovic, I.; Pullen, J.; Sherwood, C.R.

2008-01-01

In MREA and many other marine applications, it is common to have multiple models running with different grids, run by different institutions. Techniques and tools are described for low-bandwidth delivery of data from large multidimensional datasets, such as those from meteorological and oceanographic models, directly into generic analysis and visualization tools. Output is stored using the NetCDF CF Metadata Conventions, and then delivered to collaborators over the web via OPeNDAP. OPeNDAP datasets served by different institutions are then organized via THREDDS catalogs. Tools and procedures are then used which enable scientists to explore data on the original model grids using tools they are familiar with. It is also low-bandwidth, enabling users to extract just the data they require, an important feature for access from ship or remote areas. The entire implementation is simple enough to be handled by modelers working with their webmasters - no advanced programming support is necessary. ?? 2007 Elsevier B.V. All rights reserved.

Pediatric ocular trauma score as a prognostic tool in the management of pediatric traumatic cataracts.

PubMed

Shah, Mehul A; Agrawal, Rupesh; Teoh, Ryan; Shah, Shreya M; Patel, Kashyap; Gupta, Satyam; Gosai, Siddharth

2017-05-01

To introduce and validate the pediatric ocular trauma score (POTS) - a mathematical model to predict visual outcome trauma in children with traumatic cataract METHODS: In this retrospective cohort study, medical records of consecutive children with traumatic cataracts aged 18 and below were retrieved and analysed. Data collected included age, gender, visual acuity, anterior segment and posterior segment findings, nature of surgery, treatment for amblyopia, follow-up, and final outcome was recorded on a precoded data information sheet. POTS was derived based on the ocular trauma score (OTS), adjusting for age of patient and location of the injury. Visual outcome was predicted using the OTS and the POTS and using receiver operating characteristic (ROC) curves. POTS predicted outcomes were more accurate compared to that of OTS (p = 0.014). POTS is a more sensitive and specific score with more accurate predicted outcomes compared to OTS, and is a viable tool to predict visual outcomes of pediatric ocular trauma with traumatic cataract.

Building simple multiscale visualizations of outcrop geology using virtual reality modeling language (VRML)

NASA Astrophysics Data System (ADS)

Thurmond, John B.; Drzewiecki, Peter A.; Xu, Xueming

2005-08-01

Geological data collected from outcrop are inherently three-dimensional (3D) and span a variety of scales, from the megascopic to the microscopic. This presents challenges in both interpreting and communicating observations. The Virtual Reality Modeling Language provides an easy way for geoscientists to construct complex visualizations that can be viewed with free software. Field data in tabular form can be used to generate hierarchical multi-scale visualizations of outcrops, which can convey the complex relationships between a variety of data types simultaneously. An example from carbonate mud-mounds in southeastern New Mexico illustrates the embedding of three orders of magnitude of observation into a single visualization, for the purpose of interpreting depositional facies relationships in three dimensions. This type of raw data visualization can be built without software tools, yet is incredibly useful for interpreting and communicating data. Even simple visualizations can aid in the interpretation of complex 3D relationships that are frequently encountered in the geosciences.

A tool for multi-scale modelling of the renal nephron

PubMed Central

Nickerson, David P.; Terkildsen, Jonna R.; Hamilton, Kirk L.; Hunter, Peter J.

2011-01-01

We present the development of a tool, which provides users with the ability to visualize and interact with a comprehensive description of a multi-scale model of the renal nephron. A one-dimensional anatomical model of the nephron has been created and is used for visualization and modelling of tubule transport in various nephron anatomical segments. Mathematical models of nephron segments are embedded in the one-dimensional model. At the cellular level, these segment models use models encoded in CellML to describe cellular and subcellular transport kinetics. A web-based presentation environment has been developed that allows the user to visualize and navigate through the multi-scale nephron model, including simulation results, at the different spatial scales encompassed by the model description. The Zinc extension to Firefox is used to provide an interactive three-dimensional view of the tubule model and the native Firefox rendering of scalable vector graphics is used to present schematic diagrams for cellular and subcellular scale models. The model viewer is embedded in a web page that dynamically presents content based on user input. For example, when viewing the whole nephron model, the user might be presented with information on the various embedded segment models as they select them in the three-dimensional model view. Alternatively, the user chooses to focus the model viewer on a cellular model located in a particular nephron segment in order to view the various membrane transport proteins. Selecting a specific protein may then present the user with a description of the mathematical model governing the behaviour of that protein—including the mathematical model itself and various simulation experiments used to validate the model against the literature. PMID:22670210

SWATShare- A Platform for Collaborative Hydrology Research and Education with Cyber-enabled Sharing, Running and Visualization of SWAT Models

NASA Astrophysics Data System (ADS)

Rajib, M. A.; Merwade, V.; Song, C.; Zhao, L.; Kim, I. L.; Zhe, S.

2014-12-01

Setting up of any hydrologic model requires a large amount of efforts including compilation of all the data, creation of input files, calibration and validation. Given the amount of efforts involved, it is possible that models for a watershed get created multiple times by multiple groups or organizations to accomplish different research, educational or policy goals. To reduce the duplication of efforts and enable collaboration among different groups or organizations around an already existing hydrology model, a platform is needed where anyone can search for existing models, perform simple scenario analysis and visualize model results. The creator and users of a model on such a platform can then collaborate to accomplish new research or educational objectives. From this perspective, a prototype cyber-infrastructure (CI), called SWATShare, is developed for sharing, running and visualizing Soil Water Assessment Tool (SWAT) models in an interactive GIS-enabled web environment. Users can utilize SWATShare to publish or upload their own models, search and download existing SWAT models developed by others, run simulations including calibration using high performance resources provided by XSEDE and Cloud. Besides running and sharing, SWATShare hosts a novel spatio-temporal visualization system for SWAT model outputs. In temporal scale, the system creates time-series plots for all the hydrology and water quality variables available along the reach as well as in watershed-level. In spatial scale, the system can dynamically generate sub-basin level thematic maps for any variable at any user-defined date or date range; and thereby, allowing users to run animations or download the data for subsequent analyses. In addition to research, SWATShare can also be used within a classroom setting as an educational tool for modeling and comparing the hydrologic processes under different geographic and climatic settings. SWATShare is publicly available at https://www.water-hub.org/swatshare.

Meteorological Data Visualization in Multi-User Virtual Reality

NASA Astrophysics Data System (ADS)

Appleton, R.; van Maanen, P. P.; Fisher, W. I.; Krijnen, R.

2017-12-01

Due to their complexity and size, visualization of meteorological data is important. It enables the precise examining and reviewing of meteorological details and is used as a communication tool for reporting, education and to demonstrate the importance of the data to policy makers. Specifically for the UCAR community it is important to explore all of such possibilities.Virtual Reality (VR) technology enhances the visualization of volumetric and dynamical data in a more natural way as compared to a standard desktop, keyboard mouse setup. The use of VR for data visualization is not new but recent developments has made expensive hardware and complex setups unnecessary. The availability of consumer of the shelf VR hardware enabled us to create a very intuitive and low cost way to visualize meteorological data. A VR viewer has been implemented using multiple HTC Vive head sets and allows visualization and analysis of meteorological data in NetCDF format (e.g. of NCEP North America Model (NAM), see figure). Sources of atmospheric/meteorological data include radar and satellite as well as traditional weather stations. The data includes typical meteorological information such as temperature, humidity, air pressure, as well as those data described by the climate forecast (CF) model conventions (http://cfconventions.org). Other data such as lightning-strike data and ultra-high-resolution satellite data are also becoming available. The users can navigate freely around the data which is presented in a virtual room at a scale of up to 3.5 X 3.5 meters. The multiple users can manipulate the model simultaneously. Possible mutations include scaling/translating, filtering by value and using a slicing tool to cut-off specific sections of the data to get a closer look. The slicing can be done in any direction using the concept of a `virtual knife' in real-time. The users can also scoop out parts of the data and walk though successive states of the model. Future plans are (a.o.) to further improve the performance to a higher update rate (for the reduction of possible motion sickness) and to add more advanced filtering and annotation capabilities. We are looking for cooperation with data owners with use cases such as the above mentioned. This will help in further improving and developing our tool and to broaden its application into other domains.

Quantum mechanical wavefunction: visualization at undergraduate level

NASA Astrophysics Data System (ADS)

Chhabra, Mahima; Das, Ritwick

2017-01-01

Quantum mechanics (QM) forms the most crucial ingredient of modern-era physical science curricula at undergraduate level. The abstract ideas involved in QM related concepts pose a challenge towards appropriate visualization as a consequence of their counter-intuitive nature and lack of experiment-assisted visualization tools. At the heart of the quantum mechanical formulation lies the concept of ‘wavefunction’, which forms the basis for understanding the behavior of physical systems. At undergraduate level, the concept of ‘wavefunction’ is introduced in an abstract framework using mathematical tools and therefore opens up an enormous scope for alternative conceptions and erroneous visualization. The present work is an attempt towards exploring the visualization models constructed by undergraduate students for appreciating the concept of ‘wavefunction’. We present a qualitative analysis of the data obtained from administering a questionnaire containing four visualization based questions on the topic of ‘wavefunction’ to a group of ten undergraduate-level students at an institute in India which excels in teaching and research of basic sciences. Based on the written responses, all ten students were interviewed in detail to unravel the exact areas of difficulty in visualization of ‘wavefunction’. The outcome of present study not only reveals the gray areas in students’ conceptualization, but also provides a plausible route to address the issues at the pedagogical level within the classroom.

Screening methods for post-stroke visual impairment: a systematic review.

PubMed

Hanna, Kerry Louise; Hepworth, Lauren Rachel; Rowe, Fiona

2017-12-01

To provide a systematic overview of the various tools available to screen for post-stroke visual impairment. A review of the literature was conducted including randomised controlled trials, controlled trials, cohort studies, observational studies, systematic reviews and retrospective medical note reviews. All languages were included and translation was obtained. Participants included adults ≥18 years old diagnosed with a visual impairment as a direct cause of a stroke. We searched a broad range of scholarly online resources and hand-searched articles registers of published, unpublished and on-going trials. Search terms included a variety of MESH terms and alternatives in relation to stroke and visual conditions. Study selection was performed by two authors independently. The quality of the evidence and risk of bias were assessed using the STROBE, GRACE and PRISMA statements. A total of 25 articles (n = 2924) were included in this review. Articles appraised reported on tools screening solely for visual impairments or for general post-stroke disabilities inclusive of vision. The majority of identified tools screen for visual perception including visual neglect (VN), with few screening for visual acuity (VA), visual field (VF) loss or ocular motility (OM) defects. Six articles reported on nine screening tools which combined visual screening assessment alongside screening for general stroke disabilities. Of these, three included screening for VA; three screened for VF loss; three screened for OM defects and all screened for VN. Two tools screened for all visual impairments. A further 19 articles were found which reported on individual vision screening tests in stroke populations; two for VF loss; 11 for VN and six for other visual perceptual defects. Most tools cannot accurately account for those with aphasia or communicative deficits, which are common problems following a stroke. There is currently no standardised visual screening tool which can accurately assess all potential post-stroke visual impairments. The current tools screen for only a number of potential stroke-related impairments, which means many visual defects may be missed. The sensitivity of those which screen for all impairments is significantly lowered when patients are unable to report their visual symptoms. Future research is required to develop a tool capable of assessing stroke patients which encompasses all potential visual deficits and can also be easily performed by both the patients and administered by health care professionals in order to ensure all stroke survivors with visual impairment are accurately identified and managed. Implications for Rehabilitation Over 65% of stroke survivors will suffer from a visual impairment, whereas 45% of stroke units do not assess vision. Visual impairment significantly reduces the quality of life, such as being unable to return to work, driving and depression. This review outlines the available screening methods to accurately identify stroke survivors with visual impairments. Identifying visual impairment after stroke can aid general rehabilitation and thus, improve the quality of life for these patients.

Assessing Local Model Adequacy in Bayesian Hierarchical Models Using the Partitioned Deviance Information Criterion

PubMed Central

Wheeler, David C.; Hickson, DeMarc A.; Waller, Lance A.

2010-01-01

Many diagnostic tools and goodness-of-fit measures, such as the Akaike information criterion (AIC) and the Bayesian deviance information criterion (DIC), are available to evaluate the overall adequacy of linear regression models. In addition, visually assessing adequacy in models has become an essential part of any regression analysis. In this paper, we focus on a spatial consideration of the local DIC measure for model selection and goodness-of-fit evaluation. We use a partitioning of the DIC into the local DIC, leverage, and deviance residuals to assess local model fit and influence for both individual observations and groups of observations in a Bayesian framework. We use visualization of the local DIC and differences in local DIC between models to assist in model selection and to visualize the global and local impacts of adding covariates or model parameters. We demonstrate the utility of the local DIC in assessing model adequacy using HIV prevalence data from pregnant women in the Butare province of Rwanda during 1989-1993 using a range of linear model specifications, from global effects only to spatially varying coefficient models, and a set of covariates related to sexual behavior. Results of applying the diagnostic visualization approach include more refined model selection and greater understanding of the models as applied to the data. PMID:21243121

D Modelling and Visualization Based on the Unity Game Engine - Advantages and Challenges

NASA Astrophysics Data System (ADS)

Buyuksalih, I.; Bayburt, S.; Buyuksalih, G.; Baskaraca, A. P.; Karim, H.; Rahman, A. A.

2017-11-01

3D City modelling is increasingly popular and becoming valuable tools in managing big cities. Urban and energy planning, landscape, noise-sewage modelling, underground mapping and navigation are among the applications/fields which really depend on 3D modelling for their effectiveness operations. Several research areas and implementation projects had been carried out to provide the most reliable 3D data format for sharing and functionalities as well as visualization platform and analysis. For instance, BIMTAS company has recently completed a project to estimate potential solar energy on 3D buildings for the whole Istanbul and now focussing on 3D utility underground mapping for a pilot case study. The research and implementation standard on 3D City Model domain (3D data sharing and visualization schema) is based on CityGML schema version 2.0. However, there are some limitations and issues in implementation phase for large dataset. Most of the limitations were due to the visualization, database integration and analysis platform (Unity3D game engine) as highlighted in this paper.

Adapting the iSNOBAL model for improved visualization in a GIS environment

NASA Astrophysics Data System (ADS)

Johansen, W. J.; Delparte, D.

2014-12-01

Snowmelt is a primary means of crucial water resources in much of the western United States. Researchers are developing models that estimate snowmelt to aid in water resource management. One such model is the image snowcover energy and mass balance (iSNOBAL) model. It uses input climate grids to simulate the development and melting of snowpack in mountainous regions. This study looks at applying this model to the Reynolds Creek Experimental Watershed in southwestern Idaho, utilizing novel approaches incorporating geographic information systems (GIS). To improve visualization of the iSNOBAL model, we have adapted it to run in a GIS environment. This type of environment is suited to both the input grid creation and the visualization of results. The data used for input grid creation can be stored locally or on a web-server. Kriging interpolation embedded within Python scripts are used to create air temperature, soil temperature, humidity, and precipitation grids, while built-in GIS and existing tools are used to create solar radiation and wind grids. Additional Python scripting is then used to perform model calculations. The final product is a user-friendly and accessible version of the iSNOBAL model, including the ability to easily visualize and interact with model results, all within a web- or desktop-based GIS environment. This environment allows for interactive manipulation of model parameters and visualization of the resulting input grids for the model calculations. Future work is moving towards adapting the model further for use in a 3D gaming engine for improved visualization and interaction.

Evaluating the Use of Cleft Lip and Palate 3D-Printed Models as a Teaching Aid.

PubMed

AlAli, Ahmad B; Griffin, Michelle F; Calonge, Wenceslao M; Butler, Peter E

Visualization tools are essential for effective medical education, to aid students understanding of complex anatomical systems. Three dimensional (3D) printed models are showing a wide-reaching potential in the field of medical education, to aid the interpretation of 2D imaging. This study investigates the use of 3D-printed models in educational seminars on cleft lip and palate, by comparing integrated "hands-on" student seminars, with 2D presentation seminar methods. Cleft lip and palate models were manufactured using 3D-printing technology at the medical school. Sixty-seven students from two medical schools participated in the study. The students were randomly allocated to 2 groups. Knowledge was compared between the groups using a multiple-choice question test before and after the teaching intervention. Group 1 was the control group with a PowerPoint presentation-based educational seminar and group 2 was the test group, with the same PowerPoint presentation, but with the addition of a physical demonstration using 3D-printed models of unilateral and bilateral cleft lips and palate. The level of knowledge gained was established using a preseminar and postseminar assessment, in 2 different institutions, where the addition of the 3D-printed model resulted in a significant improvement in the mean percentage of knowledge gained (44.65% test group; 32.16%; control group; p = 0.038). Student experience was assessed using a postseminar survey, where students felt the 3D-printed model significantly improved the learning experience (p = 0.005) and their visualization (p = 0.001). This study highlights the benefits of the use of 3D-printed models as visualization tools in medical education and the potential of 3D-printing technology to become a standard and effective tool in the interpretation of 2D imaging. Copyright © 2018 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

Learn to Teach Chemistry Using Visual Media Tools

ERIC Educational Resources Information Center

Turkoguz, Suat

2012-01-01

The aim of this study was to investigate undergraduate students' attitudes to using visual media tools in the chemistry laboratory. One hundred and fifteen undergraduates studying science education at Dokuz Eylul University, Turkey participated in the study. They video-recorded chemistry experiments with visual media tools and assessed them on a…

Web-based visual analysis for high-throughput genomics

PubMed Central

2013-01-01

Background Visualization plays an essential role in genomics research by making it possible to observe correlations and trends in large datasets as well as communicate findings to others. Visual analysis, which combines visualization with analysis tools to enable seamless use of both approaches for scientific investigation, offers a powerful method for performing complex genomic analyses. However, there are numerous challenges that arise when creating rich, interactive Web-based visualizations/visual analysis applications for high-throughput genomics. These challenges include managing data flow from Web server to Web browser, integrating analysis tools and visualizations, and sharing visualizations with colleagues. Results We have created a platform simplifies the creation of Web-based visualization/visual analysis applications for high-throughput genomics. This platform provides components that make it simple to efficiently query very large datasets, draw common representations of genomic data, integrate with analysis tools, and share or publish fully interactive visualizations. Using this platform, we have created a Circos-style genome-wide viewer, a generic scatter plot for correlation analysis, an interactive phylogenetic tree, a scalable genome browser for next-generation sequencing data, and an application for systematically exploring tool parameter spaces to find good parameter values. All visualizations are interactive and fully customizable. The platform is integrated with the Galaxy (http://galaxyproject.org) genomics workbench, making it easy to integrate new visual applications into Galaxy. Conclusions Visualization and visual analysis play an important role in high-throughput genomics experiments, and approaches are needed to make it easier to create applications for these activities. Our framework provides a foundation for creating Web-based visualizations and integrating them into Galaxy. Finally, the visualizations we have created using the framework are useful tools for high-throughput genomics experiments. PMID:23758618

In Internet-Based Visualization System Study about Breakthrough Applet Security Restrictions

NASA Astrophysics Data System (ADS)

Chen, Jie; Huang, Yan

In the process of realization Internet-based visualization system of the protein molecules, system needs to allow users to use the system to observe the molecular structure of the local computer, that is, customers can generate the three-dimensional graphics from PDB file on the client computer. This requires Applet access to local file, related to the Applet security restrictions question. In this paper include two realization methods: 1.Use such as signature tools, key management tools and Policy Editor tools provided by the JDK to digital signature and authentication for Java Applet, breakthrough certain security restrictions in the browser. 2. Through the use of Servlet agent implement indirect access data methods, breakthrough the traditional Java Virtual Machine sandbox model restriction of Applet ability. The two ways can break through the Applet's security restrictions, but each has its own strengths.

Impact of oral health education by audio aids, braille and tactile models on the oral health status of visually impaired children of Bhopal City.

PubMed

Gautam, Anjali; Bhambal, Ajay; Moghe, Swapnil

2018-01-01

Children with special needs face unique challenges in day-to-day practice. They are dependent on their close ones for everything. To improve oral hygiene in such visually impaired children, undue training and education are required. Braille is an important language for reading and writing for the visually impaired. It helps them understand and visualize the world via touch. Audio aids are being used to impart health education to the visually impaired. Tactile models help them perceive things which they cannot visualize and hence are an important learning tool. This study aimed to assess the improvement in oral hygiene by audio aids and Braille and tactile models in visually impaired children aged 6-16 years of Bhopal city. This was a prospective study. Sixty visually impaired children aged 6-16 years were selected and randomly divided into three groups (20 children each). Group A: audio aids + Braille, Group B: audio aids + tactile models, and Group C: audio aids + Braille + tactile models. Instructions were given for maintaining good oral hygiene and brushing techniques were explained to all children. After 3 months' time, the oral hygiene status was recorded and compared using plaque and gingival index. ANNOVA test was used. The present study showed a decrease in the mean plaque and gingival scores at all time intervals in individual group as compared to that of the baseline that was statistically significant. The study depicts that the combination of audio aids, Braille and tactile models is an effective way to provide oral health education and improve oral health status of visually impaired children.

Bridging Theory with Practice: An Exploratory Study of Visualization Use and Design for Climate Model Comparison

DOE PAGES

Dasgupta, Aritra; Poco, Jorge; Wei, Yaxing; ...

2015-03-16

Evaluation methodologies in visualization have mostly focused on how well the tools and techniques cater to the analytical needs of the user. While this is important in determining the effectiveness of the tools and advancing the state-of-the-art in visualization research, a key area that has mostly been overlooked is how well established visualization theories and principles are instantiated in practice. This is especially relevant when domain experts, and not visualization researchers, design visualizations for analysis of their data or for broader dissemination of scientific knowledge. There is very little research on exploring the synergistic capabilities of cross-domain collaboration between domainmore » experts and visualization researchers. To fill this gap, in this paper we describe the results of an exploratory study of climate data visualizations conducted in tight collaboration with a pool of climate scientists. The study analyzes a large set of static climate data visualizations for identifying their shortcomings in terms of visualization design. The outcome of the study is a classification scheme that categorizes the design problems in the form of a descriptive taxonomy. The taxonomy is a first attempt for systematically categorizing the types, causes, and consequences of design problems in visualizations created by domain experts. We demonstrate the use of the taxonomy for a number of purposes, such as, improving the existing climate data visualizations, reflecting on the impact of the problems for enabling domain experts in designing better visualizations, and also learning about the gaps and opportunities for future visualization research. We demonstrate the applicability of our taxonomy through a number of examples and discuss the lessons learnt and implications of our findings.« less

Bridging Theory with Practice: An Exploratory Study of Visualization Use and Design for Climate Model Comparison

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dasgupta, Aritra; Poco, Jorge; Wei, Yaxing

Evaluation methodologies in visualization have mostly focused on how well the tools and techniques cater to the analytical needs of the user. While this is important in determining the effectiveness of the tools and advancing the state-of-the-art in visualization research, a key area that has mostly been overlooked is how well established visualization theories and principles are instantiated in practice. This is especially relevant when domain experts, and not visualization researchers, design visualizations for analysis of their data or for broader dissemination of scientific knowledge. There is very little research on exploring the synergistic capabilities of cross-domain collaboration between domainmore » experts and visualization researchers. To fill this gap, in this paper we describe the results of an exploratory study of climate data visualizations conducted in tight collaboration with a pool of climate scientists. The study analyzes a large set of static climate data visualizations for identifying their shortcomings in terms of visualization design. The outcome of the study is a classification scheme that categorizes the design problems in the form of a descriptive taxonomy. The taxonomy is a first attempt for systematically categorizing the types, causes, and consequences of design problems in visualizations created by domain experts. We demonstrate the use of the taxonomy for a number of purposes, such as, improving the existing climate data visualizations, reflecting on the impact of the problems for enabling domain experts in designing better visualizations, and also learning about the gaps and opportunities for future visualization research. We demonstrate the applicability of our taxonomy through a number of examples and discuss the lessons learnt and implications of our findings.« less

Delta: a new web-based 3D genome visualization and analysis platform.

PubMed

Tang, Bixia; Li, Feifei; Li, Jing; Zhao, Wenming; Zhang, Zhihua

2018-04-15

Delta is an integrative visualization and analysis platform to facilitate visually annotating and exploring the 3D physical architecture of genomes. Delta takes Hi-C or ChIA-PET contact matrix as input and predicts the topologically associating domains and chromatin loops in the genome. It then generates a physical 3D model which represents the plausible consensus 3D structure of the genome. Delta features a highly interactive visualization tool which enhances the integration of genome topology/physical structure with extensive genome annotation by juxtaposing the 3D model with diverse genomic assay outputs. Finally, by visually comparing the 3D model of the β-globin gene locus and its annotation, we speculated a plausible transitory interaction pattern in the locus. Experimental evidence was found to support this speculation by literature survey. This served as an example of intuitive hypothesis testing with the help of Delta. Delta is freely accessible from http://delta.big.ac.cn, and the source code is available at https://github.com/zhangzhwlab/delta. zhangzhihua@big.ac.cn. Supplementary data are available at Bioinformatics online.

Visual Illusions: An Interesting Tool to Investigate Developmental Dyslexia and Autism Spectrum Disorder

PubMed Central

Gori, Simone; Molteni, Massimo; Facoetti, Andrea

2016-01-01

A visual illusion refers to a percept that is different in some aspect from the physical stimulus. Illusions are a powerful non-invasive tool for understanding the neurobiology of vision, telling us, indirectly, how the brain processes visual stimuli. There are some neurodevelopmental disorders characterized by visual deficits. Surprisingly, just a few studies investigated illusory perception in clinical populations. Our aim is to review the literature supporting a possible role for visual illusions in helping us understand the visual deficits in developmental dyslexia and autism spectrum disorder. Future studies could develop new tools – based on visual illusions – to identify an early risk for neurodevelopmental disorders. PMID:27199702

Construction and completion of flux balance models from pathway databases.

PubMed

Latendresse, Mario; Krummenacker, Markus; Trupp, Miles; Karp, Peter D

2012-02-01

Flux balance analysis (FBA) is a well-known technique for genome-scale modeling of metabolic flux. Typically, an FBA formulation requires the accurate specification of four sets: biochemical reactions, biomass metabolites, nutrients and secreted metabolites. The development of FBA models can be time consuming and tedious because of the difficulty in assembling completely accurate descriptions of these sets, and in identifying errors in the composition of these sets. For example, the presence of a single non-producible metabolite in the biomass will make the entire model infeasible. Other difficulties in FBA modeling are that model distributions, and predicted fluxes, can be cryptic and difficult to understand. We present a multiple gap-filling method to accelerate the development of FBA models using a new tool, called MetaFlux, based on mixed integer linear programming (MILP). The method suggests corrections to the sets of reactions, biomass metabolites, nutrients and secretions. The method generates FBA models directly from Pathway/Genome Databases. Thus, FBA models developed in this framework are easily queried and visualized using the Pathway Tools software. Predicted fluxes are more easily comprehended by visualizing them on diagrams of individual metabolic pathways or of metabolic maps. MetaFlux can also remove redundant high-flux loops, solve FBA models once they are generated and model the effects of gene knockouts. MetaFlux has been validated through construction of FBA models for Escherichia coli and Homo sapiens. Pathway Tools with MetaFlux is freely available to academic users, and for a fee to commercial users. Download from: biocyc.org/download.shtml. mario.latendresse@sri.com Supplementary data are available at Bioinformatics online.

Flow visualization and modeling for education and outreach in low-income countries

NASA Astrophysics Data System (ADS)

Motanated, K.

2016-12-01

Being able to visualize the dynamic interaction between the movement of water and sediment flux is undeniably a profound tool for students and novices to understand complicated earth surface processes. In a laser-sheet flow visualization technique, a light source that is thin and monochromatic is required to illuminate sediments or tracers in the flow. However, an ideal laser sheet generator is rather expensive, especially for schools and universities residing in low-income countries. This project is proposing less-expensive options for a laser-sheet source and flow visualization experiment configuration for qualitative observation and quantitative analysis of the interaction between fluid media and sediments. Here, Fresnel lens is used to convert from point laser into sheet laser. Multiple combinations of laser diodes of various wavelength (nanometer) and power (milliwatt) and Fresnel lenses of various dimensions are analyzed. The pair that is able to produce the thinnest and brightest light sheet is not only effective but also affordable. The motion of sediments in a flow can be observed by illuminating the laser-sheet in an interested flow region. The particle motion is recorded by a video camera that is capable of taking multiple frames per second and having a narrow depth of view. The recorded video file can be played in a slow-motion mode so students can visually observe and qualitatively analyze the particle motion. An open source software package for Particle Imaging Velocimetry (PIV) can calculate the local velocity of particles from still images extracted from the video and create a vector map depicting particle motion. This flow visualization experiment is inexpensive and the configuration is simple to setup. Most importantly, this flow visualization technique serves as a fundamental tool for earth surface process education and can further be applied to sedimentary process modeling.

Visualization and simulated surgery of the left ventricle in the virtual pathological heart of the Virtual Physiological Human

PubMed Central

McFarlane, N. J. B.; Lin, X.; Zhao, Y.; Clapworthy, G. J.; Dong, F.; Redaelli, A.; Parodi, O.; Testi, D.

2011-01-01

Ischaemic heart failure remains a significant health and economic problem worldwide. This paper presents a user-friendly software system that will form a part of the virtual pathological heart of the Virtual Physiological Human (VPH2) project, currently being developed under the European Commission Virtual Physiological Human (VPH) programme. VPH2 is an integrated medicine project, which will create a suite of modelling, simulation and visualization tools for patient-specific prediction and planning in cases of post-ischaemic left ventricular dysfunction. The work presented here describes a three-dimensional interactive visualization for simulating left ventricle restoration surgery, comprising the operations of cutting, stitching and patching, and for simulating the elastic deformation of the ventricle to its post-operative shape. This will supply the quantitative measurements required for the post-operative prediction tools being developed in parallel in the same project. PMID:22670207

Visualization of risk of radiogenic second cancer in the organs and tissues of the human body.

PubMed

Zhang, Rui; Mirkovic, Dragan; Newhauser, Wayne D

2015-04-28

Radiogenic second cancer is a common late effect in long term cancer survivors. Currently there are few methods or tools available to visually evaluate the spatial distribution of risks of radiogenic late effects in the human body. We developed a risk visualization method and demonstrated it for radiogenic second cancers in tissues and organs of one patient treated with photon volumetric modulated arc therapy and one patient treated with proton craniospinal irradiation. Treatment plans were generated using radiotherapy treatment planning systems (TPS) and dose information was obtained from TPS. Linear non-threshold risk coefficients for organs at risk of second cancer incidence were taken from the Biological Effects of Ionization Radiation VII report. Alternative risk models including linear exponential model and linear plateau model were also examined. The predicted absolute lifetime risk distributions were visualized together with images of the patient anatomy. The risk distributions of second cancer for the two patients were visually presented. The risk distributions varied with tissue, dose, dose-risk model used, and the risk distribution could be similar to or very different from the dose distribution. Our method provides a convenient way to directly visualize and evaluate the risks of radiogenic second cancer in organs and tissues of the human body. In the future, visual assessment of risk distribution could be an influential determinant for treatment plan scoring.

FireMap: A Web Tool for Dynamic Data-Driven Predictive Wildfire Modeling Powered by the WIFIRE Cyberinfrastructure

NASA Astrophysics Data System (ADS)

Block, J.; Crawl, D.; Artes, T.; Cowart, C.; de Callafon, R.; DeFanti, T.; Graham, J.; Smarr, L.; Srivas, T.; Altintas, I.

2016-12-01

The NSF-funded WIFIRE project has designed a web-based wildfire modeling simulation and visualization tool called FireMap. The tool executes FARSITE to model fire propagation using dynamic weather and fire data, configuration settings provided by the user, and static topography and fuel datasets already built-in. Using GIS capabilities combined with scalable big data integration and processing, FireMap enables simple execution of the model with options for running ensembles by taking the information uncertainty into account. The results are easily viewable, sharable, repeatable, and can be animated as a time series. From these capabilities, users can model real-time fire behavior, analyze what-if scenarios, and keep a history of model runs over time for sharing with collaborators. Firemap runs FARSITE with national and local sensor networks for real-time weather data ingestion and High-Resolution Rapid Refresh (HRRR) weather for forecasted weather. The HRRR is a NOAA/NCEP operational weather prediction system comprised of a numerical forecast model and an analysis/assimilation system to initialize the model. It is run with a horizontal resolution of 3 km, has 50 vertical levels, and has a temporal resolution of 15 minutes. The HRRR requires an Environmental Data Exchange (EDEX) server to receive the feed and generate secondary products out of it for the modeling. UCSD's EDEX server, funded by NSF, makes high-resolution weather data available to researchers worldwide and enables visualization of weather systems and weather events lasting months or even years. The high-speed server aggregates weather data from the University Consortium for Atmospheric Research by way of a subscription service from the Consortium called the Internet Data Distribution system. These features are part of WIFIRE's long term goals to build an end-to-end cyberinfrastructure for real-time and data-driven simulation, prediction and visualization of wildfire behavior. Although Firemap is a research product of WIFIRE, developed in collaboration with a number of fire departments, the tool is operational in pilot form for providing big data-driven predictive fire spread modeling. Most recently, FireMap was used for situational awareness in the July 2016 Sand Fire by LA City and LA County Fire Departments.

The Tools, Approaches and Applications of Visual Literacy in the Visual Arts Department of Cross River University of Technology, Calabar, Nigeria

ERIC Educational Resources Information Center

Ecoma, Victor

2016-01-01

The paper reflects upon the tools, approaches and applications of visual literacy in the Visual Arts Department of Cross River University of Technology, Calabar, Nigeria. The objective of the discourse is to examine how the visual arts training and practice equip students with skills in visual literacy through methods of production, materials and…

Pathways to Identity: Aiding Law Enforcement in Identification Tasks With Visual Analytics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bruce, Joseph R.; Scholtz, Jean; Hodges, Duncan

The nature of identity has changed dramatically in recent years, and has grown in complexity. Identities are defined in multiple domains: biological and psychological elements strongly contribute, but also biographical and cyber elements are necessary to complete the picture. Law enforcement is beginning to adjust to these changes, recognizing its importance in criminal justice. The SuperIdentity project seeks to aid law enforcement officials in their identification tasks through research of techniques for discovering identity traits, generation of statistical models of identity and analysis of identity traits through visualization. We present use cases compiled through user interviews in multiple fields, includingmore » law enforcement, as well as the modeling and visualization tools design to aid in those use cases.« less

Pathways to Identity. Using Visualization to Aid Law Enforcement in Identification Tasks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bruce, Joseph R.; Scholtz, Jean; Hodges, Duncan

The nature of identity has changed dramatically in recent years and has grown in complexity. Identities are defined in multiple domains: biological and psychological elements strongly contribute, but biographical and cyber elements also are necessary to complete the picture. Law enforcement is beginning to adjust to these changes, recognizing identity’s importance in criminal justice. The SuperIdentity project seeks to aid law enforcement officials in their identification tasks through research of techniques for discovering identity traits, generation of statistical models of identity and analysis of identity traits through visualization. We present use cases compiled through user interviews in multiple fields, includingmore » law enforcement, and describe the modeling and visualization tools design to aid in those use cases.« less

Linking Science and Management in an Interactive Geospatial, Mutli-Criterion, Structured Decision Support Framework: Use Case Studies of the "Future Forests Geo-visualization and Decision Support Tool

NASA Astrophysics Data System (ADS)

Pontius, J.; Duncan, J.

2017-12-01

Land managers are often faced with balancing management activities to accomplish a diversity of management objectives, in systems faced with many stress agents. Advances in ecosystem modeling provide a rich source of information to inform management. Coupled with advances in decision support techniques and computing capabilities, interactive tools are now accessible for a broad audience of stakeholders. Here we present one such tool designed to capture information on how climate change may impact forested ecosystems, and how that impact varies spatially across the landscape. This tool integrates empirical models of current and future forest structure and function in a structured decision framework that allows users to customize weights for multiple management objectives and visualize suitability outcomes across the landscape. Combined with climate projections, the resulting products allow stakeholders to compare the relative success of various management objectives on a pixel by pixel basis and identify locations where management outcomes are most likely to be met. Here we demonstrate this approach with the integration of several of the preliminary models developed to map species distributions, sugar maple health, forest fragmentation risk and hemlock vulnerability to hemlock woolly adelgid under current and future climate scenarios. We compare three use case studies with objective weightings designed to: 1) Identify key parcels for sugarbush conservation and management, 2) Target state lands that may serve as hemlock refugia from hemlock woolly adelgid induced mortality, and 3) Examine how climate change may alter the success of managing for both sugarbush and hemlock across privately owned lands. This tool highlights the value of flexible models that can be easily run with customized weightings in a dynamic, integrated assessment that allows users to hone in on their potentially complex management objectives, and to visualize and prioritize locations across the landscape. It also demonstrates the importance of including climate considerations for long-term management. This merging of scientific knowledge with the diversity of stakeholder needs is an important step towards using science to inform management and policy decisions.

Collaboratively Conceived, Designed and Implemented: Matching Visualization Tools with Geoscience Data Collections and Geoscience Data Collections with Visualization Tools via the ToolMatch Service.

NASA Astrophysics Data System (ADS)

Hoebelheinrich, N. J.; Lynnes, C.; West, P.; Ferritto, M.

2014-12-01

Two problems common to many geoscience domains are the difficulties in finding tools to work with a given dataset collection, and conversely, the difficulties in finding data for a known tool. A collaborative team from the Earth Science Information Partnership (ESIP) has gotten together to design and create a web service, called ToolMatch, to address these problems. The team began their efforts by defining an initial, relatively simple conceptual model that addressed the two uses cases briefly described above. The conceptual model is expressed as an ontology using OWL (Web Ontology Language) and DCterms (Dublin Core Terms), and utilizing standard ontologies such as DOAP (Description of a Project), FOAF (Friend of a Friend), SKOS (Simple Knowledge Organization System) and DCAT (Data Catalog Vocabulary). The ToolMatch service will be taking advantage of various Semantic Web and Web standards, such as OpenSearch, RESTful web services, SWRL (Semantic Web Rule Language) and SPARQL (Simple Protocol and RDF Query Language). The first version of the ToolMatch service was deployed in early fall 2014. While more complete testing is required, a number of communities besides ESIP member organizations have expressed interest in collaborating to create, test and use the service and incorporate it into their own web pages, tools and / or services including the USGS Data Catalog service, DataONE, the Deep Carbon Observatory, Virtual Solar Terrestrial Observatory (VSTO), and the U.S. Global Change Research Program. In this session, presenters will discuss the inception and development of the ToolMatch service, the collaborative process used to design, refine, and test the service, and future plans for the service.

Virtual reality hardware for use in interactive 3D data fusion and visualization

NASA Astrophysics Data System (ADS)

Gourley, Christopher S.; Abidi, Mongi A.

1997-09-01

Virtual reality has become a tool for use in many areas of research. We have designed and built a VR system for use in range data fusion and visualization. One major VR tool is the CAVE. This is the ultimate visualization tool, but comes with a large price tag. Our design uses a unique CAVE whose graphics are powered by a desktop computer instead of a larger rack machine making it much less costly. The system consists of a screen eight feet tall by twenty-seven feet wide giving a variable field-of-view currently set at 160 degrees. A silicon graphics Indigo2 MaxImpact with the impact channel option is used for display. This gives the capability to drive three projectors at a resolution of 640 by 480 for use in displaying the virtual environment and one 640 by 480 display for a user control interface. This machine is also the first desktop package which has built-in hardware texture mapping. This feature allows us to quickly fuse the range and intensity data and other multi-sensory data. The final goal is a complete 3D texture mapped model of the environment. A dataglove, magnetic tracker, and spaceball are to be used for manipulation of the data and navigation through the virtual environment. This system gives several users the ability to interactively create 3D models from multiple range images.

2014 Earth System Grid Federation and Ultrascale Visualization Climate Data Analysis Tools Conference Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, Dean N.

2015-01-27

The climate and weather data science community met December 9–11, 2014, in Livermore, California, for the fourth annual Earth System Grid Federation (ESGF) and Ultrascale Visualization Climate Data Analysis Tools (UV-CDAT) Face-to-Face (F2F) Conference, hosted by the Department of Energy, National Aeronautics and Space Administration, National Oceanic and Atmospheric Administration, the European Infrastructure for the European Network of Earth System Modelling, and the Australian Department of Education. Both ESGF and UVCDATremain global collaborations committed to developing a new generation of open-source software infrastructure that provides distributed access and analysis to simulated and observed data from the climate and weather communities.more » The tools and infrastructure created under these international multi-agency collaborations are critical to understanding extreme weather conditions and long-term climate change. In addition, the F2F conference fosters a stronger climate and weather data science community and facilitates a stronger federated software infrastructure. The 2014 F2F conference detailed the progress of ESGF, UV-CDAT, and other community efforts over the year and sets new priorities and requirements for existing and impending national and international community projects, such as the Coupled Model Intercomparison Project Phase Six. Specifically discussed at the conference were project capabilities and enhancements needs for data distribution, analysis, visualization, hardware and network infrastructure, standards, and resources.« less

Resources for Designing, Selecting and Teaching with Visualizations in the Geoscience Classroom

NASA Astrophysics Data System (ADS)

Kirk, K. B.; Manduca, C. A.; Ormand, C. J.; McDaris, J. R.

2009-12-01

Geoscience is a highly visual field, and effective use of visualizations can enhance student learning, appeal to students’ emotions and help them acquire skills for interpreting visual information. The On the Cutting Edge website, “Teaching Geoscience with Visualizations” presents information of interest to faculty who are teaching with visualizations, as well as those who are designing visualizations. The website contains best practices for effective visualizations, drawn from the educational literature and from experts in the field. For example, a case is made for careful selection of visualizations so that faculty can align the correct visualization with their teaching goals and audience level. Appropriate visualizations will contain the desired geoscience content without adding extraneous information that may distract or confuse students. Features such as labels, arrows and contextual information can help guide students through imagery and help to explain the relevant concepts. Because students learn by constructing their own mental image of processes, it is helpful to select visualizations that reflect the same type of mental picture that students should create. A host of recommended readings and presentations from the On the Cutting Edge visualization workshops can provide further grounding for the educational uses of visualizations. Several different collections of visualizations, datasets with visualizations and visualization tools are available on the website. Examples include animations of tsunamis, El Nino conditions, braided stream formation and mountain uplift. These collections are grouped by topic and range from simple animations to interactive models. A series of example activities that incorporate visualizations into classroom and laboratory activities illustrate various tactics for using these materials in different types of settings. Activities cover topics such as ocean circulation, land use changes, earthquake simulations and the use of Google Earth to explore geologic processes. These materials can be found at http://serc.carleton.edu/NAGTWorkshops/visualization. Faculty and developers of visualization tools are encouraged to submit teaching activities, references or visualizations to the collections.

Identifying and tracking attacks on networks: C3I displays and related technologies

NASA Astrophysics Data System (ADS)

Manes, Gavin W.; Dawkins, J.; Shenoi, Sujeet; Hale, John C.

2003-09-01

Converged network security is extremely challenging for several reasons; expanded system and technology perimeters, unexpected feature interaction, and complex interfaces all conspire to provide hackers with greater opportunities for compromising large networks. Preventive security services and architectures are essential, but in and of themselves do not eliminate all threat of compromise. Attack management systems mitigate this residual risk by facilitating incident detection, analysis and response. There are a wealth of attack detection and response tools for IP networks, but a dearth of such tools for wireless and public telephone networks. Moreover, methodologies and formalisms have yet to be identified that can yield a common model for vulnerabilities and attacks in converged networks. A comprehensive attack management system must coordinate detection tools for converged networks, derive fully-integrated attack and network models, perform vulnerability and multi-stage attack analysis, support large-scale attack visualization, and orchestrate strategic responses to cyber attacks that cross network boundaries. We present an architecture that embodies these principles for attack management. The attack management system described engages a suite of detection tools for various networking domains, feeding real-time attack data to a comprehensive modeling, analysis and visualization subsystem. The resulting early warning system not only provides network administrators with a heads-up cockpit display of their entire network, it also supports guided response and predictive capabilities for multi-stage attacks in converged networks.

Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms

PubMed Central

Stone, John E.; Hynninen, Antti-Pekka; Phillips, James C.; Schulten, Klaus

2017-01-01

All-atom molecular dynamics simulations of biomolecules provide a powerful tool for exploring the structure and dynamics of large protein complexes within realistic cellular environments. Unfortunately, such simulations are extremely demanding in terms of their computational requirements, and they present many challenges in terms of preparation, simulation methodology, and analysis and visualization of results. We describe our early experiences porting the popular molecular dynamics simulation program NAMD and the simulation preparation, analysis, and visualization tool VMD to GPU-accelerated OpenPOWER hardware platforms. We report our experiences with compiler-provided autovectorization and compare with hand-coded vector intrinsics for the POWER8 CPU. We explore the performance benefits obtained from unique POWER8 architectural features such as 8-way SMT and its value for particular molecular modeling tasks. Finally, we evaluate the performance of several GPU-accelerated molecular modeling kernels and relate them to other hardware platforms. PMID:29202130

Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology

PubMed Central

Latendresse, Mario; Paley, Suzanne M.; Krummenacker, Markus; Ong, Quang D.; Billington, Richard; Kothari, Anamika; Weaver, Daniel; Lee, Thomas; Subhraveti, Pallavi; Spaulding, Aaron; Fulcher, Carol; Keseler, Ingrid M.; Caspi, Ron

2016-01-01

Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions. This article outlines the advances in Pathway Tools in the past 5 years. Major additions include components for metabolic modeling, metabolic route search, computation of atom mappings and estimation of compound Gibbs free energies of formation; addition of editors for signaling pathways, for genome sequences and for cellular architecture; storage of gene essentiality data and phenotype data; display of multiple alignments, and of signaling and electron-transport pathways; and development of Python and web-services application programming interfaces. Scientists around the world have created more than 9800 Pathway/Genome Databases by using Pathway Tools, many of which are curated databases for important model organisms. PMID:26454094

Web-based, GPU-accelerated, Monte Carlo simulation and visualization of indirect radiation imaging detector performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dong, Han; Sharma, Diksha; Badano, Aldo, E-mail: aldo.badano@fda.hhs.gov

2014-12-15

Purpose: Monte Carlo simulations play a vital role in the understanding of the fundamental limitations, design, and optimization of existing and emerging medical imaging systems. Efforts in this area have resulted in the development of a wide variety of open-source software packages. One such package, hybridMANTIS, uses a novel hybrid concept to model indirect scintillator detectors by balancing the computational load using dual CPU and graphics processing unit (GPU) processors, obtaining computational efficiency with reasonable accuracy. In this work, the authors describe two open-source visualization interfaces, webMANTIS and visualMANTIS to facilitate the setup of computational experiments via hybridMANTIS. Methods: Themore » visualization tools visualMANTIS and webMANTIS enable the user to control simulation properties through a user interface. In the case of webMANTIS, control via a web browser allows access through mobile devices such as smartphones or tablets. webMANTIS acts as a server back-end and communicates with an NVIDIA GPU computing cluster that can support multiuser environments where users can execute different experiments in parallel. Results: The output consists of point response and pulse-height spectrum, and optical transport statistics generated by hybridMANTIS. The users can download the output images and statistics through a zip file for future reference. In addition, webMANTIS provides a visualization window that displays a few selected optical photon path as they get transported through the detector columns and allows the user to trace the history of the optical photons. Conclusions: The visualization tools visualMANTIS and webMANTIS provide features such as on the fly generation of pulse-height spectra and response functions for microcolumnar x-ray imagers while allowing users to save simulation parameters and results from prior experiments. The graphical interfaces simplify the simulation setup and allow the user to go directly from specifying input parameters to receiving visual feedback for the model predictions.« less

GABBs: Cyberinfrastructure for Self-Service Geospatial Data Exploration, Computation, and Sharing

NASA Astrophysics Data System (ADS)

Song, C. X.; Zhao, L.; Biehl, L. L.; Merwade, V.; Villoria, N.

2016-12-01

Geospatial data are present everywhere today with the proliferation of location-aware computing devices. This is especially true in the scientific community where large amounts of data are driving research and education activities in many domains. Collaboration over geospatial data, for example, in modeling, data analysis and visualization, must still overcome the barriers of specialized software and expertise among other challenges. In addressing these needs, the Geospatial data Analysis Building Blocks (GABBs) project aims at building geospatial modeling, data analysis and visualization capabilities in an open source web platform, HUBzero. Funded by NSF's Data Infrastructure Building Blocks initiative, GABBs is creating a geospatial data architecture that integrates spatial data management, mapping and visualization, and interfaces in the HUBzero platform for scientific collaborations. The geo-rendering enabled Rappture toolkit, a generic Python mapping library, geospatial data exploration and publication tools, and an integrated online geospatial data management solution are among the software building blocks from the project. The GABBS software will be available through Amazon's AWS Marketplace VM images and open source. Hosting services are also available to the user community. The outcome of the project will enable researchers and educators to self-manage their scientific data, rapidly create GIS-enable tools, share geospatial data and tools on the web, and build dynamic workflows connecting data and tools, all without requiring significant software development skills, GIS expertise or IT administrative privileges. This presentation will describe the GABBs architecture, toolkits and libraries, and showcase the scientific use cases that utilize GABBs capabilities, as well as the challenges and solutions for GABBs to interoperate with other cyberinfrastructure platforms.

Graphical Technique to Support the Teaching/Learning Process of Software Process Reference Models

NASA Astrophysics Data System (ADS)

Espinosa-Curiel, Ismael Edrein; Rodríguez-Jacobo, Josefina; Fernández-Zepeda, José Alberto

In this paper, we propose a set of diagrams to visualize software process reference models (PRM). The diagrams, called dimods, are the combination of some visual and process modeling techniques such as rich pictures, mind maps, IDEF and RAD diagrams. We show the use of this technique by designing a set of dimods for the Mexican Software Industry Process Model (MoProSoft). Additionally, we perform an evaluation of the usefulness of dimods. The result of the evaluation shows that dimods may be a support tool that facilitates the understanding, memorization, and learning of software PRMs in both, software development organizations and universities. The results also show that dimods may have advantages over the traditional description methods for these types of models.

Boxes of Model Building and Visualization.

PubMed

Turk, Dušan

2017-01-01

Macromolecular crystallography and electron microscopy (single-particle and in situ tomography) are merging into a single approach used by the two coalescing scientific communities. The merger is a consequence of technical developments that enabled determination of atomic structures of macromolecules by electron microscopy. Technological progress in experimental methods of macromolecular structure determination, computer hardware, and software changed and continues to change the nature of model building and visualization of molecular structures. However, the increase in automation and availability of structure validation are reducing interactive manual model building to fiddling with details. On the other hand, interactive modeling tools increasingly rely on search and complex energy calculation procedures, which make manually driven changes in geometry increasingly powerful and at the same time less demanding. Thus, the need for accurate manual positioning of a model is decreasing. The user's push only needs to be sufficient to bring the model within the increasing convergence radius of the computing tools. It seems that we can now better than ever determine an average single structure. The tools work better, requirements for engagement of human brain are lowered, and the frontier of intellectual and scientific challenges has moved on. The quest for resolution of new challenges requires out-of-the-box thinking. A few issues such as model bias and correctness of structure, ongoing developments in parameters defining geometric restraints, limitations of the ideal average single structure, and limitations of Bragg spot data are discussed here, together with the challenges that lie ahead.

VFMA: Topographic Analysis of Sensitivity Data From Full-Field Static Perimetry

PubMed Central

Weleber, Richard G.; Smith, Travis B.; Peters, Dawn; Chegarnov, Elvira N.; Gillespie, Scott P.; Francis, Peter J.; Gardiner, Stuart K.; Paetzold, Jens; Dietzsch, Janko; Schiefer, Ulrich; Johnson, Chris A.

2015-01-01

Purpose: To analyze static visual field sensitivity with topographic models of the hill of vision (HOV), and to characterize several visual function indices derived from the HOV volume. Methods: A software application, Visual Field Modeling and Analysis (VFMA), was developed for static perimetry data visualization and analysis. Three-dimensional HOV models were generated for 16 healthy subjects and 82 retinitis pigmentosa patients. Volumetric visual function indices, which are measures of quantity and comparable regardless of perimeter test pattern, were investigated. Cross-validation, reliability, and cross-sectional analyses were performed to assess this methodology and compare the volumetric indices to conventional mean sensitivity and mean deviation. Floor effects were evaluated by computer simulation. Results: Cross-validation yielded an overall R2 of 0.68 and index of agreement of 0.89, which were consistent among subject groups, indicating good accuracy. Volumetric and conventional indices were comparable in terms of test–retest variability and discriminability among subject groups. Simulated floor effects did not negatively impact the repeatability of any index, but large floor changes altered the discriminability for regional volumetric indices. Conclusions: VFMA is an effective tool for clinical and research analyses of static perimetry data. Topographic models of the HOV aid the visualization of field defects, and topographically derived indices quantify the magnitude and extent of visual field sensitivity. Translational Relevance: VFMA assists with the interpretation of visual field data from any perimetric device and any test location pattern. Topographic models and volumetric indices are suitable for diagnosis, monitoring of field loss, patient counseling, and endpoints in therapeutic trials. PMID:25938002

Weather from 250 Miles Up: Visualizing Precipitation Satellite Data (and Other Weather Applications) Using CesiumJS

NASA Technical Reports Server (NTRS)

Lammers, Matt

2017-01-01

Geospatial weather visualization remains predominately a two-dimensional endeavor. Even popular advanced tools like the Nullschool Earth display 2-dimensional fields on a 3-dimensional globe. Yet much of the observational data and model output contains detailed three-dimensional fields. In 2014, NASA and JAXA (Japanese Space Agency) launched the Global Precipitation Measurement (GPM) satellite. Its two instruments, the Dual-frequency Precipitation Radar (DPR) and GPM Microwave Imager (GMI) observe much of the Earth's atmosphere between 65 degrees North Latitude and 65 degrees South Latitude. As part of the analysis and visualization tools developed by the Precipitation Processing System (PPS) Group at NASA Goddard, a series of CesiumJS [Using Cesium Markup Language (CZML), JavaScript (JS) and JavaScript Object Notation (JSON)] -based globe viewers have been developed to improve data acquisition decision making and to enhance scientific investigation of the satellite data. Other demos have also been built to illustrate the capabilities of CesiumJS in presenting atmospheric data, including model forecasts of hurricanes, observed surface radar data, and gridded analyses of global precipitation. This talk will present these websites and the various workflows used to convert binary satellite and model data into a form easily integrated with CesiumJS.

Space-Based Telescopes for the Actionable Refinement of Ephemeris Systems and Test Engineering

DTIC Science & Technology

2011-12-01

Space Surveillance Network STARE Space-based Telescopes for the Actionable Refinement of Ephemeris STK Satellite Toolkit SV Space Vehicle TAMU...vacuum bake out and visual inspection. Additionally, it is prescribed that these tests be performed in accordance with GSFC-STD-7000, more commonly...environment that a FV will see in orbit. Tools such as Solid Works and NX-Ideas can be used to build CAD models to visually validate engineering

VERAView

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Ronald W.; Collins, Benjamin S.; Godfrey, Andrew T.

2016-12-09

In order to support engineering analysis of Virtual Environment for Reactor Analysis (VERA) model results, the Consortium for Advanced Simulation of Light Water Reactors (CASL) needs a tool that provides visualizations of HDF5 files that adhere to the VERAOUT specification. VERAView provides an interactive graphical interface for the visualization and engineering analyses of output data from VERA. The Python-based software provides instantaneous 2D and 3D images, 1D plots, and alphanumeric data from VERA multi-physics simulations.

Visualization Techniques for Computer Network Defense

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beaver, Justin M; Steed, Chad A; Patton, Robert M

2011-01-01

Effective visual analysis of computer network defense (CND) information is challenging due to the volume and complexity of both the raw and analyzed network data. A typical CND is comprised of multiple niche intrusion detection tools, each of which performs network data analysis and produces a unique alerting output. The state-of-the-practice in the situational awareness of CND data is the prevalent use of custom-developed scripts by Information Technology (IT) professionals to retrieve, organize, and understand potential threat events. We propose a new visual analytics framework, called the Oak Ridge Cyber Analytics (ORCA) system, for CND data that allows an operatormore » to interact with all detection tool outputs simultaneously. Aggregated alert events are presented in multiple coordinated views with timeline, cluster, and swarm model analysis displays. These displays are complemented with both supervised and semi-supervised machine learning classifiers. The intent of the visual analytics framework is to improve CND situational awareness, to enable an analyst to quickly navigate and analyze thousands of detected events, and to combine sophisticated data analysis techniques with interactive visualization such that patterns of anomalous activities may be more easily identified and investigated.« less

Advanced engineering environment collaboration project.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lamph, Jane Ann; Pomplun, Alan R.; Kiba, Grant W.

2008-12-01

The Advanced Engineering Environment (AEE) is a model for an engineering design and communications system that will enhance project collaboration throughout the nuclear weapons complex (NWC). Sandia National Laboratories and Parametric Technology Corporation (PTC) worked together on a prototype project to evaluate the suitability of a portion of PTC's Windchill 9.0 suite of data management, design and collaboration tools as the basis for an AEE. The AEE project team implemented Windchill 9.0 development servers in both classified and unclassified domains and used them to test and evaluate the Windchill tool suite relative to the needs of the NWC using weaponsmore » project use cases. A primary deliverable was the development of a new real time collaborative desktop design and engineering process using PDMLink (data management tool), Pro/Engineer (mechanical computer aided design tool) and ProductView Lite (visualization tool). Additional project activities included evaluations of PTC's electrical computer aided design, visualization, and engineering calculations applications. This report documents the AEE project work to share information and lessons learned with other NWC sites. It also provides PTC with recommendations for improving their products for NWC applications.« less

A Visual Training Tool for Teaching Kanji to Children with Developmental Dyslexia

ERIC Educational Resources Information Center

Ikeshita-Yamazoe, Hanae; Miyao, Masutomo

2016-01-01

We developed a visual training tool to assist children with developmental dyslexia in learning to recognize and understand Chinese characters (kanji). The visual training tool presents the strokes of a kanji character as separate shapes and requires students to use these fragments to construct the character. Two types of experiments were conducted…

An Exploratory Study of Interactivity in Visualization Tools: "Flow" of Interaction

ERIC Educational Resources Information Center

Liang, Hai-Ning; Parsons, Paul C.; Wu, Hsien-Chi; Sedig, Kamran

2010-01-01

This paper deals with the design of interactivity in visualization tools. There are several factors that can be used to guide the analysis and design of the interactivity of these tools. One such factor is flow, which is concerned with the duration of interaction with visual representations of information--interaction being the actions performed…

AR4VI: AR as an Accessibility Tool for People with Visual Impairments

PubMed Central

Coughlan, James M.; Miele, Joshua

2017-01-01

Although AR technology has been largely dominated by visual media, a number of AR tools using both visual and auditory feedback have been developed specifically to assist people with low vision or blindness – an application domain that we term Augmented Reality for Visual Impairment (AR4VI). We describe two AR4VI tools developed at Smith-Kettlewell, as well as a number of pre-existing examples. We emphasize that AR4VI is a powerful tool with the potential to remove or significantly reduce a range of accessibility barriers. Rather than being restricted to use by people with visual impairments, AR4VI is a compelling universal design approach offering benefits for mainstream applications as well. PMID:29303163

AR4VI: AR as an Accessibility Tool for People with Visual Impairments.

PubMed

Coughlan, James M; Miele, Joshua

2017-10-01

Although AR technology has been largely dominated by visual media, a number of AR tools using both visual and auditory feedback have been developed specifically to assist people with low vision or blindness - an application domain that we term Augmented Reality for Visual Impairment (AR4VI). We describe two AR4VI tools developed at Smith-Kettlewell, as well as a number of pre-existing examples. We emphasize that AR4VI is a powerful tool with the potential to remove or significantly reduce a range of accessibility barriers. Rather than being restricted to use by people with visual impairments, AR4VI is a compelling universal design approach offering benefits for mainstream applications as well.

Virtual Earth System Laboratory (VESL): Effective Visualization of Earth System Data and Process Simulations

NASA Astrophysics Data System (ADS)

Quinn, J. D.; Larour, E. Y.; Cheng, D. L. C.; Halkides, D. J.

2016-12-01

The Virtual Earth System Laboratory (VESL) is a Web-based tool, under development at the Jet Propulsion Laboratory and UC Irvine, for the visualization of Earth System data and process simulations. It contains features geared toward a range of applications, spanning research and outreach. It offers an intuitive user interface, in which model inputs are changed using sliders and other interactive components. Current capabilities include simulation of polar ice sheet responses to climate forcing, based on NASA's Ice Sheet System Model (ISSM). We believe that the visualization of data is most effective when tailored to the target audience, and that many of the best practices for modern Web design/development can be applied directly to the visualization of data: use of negative space, color schemes, typography, accessibility standards, tooltips, etc cetera. We present our prototype website, and invite input from potential users, including researchers, educators, and students.

Interactive Visualizations of Complex Seismic Data and Models

NASA Astrophysics Data System (ADS)

Chai, C.; Ammon, C. J.; Maceira, M.; Herrmann, R. B.

2016-12-01

The volume and complexity of seismic data and models have increased dramatically thanks to dense seismic station deployments and advances in data modeling and processing. Seismic observations such as receiver functions and surface-wave dispersion are multidimensional: latitude, longitude, time, amplitude and latitude, longitude, period, and velocity. Three-dimensional seismic velocity models are characterized with three spatial dimensions and one additional dimension for the speed. In these circumstances, exploring the data and models and assessing the data fits is a challenge. A few professional packages are available to visualize these complex data and models. However, most of these packages rely on expensive commercial software or require a substantial time investment to master, and even when that effort is complete, communicating the results to others remains a problem. A traditional approach during the model interpretation stage is to examine data fits and model features using a large number of static displays. Publications include a few key slices or cross-sections of these high-dimensional data, but this prevents others from directly exploring the model and corresponding data fits. In this presentation, we share interactive visualization examples of complex seismic data and models that are based on open-source tools and are easy to implement. Model and data are linked in an intuitive and informative web-browser based display that can be used to explore the model and the features in the data that influence various aspects of the model. We encode the model and data into HTML files and present high-dimensional information using two approaches. The first uses a Python package to pack both data and interactive plots in a single file. The second approach uses JavaScript, CSS, and HTML to build a dynamic webpage for seismic data visualization. The tools have proven useful and led to deeper insight into 3D seismic models and the data that were used to construct them. Such easy-to-use interactive displays are essential in teaching environments - user-friendly interactivity allows students to explore large, complex data sets and models at their own pace, enabling a more accessible learning experience.

A tool for the estimation of the distribution of landslide area in R

NASA Astrophysics Data System (ADS)

Rossi, M.; Cardinali, M.; Fiorucci, F.; Marchesini, I.; Mondini, A. C.; Santangelo, M.; Ghosh, S.; Riguer, D. E. L.; Lahousse, T.; Chang, K. T.; Guzzetti, F.

2012-04-01

We have developed a tool in R (the free software environment for statistical computing, http://www.r-project.org/) to estimate the probability density and the frequency density of landslide area. The tool implements parametric and non-parametric approaches to the estimation of the probability density and the frequency density of landslide area, including: (i) Histogram Density Estimation (HDE), (ii) Kernel Density Estimation (KDE), and (iii) Maximum Likelihood Estimation (MLE). The tool is available as a standard Open Geospatial Consortium (OGC) Web Processing Service (WPS), and is accessible through the web using different GIS software clients. We tested the tool to compare Double Pareto and Inverse Gamma models for the probability density of landslide area in different geological, morphological and climatological settings, and to compare landslides shown in inventory maps prepared using different mapping techniques, including (i) field mapping, (ii) visual interpretation of monoscopic and stereoscopic aerial photographs, (iii) visual interpretation of monoscopic and stereoscopic VHR satellite images and (iv) semi-automatic detection and mapping from VHR satellite images. Results show that both models are applicable in different geomorphological settings. In most cases the two models provided very similar results. Non-parametric estimation methods (i.e., HDE and KDE) provided reasonable results for all the tested landslide datasets. For some of the datasets, MLE failed to provide a result, for convergence problems. The two tested models (Double Pareto and Inverse Gamma) resulted in very similar results for large and very large datasets (> 150 samples). Differences in the modeling results were observed for small datasets affected by systematic biases. A distinct rollover was observed in all analyzed landslide datasets, except for a few datasets obtained from landslide inventories prepared through field mapping or by semi-automatic mapping from VHR satellite imagery. The tool can also be used to evaluate the probability density and the frequency density of landslide volume.

Information visualisation based on graph models

NASA Astrophysics Data System (ADS)

Kasyanov, V. N.; Kasyanova, E. V.

2013-05-01

Information visualisation is a key component of support tools for many applications in science and engineering. A graph is an abstract structure that is widely used to model information for its visualisation. In this paper, we consider practical and general graph formalism called hierarchical graphs and present the Higres and Visual Graph systems aimed at supporting information visualisation on the base of hierarchical graph models.

Teaching Tip: Using Activity Diagrams to Model Systems Analysis Techniques: Teaching What We Preach

ERIC Educational Resources Information Center

Lending, Diane; May, Jeffrey

2013-01-01

Activity diagrams are used in Systems Analysis and Design classes as a visual tool to model the business processes of "as-is" and "to-be" systems. This paper presents the idea of using these same activity diagrams in the classroom to model the actual processes (practices and techniques) of Systems Analysis and Design. This tip…

Information Extraction for System-Software Safety Analysis: Calendar Year 2007 Year-End Report

NASA Technical Reports Server (NTRS)

Malin, Jane T.

2008-01-01

This annual report describes work to integrate a set of tools to support early model-based analysis of failures and hazards due to system-software interactions. The tools perform and assist analysts in the following tasks: 1) extract model parts from text for architecture and safety/hazard models; 2) combine the parts with library information to develop the models for visualization and analysis; 3) perform graph analysis on the models to identify possible paths from hazard sources to vulnerable entities and functions, in nominal and anomalous system-software configurations; 4) perform discrete-time-based simulation on the models to investigate scenarios where these paths may play a role in failures and mishaps; and 5) identify resulting candidate scenarios for software integration testing. This paper describes new challenges in a NASA abort system case, and enhancements made to develop the integrated tool set.

Image processing, geometric modeling and data management for development of a virtual bone surgery system.

PubMed

Niu, Qiang; Chi, Xiaoyi; Leu, Ming C; Ochoa, Jorge

2008-01-01

This paper describes image processing, geometric modeling and data management techniques for the development of a virtual bone surgery system. Image segmentation is used to divide CT scan data into different segments representing various regions of the bone. A region-growing algorithm is used to extract cortical bone and trabecular bone structures systematically and efficiently. Volume modeling is then used to represent the bone geometry based on the CT scan data. Material removal simulation is achieved by continuously performing Boolean subtraction of the surgical tool model from the bone model. A quadtree-based adaptive subdivision technique is developed to handle the large set of data in order to achieve the real-time simulation and visualization required for virtual bone surgery. A Marching Cubes algorithm is used to generate polygonal faces from the volumetric data. Rendering of the generated polygons is performed with the publicly available VTK (Visualization Tool Kit) software. Implementation of the developed techniques consists of developing a virtual bone-drilling software program, which allows the user to manipulate a virtual drill to make holes with the use of a PHANToM device on a bone model derived from real CT scan data.

Dose-Response Calculator for ArcGIS

USGS Publications Warehouse

Hanser, Steven E.; Aldridge, Cameron L.; Leu, Matthias; Nielsen, Scott E.

2011-01-01

The Dose-Response Calculator for ArcGIS is a tool that extends the Environmental Systems Research Institute (ESRI) ArcGIS 10 Desktop application to aid with the visualization of relationships between two raster GIS datasets. A dose-response curve is a line graph commonly used in medical research to examine the effects of different dosage rates of a drug or chemical (for example, carcinogen) on an outcome of interest (for example, cell mutations) (Russell and others, 1982). Dose-response curves have recently been used in ecological studies to examine the influence of an explanatory dose variable (for example, percentage of habitat cover, distance to disturbance) on a predicted response (for example, survival, probability of occurrence, abundance) (Aldridge and others, 2008). These dose curves have been created by calculating the predicted response value from a statistical model at different levels of the explanatory dose variable while holding values of other explanatory variables constant. Curves (plots) developed using the Dose-Response Calculator overcome the need to hold variables constant by using values extracted from the predicted response surface of a spatially explicit statistical model fit in a GIS, which include the variation of all explanatory variables, to visualize the univariate response to the dose variable. Application of the Dose-Response Calculator can be extended beyond the assessment of statistical model predictions and may be used to visualize the relationship between any two raster GIS datasets (see example in tool instructions). This tool generates tabular data for use in further exploration of dose-response relationships and a graph of the dose-response curve.

The Geoinformatica free and open source software stack

NASA Astrophysics Data System (ADS)

Jolma, A.

2012-04-01

The Geoinformatica free and open source software (FOSS) stack is based mainly on three established FOSS components, namely GDAL, GTK+, and Perl. GDAL provides access to a very large selection of geospatial data formats and data sources, a generic geospatial data model, and a large collection of geospatial analytical and processing functionality. GTK+ and the Cairo graphics library provide generic graphics and graphical user interface capabilities. Perl is a programming language, for which there is a very large set of FOSS modules for a wide range of purposes and which can be used as an integrative tool for building applications. In the Geoinformatica stack, data storages such as FOSS RDBMS PostgreSQL with its geospatial extension PostGIS can be used below the three above mentioned components. The top layer of Geoinformatica consists of a C library and several Perl modules. The C library comprises a general purpose raster algebra library, hydrological terrain analysis functions, and visualization code. The Perl modules define a generic visualized geospatial data layer and subclasses for raster and vector data and graphs. The hydrological terrain functions are already rather old and they suffer for example from the requirement of in-memory rasters. Newer research conducted using the platform include basic geospatial simulation modeling, visualization of ecological data, linking with a Bayesian network engine for spatial risk assessment in coastal areas, and developing standards-based distributed water resources information systems in Internet. The Geoinformatica stack constitutes a platform for geospatial research, which is targeted towards custom analytical tools, prototyping and linking with external libraries. Writing custom analytical tools is supported by the Perl language and the large collection of tools that are available especially in GDAL and Perl modules. Prototyping is supported by the GTK+ library, the GUI tools, and the support for object-oriented programming in Perl. New feature types, geospatial layer classes, and tools as extensions with specific features can be defined, used, and studied. Linking with external libraries is possible using the Perl foreign function interface tools or with generic tools such as Swig. We are interested in implementing and testing linking Geoinformatica with existing or new more specific hydrological FOSS.

Development of efficient and cost-effective distributed hydrological modeling tool MWEasyDHM based on open-source MapWindow GIS

NASA Astrophysics Data System (ADS)

Lei, Xiaohui; Wang, Yuhui; Liao, Weihong; Jiang, Yunzhong; Tian, Yu; Wang, Hao

2011-09-01

Many regions are still threatened with frequent floods and water resource shortage problems in China. Consequently, the task of reproducing and predicting the hydrological process in watersheds is hard and unavoidable for reducing the risks of damage and loss. Thus, it is necessary to develop an efficient and cost-effective hydrological tool in China as many areas should be modeled. Currently, developed hydrological tools such as Mike SHE and ArcSWAT (soil and water assessment tool based on ArcGIS) show significant power in improving the precision of hydrological modeling in China by considering spatial variability both in land cover and in soil type. However, adopting developed commercial tools in such a large developing country comes at a high cost. Commercial modeling tools usually contain large numbers of formulas, complicated data formats, and many preprocessing or postprocessing steps that may make it difficult for the user to carry out simulation, thus lowering the efficiency of the modeling process. Besides, commercial hydrological models usually cannot be modified or improved to be suitable for some special hydrological conditions in China. Some other hydrological models are open source, but integrated into commercial GIS systems. Therefore, by integrating hydrological simulation code EasyDHM, a hydrological simulation tool named MWEasyDHM was developed based on open-source MapWindow GIS, the purpose of which is to establish the first open-source GIS-based distributed hydrological model tool in China by integrating modules of preprocessing, model computation, parameter estimation, result display, and analysis. MWEasyDHM provides users with a friendly manipulating MapWindow GIS interface, selectable multifunctional hydrological processing modules, and, more importantly, an efficient and cost-effective hydrological simulation tool. The general construction of MWEasyDHM consists of four major parts: (1) a general GIS module for hydrological analysis, (2) a preprocessing module for modeling inputs, (3) a model calibration module, and (4) a postprocessing module. The general GIS module for hydrological analysis is developed on the basis of totally open-source GIS software, MapWindow, which contains basic GIS functions. The preprocessing module is made up of three submodules including a DEM-based submodule for hydrological analysis, a submodule for default parameter calculation, and a submodule for the spatial interpolation of meteorological data. The calibration module contains parallel computation, real-time computation, and visualization. The postprocessing module includes model calibration and model results spatial visualization using tabular form and spatial grids. MWEasyDHM makes it possible for efficient modeling and calibration of EasyDHM, and promises further development of cost-effective applications in various watersheds.

Monocular tool control, eye dominance, and laterality in New Caledonian crows.

PubMed

Martinho, Antone; Burns, Zackory T; von Bayern, Auguste M P; Kacelnik, Alex

2014-12-15

Tool use, though rare, is taxonomically widespread, but morphological adaptations for tool use are virtually unknown. We focus on the New Caledonian crow (NCC, Corvus moneduloides), which displays some of the most innovative tool-related behavior among nonhumans. One of their major food sources is larvae extracted from burrows with sticks held diagonally in the bill, oriented with individual, but not species-wide, laterality. Among possible behavioral and anatomical adaptations for tool use, NCCs possess unusually wide binocular visual fields (up to 60°), suggesting that extreme binocular vision may facilitate tool use. Here, we establish that during natural extractions, tool tips can only be viewed by the contralateral eye. Thus, maintaining binocular view of tool tips is unlikely to have selected for wide binocular fields; the selective factor is more likely to have been to allow each eye to see far enough across the midsagittal line to view the tool's tip monocularly. Consequently, we tested the hypothesis that tool side preference follows eye preference and found that eye dominance does predict tool laterality across individuals. This contrasts with humans' species-wide motor laterality and uncorrelated motor-visual laterality, possibly because bill-held tools are viewed monocularly and move in concert with eyes, whereas hand-held tools are visible to both eyes and allow independent combinations of eye preference and handedness. This difference may affect other models of coordination between vision and mechanical control, not necessarily involving tools. Copyright © 2014 Elsevier Ltd. All rights reserved.

VCS: Tool for Visualizing Copy Number Variation and Single Nucleotide Polymorphism.

PubMed

Kim, HyoYoung; Sung, Samsun; Cho, Seoae; Kim, Tae-Hun; Seo, Kangseok; Kim, Heebal

2014-12-01

Copy number variation (CNV) or single nucleotide phlyorphism (SNP) is useful genetic resource to aid in understanding complex phenotypes or deseases susceptibility. Although thousands of CNVs and SNPs are currently avaliable in the public databases, they are somewhat difficult to use for analyses without visualization tools. We developed a web-based tool called the VCS (visualization of CNV or SNP) to visualize the CNV or SNP detected. The VCS tool can assist to easily interpret a biological meaning from the numerical value of CNV and SNP. The VCS provides six visualization tools: i) the enrichment of genome contents in CNV; ii) the physical distribution of CNV or SNP on chromosomes; iii) the distribution of log2 ratio of CNVs with criteria of interested; iv) the number of CNV or SNP per binning unit; v) the distribution of homozygosity of SNP genotype; and vi) cytomap of genes within CNV or SNP region.

Experiences in using DISCUS for visualizing human communication

NASA Astrophysics Data System (ADS)

Groehn, Matti; Nieminen, Marko; Haho, Paeivi; Smeds, Riitta

2000-02-01

In this paper, we present further improvement to the DISCUS software that can be used to record and analyze the flow and constants of business process simulation session discussion. The tool was initially introduced in 'visual data exploration and analysis IV' conference. The initial features of the tool enabled the visualization of discussion flow in business process simulation sessions and the creation of SOM analyses. The improvements of the tool consists of additional visualization possibilities that enable quick on-line analyses and improved graphical statistics. We have also created the very first interface to audio data and implemented two ways to visualize it. We also outline additional possibilities to use the tool in other application areas: these include usability testing and the possibility to use the tool for capturing design rationale in a product development process. The data gathered with DISCUS may be used in other applications, and further work may be done with data ming techniques.

Visualizing the ground motions of the 1906 San Francisco earthquake

USGS Publications Warehouse

Chourasia, A.; Cutchin, S.; Aagaard, Brad T.

2008-01-01

With advances in computational capabilities and refinement of seismic wave-propagation models in the past decade large three-dimensional simulations of earthquake ground motion have become possible. The resulting datasets from these simulations are multivariate, temporal and multi-terabyte in size. Past visual representations of results from seismic studies have been largely confined to static two-dimensional maps. New visual representations provide scientists with alternate ways of viewing and interacting with these results potentially leading to new and significant insight into the physical phenomena. Visualizations can also be used for pedagogic and general dissemination purposes. We present a workflow for visual representation of the data from a ground motion simulation of the great 1906 San Francisco earthquake. We have employed state of the art animation tools for visualization of the ground motions with a high degree of accuracy and visual realism. ?? 2008 Elsevier Ltd.

New developments in UTMOST : application to electronic stability control.

DOT National Transportation Integrated Search

2009-10-01

The Unified Tool for Mapping Opportunities for Safety Technology (UTMOST) : is a model of crash data that incorporates the complex relationships among different : vehicle and driver variables. It is designed to visualize the effect of multiple safety...

Cal-Adapt: California's Climate Data Resource and Interactive Toolkit

NASA Astrophysics Data System (ADS)

Thomas, N.; Mukhtyar, S.; Wilhelm, S.; Galey, B.; Lehmer, E.

2016-12-01

Cal-Adapt is a web-based application that provides an interactive toolkit and information clearinghouse to help agencies, communities, local planners, resource managers, and the public understand climate change risks and impacts at the local level. The website offers interactive, visually compelling, and useful data visualization tools that show how climate change might affect California using downscaled continental climate data. Cal-Adapt is supporting California's Fourth Climate Change Assessment through providing access to the wealth of modeled and observed data and adaption-related information produced by California's scientific community. The site has been developed by UC Berkeley's Geospatial Innovation Facility (GIF) in collaboration with the California Energy Commission's (CEC) Research Program. The Cal-Adapt website allows decision makers, scientists and residents of California to turn research results and climate projections into effective adaptation decisions and policies. Since its release to the public in June 2011, Cal-Adapt has been visited by more than 94,000 unique visitors from over 180 countries, all 50 U.S. states, and 689 California localities. We will present several key visualizations that have been employed by Cal-Adapt's users to support their efforts to understand local impacts of climate change, indicate the breadth of data available, and delineate specific use cases. Recently, CEC and GIF have been developing and releasing Cal-Adapt 2.0, which includes updates and enhancements that are increasing its ease of use, information value, visualization tools, and data accessibility. We showcase how Cal-Adapt is evolving in response to feedback from a variety of sources to present finer-resolution downscaled data, and offer an open API that allows other organization to access Cal-Adapt climate data and build domain specific visualization and planning tools. Through a combination of locally relevant information, visualization tools, and access to primary data, Cal-Adapt allows users to investigate how the climate is projected to change in their areas of interest.

Computer aided drug design

NASA Astrophysics Data System (ADS)

Jain, A.

2017-08-01

Computer based method can help in discovery of leads and can potentially eliminate chemical synthesis and screening of many irrelevant compounds, and in this way, it save time as well as cost. Molecular modeling systems are powerful tools for building, visualizing, analyzing and storing models of complex molecular structure that can help to interpretate structure activity relationship. The use of various techniques of molecular mechanics and dynamics and software in Computer aided drug design along with statistics analysis is powerful tool for the medicinal chemistry to synthesis therapeutic and effective drugs with minimum side effect.

NCWin — A Component Object Model (COM) for processing and visualizing NetCDF data

USGS Publications Warehouse

Liu, Jinxun; Chen, J.M.; Price, D.T.; Liu, S.

2005-01-01

NetCDF (Network Common Data Form) is a data sharing protocol and library that is commonly used in large-scale atmospheric and environmental data archiving and modeling. The NetCDF tool described here, named NCWin and coded with Borland C + + Builder, was built as a standard executable as well as a COM (component object model) for the Microsoft Windows environment. COM is a powerful technology that enhances the reuse of applications (as components). Environmental model developers from different modeling environments, such as Python, JAVA, VISUAL FORTRAN, VISUAL BASIC, VISUAL C + +, and DELPHI, can reuse NCWin in their models to read, write and visualize NetCDF data. Some Windows applications, such as ArcGIS and Microsoft PowerPoint, can also call NCWin within the application. NCWin has three major components: 1) The data conversion part is designed to convert binary raw data to and from NetCDF data. It can process six data types (unsigned char, signed char, short, int, float, double) and three spatial data formats (BIP, BIL, BSQ); 2) The visualization part is designed for displaying grid map series (playing forward or backward) with simple map legend, and displaying temporal trend curves for data on individual map pixels; and 3) The modeling interface is designed for environmental model development by which a set of integrated NetCDF functions is provided for processing NetCDF data. To demonstrate that the NCWin can easily extend the functions of some current GIS software and the Office applications, examples of calling NCWin within ArcGIS and MS PowerPoint for showing NetCDF map animations are given.

FROMS3D: New Software for 3-D Visualization of Fracture Network System in Fractured Rock Masses

NASA Astrophysics Data System (ADS)

Noh, Y. H.; Um, J. G.; Choi, Y.

2014-12-01

A new software (FROMS3D) is presented to visualize fracture network system in 3-D. The software consists of several modules that play roles in management of borehole and field fracture data, fracture network modelling, visualization of fracture geometry in 3-D and calculation and visualization of intersections and equivalent pipes between fractures. Intel Parallel Studio XE 2013, Visual Studio.NET 2010 and the open source VTK library were utilized as development tools to efficiently implement the modules and the graphical user interface of the software. The results have suggested that the developed software is effective in visualizing 3-D fracture network system, and can provide useful information to tackle the engineering geological problems related to strength, deformability and hydraulic behaviors of the fractured rock masses.

Entering AN ERA of Synthesis of Modeling

NASA Astrophysics Data System (ADS)

Guerin, Stephen

First, I believe we're entering an era of synthesis of modeling. Over the past 20 years, we've seen the proliferation of many isolated complex systems models. I think we now need tools for researchers, policy makers and the public to share models. Sharing could happen by stacking different layers of spatial agent-based models in geographic information systems and projecting interactive visualization out onto shared surfaces. Further, we need to make model authoring tools much more accessible to the point where motivated policy makers can author on their own. With the increased ability to author and share models, I believe this will allow us to scale our research to understand and manage the many interacting systems that make up our complex world...

Mass spectrometric imaging of red fluorescent protein in breast tumor xenografts.

PubMed

Chughtai, Kamila; Jiang, Lu; Post, Harm; Winnard, Paul T; Greenwood, Tiffany R; Raman, Venu; Bhujwalla, Zaver M; Heeren, Ron M A; Glunde, Kristine

2013-05-01

Mass spectrometric imaging (MSI) in combination with electrospray mass spectrometry (ESI-MS) is a powerful technique for visualization and identification of a variety of different biomolecules directly from thin tissue sections. As commonly used tools for molecular reporting, fluorescent proteins are molecular reporter tools that have enabled the elucidation of a multitude of biological pathways and processes. To combine these two approaches, we have performed targeted MS analysis and MALDI-MSI visualization of a tandem dimer (td)Tomato red fluorescent protein, which was expressed exclusively in the hypoxic regions of a breast tumor xenograft model. For the first time, a fluorescent protein has been visualized by both optical microscopy and MALDI-MSI. Visualization of tdTomato by MALDI-MSI directly from breast tumor tissue sections will allow us to simultaneously detect and subsequently identify novel molecules present in hypoxic regions of the tumor. MS and MALDI-MSI of fluorescent proteins, as exemplified in our study, is useful for studies in which the advantages of MS and MSI will benefit from the combination with molecular approaches that use fluorescent proteins as reporters.

TopoDrive and ParticleFlow--Two Computer Models for Simulation and Visualization of Ground-Water Flow and Transport of Fluid Particles in Two Dimensions

USGS Publications Warehouse

Hsieh, Paul A.

2001-01-01

This report serves as a user?s guide for two computer models: TopoDrive and ParticleFlow. These two-dimensional models are designed to simulate two ground-water processes: topography-driven flow and advective transport of fluid particles. To simulate topography-driven flow, the user may specify the shape of the water table, which bounds the top of the vertical flow section. To simulate transport of fluid particles, the model domain is a rectangle with overall flow from left to right. In both cases, the flow is under steady state, and the distribution of hydraulic conductivity may be specified by the user. The models compute hydraulic head, ground-water flow paths, and the movement of fluid particles. An interactive visual interface enables the user to easily and quickly explore model behavior, and thereby better understand ground-water flow processes. In this regard, TopoDrive and ParticleFlow are not intended to be comprehensive modeling tools, but are designed for modeling at the exploratory or conceptual level, for visual demonstration, and for educational purposes.

The 3D widgets for exploratory scientific visualization

NASA Technical Reports Server (NTRS)

Herndon, Kenneth P.; Meyer, Tom

1995-01-01

Computational fluid dynamics (CFD) techniques are used to simulate flows of fluids like air or water around such objects as airplanes and automobiles. These techniques usually generate very large amounts of numerical data which are difficult to understand without using graphical scientific visualization techniques. There are a number of commercial scientific visualization applications available today which allow scientists to control visualization tools via textual and/or 2D user interfaces. However, these user interfaces are often difficult to use. We believe that 3D direct-manipulation techniques for interactively controlling visualization tools will provide opportunities for powerful and useful interfaces with which scientists can more effectively explore their datasets. A few systems have been developed which use these techniques. In this paper, we will present a variety of 3D interaction techniques for manipulating parameters of visualization tools used to explore CFD datasets, and discuss in detail various techniques for positioning tools in a 3D scene.

Survey of Network Visualization Tools

DTIC Science & Technology

2007-12-01

Dimensionality • 2D Comments: Deployment Type: • Components for tool building • Standalone Tool OS: • Windows Extensibility • ActiveX ...Visual Basic Comments: Interoperability Daisy is fully compliant with Microsoft’s ActiveX , therefore, other Windows based programs can...other functions that improve analytic decision making. Available in ActiveX , C++, Java, and .NET editions. • Tom Sawyer Visualization: Enables you to

Do Bedside Visual Tools Improve Patient and Caregiver Satisfaction? A Systematic Review of the Literature.

PubMed

Goyal, Anupama A; Tur, Komalpreet; Mann, Jason; Townsend, Whitney; Flanders, Scott A; Chopra, Vineet

2017-11-01

Although common, the impact of low-cost bedside visual tools, such as whiteboards, on patient care is unclear. To systematically review the literature and assess the influence of bedside visual tools on patient satisfaction. Medline, Embase, SCOPUS, Web of Science, CINAHL, and CENTRAL. Studies of adult or pediatric hospitalized patients reporting physician identification, understanding of provider roles, patient-provider communication, and satisfaction with care from the use of visual tools were included. Outcomes were categorized as positive, negative, or neutral based on survey responses for identification, communication, and satisfaction. Two reviewers screened studies, extracted data, and assessed the risk of study bias. Sixteen studies met the inclusion criteria. Visual tools included whiteboards (n = 4), physician pictures (n = 7), whiteboard and picture (n = 1), electronic medical record-based patient portals (n = 3), and formatted notepads (n = 1). Tools improved patients' identification of providers (13/13 studies). The impact on understanding the providers' roles was largely positive (8/10 studies). Visual tools improved patient-provider communication (4/5 studies) and satisfaction (6/8 studies). In adults, satisfaction varied between positive with the use of whiteboards (2/5 studies) and neutral with pictures (1/5 studies). Satisfaction related to pictures in pediatric patients was either positive (1/3 studies) or neutral (1/3 studies). Differences in tool format (individual pictures vs handouts with pictures of all providers) and study design (randomized vs cohort) may explain variable outcomes. The use of bedside visual tools appears to improve patient recognition of providers and patient-provider communication. Future studies that include better design and outcome assessment are necessary before widespread use can be recommended. © 2017 Society of Hospital Medicine

Visual Impairment Screening Assessment (VISA) tool: pilot validation.

PubMed

Rowe, Fiona J; Hepworth, Lauren R; Hanna, Kerry L; Howard, Claire

2018-03-06

To report and evaluate a new Vision Impairment Screening Assessment (VISA) tool intended for use by the stroke team to improve identification of visual impairment in stroke survivors. Prospective case cohort comparative study. Stroke units at two secondary care hospitals and one tertiary centre. 116 stroke survivors were screened, 62 by naïve and 54 by non-naïve screeners. Both the VISA screening tool and the comprehensive specialist vision assessment measured case history, visual acuity, eye alignment, eye movements, visual field and visual inattention. Full completion of VISA tool and specialist vision assessment was achieved for 89 stroke survivors. Missing data for one or more sections typically related to patient's inability to complete the assessment. Sensitivity and specificity of the VISA screening tool were 90.24% and 85.29%, respectively; the positive and negative predictive values were 93.67% and 78.36%, respectively. Overall agreement was significant; k=0.736. Lowest agreement was found for screening of eye movement and visual inattention deficits. This early validation of the VISA screening tool shows promise in improving detection accuracy for clinicians involved in stroke care who are not specialists in vision problems and lack formal eye training, with potential to lead to more prompt referral with fewer false positives and negatives. Pilot validation indicates acceptability of the VISA tool for screening of visual impairment in stroke survivors. Sensitivity and specificity were high indicating the potential accuracy of the VISA tool for screening purposes. Results of this study have guided the revision of the VISA screening tool ahead of full clinical validation. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Audio-video decision support for patients: the documentary genré as a basis for decision aids.

PubMed

Volandes, Angelo E; Barry, Michael J; Wood, Fiona; Elwyn, Glyn

2013-09-01

Decision support tools are increasingly using audio-visual materials. However, disagreement exists about the use of audio-visual materials as they may be subjective and biased. This is a literature review of the major texts for documentary film studies to extrapolate issues of objectivity and bias from film to decision support tools. The key features of documentary films are that they attempt to portray real events and that the attempted reality is always filtered through the lens of the filmmaker. The same key features can be said of decision support tools that use audio-visual materials. Three concerns arising from documentary film studies as they apply to the use of audio-visual materials in decision support tools include whose perspective matters (stakeholder bias), how to choose among audio-visual materials (selection bias) and how to ensure objectivity (editorial bias). Decision science needs to start a debate about how audio-visual materials are to be used in decision support tools. Simply because audio-visual materials may be subjective and open to bias does not mean that we should not use them. Methods need to be found to ensure consensus around balance and editorial control, such that audio-visual materials can be used. © 2011 John Wiley & Sons Ltd.

Audio‐video decision support for patients: the documentary genré as a basis for decision aids

PubMed Central

Volandes, Angelo E.; Barry, Michael J.; Wood, Fiona; Elwyn, Glyn

2011-01-01

Abstract Objective  Decision support tools are increasingly using audio‐visual materials. However, disagreement exists about the use of audio‐visual materials as they may be subjective and biased. Methods  This is a literature review of the major texts for documentary film studies to extrapolate issues of objectivity and bias from film to decision support tools. Results  The key features of documentary films are that they attempt to portray real events and that the attempted reality is always filtered through the lens of the filmmaker. The same key features can be said of decision support tools that use audio‐visual materials. Three concerns arising from documentary film studies as they apply to the use of audio‐visual materials in decision support tools include whose perspective matters (stakeholder bias), how to choose among audio‐visual materials (selection bias) and how to ensure objectivity (editorial bias). Discussion  Decision science needs to start a debate about how audio‐visual materials are to be used in decision support tools. Simply because audio‐visual materials may be subjective and open to bias does not mean that we should not use them. Conclusion  Methods need to be found to ensure consensus around balance and editorial control, such that audio‐visual materials can be used. PMID:22032516

The Shale Hills Sensorium for Embedded Sensors, Simulation, & Visualization: A Prototype for Land-Vegetation-Atmosphere Interactions

NASA Astrophysics Data System (ADS)

Duffy, C.

2008-12-01

The future of environmental observing systems will utilize embedded sensor networks with continuous real- time measurement of hydrologic, atmospheric, biogeochemical, and ecological variables across diverse terrestrial environments. Embedded environmental sensors, benefitting from advances in information sciences, networking technology, materials science, computing capacity, and data synthesis methods, are undergoing revolutionary change. It is now possible to field spatially-distributed, multi-node sensor networks that provide density and spatial coverage previously accessible only via numerical simulation. At the same time, computational tools are advancing rapidly to the point where it is now possible to simulate the physical processes controlling individual parcels of water and solutes through the complete terrestrial water cycle. Our goal for the Penn State Critical Zone Observatory is to apply environmental sensor arrays, integrated hydrologic models, and state-of-the-art visualization deployed and coordinated at a testbed within the Penn State Experimental Forest. The Shale Hills Hydro_Sensorium prototype proposed here is designed to observe land-atmosphere interactions in four-dimensional (space and time). The term Hydro_Sensorium implies the totality of physical sensors, models and visualization tools that allow us to perceive the detailed space and time complexities of the water and energy cycle for a watershed or river basin for all physical states and fluxes (groundwater, soil moisture, temperature, streamflow, latent heat, snowmelt, chemistry, isotopes etc.). This research will ultimately catalyze the study of complex interactions between the land surface, subsurface, biological and atmospheric systems over a broad range of scales. The sensor array would be real-time and fully controllable by remote users for "computational steering" and data fusion. Presently fully-coupled physical models are being developed that link the atmosphere-land-vegetation-subsurface system into a fully-coupled distributed system. During the last 5 years the Penn State Integrated Hydrologic Modeling System has been under development as an open-source community modeling project funded by NSF EAR/GEO and NSF CBET/ENG. PIHM represents a strategy for the formulation and solution of fully-coupled process equations at the watershed and river basin scales, and includes a tightly coupled GIS tool for data handling, domain decomposition, optimal unstructured grid generation, and model parameterization. The sensor and simulation system has the following elements: 1) extensive, spatially-distributed, non- invasive, smart sensor networks to gather massive geologic, hydrologic, and geochemical data; 2) stochastic information fusion methods; 3) spatially-explicit multiphysics models/solutions of the land-vegetation- atmosphere system; and 4) asynchronous, parallel/distributed, adaptive algorithms for rapidly simulating the states of a basin at high resolution, 5) signal processing tools for data mining and parameter estimation, and 6) visualization tools. The prototype proposed sensor array and simulation system proposed here will offer a coherent new approach to environmental predictions with a fully integrated observing system design. We expect that the Shale Hills Hydro_Sensorium may provide the needed synthesis of information and conceptualization necessary to advance predictive understanding in complex hydrologic systems.

Solar System Treks: Interactive Web Portals or STEM, Exploration and Beyond

NASA Astrophysics Data System (ADS)

Law, E.; Day, B. H.; Viotti, M.

2017-12-01

NASA's Solar System Treks project produces a suite of online visualization and analysis tools for lunar and planetary mapping and modeling. These portals offer great benefits for education and public outreach, providing access to data from a wide range of instruments aboard a variety of past and current missions. As a component of NASA's STEM Activation Infrastructure, they are available as resources for NASA STEM programs, and to the greater STEM community. As new missions are planned to a variety of planetary bodies, these tools facilitate public understanding of the missions and engage the public in the process of identifying and selecting where these missions will land. There are currently three web portals in the program: Moon Trek (https://moontrek.jpl.nasa.gov), Mars Trek (https://marstrek.jpl.nasa.gov), and Vesta Trek (https://vestatrek.jpl.nasa.gov). A new release of Mars Trek includes new tools and data products focusing on human landing site selection. Backed by evidence-based cognitive and computer science findings, an additional version is available for educational and public audiences in support of earning along novice-to-expert pathways, enabling authentic, real-world interaction with planetary data. Portals for additional planetary bodies are planned. As web-based toolsets, the portals do not require users to purchase or install any software beyond current web browsers. The portals provide analysis tools for measurement and study of planetary terrain. They allow data to be layered and adjusted to optimize visualization. Visualizations are easily stored and shared. The portals provide 3D visualization and give users the ability to mark terrain for generation of STL/OBJ files that can be directed to 3D printers. Such 3D prints are valuable tools in museums, public exhibits, and classrooms - especially for the visually impaired. The program supports additional clients, web services, and APIs facilitating dissemination of planetary data to external applications and venues. NASA challenges and hackathons also provide members of the software development community opportunities to participate in tool development and leverage data from the portals.

Visualization and Interaction in Research, Teaching, and Scientific Communication

NASA Astrophysics Data System (ADS)

Ammon, C. J.

2017-12-01

Modern computing provides many tools for exploring observations, numerical calculations, and theoretical relationships. The number of options is, in fact, almost overwhelming. But the choices provide those with modest programming skills opportunities to create unique views of scientific information and to develop deeper insights into their data, their computations, and the underlying theoretical data-model relationships. I present simple examples of using animation and human-computer interaction to explore scientific data and scientific-analysis approaches. I illustrate how valuable a little programming ability can free scientists from the constraints of existing tools and can facilitate the development of deeper appreciation data and models. I present examples from a suite of programming languages ranging from C to JavaScript including the Wolfram Language. JavaScript is valuable for sharing tools and insight (hopefully) with others because it is integrated into one of the most powerful communication tools in human history, the web browser. Although too much of that power is often spent on distracting advertisements, the underlying computation and graphics engines are efficient, flexible, and almost universally available in desktop and mobile computing platforms. Many are working to fulfill the browser's potential to become the most effective tool for interactive study. Open-source frameworks for visualizing everything from algorithms to data are available, but advance rapidly. One strategy for dealing with swiftly changing tools is to adopt common, open data formats that are easily adapted (often by framework or tool developers). I illustrate the use of animation and interaction in research and teaching with examples from earthquake seismology.

DEVA: An extensible ontology-based annotation model for visual document collections

NASA Astrophysics Data System (ADS)

Jelmini, Carlo; Marchand-Maillet, Stephane

2003-01-01

The description of visual documents is a fundamental aspect of any efficient information management system, but the process of manually annotating large collections of documents is tedious and far from being perfect. The need for a generic and extensible annotation model therefore arises. In this paper, we present DEVA, an open, generic and expressive multimedia annotation framework. DEVA is an extension of the Dublin Core specification. The model can represent the semantic content of any visual document. It is described in the ontology language DAML+OIL and can easily be extended with external specialized ontologies, adapting the vocabulary to the given application domain. In parallel, we present the Magritte annotation tool, which is an early prototype that validates the DEVA features. Magritte allows to manually annotating image collections. It is designed with a modular and extensible architecture, which enables the user to dynamically adapt the user interface to specialized ontologies merged into DEVA.

Visual analytics in healthcare education: exploring novel ways to analyze and represent big data in undergraduate medical education

PubMed Central

Nilsson, Gunnar; Zary, Nabil

2014-01-01

Introduction. The big data present in the medical curriculum that informs undergraduate medical education is beyond human abilities to perceive and analyze. The medical curriculum is the main tool used by teachers and directors to plan, design, and deliver teaching and assessment activities and student evaluations in medical education in a continuous effort to improve it. Big data remains largely unexploited for medical education improvement purposes. The emerging research field of visual analytics has the advantage of combining data analysis and manipulation techniques, information and knowledge representation, and human cognitive strength to perceive and recognize visual patterns. Nevertheless, there is a lack of research on the use and benefits of visual analytics in medical education. Methods. The present study is based on analyzing the data in the medical curriculum of an undergraduate medical program as it concerns teaching activities, assessment methods and learning outcomes in order to explore visual analytics as a tool for finding ways of representing big data from undergraduate medical education for improvement purposes. Cytoscape software was employed to build networks of the identified aspects and visualize them. Results. After the analysis of the curriculum data, eleven aspects were identified. Further analysis and visualization of the identified aspects with Cytoscape resulted in building an abstract model of the examined data that presented three different approaches; (i) learning outcomes and teaching methods, (ii) examination and learning outcomes, and (iii) teaching methods, learning outcomes, examination results, and gap analysis. Discussion. This study identified aspects of medical curriculum that play an important role in how medical education is conducted. The implementation of visual analytics revealed three novel ways of representing big data in the undergraduate medical education context. It appears to be a useful tool to explore such data with possible future implications on healthcare education. It also opens a new direction in medical education informatics research. PMID:25469323

Visual analytics in healthcare education: exploring novel ways to analyze and represent big data in undergraduate medical education.

PubMed

Vaitsis, Christos; Nilsson, Gunnar; Zary, Nabil

2014-01-01

Introduction. The big data present in the medical curriculum that informs undergraduate medical education is beyond human abilities to perceive and analyze. The medical curriculum is the main tool used by teachers and directors to plan, design, and deliver teaching and assessment activities and student evaluations in medical education in a continuous effort to improve it. Big data remains largely unexploited for medical education improvement purposes. The emerging research field of visual analytics has the advantage of combining data analysis and manipulation techniques, information and knowledge representation, and human cognitive strength to perceive and recognize visual patterns. Nevertheless, there is a lack of research on the use and benefits of visual analytics in medical education. Methods. The present study is based on analyzing the data in the medical curriculum of an undergraduate medical program as it concerns teaching activities, assessment methods and learning outcomes in order to explore visual analytics as a tool for finding ways of representing big data from undergraduate medical education for improvement purposes. Cytoscape software was employed to build networks of the identified aspects and visualize them. Results. After the analysis of the curriculum data, eleven aspects were identified. Further analysis and visualization of the identified aspects with Cytoscape resulted in building an abstract model of the examined data that presented three different approaches; (i) learning outcomes and teaching methods, (ii) examination and learning outcomes, and (iii) teaching methods, learning outcomes, examination results, and gap analysis. Discussion. This study identified aspects of medical curriculum that play an important role in how medical education is conducted. The implementation of visual analytics revealed three novel ways of representing big data in the undergraduate medical education context. It appears to be a useful tool to explore such data with possible future implications on healthcare education. It also opens a new direction in medical education informatics research.

Ultra-scale Visualization Climate Data Analysis Tools (UV-CDAT)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, Dean N.

2011-07-20

This report summarizes work carried out by the Ultra-scale Visualization Climate Data Analysis Tools (UV-CDAT) Team for the period of January 1, 2011 through June 30, 2011. It discusses highlights, overall progress, period goals, and collaborations and lists papers and presentations. To learn more about our project, please visit our UV-CDAT website (URL: http://uv-cdat.org). This report will be forwarded to the program manager for the Department of Energy (DOE) Office of Biological and Environmental Research (BER), national and international collaborators and stakeholders, and to researchers working on a wide range of other climate model, reanalysis, and observation evaluation activities. Themore » UV-CDAT executive committee consists of Dean N. Williams of Lawrence Livermore National Laboratory (LLNL); Dave Bader and Galen Shipman of Oak Ridge National Laboratory (ORNL); Phil Jones and James Ahrens of Los Alamos National Laboratory (LANL), Claudio Silva of Polytechnic Institute of New York University (NYU-Poly); and Berk Geveci of Kitware, Inc. The UV-CDAT team consists of researchers and scientists with diverse domain knowledge whose home institutions also include the National Aeronautics and Space Administration (NASA) and the University of Utah. All work is accomplished under DOE open-source guidelines and in close collaboration with the project's stakeholders, domain researchers, and scientists. Working directly with BER climate science analysis projects, this consortium will develop and deploy data and computational resources useful to a wide variety of stakeholders, including scientists, policymakers, and the general public. Members of this consortium already collaborate with other institutions and universities in researching data discovery, management, visualization, workflow analysis, and provenance. The UV-CDAT team will address the following high-level visualization requirements: (1) Alternative parallel streaming statistics and analysis pipelines - Data parallelism, Task parallelism, Visualization parallelism; (2) Optimized parallel input/output (I/O); (3) Remote interactive execution; (4) Advanced intercomparison visualization; (5) Data provenance processing and capture; and (6) Interfaces for scientists - Workflow data analysis and visualization construction tools, and Visualization interfaces.« less

BioNSi: A Discrete Biological Network Simulator Tool.

PubMed

Rubinstein, Amir; Bracha, Noga; Rudner, Liat; Zucker, Noga; Sloin, Hadas E; Chor, Benny

2016-08-05

Modeling and simulation of biological networks is an effective and widely used research methodology. The Biological Network Simulator (BioNSi) is a tool for modeling biological networks and simulating their discrete-time dynamics, implemented as a Cytoscape App. BioNSi includes a visual representation of the network that enables researchers to construct, set the parameters, and observe network behavior under various conditions. To construct a network instance in BioNSi, only partial, qualitative biological data suffices. The tool is aimed for use by experimental biologists and requires no prior computational or mathematical expertise. BioNSi is freely available at http://bionsi.wix.com/bionsi , where a complete user guide and a step-by-step manual can also be found.

Experience Report: Visual Programming in the Real World

NASA Technical Reports Server (NTRS)

Baroth, E.; Hartsough, C

1994-01-01

This paper reports direct experience with two commercial, widely used visual programming environments. While neither of these systems is object oriented, the tools have transformed the development process and indicate a direction for visual object oriented tools to proceed.

The Science Behind the NASA/NOAA Electronic Theater 2002

NASA Technical Reports Server (NTRS)

Hasler, A. Fritz; Starr, David (Technical Monitor)

2002-01-01

Details of the science stories and scientific results behind the Etheater Earth Science Visualizations from the major remote sensing institutions around the country will be explained. The NASA Electronic Theater presents Earth science observations and visualizations in a historical perspective. Fly in from outer space to Temple Square and the University of Utah Campus. Go back to the early weather satellite images from the 1960s see them contrasted with the latest US/Europe/Japan global weather data. See the latest images and image sequences from NASA & NOAA missions like Terra, GOES, NOAA, TRMM, SeaWiFS, Landsat 7 visualized with state-of-the art tools. A similar retrospective of numerical weather models from the 1960s will be compared with the latest "year 2002" high-resolution models. See the inner workings of a powerful hurricane as it is sliced and dissected using the University of Wisconsin Vis-5D interactive visualization system. The largest super computers are now capable of realistic modeling of the global oceans. See ocean vortexes and currents that bring up the nutrients to feed phitoplankton and zooplankton as well as draw the crill fish, whales and fisherman. See the how the ocean blooms in response to these currents and El Nino/La Nina climate regimes. The Internet and networks have appeared while computers and visualizations have vastly improved over the last 40 years. These advances make it possible to present the broad scope and detailed structure of the huge new observed and simulated datasets in a compelling and instructive manner. New visualization tools allow us to interactively roam & zoom through massive global images larger than 40,000 x 20,000 pixels. Powerful movie players allow us to interactively roam, zoom & loop through 4000 x 4000 pixel bigger than HDTV movies of up to 5000 frames. New 3D tools allow highly interactive manipulation of detailed perspective views of many changing model quantities. See the 1m resolution before and after shots of lower Manhattan and the Pentagon after the September 11 disaster as well as shots of Afghanistan from the Space Imaging IKONOS as well as debris plume images from Terra MODIS and SPOT Image. Shown by the SGI-Octane Graphics-Supercomputer are visualizations of hurricanes Michelle 2001, Floyd, Mitch, Fran and Linda. Our visualizations of these storms have been featured on the covers of the National Geographic, Time, Newsweek and Popular Science. Highlights will be shown from the NASA's large collection of High Definition TV (HDTV) visualizations clips New visualizations of a Los Alamos global ocean model, and high-resolution results of a NASA/JPL Atlantic ocean basin model showing currents, and salinity features will be shown. El Nino/La Nina effects on sea surface temperature and sea surface height of the Pacific Ocean will also be shown. The SST simulations will be compared with GOES Gulf Stream animations and ocean productivity observations. Tours will be given of the entire Earth's land surface at 500 m resolution from recently composited Terra MODIS data, Visualizations will be shown from the Earth Science Etheater 2001 recently presented over the last years in New Zealand, Johannesburg, Tokyo, Paris, Munich, Sydney, Melbourne, Honolulu, Washington, New York City, Pasadena, UCAR/Boulder, and Penn State University. The presentation will use a 2-CPU SGI/CRAY Octane Super Graphics workstation with 4 GB RAM and terabyte disk array at 2048 x 768 resolution plus multimedia laptop with three high resolution projectors. Visualizations will also be featured from museum exhibits and presentations including: the Smithsonian Air & Space Museum in Washington, IMAX theater at the Maryland Science Center in Baltimore, the James Lovell Discovery World Science museum in Milwaukee, the American Museum of Natural History (NYC) Hayden Planetarium IMAX theater, etc. The Etheater is sponsored by NASA, NOAA and the American Meteorological Society. This presentation is brought to you by the University of Utah College of Mines and Earth Sciences and, the Utah Museum of Natural History.

Cross-sectoral optimization and visualization of transformation processes in urban water infrastructures in rural areas.

PubMed

Baron, S; Kaufmann Alves, I; Schmitt, T G; Schöffel, S; Schwank, J

2015-01-01

Predicted demographic, climatic and socio-economic changes will require adaptations of existing water supply and wastewater disposal systems. Especially in rural areas, these new challenges will affect the functionality of the present systems. This paper presents a joint interdisciplinary research project with the objective of developing an innovative software-based optimization and decision support system for the implementation of long-term transformations of existing infrastructures of water supply, wastewater and energy. The concept of the decision support and optimization tool is described and visualization methods for the presentation of results are illustrated. The model is tested in a rural case study region in the Southwest of Germany. A transformation strategy for a decentralized wastewater treatment concept and its visualization are presented for a model village.

A Colour Opponent Model That Explains Tsetse Fly Attraction to Visual Baits and Can Be Used to Investigate More Efficacious Bait Materials

PubMed Central

Santer, Roger D.

2014-01-01

Palpalis group tsetse flies are the major vectors of human African trypanosomiasis, and visually-attractive targets and traps are important tools for their control. Considerable efforts are underway to optimise these visual baits, and one factor that has been investigated is coloration. Analyses of the link between visual bait coloration and tsetse fly catches have used methods which poorly replicate sensory processing in the fly visual system, but doing so would allow the visual information driving tsetse attraction to these baits to be more fully understood, and the reflectance spectra of candidate visual baits to be more completely analysed. Following methods well established for other species, I reanalyse the numbers of tsetse flies caught at visual baits based upon the calculated photoreceptor excitations elicited by those baits. I do this for large sets of previously published data for Glossina fuscipes fuscipes (Lindh et al. (2012). PLoS Negl Trop Dis 6: e1661), G. palpalis palpalis (Green (1988). Bull Ent Res 78: 591), and G. pallidipes (Green and Flint (1986). Bull Ent Res 76: 409). Tsetse attraction to visual baits in these studies can be explained by a colour opponent mechanism to which the UV-blue photoreceptor R7y contributes positively, and both the green-yellow photoreceptor R8y, and the low-wavelength UV photoreceptor R7p, contribute negatively. A tool for calculating fly photoreceptor excitations is made available with this paper, and this will facilitate a complete and biologically authentic description of visual bait reflectance spectra that can be employed in the search for more efficacious visual baits, or the analysis of future studies of tsetse fly attraction. PMID:25473844

A colour opponent model that explains tsetse fly attraction to visual baits and can be used to investigate more efficacious bait materials.

PubMed

Santer, Roger D

2014-12-01

Palpalis group tsetse flies are the major vectors of human African trypanosomiasis, and visually-attractive targets and traps are important tools for their control. Considerable efforts are underway to optimise these visual baits, and one factor that has been investigated is coloration. Analyses of the link between visual bait coloration and tsetse fly catches have used methods which poorly replicate sensory processing in the fly visual system, but doing so would allow the visual information driving tsetse attraction to these baits to be more fully understood, and the reflectance spectra of candidate visual baits to be more completely analysed. Following methods well established for other species, I reanalyse the numbers of tsetse flies caught at visual baits based upon the calculated photoreceptor excitations elicited by those baits. I do this for large sets of previously published data for Glossina fuscipes fuscipes (Lindh et al. (2012). PLoS Negl Trop Dis 6: e1661), G. palpalis palpalis (Green (1988). Bull Ent Res 78: 591), and G. pallidipes (Green and Flint (1986). Bull Ent Res 76: 409). Tsetse attraction to visual baits in these studies can be explained by a colour opponent mechanism to which the UV-blue photoreceptor R7y contributes positively, and both the green-yellow photoreceptor R8y, and the low-wavelength UV photoreceptor R7p, contribute negatively. A tool for calculating fly photoreceptor excitations is made available with this paper, and this will facilitate a complete and biologically authentic description of visual bait reflectance spectra that can be employed in the search for more efficacious visual baits, or the analysis of future studies of tsetse fly attraction.

Focal activation of primary visual cortex following supra-choroidal electrical stimulation of the retina: Intrinsic signal imaging and linear model analysis.

PubMed

Cloherty, Shaun L; Hietanen, Markus A; Suaning, Gregg J; Ibbotson, Michael R

2010-01-01

We performed optical intrinsic signal imaging of cat primary visual cortex (Area 17 and 18) while delivering bipolar electrical stimulation to the retina by way of a supra-choroidal electrode array. Using a general linear model (GLM) analysis we identified statistically significant (p < 0.01) activation in a localized region of cortex following supra-threshold electrical stimulation at a single retinal locus. (1) demonstrate that intrinsic signal imaging combined with linear model analysis provides a powerful tool for assessing cortical responses to prosthetic stimulation, and (2) confirm that supra-choroidal electrical stimulation can achieve localized activation of the cortex consistent with focal activation of the retina.

Intuitive and interpretable visual communication of a complex statistical model of disease progression and risk.

PubMed

Jieyi Li; Arandjelovic, Ognjen

2017-07-01

Computer science and machine learning in particular are increasingly lauded for their potential to aid medical practice. However, the highly technical nature of the state of the art techniques can be a major obstacle in their usability by health care professionals and thus, their adoption and actual practical benefit. In this paper we describe a software tool which focuses on the visualization of predictions made by a recently developed method which leverages data in the form of large scale electronic records for making diagnostic predictions. Guided by risk predictions, our tool allows the user to explore interactively different diagnostic trajectories, or display cumulative long term prognostics, in an intuitive and easily interpretable manner.

Reducing energy use and emissions through innovative technologies and community designs.

DOT National Transportation Integrated Search

2016-05-01

This project aimed to quantify the impacts of growth and technology strategies at the regional level by using modeling, simulation, and visualization tools, with the overall goal of enhancing livability and sustainability. A key research outcome is t...

Fostering Outreach, Education and Exploration of the Moon Using the Lunar Mapping & Modeling Portal

NASA Astrophysics Data System (ADS)

Dodge, K.; Law, E.; Malhotra, S.; Chang, G.; Kim, R. M.; Bui, B.; Sadaqathullah, S.; Day, B. H.

2014-12-01

The Lunar Mapping and Modeling Portal (LMMP)[1], is a web-based Portal and a suite of interactive visualization and analysis tools for users to access mapped lunar data products (including image mosaics, digital elevation models, etc.) from past and current lunar missions (e.g., Lunar Reconnaissance Orbiter, Apollo, etc.). Originally designed as a mission planning tool for the Constellation Program, LMMP has grown into a generalized suite of tools facilitating a wide range of activities in support of lunar exploration including public outreach, education, lunar mission planning and scientific research. LMMP fosters outreach, education, and exploration of the Moon by educators, students, amateur astronomers, and the general public. These efforts are enhanced by Moon Tours, LMMP's mobile application, which makes LMMP's information accessible to people of all ages, putting opportunities for real lunar exploration in the palms of their hands. Our talk will include an overview of LMMP and a demonstration of its technologies (web portals, mobile apps), to show how it serves NASA data as commodities for use by advanced visualization facilities (e.g., planetariums) and how it contributes to improving teaching and learning, increasing scientific literacy of the general public, and enriching STEM efforts. References:[1] http://www.lmmp.nasa.gov

Advances in visual representation of molecular potentials.

PubMed

Du, Qi-Shi; Huang, Ri-Bo; Chou, Kuo-Chen

2010-06-01

The recent advances in visual representations of molecular properties in 3D space are summarized, and their applications in molecular modeling study and rational drug design are introduced. The visual representation methods provide us with detailed insights into protein-ligand interactions, and hence can play a major role in elucidating the structure or reactivity of a biomolecular system. Three newly developed computation and visualization methods for studying the physical and chemical properties of molecules are introduced, including their electrostatic potential, lipophilicity potential and excess chemical potential. The newest application examples of visual representations in structure-based rational drug are presented. The 3D electrostatic potentials, calculated using the empirical method (EM-ESP), in which the classical Coulomb equation and traditional atomic partial changes are discarded, are highly consistent with the results by the higher level quantum chemical method. The 3D lipophilicity potentials, computed by the heuristic molecular lipophilicity potential method based on the principles of quantum mechanics and statistical mechanics, are more accurate and reliable than those by using the traditional empirical methods. The 3D excess chemical potentials, derived by the reference interaction site model-hypernetted chain theory, provide a new tool for computational chemistry and molecular modeling. For structure-based drug design, the visual representations of molecular properties will play a significant role in practical applications. It is anticipated that the new advances in computational chemistry will stimulate the development of molecular modeling methods, further enriching the visual representation techniques for rational drug design, as well as other relevant fields in life science.

Can Interactive Visualization Tools Engage and Support Pre-University Students in Exploring Non-Trivial Mathematical Concepts?

ERIC Educational Resources Information Center

Liang, Hai-Ning; Sedig, Kamran

2010-01-01

Many students find it difficult to engage with mathematical concepts. As a relatively new class of learning tools, visualization tools may be able to promote higher levels of engagement with mathematical concepts. Often, development of new tools may outpace empirical evaluations of the effectiveness of these tools, especially in educational…

Using NASA's Giovanni Web Portal to Access and Visualize Satellite-Based Earth Science Data in the Classroom

NASA Astrophysics Data System (ADS)

Lloyd, S. A.; Acker, J. G.; Prados, A. I.; Leptoukh, G. G.

2008-12-01

One of the biggest obstacles for the average Earth science student today is locating and obtaining satellite- based remote sensing datasets in a format that is accessible and optimal for their data analysis needs. At the Goddard Earth Sciences Data and Information Services Center (GES-DISC) alone, on the order of hundreds of Terabytes of data are available for distribution to scientists, students and the general public. The single biggest and time-consuming hurdle for most students when they begin their study of the various datasets is how to slog through this mountain of data to arrive at a properly sub-setted and manageable dataset to answer their science question(s). The GES DISC provides a number of tools for data access and visualization, including the Google-like Mirador search engine and the powerful GES-DISC Interactive Online Visualization ANd aNalysis Infrastructure (Giovanni) web interface. Giovanni provides a simple way to visualize, analyze and access vast amounts of satellite-based Earth science data. Giovanni's features and practical examples of its use will be demonstrated, with an emphasis on how satellite remote sensing can help students understand recent events in the atmosphere and biosphere. Giovanni is actually a series of sixteen similar web-based data interfaces, each of which covers a single satellite dataset (such as TRMM, TOMS, OMI, AIRS, MLS, HALOE, etc.) or a group of related datasets (such as MODIS and MISR for aerosols, SeaWIFS and MODIS for ocean color, and the suite of A-Train observations co-located along the CloudSat orbital path). Recently, ground-based datasets have been included in Giovanni, including the Northern Eurasian Earth Science Partnership Initiative (NEESPI), and EPA fine particulate matter (PM2.5) for air quality. Model data such as the Goddard GOCART model and MERRA meteorological reanalyses (in process) are being increasingly incorporated into Giovanni to facilitate model- data intercomparison. A full suite of data analysis and visualization tools is also available within Giovanni. The GES DISC is currently developing a systematic series of training modules for Earth science satellite data, associated with our development of additional datasets and data visualization tools for Giovanni. Training sessions will include an overview of the Earth science datasets archived at Goddard, an overview of terms and techniques associated with satellite remote sensing, dataset-specific issues, an overview of Giovanni functionality, and a series of examples of how data can be readily accessed and visualized.

Concept mapping One-Carbon Metabolism to model future ontologies for nutrient-gene-phenotype interactions.

PubMed

Joslin, A C; Green, R; German, J B; Lange, M C

2014-09-01

Advances in the development of bioinformatic tools continue to improve investigators' ability to interrogate, organize, and derive knowledge from large amounts of heterogeneous information. These tools often require advanced technical skills not possessed by life scientists. User-friendly, low-barrier-to-entry methods of visualizing nutrigenomics information are yet to be developed. We utilized concept mapping software from the Institute for Human and Machine Cognition to create a conceptual model of diet and health-related data that provides a foundation for future nutrigenomics ontologies describing published nutrient-gene/polymorphism-phenotype data. In this model, maps containing phenotype, nutrient, gene product, and genetic polymorphism interactions are visualized as triples of two concepts linked together by a linking phrase. These triples, or "knowledge propositions," contextualize aggregated data and information into easy-to-read knowledge maps. Maps of these triples enable visualization of genes spanning the One-Carbon Metabolism (OCM) pathway, their sequence variants, and multiple literature-mined associations including concepts relevant to nutrition, phenotypes, and health. The concept map development process documents the incongruity of information derived from pathway databases versus literature resources. This conceptual model highlights the importance of incorporating information about genes in upstream pathways that provide substrates, as well as downstream pathways that utilize products of the pathway under investigation, in this case OCM. Other genes and their polymorphisms, such as TCN2 and FUT2, although not directly involved in OCM, potentially alter OCM pathway functionality. These upstream gene products regulate substrates such as B12. Constellations of polymorphisms affecting the functionality of genes along OCM, together with substrate and cofactor availability, may impact resultant phenotypes. These conceptual maps provide a foundational framework for development of nutrient-gene/polymorphism-phenotype ontologies and systems visualization.

Web-based, GPU-accelerated, Monte Carlo simulation and visualization of indirect radiation imaging detector performance.

PubMed

Dong, Han; Sharma, Diksha; Badano, Aldo

2014-12-01

Monte Carlo simulations play a vital role in the understanding of the fundamental limitations, design, and optimization of existing and emerging medical imaging systems. Efforts in this area have resulted in the development of a wide variety of open-source software packages. One such package, hybridmantis, uses a novel hybrid concept to model indirect scintillator detectors by balancing the computational load using dual CPU and graphics processing unit (GPU) processors, obtaining computational efficiency with reasonable accuracy. In this work, the authors describe two open-source visualization interfaces, webmantis and visualmantis to facilitate the setup of computational experiments via hybridmantis. The visualization tools visualmantis and webmantis enable the user to control simulation properties through a user interface. In the case of webmantis, control via a web browser allows access through mobile devices such as smartphones or tablets. webmantis acts as a server back-end and communicates with an NVIDIA GPU computing cluster that can support multiuser environments where users can execute different experiments in parallel. The output consists of point response and pulse-height spectrum, and optical transport statistics generated by hybridmantis. The users can download the output images and statistics through a zip file for future reference. In addition, webmantis provides a visualization window that displays a few selected optical photon path as they get transported through the detector columns and allows the user to trace the history of the optical photons. The visualization tools visualmantis and webmantis provide features such as on the fly generation of pulse-height spectra and response functions for microcolumnar x-ray imagers while allowing users to save simulation parameters and results from prior experiments. The graphical interfaces simplify the simulation setup and allow the user to go directly from specifying input parameters to receiving visual feedback for the model predictions.

Three-Dimensional Online Visualization and Engagement Tools for the Geosciences

NASA Astrophysics Data System (ADS)

Cockett, R.; Moran, T.; Pidlisecky, A.

2013-12-01

Educational tools often sacrifice interactivity in favour of scalability so they can reach more users. This compromise leads to tools that may be viewed as second tier when compared to more engaging activities performed in a laboratory; however, the resources required to deliver laboratory exercises that are scalable is often impractical. Geoscience education is well situated to benefit from interactive online learning tools that allow users to work in a 3D environment. Visible Geology (http://3ptscience.com/visiblegeology) is an innovative web-based application designed to enable visualization of geologic structures and processes through the use of interactive 3D models. The platform allows users to conceptualize difficult, yet important geologic principles in a scientifically accurate manner by developing unique geologic models. The environment allows students to interactively practice their visualization and interpretation skills by creating and interacting with their own models and terrains. Visible Geology has been designed from a user centric perspective resulting in a simple and intuitive interface. The platform directs students to build there own geologic models by adding beds and creating geologic events such as tilting, folding, or faulting. The level of ownership and interactivity encourages engagement, leading learners to discover geologic relationships on their own, in the context of guided assignments. In January 2013, an interactive geologic history assignment was developed for a 700-student introductory geology class at The University of British Columbia. The assignment required students to distinguish the relative age of geologic events to construct a geologic history. Traditionally this type of exercise has been taught through the use of simple geologic cross-sections showing crosscutting relationships; from these cross-sections students infer the relative age of geologic events. In contrast, the Visible Geology assignment offers students a unique experience where they first create their own geologic events allowing them to directly see how the timing of a geologic event manifests in the model and resulting cross-sections. By creating each geologic event in the model themselves, the students gain a deeper understanding of the processes and relative order of events. The resulting models can be shared amongst students, and provide instructors with a basis for guiding inquiry to address misconceptions. The ease of use of the assignment, including automatic assessment, made this tool practical for deployment in this 700 person class. The outcome of this type of large scale deployment is that students, who would normally not experience a lab exercise, gain exposure to interactive 3D thinking. Engaging tools and software that puts the user in control of their learning experiences is critical for moving to scalable, yet engaging, online learning environments.

Got Graphs? An Assessment of Data Visualization Tools

NASA Technical Reports Server (NTRS)

Schaefer, C. M.; Foy, M.

2015-01-01

Graphs are powerful tools for simplifying complex data. They are useful for quickly assessing patterns and relationships among one or more variables from a dataset. As the amount of data increases, it becomes more difficult to visualize potential associations. Lifetime Surveillance of Astronaut Health (LSAH) was charged with assessing its current visualization tools along with others on the market to determine whether new tools would be useful for supporting NASA's occupational surveillance effort. It was concluded by members of LSAH that the current tools hindered their ability to provide quick results to researchers working with the department. Due to the high volume of data requests and the many iterations of visualizations requested by researchers, software with a better ability to replicate graphs and edit quickly could improve LSAH's efficiency and lead to faster research results.

Web-Based Geospatial Visualization of GPM Data with CesiumJS

NASA Technical Reports Server (NTRS)

Lammers, Matt

2018-01-01

Advancements in the capabilities of JavaScript frameworks and web browsing technology have made online visualization of large geospatial datasets such as those coming from precipitation satellites viable. These data benefit from being visualized on and above a three-dimensional surface. The open-source JavaScript framework CesiumJS (http://cesiumjs.org), developed by Analytical Graphics, Inc., leverages the WebGL protocol to do just that. This presentation will describe how CesiumJS has been used in three-dimensional visualization products developed as part of the NASA Precipitation Processing System (PPS) STORM data-order website. Existing methods of interacting with Global Precipitation Measurement (GPM) Mission data primarily focus on two-dimensional static images, whether displaying vertical slices or horizontal surface/height-level maps. These methods limit interactivity with the robust three-dimensional data coming from the GPM core satellite. Integrating the data with CesiumJS in a web-based user interface has allowed us to create the following products. We have linked with the data-order interface an on-the-fly visualization tool for any GPM/partner satellite orbit. A version of this tool also focuses on high-impact weather events. It enables viewing of combined radar and microwave-derived precipitation data on mobile devices and in a way that can be embedded into other websites. We also have used CesiumJS to visualize a method of integrating gridded precipitation data with modeled wind speeds that animates over time. Emphasis in the presentation will be placed on how a variety of technical methods were used to create these tools, and how the flexibility of the CesiumJS framework facilitates creative approaches to interact with the data.

Computerized Biomechanical Man-Model

DTIC Science & Technology

1976-07-01

Force Systems Command Wright-Patterson AFB, Ohio ABSTRACT The COMputerized BIomechanical MAN-Model (called COMBIMAN) is a computer interactive graphics...concept was to build a mock- The use of mock-ups for biomechanical evalua- up which permitted the designer to visualize the tion has long been a tool...of the can become an obstacle to design change. Aerospace Medical Research Laboratory, we are developing a computerized biomechanical man-model

50 Years of Army Computing From ENIAC to MSRC

DTIC Science & Technology

2000-09-01

processing capability. The scientifi c visualization program was started in 1984 to provide tools and expertise to help researchers graphically...and materials, forces modeling, nanoelectronics, electromagnetics and acoustics, signal image processing , and simulation and modeling. The ARL...mechanical and electrical calculating equipment, punch card data processing equipment, analog computers, and early digital machines. Before beginning, we

Using component technologies for web based wavelet enhanced mammographic image visualization.

PubMed

Sakellaropoulos, P; Costaridou, L; Panayiotakis, G

2000-01-01

The poor contrast detectability of mammography can be dealt with by domain specific software visualization tools. Remote desktop client access and time performance limitations of a previously reported visualization tool are addressed, aiming at more efficient visualization of mammographic image resources existing in web or PACS image servers. This effort is also motivated by the fact that at present, web browsers do not support domain-specific medical image visualization. To deal with desktop client access the tool was redesigned by exploring component technologies, enabling the integration of stand alone domain specific mammographic image functionality in a web browsing environment (web adaptation). The integration method is based on ActiveX Document Server technology. ActiveX Document is a part of Object Linking and Embedding (OLE) extensible systems object technology, offering new services in existing applications. The standard DICOM 3.0 part 10 compatible image-format specification Papyrus 3.0 is supported, in addition to standard digitization formats such as TIFF. The visualization functionality of the tool has been enhanced by including a fast wavelet transform implementation, which allows for real time wavelet based contrast enhancement and denoising operations. Initial use of the tool with mammograms of various breast structures demonstrated its potential in improving visualization of diagnostic mammographic features. Web adaptation and real time wavelet processing enhance the potential of the previously reported tool in remote diagnosis and education in mammography.

Desktop chaotic systems: Intuition and visualization

NASA Technical Reports Server (NTRS)

Bright, Michelle M.; Melcher, Kevin J.; Qammar, Helen K.; Hartley, Tom T.

1993-01-01

This paper presents a dynamic study of the Wildwood Pendulum, a commercially available desktop system which exhibits a strange attractor. The purpose of studying this chaotic pendulum is twofold: to gain insight in the paradigmatic approach of modeling, simulating, and determining chaos in nonlinear systems; and to provide a desktop model of chaos as a visual tool. For this study, the nonlinear behavior of this chaotic pendulum is modeled, a computer simulation is performed, and an experimental performance is measured. An assessment of the pendulum in the phase plane shows the strange attractor. Through the use of a box-assisted correlation dimension methodology, the attractor dimension is determined for both the model and the experimental pendulum systems. Correlation dimension results indicate that the pendulum and the model are chaotic and their fractal dimensions are similar.

cellVIEW: a Tool for Illustrative and Multi-Scale Rendering of Large Biomolecular Datasets

PubMed Central

Le Muzic, Mathieu; Autin, Ludovic; Parulek, Julius; Viola, Ivan

2017-01-01

In this article we introduce cellVIEW, a new system to interactively visualize large biomolecular datasets on the atomic level. Our tool is unique and has been specifically designed to match the ambitions of our domain experts to model and interactively visualize structures comprised of several billions atom. The cellVIEW system integrates acceleration techniques to allow for real-time graphics performance of 60 Hz display rate on datasets representing large viruses and bacterial organisms. Inspired by the work of scientific illustrators, we propose a level-of-detail scheme which purpose is two-fold: accelerating the rendering and reducing visual clutter. The main part of our datasets is made out of macromolecules, but it also comprises nucleic acids strands which are stored as sets of control points. For that specific case, we extend our rendering method to support the dynamic generation of DNA strands directly on the GPU. It is noteworthy that our tool has been directly implemented inside a game engine. We chose to rely on a third party engine to reduce software development work-load and to make bleeding-edge graphics techniques more accessible to the end-users. To our knowledge cellVIEW is the only suitable solution for interactive visualization of large bimolecular landscapes on the atomic level and is freely available to use and extend. PMID:29291131

Improve Problem Solving Skills through Adapting Programming Tools

NASA Technical Reports Server (NTRS)

Shaykhian, Linda H.; Shaykhian, Gholam Ali

2007-01-01

There are numerous ways for engineers and students to become better problem-solvers. The use of command line and visual programming tools can help to model a problem and formulate a solution through visualization. The analysis of problem attributes and constraints provide insight into the scope and complexity of the problem. The visualization aspect of the problem-solving approach tends to make students and engineers more systematic in their thought process and help them catch errors before proceeding too far in the wrong direction. The problem-solver identifies and defines important terms, variables, rules, and procedures required for solving a problem. Every step required to construct the problem solution can be defined in program commands that produce intermediate output. This paper advocates improved problem solving skills through using a programming tool. MatLab created by MathWorks, is an interactive numerical computing environment and programming language. It is a matrix-based system that easily lends itself to matrix manipulation, and plotting of functions and data. MatLab can be used as an interactive command line or a sequence of commands that can be saved in a file as a script or named functions. Prior programming experience is not required to use MatLab commands. The GNU Octave, part of the GNU project, a free computer program for performing numerical computations, is comparable to MatLab. MatLab visual and command programming are presented here.

Visual quality assessment of alternative silvicultural practices in upland hardwood management

Treesearch

Tim McDonald; Bryce Stokes

1997-01-01

Visual impacts of forest operations are of increasing concern to forest managers. Tools are available for evaluating, and potentially avoiding, problems in visual quality resulting from poorly designed harvest unit boundaries. One of these visualization tools is applied in comparing various harvest unit shape alternatives in an upland hardwood stand on steeply sloping...

Application of Frameworks in the Analysis and (Re)design of Interactive Visual Learning Tools

ERIC Educational Resources Information Center

Liang, Hai-Ning; Sedig, Kamran

2009-01-01

Interactive visual learning tools (IVLTs) are software environments that encode and display information visually and allow learners to interact with the visual information. This article examines the application and utility of frameworks in the analysis and design of IVLTs at the micro level. Frameworks play an important role in any design. They…

Examining Chemistry Students Visual-Perceptual Skills Using the VSCS Tool and Interview Data

ERIC Educational Resources Information Center

Christian, Caroline

2010-01-01

The Visual-Spatial Chemistry Specific (VSCS) assessment tool was developed to test students' visual-perceptual skills, which are required to form a mental image of an object. The VSCS was designed around the theoretical framework of Rochford and Archer that provides eight distinct and well-defined visual-perceptual skills with identified problems…

Integrated network analysis and effective tools in plant systems biology

PubMed Central

Fukushima, Atsushi; Kanaya, Shigehiko; Nishida, Kozo

2014-01-01

One of the ultimate goals in plant systems biology is to elucidate the genotype-phenotype relationship in plant cellular systems. Integrated network analysis that combines omics data with mathematical models has received particular attention. Here we focus on the latest cutting-edge computational advances that facilitate their combination. We highlight (1) network visualization tools, (2) pathway analyses, (3) genome-scale metabolic reconstruction, and (4) the integration of high-throughput experimental data and mathematical models. Multi-omics data that contain the genome, transcriptome, proteome, and metabolome and mathematical models are expected to integrate and expand our knowledge of complex plant metabolisms. PMID:25408696

Model My Watershed: A high-performance cloud application for public engagement, watershed modeling and conservation decision support

NASA Astrophysics Data System (ADS)

Aufdenkampe, A. K.; Tarboton, D. G.; Horsburgh, J. S.; Mayorga, E.; McFarland, M.; Robbins, A.; Haag, S.; Shokoufandeh, A.; Evans, B. M.; Arscott, D. B.

2017-12-01

The Model My Watershed Web app (https://app.wikiwatershed.org/) and the BiG-CZ Data Portal (http://portal.bigcz.org/) and are web applications that share a common codebase and a common goal to deliver high-performance discovery, visualization and analysis of geospatial data in an intuitive user interface in web browser. Model My Watershed (MMW) was designed as a decision support system for watershed conservation implementation. BiG CZ Data Portal was designed to provide context and background data for research sites. Users begin by creating an Area of Interest, via an automated watershed delineation tool, a free draw tool, selection of a predefined area such as a county or USGS Hydrological Unit (HUC), or uploading a custom polygon. Both Web apps visualize and provide summary statistics of land use, soil groups, streams, climate and other geospatial information. MMW then allows users to run a watershed model to simulate different scenarios of human impacts on stormwater runoff and water-quality. BiG CZ Data Portal allows users to search for scientific and monitoring data within the Area of Interest, which also serves as a prototype for the upcoming Monitor My Watershed web app. Both systems integrate with CUAHSI cyberinfrastructure, including visualizing observational data from CUAHSI Water Data Center and storing user data via CUAHSI HydroShare. Both systems also integrate with the new EnviroDIY Water Quality Data Portal (http://data.envirodiy.org/), a system for crowd-sourcing environmental monitoring data using open-source sensor stations (http://envirodiy.org/mayfly/) and based on the Observations Data Model v2.

Increasing awareness and preparedness by an exhibition and studying the effect of visuals

NASA Astrophysics Data System (ADS)

Charrière, Marie; Bogaard, Thom; Malet, Jean-Philippe; Mostert, Erik

2013-04-01

Damages caused by natural hazards can be reduced not only by protection, management and intervention activities, but also by information and communication to improve awareness and preparedness of local communities and tourists. Risk communication is particularly crucial for mountainous areas, such as the Ubaye Valley (France), as they are affected by multiple hazards and are particularly sensitive to the potential effects of climate and socio-economic changes which may increase the risk associated with natural hazards significantly. An exhibition is a powerful tool to communicate with the general public. It allows1: (1) targeting specific audiences, (2) transmitting technical and scientific knowledge using a suitable language, (3) anchoring the collective memory of past events, (4) visualize and emotionalize the topic of natural hazards, (5) strengthening the communication between peers, and (6) highlighting local resources and knowledge. In addition to these theoretical advantages, an exhibition may fulfill the requirements of a community. In the Ubaye Valley (France), this tool was proposed by the stakeholders themselves to increase awareness and preparedness of the general public. To meet this demand, the exhibition was designed following three general topics: (1) the natural phenomena and their potential consequences on the elements at risk, (2) the management and protection measures (individual and collective) and (3) the evolution of events and knowledge throughout past up to the present and the anticipation of the future situations. Besides being a real risk communication practice, this exhibition will be the setting for an extensive research project studying the effect of the use of visualization tools on the awareness and preparedness of a community. A wide range of visuals (photos, videos, maps, models, animations, multimedia, etc.) will present many dimensions of locally occurring natural hazards and risk problems. The aim of the research is (1) to verify the theoretical advantages of visual communication, such as conveying strong messages and making them easy to remember2, (2) to measure the change of awareness and preparedness after being exposed to such media, and (3) to propose guidelines for further development and use of visual tools for natural hazard risk communication. To conduct this analysis, questionnaires and direct observation will be applied. The first method will allow to measure changes in knowledge and perceptions as the same questionnaire will be filled by visitors prior and after their attendance to the exhibition. Additional items of the questionnaire will deal with the opinions on the different visualization tools, i.e. fulfillment of needs and requirements of the visitors. Direct observation will be used for analyzing the relative attraction of each of the visualization tools. This research will help to determine which tool is more suitable to communicate to the community not only as a whole, but also by its sub-groups, i.e. children or adults, locals or tourists, etc.

Generating community-built tools for data sharing and analysis in environmental networks

USGS Publications Warehouse

Read, Jordan S.; Gries, Corinna; Read, Emily K.; Klug, Jennifer; Hanson, Paul C.; Hipsey, Matthew R.; Jennings, Eleanor; O'Reilley, Catherine; Winslow, Luke A.; Pierson, Don; McBride, Christopher G.; Hamilton, David

2016-01-01

Rapid data growth in many environmental sectors has necessitated tools to manage and analyze these data. The development of tools often lags behind the proliferation of data, however, which may slow exploratory opportunities and scientific progress. The Global Lake Ecological Observatory Network (GLEON) collaborative model supports an efficient and comprehensive data–analysis–insight life cycle, including implementations of data quality control checks, statistical calculations/derivations, models, and data visualizations. These tools are community-built and openly shared. We discuss the network structure that enables tool development and a culture of sharing, leading to optimized output from limited resources. Specifically, data sharing and a flat collaborative structure encourage the development of tools that enable scientific insights from these data. Here we provide a cross-section of scientific advances derived from global-scale analyses in GLEON. We document enhancements to science capabilities made possible by the development of analytical tools and highlight opportunities to expand this framework to benefit other environmental networks.

CDPP Tools in the IMPEx infrastructure

NASA Astrophysics Data System (ADS)

Gangloff, Michel; Génot, Vincent; Bourrel, Nataliya; Hess, Sébastien; Khodachenko, Maxim; Modolo, Ronan; Kallio, Esa; Alexeev, Igor; Al-Ubaidi, Tarek; Cecconi, Baptiste; André, Nicolas; Budnik, Elena; Bouchemit, Myriam; Dufourg, Nicolas; Beigbeder, Laurent

2014-05-01

The CDPP (Centre de Données de la Physique des Plasmas, http://cdpp.eu/), the French data center for plasma physics, is engaged for more than a decade in the archiving and dissemination of plasma data products from space missions and ground observatories. Besides these activities, the CDPP developed services like AMDA (http://amda.cdpp.eu/) which enables in depth analysis of large amount of data through dedicated functionalities such as: visualization, conditional search, cataloguing, and 3DView (http://3dview.cdpp.eu/) which provides immersive visualisations in planetary environments and is further developed to include simulation and observational data. Both tools implement the IMPEx protocol (http://impexfp7.oeaw.ac.at/) to give access to outputs of simulation runs and models in planetary sciences from several providers like LATMOS, FMI , SINP; prototypes have also been built to access some UCLA and CCMC simulations. These tools and their interaction will be presented together with the IMPEx simulation data model (http://impex.latmos.ipsl.fr/tools/DataModel.htm) used for the interface to model databases.

ASCI visualization tool evaluation, Version 2.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kegelmeyer, P.

1997-04-01

The charter of the ASCI Visualization Common Tools subgroup was to investigate and evaluate 3D scientific visualization tools. As part of that effort, a Tri-Lab evaluation effort was launched in February of 1996. The first step was to agree on a thoroughly documented list of 32 features against which all tool candidates would be evaluated. These evaluation criteria were both gleaned from a user survey and determined from informed extrapolation into the future, particularly as concerns the 3D nature and extremely large size of ASCI data sets. The second step was to winnow a field of 41 candidate tools downmore » to 11. The selection principle was to be as inclusive as practical, retaining every tool that seemed to hold any promise of fulfilling all of ASCI`s visualization needs. These 11 tools were then closely investigated by volunteer evaluators distributed across LANL, LLNL, and SNL. This report contains the results of those evaluations, as well as a discussion of the evaluation philosophy and criteria.« less

Scalable Predictive Analysis in Critically Ill Patients Using a Visual Open Data Analysis Platform

PubMed Central

Poucke, Sven Van; Zhang, Zhongheng; Schmitz, Martin; Vukicevic, Milan; Laenen, Margot Vander; Celi, Leo Anthony; Deyne, Cathy De

2016-01-01

With the accumulation of large amounts of health related data, predictive analytics could stimulate the transformation of reactive medicine towards Predictive, Preventive and Personalized (PPPM) Medicine, ultimately affecting both cost and quality of care. However, high-dimensionality and high-complexity of the data involved, prevents data-driven methods from easy translation into clinically relevant models. Additionally, the application of cutting edge predictive methods and data manipulation require substantial programming skills, limiting its direct exploitation by medical domain experts. This leaves a gap between potential and actual data usage. In this study, the authors address this problem by focusing on open, visual environments, suited to be applied by the medical community. Moreover, we review code free applications of big data technologies. As a showcase, a framework was developed for the meaningful use of data from critical care patients by integrating the MIMIC-II database in a data mining environment (RapidMiner) supporting scalable predictive analytics using visual tools (RapidMiner’s Radoop extension). Guided by the CRoss-Industry Standard Process for Data Mining (CRISP-DM), the ETL process (Extract, Transform, Load) was initiated by retrieving data from the MIMIC-II tables of interest. As use case, correlation of platelet count and ICU survival was quantitatively assessed. Using visual tools for ETL on Hadoop and predictive modeling in RapidMiner, we developed robust processes for automatic building, parameter optimization and evaluation of various predictive models, under different feature selection schemes. Because these processes can be easily adopted in other projects, this environment is attractive for scalable predictive analytics in health research. PMID:26731286

Scalable Predictive Analysis in Critically Ill Patients Using a Visual Open Data Analysis Platform.

PubMed

Van Poucke, Sven; Zhang, Zhongheng; Schmitz, Martin; Vukicevic, Milan; Laenen, Margot Vander; Celi, Leo Anthony; De Deyne, Cathy

2016-01-01

With the accumulation of large amounts of health related data, predictive analytics could stimulate the transformation of reactive medicine towards Predictive, Preventive and Personalized (PPPM) Medicine, ultimately affecting both cost and quality of care. However, high-dimensionality and high-complexity of the data involved, prevents data-driven methods from easy translation into clinically relevant models. Additionally, the application of cutting edge predictive methods and data manipulation require substantial programming skills, limiting its direct exploitation by medical domain experts. This leaves a gap between potential and actual data usage. In this study, the authors address this problem by focusing on open, visual environments, suited to be applied by the medical community. Moreover, we review code free applications of big data technologies. As a showcase, a framework was developed for the meaningful use of data from critical care patients by integrating the MIMIC-II database in a data mining environment (RapidMiner) supporting scalable predictive analytics using visual tools (RapidMiner's Radoop extension). Guided by the CRoss-Industry Standard Process for Data Mining (CRISP-DM), the ETL process (Extract, Transform, Load) was initiated by retrieving data from the MIMIC-II tables of interest. As use case, correlation of platelet count and ICU survival was quantitatively assessed. Using visual tools for ETL on Hadoop and predictive modeling in RapidMiner, we developed robust processes for automatic building, parameter optimization and evaluation of various predictive models, under different feature selection schemes. Because these processes can be easily adopted in other projects, this environment is attractive for scalable predictive analytics in health research.

Virtual skeletal complex model- and landmark-guided orthognathic surgery system.

PubMed

Lee, Sang-Jeong; Woo, Sang-Yoon; Huh, Kyung-Hoe; Lee, Sam-Sun; Heo, Min-Suk; Choi, Soon-Chul; Han, Jeong Joon; Yang, Hoon Joo; Hwang, Soon Jung; Yi, Won-Jin

2016-05-01

In this study, correction of the maxillofacial deformities was performed by repositioning bone segments to an appropriate location according to the preoperative planning in orthognathic surgery. The surgery was planned using the patient's virtual skeletal models fused with optically scanned three-dimensional dentition. The virtual maxillomandibular complex (MMC) model of the patient's final occlusal relationship was generated by fusion of the maxillary and mandibular models with scanned occlusion. The final position of the MMC was simulated preoperatively by planning and was used as a goal model for guidance. During surgery, the intraoperative registration was finished immediately using only software processing. For accurate repositioning, the intraoperative MMC model was visualized on the monitor with respect to the simulated MMC model, and the intraoperative positions of multiple landmarks were also visualized on the MMC surface model. The deviation errors between the intraoperative and the final positions of each landmark were visualized quantitatively. As a result, the surgeon could easily recognize the three-dimensional deviation of the intraoperative MMC state from the final goal model without manually applying a pointing tool, and could also quickly determine the amount and direction of further MMC movements needed to reach the goal position. The surgeon could also perform various osteotomies and remove bone interference conveniently, as the maxillary tracking tool could be separated from the MMC. The root mean square (RMS) difference between the preoperative planning and the intraoperative guidance was 1.16 ± 0.34 mm immediately after repositioning. After surgery, the RMS differences between the planning and the postoperative computed tomographic model were 1.31 ± 0.28 mm and 1.74 ± 0.73 mm for the maxillary and mandibular landmarks, respectively. Our method provides accurate and flexible guidance for bimaxillary orthognathic surgery based on intraoperative visualization and quantification of deviations for simulated postoperative MMC and landmarks. The guidance using simulated skeletal models and landmarks can complement and improve conventional navigational surgery for bone repositioning in the craniomaxillofacial area. Copyright © 2016 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Application of Mathematical and Three-Dimensional Computer Modeling Tools in the Planning of Processes of Fuel and Energy Complexes

NASA Astrophysics Data System (ADS)

Aksenova, Olesya; Nikolaeva, Evgenia; Cehlár, Michal

2017-11-01

This work aims to investigate the effectiveness of mathematical and three-dimensional computer modeling tools in the planning of processes of fuel and energy complexes at the planning and design phase of a thermal power plant (TPP). A solution for purification of gas emissions at the design development phase of waste treatment systems is proposed employing mathematical and three-dimensional computer modeling - using the E-nets apparatus and the development of a 3D model of the future gas emission purification system. Which allows to visualize the designed result, to select and scientifically prove economically feasible technology, as well as to ensure the high environmental and social effect of the developed waste treatment system. The authors present results of a treatment of planned technological processes and the system for purifying gas emissions in terms of E-nets. using mathematical modeling in the Simulink application. What allowed to create a model of a device from the library of standard blocks and to perform calculations. A three-dimensional model of a system for purifying gas emissions has been constructed. It allows to visualize technological processes and compare them with the theoretical calculations at the design phase of a TPP and. if necessary, make adjustments.

Decision exploration lab: a visual analytics solution for decision management.

PubMed

Broeksema, Bertjan; Baudel, Thomas; Telea, Arthur G; Crisafulli, Paolo

2013-12-01

We present a visual analytics solution designed to address prevalent issues in the area of Operational Decision Management (ODM). In ODM, which has its roots in Artificial Intelligence (Expert Systems) and Management Science, it is increasingly important to align business decisions with business goals. In our work, we consider decision models (executable models of the business domain) as ontologies that describe the business domain, and production rules that describe the business logic of decisions to be made over this ontology. Executing a decision model produces an accumulation of decisions made over time for individual cases. We are interested, first, to get insight in the decision logic and the accumulated facts by themselves. Secondly and more importantly, we want to see how the accumulated facts reveal potential divergences between the reality as captured by the decision model, and the reality as captured by the executed decisions. We illustrate the motivation, added value for visual analytics, and our proposed solution and tooling through a business case from the car insurance industry.

Coastal On-line Assessment and Synthesis Tool 2.0

NASA Technical Reports Server (NTRS)

Brown, Richard; Navard, Andrew; Nguyen, Beth

2011-01-01

COAST (Coastal On-line Assessment and Synthesis Tool) is a 3D, open-source Earth data browser developed by leveraging and enhancing previous NASA open-source tools. These tools use satellite imagery and elevation data in a way that allows any user to zoom from orbit view down into any place on Earth, and enables the user to experience Earth terrain in a visually rich 3D view. The benefits associated with taking advantage of an open-source geo-browser are that it is free, extensible, and offers a worldwide developer community that is available to provide additional development and improvement potential. What makes COAST unique is that it simplifies the process of locating and accessing data sources, and allows a user to combine them into a multi-layered and/or multi-temporal visual analytical look into possible data interrelationships and coeffectors for coastal environment phenomenology. COAST provides users with new data visual analytic capabilities. COAST has been upgraded to maximize use of open-source data access, viewing, and data manipulation software tools. The COAST 2.0 toolset has been developed to increase access to a larger realm of the most commonly implemented data formats used by the coastal science community. New and enhanced functionalities that upgrade COAST to COAST 2.0 include the development of the Temporal Visualization Tool (TVT) plug-in, the Recursive Online Remote Data-Data Mapper (RECORD-DM) utility, the Import Data Tool (IDT), and the Add Points Tool (APT). With these improvements, users can integrate their own data with other data sources, and visualize the resulting layers of different data types (such as spatial and spectral, for simultaneous visual analysis), and visualize temporal changes in areas of interest.

Visualizing Uncertainty for Probabilistic Weather Forecasting based on Reforecast Analogs

NASA Astrophysics Data System (ADS)

Pelorosso, Leandro; Diehl, Alexandra; Matković, Krešimir; Delrieux, Claudio; Ruiz, Juan; Gröeller, M. Eduard; Bruckner, Stefan

2016-04-01

Numerical weather forecasts are prone to uncertainty coming from inaccuracies in the initial and boundary conditions and lack of precision in numerical models. Ensemble of forecasts partially addresses these problems by considering several runs of the numerical model. Each forecast is generated with different initial and boundary conditions and different model configurations [GR05]. The ensembles can be expressed as probabilistic forecasts, which have proven to be very effective in the decision-making processes [DE06]. The ensemble of forecasts represents only some of the possible future atmospheric states, usually underestimating the degree of uncertainty in the predictions [KAL03, PH06]. Hamill and Whitaker [HW06] introduced the "Reforecast Analog Regression" (RAR) technique to overcome the limitations of ensemble forecasting. This technique produces probabilistic predictions based on the analysis of historical forecasts and observations. Visual analytics provides tools for processing, visualizing, and exploring data to get new insights and discover hidden information patterns in an interactive exchange between the user and the application [KMS08]. In this work, we introduce Albero, a visual analytics solution for probabilistic weather forecasting based on the RAR technique. Albero targets at least two different type of users: "forecasters", who are meteorologists working in operational weather forecasting and "researchers", who work in the construction of numerical prediction models. Albero is an efficient tool for analyzing precipitation forecasts, allowing forecasters to make and communicate quick decisions. Our solution facilitates the analysis of a set of probabilistic forecasts, associated statistical data, observations and uncertainty. A dashboard with small-multiples of probabilistic forecasts allows the forecasters to analyze at a glance the distribution of probabilities as a function of time, space, and magnitude. It provides the user with a more accurate measure of forecast uncertainty that could result in better decision-making. It offers different level of abstractions to help with the recalibration of the RAR method. It also has an inspection tool that displays the selected analogs, their observations and statistical data. It gives the users access to inner parts of the method, unveiling hidden information. References [GR05] GNEITING T., RAFTERY A. E.: Weather forecasting with ensemble methods. Science 310, 5746, 248-249, 2005. [KAL03] KALNAY E.: Atmospheric modeling, data assimilation and predictability. Cambridge University Press, 2003. [PH06] PALMER T., HAGEDORN R.: Predictability of weather and climate. Cambridge University Press, 2006. [HW06] HAMILL T. M., WHITAKER J. S.: Probabilistic quantitative precipitation forecasts based on reforecast analogs: Theory and application. Monthly Weather Review 134, 11, 3209-3229, 2006. [DE06] DEITRICK S., EDSALL R.: The influence of uncertainty visualization on decision making: An empirical evaluation. Springer, 2006. [KMS08] KEIM D. A., MANSMANN F., SCHNEIDEWIND J., THOMAS J., ZIEGLER H.: Visual analytics: Scope and challenges. Springer, 2008.

Latest Community Coordinated Modeling Center (CCMC) services and innovative tools supporting the space weather research and operational communities.

NASA Astrophysics Data System (ADS)

Mendoza, A. M. M.; Rastaetter, L.; Kuznetsova, M. M.; Mays, M. L.; Chulaki, A.; Shim, J. S.; MacNeice, P. J.; Taktakishvili, A.; Collado-Vega, Y. M.; Weigand, C.; Zheng, Y.; Mullinix, R.; Patel, K.; Pembroke, A. D.; Pulkkinen, A. A.; Boblitt, J. M.; Bakshi, S. S.; Tsui, T.

2017-12-01

The Community Coordinated Modeling Center (CCMC), with the fundamental goal of aiding the transition of modern space science models into space weather forecasting while supporting space science research, has been serving as an integral hub for over 15 years, providing invaluable resources to both space weather scientific and operational communities. CCMC has developed and provided innovative web-based point of access tools varying from: Runs-On-Request System - providing unprecedented global access to the largest collection of state-of-the-art solar and space physics models, Integrated Space Weather Analysis (iSWA) - a powerful dissemination system for space weather information, Advanced Online Visualization and Analysis tools for more accurate interpretation of model results, Standard Data formats for Simulation Data downloads, and Mobile apps to view space weather data anywhere to the scientific community. In addition to supporting research and performing model evaluations, CCMC also supports space science education by hosting summer students through local universities. In this poster, we will showcase CCMC's latest innovative tools and services, and CCMC's tools that revolutionized the way we do research and improve our operational space weather capabilities. CCMC's free tools and resources are all publicly available online (http://ccmc.gsfc.nasa.gov).

Juniper Encroachment and Management in the Intermountain West Relative to Wildfires Utilizing Remote Sensing

NASA Astrophysics Data System (ADS)

Williams, J.; Howerton, R.; Ramos, S.; Simpson, Z.; Weber, K.

2016-12-01

One of the most pronounced vegetation changes in recent history is the expansion of junipers (Juniperus spp.) throughout the intermountain west United States. These native species have expanded from their traditional fire-safe habitats into fire-dependent communities as a result of climatic fluctuations, grazing patterns, and wildfire suppression efforts. As junipers expand their range, they begin to dominate plant communities resulting in the recession of shrubs, grasses, and forbs. Land management agencies have a strong commitment to find areas that are vulnerable to juniper encroachment, so that these areas can be studied and more effectively managed. Aiding in this effort, this project used remote sensing to develop two tools that determine fire intensity on a per pixel basis and identify different phases of juniper encroachment, respectively. Landsat 8, representing land cover data was combined with topography information (slope and aspect) in a linear regression model that quantified fire intensity on a per pixel basis, identifying areas that would burn hotter and longer based on fuel type. The overall accuracy of the model was 86% with a kappa coefficient of 0.81. Visual validation using NAIP imagery in comparison with the fuel classification result showed good visual correlation of the fuel model with dense juniper stands. The second output of the project was an image/object based classification tool that uses multispectral imagery and supervised point classification to classify different vegetation types according to the spectral detail of the objects. The goal of the model is to improve phase identification of juniper stands. Initial visual verification with NAIP shows the model to be performing very satisfactorily but is dependent on the spatial resolution of the user fed input imagery. Furnishing land managers with these tools will assist in forecasting areas prone to juniper invasion based upon surrounding seedbanks, as well as, predict the ensuing intensity of fires should ignition occur.

WetDATA Hub: Democratizing Access to Water Data to Accelerate Innovation through Data Visualization, Predictive Analytics and Artificial Intelligence Applications

NASA Astrophysics Data System (ADS)

Sarni, W.

2017-12-01

Water scarcity and poor quality impacts economic development, business growth, and social well-being. Water has become, in our generation, the foremost critical local, regional, and global issue of our time. Despite these needs, there is no water hub or water technology accelerator solely dedicated to water data and tools. There is a need by the public and private sectors for vastly improved data management and visualization tools. This is the WetDATA opportunity - to develop a water data tech hub dedicated to water data acquisition, analytics, and visualization tools for informed policy and business decisions. WetDATA's tools will help incubate disruptive water data technologies and accelerate adoption of current water data solutions. WetDATA is a Colorado-based (501c3), global hub for water data analytics and technology innovation. WetDATA's vision is to be a global leader in water information, data technology innovation and collaborate with other US and global water technology hubs. ROADMAP * Portal (www.wetdata.org) to provide stakeholders with tools/resources to understand related water risks. * The initial activities will provide education, awareness and tools to stakeholders to support the implementation of the Colorado State Water Plan. * Leverage the Western States Water Council Water Data Exchange database. * Development of visualization, predictive analytics and AI tools to engage with stakeholders and provide actionable data and information. TOOLS Education: Provide information on water issues and risks at the local, state, national and global scale. Visualizations: Development of data analytics and visualization tools based upon the 2030 Water Resources Group methodology to support the implementation of the Colorado State Water Plan. Predictive Analytics: Accessing publically available water databases and using machine learning to develop water availability forecasting tools, and time lapse images to support city / urban planning.

Declarative language design for interactive visualization.

PubMed

Heer, Jeffrey; Bostock, Michael

2010-01-01

We investigate the design of declarative, domain-specific languages for constructing interactive visualizations. By separating specification from execution, declarative languages can simplify development, enable unobtrusive optimization, and support retargeting across platforms. We describe the design of the Protovis specification language and its implementation within an object-oriented, statically-typed programming language (Java). We demonstrate how to support rich visualizations without requiring a toolkit-specific data model and extend Protovis to enable declarative specification of animated transitions. To support cross-platform deployment, we introduce rendering and event-handling infrastructures decoupled from the runtime platform, letting designers retarget visualization specifications (e.g., from desktop to mobile phone) with reduced effort. We also explore optimizations such as runtime compilation of visualization specifications, parallelized execution, and hardware-accelerated rendering. We present benchmark studies measuring the performance gains provided by these optimizations and compare performance to existing Java-based visualization tools, demonstrating scalability improvements exceeding an order of magnitude.

Fundamental Study of Material Flow in Friction Stir Welds

NASA Technical Reports Server (NTRS)

Reynolds, Anthony P.

1999-01-01

The presented research project consists of two major parts. First, the material flow in solid-state, friction stir, butt-welds as been investigated using a marker insert technique. Changes in material flow due to welding parameter as well as tool geometry variations have been examined for different materials. The method provides a semi-quantitative, three-dimensional view of the material transport in the welded zone. Second, a FSW process model has been developed. The fully coupled model is based on fluid mechanics; the solid-state material transport during welding is treated as a laminar, viscous flow of a non-Newtonian fluid past a rotating circular cylinder. The heat necessary for the material softening is generated by deformation of the material. As a first step, a two-dimensional model, which contains only the pin of the FSW tool, has been created to test the suitability of the modeling approach and to perform parametric studies of the boundary conditions. The material flow visualization experiments agree very well with the predicted flow field. Accordingly, material within the pin diameter is transported only in the rotation direction around the pin. Due to the simplifying assumptions inherent in the 2-D model, other experimental data such as forces on the pin, torque, and weld energy cannot be directly used for validation. However, the 2-D model predicts the same trends as shown in the experiments. The model also predicts a deviation from the "normal" material flow at certain combinations of welding parameters, suggesting a possible mechanism for the occurrence of some typical FSW defects. The next step has been the development of a three-dimensional process model. The simplified FSW tool has been designed as a flat shoulder rotating on the top of the workpiece and a rotating, cylindrical pin, which extends throughout the total height of the flow domain. The thermal boundary conditions at the tool and at the contact area to the backing plate have been varied to fit experimental data such as temperature profiles, torque and tool forces. General aspects of the experimentally visualized material flow pattern are confirmed by the 3-D model.

A Java-based tool for creating KML files from GPS waypoints

NASA Astrophysics Data System (ADS)

Kinnicutt, P. G.; Rivard, C.; Rimer, S.

2008-12-01

Google Earth provides a free tool with powerful capabilities for visualizing geoscience images and data. Commercial software tools exist for doing sophisticated digitizing and spatial modeling , but for the purposes of presentation, visualization and overlaying aerial images with data Google Earth provides much of the functionality. Likewise, with current technologies in GPS (Global Positioning System) systems and with Google Earth Plus, it is possible to upload GPS waypoints, tracks and routes directly into Google Earth for visualization. However, older technology GPS units and even low-cost GPS units found today may lack the necessary communications interface to a computer (e.g. no Bluetooth, no WiFi, no USB, no Serial, etc.) or may have an incompatible interface, such as a Serial port but no USB adapter available. In such cases, any waypoints, tracks and routes saved in the GPS unit or recorded in a field notebook must be manually transferred to a computer for use in a GIS system or other program. This presentation describes a Java-based tool developed by the author which enables users to enter GPS coordinates in a user-friendly manner, then save these coordinates in a Keyhole MarkUp Language (KML) file format, for visualization in Google Earth. This tool either accepts user-interactive input or accepts input from a CSV (Comma Separated Value) file, which can be generated from any spreadsheet program. This tool accepts input in the form of lat/long or UTM (Universal Transverse Mercator) coordinates. This presentation describes this system's applicability through several small case studies. This free and lightweight tool simplifies the task of manually inputting GPS data into Google Earth for people working in the field without an automated mechanism for uploading the data; for instance, the user may not have internet connectivity or may not have the proper hardware or software. Since it is a Java application and not a web- based tool, it can be installed on one's field laptop and the GPS data can be manually entered without the need for internet connectivity. This tool provides a table view of the GPS data, but lacks a KML viewer to view the data overlain on top of an aerial view, as this viewer functionality is provided in Google Earth. The tool's primary contribution lies in its more convenient method for entering the GPS data manually when automated technologies are not available.

Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.

PubMed

Karp, Peter D; Latendresse, Mario; Paley, Suzanne M; Krummenacker, Markus; Ong, Quang D; Billington, Richard; Kothari, Anamika; Weaver, Daniel; Lee, Thomas; Subhraveti, Pallavi; Spaulding, Aaron; Fulcher, Carol; Keseler, Ingrid M; Caspi, Ron

2016-09-01

Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions. This article outlines the advances in Pathway Tools in the past 5 years. Major additions include components for metabolic modeling, metabolic route search, computation of atom mappings and estimation of compound Gibbs free energies of formation; addition of editors for signaling pathways, for genome sequences and for cellular architecture; storage of gene essentiality data and phenotype data; display of multiple alignments, and of signaling and electron-transport pathways; and development of Python and web-services application programming interfaces. Scientists around the world have created more than 9800 Pathway/Genome Databases by using Pathway Tools, many of which are curated databases for important model organisms. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Master Middle Ware: A Tool to Integrate Water Resources and Fish Population Dynamics Models

NASA Astrophysics Data System (ADS)

Yi, S.; Sandoval Solis, S.; Thompson, L. C.; Kilduff, D. P.

2017-12-01

Linking models that investigate separate components of ecosystem processes has the potential to unify messages regarding management decisions by evaluating potential trade-offs in a cohesive framework. This project aimed to improve the ability of riparian resource managers to forecast future water availability conditions and resultant fish habitat suitability, in order to better inform their management decisions. To accomplish this goal, we developed a middleware tool that is capable of linking and overseeing the operations of two existing models, a water resource planning tool Water Evaluation and Planning (WEAP) model and a habitat-based fish population dynamics model (WEAPhish). First, we designed the Master Middle Ware (MMW) software in Visual Basic for Application® in one Excel® file that provided a familiar framework for both data input and output Second, MMW was used to link and jointly operate WEAP and WEAPhish, using Visual Basic Application (VBA) macros to implement system level calls to run the models. To demonstrate the utility of this approach, hydrological, biological, and middleware model components were developed for the Butte Creek basin. This tributary of the Sacramento River, California is managed for both hydropower and the persistence of a threatened population of spring-run Chinook salmon (Oncorhynchus tschawytscha). While we have demonstrated the use of MMW for a particular watershed and fish population, MMW can be customized for use with different rivers and fish populations, assuming basic data requirements are met. This model integration improves on ad hoc linkages for managing data transfer between software programs by providing a consistent, user-friendly, and familiar interface across different model implementations. Furthermore, the data-viewing capabilities of MMW facilitate the rapid interpretation of model results by hydrologists, fisheries biologists, and resource managers, in order to accelerate learning and management decision making.

BMDExpress Data Viewer: A Visualization Tool to Analyze BMDExpress Datasets(SoTC)

EPA Science Inventory

Background: Benchmark Dose (BMD) modelling is a mathematical approach used to determine where a dose-response change begins to take place relative to controls following chemical exposure. BMDs are being increasingly applied in regulatory toxicology to estimate acceptable exposure...

BMDExpress Data Viewer: A Visualization Tool to Analyze BMDExpress Datasets (STC symposium)

EPA Science Inventory

Background: Benchmark Dose (BMD) modelling is a mathematical approach used to determine where a dose-response change begins to take place relative to controls following chemical exposure. BMDs are being increasingly applied in regulatory toxicology to estimate acceptable exposure...

Tradespace Exploration for the Engineering of Resilient Systems

DTIC Science & Technology

2015-05-01

world scenarios. The types of tools within the SAE set include visualization, decision analysis, and M&S, so it is difficult to categorize this toolset... overpopulated , or questionable. ERS Tradespace Workshop Create predictive models using multiple techniques (e.g., regression, Kriging, neural nets

Evaluation of Visualization Tools for Computer Network Defense Analysts: Display Design, Methods, and Results for a User Study

DTIC Science & Technology

2016-11-01

Display Design, Methods , and Results for a User Study by Christopher J Garneau and Robert F Erbacher Approved for public...NOV 2016 US Army Research Laboratory Evaluation of Visualization Tools for Computer Network Defense Analysts: Display Design, Methods ...January 2013–September 2015 4. TITLE AND SUBTITLE Evaluation of Visualization Tools for Computer Network Defense Analysts: Display Design, Methods

A framework for interactive visualization of digital medical images.

PubMed

Koehring, Andrew; Foo, Jung Leng; Miyano, Go; Lobe, Thom; Winer, Eliot

2008-10-01

The visualization of medical images obtained from scanning techniques such as computed tomography and magnetic resonance imaging is a well-researched field. However, advanced tools and methods to manipulate these data for surgical planning and other tasks have not seen widespread use among medical professionals. Radiologists have begun using more advanced visualization packages on desktop computer systems, but most physicians continue to work with basic two-dimensional grayscale images or not work directly with the data at all. In addition, new display technologies that are in use in other fields have yet to be fully applied in medicine. It is our estimation that usability is the key aspect in keeping this new technology from being more widely used by the medical community at large. Therefore, we have a software and hardware framework that not only make use of advanced visualization techniques, but also feature powerful, yet simple-to-use, interfaces. A virtual reality system was created to display volume-rendered medical models in three dimensions. It was designed to run in many configurations, from a large cluster of machines powering a multiwalled display down to a single desktop computer. An augmented reality system was also created for, literally, hands-on interaction when viewing models of medical data. Last, a desktop application was designed to provide a simple visualization tool, which can be run on nearly any computer at a user's disposal. This research is directed toward improving the capabilities of medical professionals in the tasks of preoperative planning, surgical training, diagnostic assistance, and patient education.

Y0: An innovative tool for spatial data analysis

NASA Astrophysics Data System (ADS)

Wilson, Jeremy C.

1993-08-01

This paper describes an advanced analysis and visualization tool, called Y0 (pronounced ``Why not?!''), that has been developed to directly support the scientific process for earth and space science research. Y0 aids the scientific research process by enabling the user to formulate algorithms and models within an integrated environment, and then interactively explore the solution space with the aid of appropriate visualizations. Y0 has been designed to provide strong support for both quantitative analysis and rich visualization. The user's algorithm or model is defined in terms of algebraic formulas in cells on worksheets, in a similar fashion to spreadsheet programs. Y0 is specifically designed to provide the data types and rich function set necessary for effective analysis and manipulation of remote sensing data. This includes various types of arrays, geometric objects, and objects for representing geographic coordinate system mappings. Visualization of results is tailored to the needs of remote sensing, with straightforward methods of composing, comparing, and animating imagery and graphical information, with reference to geographical coordinate systems. Y0 is based on advanced object-oriented technology. It is implemented in C++ for use in Unix environments, with a user interface based on the X window system. Y0 has been delivered under contract to Unidata, a group which provides data and software support to atmospheric researches in universities affiliated with UCAR. This paper will explore the key concepts in Y0, describe its utility for remote sensing analysis and visualization, and will give a specific example of its application to the problem of measuring glacier flow rates from Landsat imagery.

High resolution renderings and interactive visualization of the 2006 Huntington Beach experiment

NASA Astrophysics Data System (ADS)

Im, T.; Nayak, A.; Keen, C.; Samilo, D.; Matthews, J.

2006-12-01

The Visualization Center at the Scripps Institution of Oceanography investigates innovative ways to represent graphically interactive 3D virtual landscapes and to produce high resolution, high quality renderings of Earth sciences data and the sensors and instruments used to collect the data . Among the Visualization Center's most recent work is the visualization of the Huntington Beach experiment, a study launched in July 2006 by the Southern California Ocean Observing System (http://www.sccoos.org/) to record and synthesize data of the Huntington Beach coastal region. Researchers and students at the Visualization Center created visual presentations that combine bathymetric data provided by SCCOOS with USGS aerial photography and with 3D polygonal models of sensors created in Maya into an interactive 3D scene using the Fledermaus suite of visualization tools (http://www.ivs3d.com). In addition, the Visualization Center has produced high definition (HD) animations of SCCOOS sensor instruments (e.g. REMUS, drifters, spray glider, nearshore mooring, OCSD/USGS mooring and CDIP mooring) using the Maya modeling and animation software and rendered over multiple nodes of the OptIPuter Visualization Cluster at Scripps. These visualizations are aimed at providing researchers with a broader context of sensor locations relative to geologic characteristics, to promote their use as an educational resource for informal education settings and increasing public awareness, and also as an aid for researchers' proposals and presentations. These visualizations are available for download on the Visualization Center website at http://siovizcenter.ucsd.edu/sccoos/hb2006.php.

Visual impairment and traits of autism in children.

PubMed

Wrzesińska, Magdalena; Kapias, Joanna; Nowakowska-Domagała, Katarzyna; Kocur, Józef

2017-04-30

Visual impairment present from birth or from an early childhood may lead to psychosocial and emotional disorders. 11-40% of children in the group with visual impairment show traits of autism. The aim of this paper was to present the selected examples of how visual impairment in children is related to the occurrence of autism and to describe the available tools for diagnosing autism in children with visual impairment. So far the relation between visual impairment in children and autism has not been sufficiently confirmed. Psychiatric and psychological diagnosis of children with visual impairment has some difficulties in differentiating between "blindism" and traits typical for autism resulting from a lack of standardized diagnostic tools used to diagnosing children with visual impairment. Another difficulty in diagnosing autism in children with visual impairment is the coexistence of other disabilities in case of most children with vision impairment. Additionally, apart from difficulties in diagnosing autistic disorders in children with eye dysfunctions there is also a question of what tools should be used in therapy and rehabilitation of patients.

Construction of a Distributed-network Digital Watershed Management System with B/S Techniques

NASA Astrophysics Data System (ADS)

Zhang, W. C.; Liu, Y. M.; Fang, J.

2017-07-01

Integrated watershed assessment tools for supporting land management and hydrologic research are becoming established tools in both basic and applied research. The core of these tools are mainly spatially distributed hydrologic models as they can provide a mechanism for investigating interactions among climate, topography, vegetation, and soil. However, the extensive data requirements and the difficult task of building input parameter files for driving these distributed models, have long been an obstacle to the timely and cost-effective use of such complex models by watershed managers and policy-makers. Recently, a web based geographic information system (GIS) tool to facilitate this process has been developed for a large watersheds of Jinghe and Weihe catchments located in the loess plateau of the Huanghe River basin in north-western China. A web-based GIS provides the framework within which spatially distributed data are collected and used to prepare model input files of these two watersheds and evaluate model results as well as to provide the various clients for watershed information inquiring, visualizing and assessment analysis. This Web-based Automated Geospatial Watershed Assessment GIS (WAGWA-GIS) tool uses widely available standardized spatial datasets that can be obtained via the internet oracle databank designed with association of Map Guide platform to develop input parameter files for online simulation at different spatial and temporal scales with Xing’anjiang and TOPMODEL that integrated with web-based digital watershed. WAGWA-GIS automates the process of transforming both digital data including remote sensing data, DEM, Land use/cover, soil digital maps and meteorological and hydrological station geo-location digital maps and text files containing meteorological and hydrological data obtained from stations of the watershed into hydrological models for online simulation and geo-spatial analysis and provides a visualization tool to help the user interpret results. The utility of WAGWA-GIS in jointing hydrologic and ecological investigations has been demonstrated on such diverse landscapes as Jinhe and Weihe watersheds, and will be extended to be utilized in the other watersheds in China step by step in coming years

A cognitive task analysis of a visual analytic workflow: Exploring molecular interaction networks in systems biology.

PubMed

Mirel, Barbara; Eichinger, Felix; Keller, Benjamin J; Kretzler, Matthias

2011-03-21

Bioinformatics visualization tools are often not robust enough to support biomedical specialists’ complex exploratory analyses. Tools need to accommodate the workflows that scientists actually perform for specific translational research questions. To understand and model one of these workflows, we conducted a case-based, cognitive task analysis of a biomedical specialist’s exploratory workflow for the question: What functional interactions among gene products of high throughput expression data suggest previously unknown mechanisms of a disease? From our cognitive task analysis four complementary representations of the targeted workflow were developed. They include: usage scenarios, flow diagrams, a cognitive task taxonomy, and a mapping between cognitive tasks and user-centered visualization requirements. The representations capture the flows of cognitive tasks that led a biomedical specialist to inferences critical to hypothesizing. We created representations at levels of detail that could strategically guide visualization development, and we confirmed this by making a trial prototype based on user requirements for a small portion of the workflow. Our results imply that visualizations should make available to scientific users “bundles of features” consonant with the compositional cognitive tasks purposefully enacted at specific points in the workflow. We also highlight certain aspects of visualizations that: (a) need more built-in flexibility; (b) are critical for negotiating meaning; and (c) are necessary for essential metacognitive support.

CGDV: a webtool for circular visualization of genomics and transcriptomics data.

PubMed

Jha, Vineet; Singh, Gulzar; Kumar, Shiva; Sonawane, Amol; Jere, Abhay; Anamika, Krishanpal

2017-10-24

Interpretation of large-scale data is very challenging and currently there is scarcity of web tools which support automated visualization of a variety of high throughput genomics and transcriptomics data and for a wide variety of model organisms along with user defined karyotypes. Circular plot provides holistic visualization of high throughput large scale data but it is very complex and challenging to generate as most of the available tools need informatics expertise to install and run them. We have developed CGDV (Circos for Genomics and Transcriptomics Data Visualization), a webtool based on Circos, for seamless and automated visualization of a variety of large scale genomics and transcriptomics data. CGDV takes output of analyzed genomics or transcriptomics data of different formats, such as vcf, bed, xls, tab limited matrix text file, CNVnator raw output and Gene fusion raw output, to plot circular view of the sample data. CGDV take cares of generating intermediate files required for circos. CGDV is freely available at https://cgdv-upload.persistent.co.in/cgdv/ . The circular plot for each data type is tailored to gain best biological insights into the data. The inter-relationship between data points, homologous sequences, genes involved in fusion events, differential expression pattern, sequencing depth, types and size of variations and enrichment of DNA binding proteins can be seen using CGDV. CGDV thus helps biologists and bioinformaticians to visualize a variety of genomics and transcriptomics data seamlessly.

An integrated network visualization framework towards metabolic engineering applications.

PubMed

Noronha, Alberto; Vilaça, Paulo; Rocha, Miguel

2014-12-30

Over the last years, several methods for the phenotype simulation of microorganisms, under specified genetic and environmental conditions have been proposed, in the context of Metabolic Engineering (ME). These methods provided insight on the functioning of microbial metabolism and played a key role in the design of genetic modifications that can lead to strains of industrial interest. On the other hand, in the context of Systems Biology research, biological network visualization has reinforced its role as a core tool in understanding biological processes. However, it has been scarcely used to foster ME related methods, in spite of the acknowledged potential. In this work, an open-source software that aims to fill the gap between ME and metabolic network visualization is proposed, in the form of a plugin to the OptFlux ME platform. The framework is based on an abstract layer, where the network is represented as a bipartite graph containing minimal information about the underlying entities and their desired relative placement. The framework provides input/output support for networks specified in standard formats, such as XGMML, SBGN or SBML, providing a connection to genome-scale metabolic models. An user-interface makes it possible to edit, manipulate and query nodes in the network, providing tools to visualize diverse effects, including visual filters and aspect changing (e.g. colors, shapes and sizes). These tools are particularly interesting for ME, since they allow overlaying phenotype simulation results or elementary flux modes over the networks. The framework and its source code are freely available, together with documentation and other resources, being illustrated with well documented case studies.

The Blue DRAGON--a system for monitoring the kinematics and the dynamics of endoscopic tools in minimally invasive surgery for objective laparoscopic skill assessment.

PubMed

Rosen, Jacob; Brown, Jeffrey D; Barreca, Marco; Chang, Lily; Hannaford, Blake; Sinanan, Mika

2002-01-01

Minimally invasive surgeiy (MIS) involves a multi-dimensional series of tasks requiring a synthesis between visual information and the kinematics and dynamics of the surgical tools. Analysis of these sources of information is a key step in mastering MIS surgery but may also be used to define objective criteria for characterizing surgical performance. The BIueDRAGON is a new system for acquiring the kinematics and the dynamics of two endoscopic tools along with the visual view of the surgical scene. It includes two four-bar mechanisms equipped with position and force torque sensors for measuring the positions and the orientations (P/O) of two endoscopic tools along with the forces and torques applied by the surgeons hands. The methodology of decomposing the surgical task is based on a fully connected, finite-states (28 states) Markov model where each states corresponded to a fundamental tool/tissue interaction based on the tool kinematics and associated with unique F/T signatures. The experimental protocol included seven MIS tasks performed on an animal model (pig) by 30 surgeons at different levels of their residency training. Preliminary analysis of these data showed that major differences between residents at different skill levels were: (i) the types of tool/tissue interactions being used, (ii) the transitions between tool/tissue interactions being applied by each hand, (iii) time spent while perfonning each tool/tissue interaction, (iv) the overall completion time, and (v) the variable F/T magnitudes being applied by the subjects through the endoscopic tools. Systems like surgical robots or virtual reality simulators that inherently measure the kinematics and the dynamics of the surgical tool may benefit from inclusion of the proposed methodology for analysis of efficacy and objective evaluation of surgical skills during training.

Interactive Visualization of Dependencies

ERIC Educational Resources Information Center

Moreno, Camilo Arango; Bischof, Walter F.; Hoover, H. James

2012-01-01

We present an interactive tool for browsing course requisites as a case study of dependency visualization. This tool uses multiple interactive visualizations to allow the user to explore the dependencies between courses. A usability study revealed that the proposed browser provides significant advantages over traditional methods, in terms of…

Visualizing Qualitative Information

ERIC Educational Resources Information Center

Slone, Debra J.

2009-01-01

The abundance of qualitative data in today's society and the need to easily scrutinize, digest, and share this information calls for effective visualization and analysis tools. Yet, no existing qualitative tools have the analytic power, visual effectiveness, and universality of familiar quantitative instruments like bar charts, scatter-plots, and…

The Lunar Mapping and Modeling Portal: Capabilities and Lunar Data Products to support Return to the Moon

NASA Astrophysics Data System (ADS)

Law, E.; Bui, B.; Chang, G.; Goodale, C. E.; Kim, R.; Malhotra, S.; Ramirez, P.; Rodriguez, L.; Sadaqathulla, S.; Nall, M.; Muery, K.

2012-12-01

The Lunar Mapping and Modeling Portal (LMMP), is a multi-center project led by NASA's Marshall Space Flight Center. The LMMP is a web-based Portal and a suite of interactive visualization and analysis tools to enable lunar scientists, engineers, and mission planners to access mapped lunar data products from past and current lunar missions, e.g., Lunar Reconnaissance Orbiter, Apollo, Lunar Orbiter, Lunar Prospector, and Clementine. The Portal allows users to search, view and download a vast number of the most recent lunar digital products including image mosaics, digital elevation models, and in situ lunar resource maps such as iron and hydrogen abundance. The Portal also provides a number of visualization and analysis tools that perform lighting analysis and local hazard assessments, such as, slope, surface roughness and crater/boulder distribution. In this talk, we will give a brief overview of the project. After that, we will highlight various key features and Lunar data products. We will further demonstrate image viewing and layering of lunar map images via our web portal as well as mobile devices.

NASTRAN data generation and management using interactive graphics

NASA Technical Reports Server (NTRS)

Smootkatow, M.; Cooper, B. M.

1972-01-01

A method of using an interactive graphics device to generate a large portion of the input bulk data with visual checks of the structure and the card images is described. The generation starts from GRID and PBAR cards. The visual checks result from a three-dimensional display of the model in any rotated position. By detailing the steps, the time saving and cost effectiveness of this method may be judged, and its potential as a useful tool for the structural analyst may be established.

Moon Trek: An Interactive Web Portal for Current and Future Lunar Missions

NASA Technical Reports Server (NTRS)

Day, B; Law, Emily S.

2017-01-01

NASA's Moon Trek (https://moontrek.jpl.nasa.gov) is the successor to and replacement for NASA's Lunar Mapping and Modeling Portal (LMMP). Released in 2017, Moon Trek features a new interface with improved ways to access, visualize, and analyze data. Moon Trek provides a web-based Portal and a suite of interactive visualization and analysis tools to enable mission planners, lunar scientists, and engineers to access mapped lunar data products from past and current lunar missions.

Analysis of eye-tracking experiments performed on a Tobii T60

DOE Office of Scientific and Technical Information (OSTI.GOV)

Banks, David C

2008-01-01

Commercial eye-gaze trackers have the potential to be an important tool for quantifying the benefits of new visualization techniques. The expense of such trackers has made their use relatively infrequent in visualization studies. As such, it is difficult for researchers to compare multiple devices obtaining several demonstration models is impractical in cost and time, and quantitative measures from real-world use are not readily available. In this paper, we present a sample protocol to determine the accuracy of a gaze-tacking device.

Moon Trek: An Interactive Web Portal for Current and Future Lunar Missions

NASA Astrophysics Data System (ADS)

Day, B.; Law, E.

2017-09-01

NASA's Moon Trek (https://moontrek.jpl.nasa.gov) is the successor to and replacement for NASA's Lunar Mapping and Modeling Portal (LMMP). Released in 2017, Moon Trek features a new interface with improved ways to access, visualize, and analyse data. Moon Trek provides a web-based Portal and a suite of interactive visualization and analysis tools to enable mission planners, lunar scientists, and engineers to access mapped lunar data products from past and current lunar missions.

Explicit criteria for prioritization of cataract surgery

PubMed Central

Ma Quintana, José; Escobar, Antonio; Bilbao, Amaia

2006-01-01

Background Consensus techniques have been used previously to create explicit criteria to prioritize cataract extraction; however, the appropriateness of the intervention was not included explicitly in previous studies. We developed a prioritization tool for cataract extraction according to the RAND method. Methods Criteria were developed using a modified Delphi panel judgment process. A panel of 11 ophthalmologists was assembled. Ratings were analyzed regarding the level of agreement among panelists. We studied the effect of all variables on the final panel score using general linear and logistic regression models. Priority scoring systems were developed by means of optimal scaling and general linear models. The explicit criteria developed were summarized by means of regression tree analysis. Results Eight variables were considered to create the indications. Of the 310 indications that the panel evaluated, 22.6% were considered high priority, 52.3% intermediate priority, and 25.2% low priority. Agreement was reached for 31.9% of the indications and disagreement for 0.3%. Logistic regression and general linear models showed that the preoperative visual acuity of the cataractous eye, visual function, and anticipated visual acuity postoperatively were the most influential variables. Alternative and simple scoring systems were obtained by optimal scaling and general linear models where the previous variables were also the most important. The decision tree also shows the importance of the previous variables and the appropriateness of the intervention. Conclusion Our results showed acceptable validity as an evaluation and management tool for prioritizing cataract extraction. It also provides easy algorithms for use in clinical practice. PMID:16512893

A pandemic influenza modeling and visualization tool

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maciejewski, Ross; Livengood, Philip; Rudolph, Stephen

2011-08-01

The National Strategy for Pandemic Influenza outlines a plan for community response to a potential pandemic. In this outline, state and local communities are charged with enhancing their preparedness. In order to help public health officials better understand these charges, we have developed a modeling and visualization toolkit (PanViz) for analyzing the effect of decision measures implemented during a simulated pandemic influenza scenario. Spread vectors based on the point of origin and distance traveled over time are calculated and the factors of age distribution and population density are taken into effect. Healthcare officials are able to explore the effects ofmore » the pandemic on the population through a spatiotemporal view, moving forward and backward through time and inserting decision points at various days to determine the impact. Linked statistical displays are also shown, providing county level summaries of data in terms of the number of sick, hospitalized and dead as a result of the outbreak. Currently, this tool has been deployed in Indiana State Department of Health planning and preparedness exercises, and as an educational tool for demonstrating the impact of social distancing strategies during the recent H1N1 (swine flu) outbreak.« less

Visualization of protein interaction networks: problems and solutions

PubMed Central

2013-01-01

Background Visualization concerns the representation of data visually and is an important task in scientific research. Protein-protein interactions (PPI) are discovered using either wet lab techniques, such mass spectrometry, or in silico predictions tools, resulting in large collections of interactions stored in specialized databases. The set of all interactions of an organism forms a protein-protein interaction network (PIN) and is an important tool for studying the behaviour of the cell machinery. Since graphic representation of PINs may highlight important substructures, e.g. protein complexes, visualization is more and more used to study the underlying graph structure of PINs. Although graphs are well known data structures, there are different open problems regarding PINs visualization: the high number of nodes and connections, the heterogeneity of nodes (proteins) and edges (interactions), the possibility to annotate proteins and interactions with biological information extracted by ontologies (e.g. Gene Ontology) that enriches the PINs with semantic information, but complicates their visualization. Methods In these last years many software tools for the visualization of PINs have been developed. Initially thought for visualization only, some of them have been successively enriched with new functions for PPI data management and PIN analysis. The paper analyzes the main software tools for PINs visualization considering four main criteria: (i) technology, i.e. availability/license of the software and supported OS (Operating System) platforms; (ii) interoperability, i.e. ability to import/export networks in various formats, ability to export data in a graphic format, extensibility of the system, e.g. through plug-ins; (iii) visualization, i.e. supported layout and rendering algorithms and availability of parallel implementation; (iv) analysis, i.e. availability of network analysis functions, such as clustering or mining of the graph, and the possibility to interact with external databases. Results Currently, many tools are available and it is not easy for the users choosing one of them. Some tools offer sophisticated 2D and 3D network visualization making available many layout algorithms, others tools are more data-oriented and support integration of interaction data coming from different sources and data annotation. Finally, some specialistic tools are dedicated to the analysis of pathways and cellular processes and are oriented toward systems biology studies, where the dynamic aspects of the processes being studied are central. Conclusion A current trend is the deployment of open, extensible visualization tools (e.g. Cytoscape), that may be incrementally enriched by the interactomics community with novel and more powerful functions for PIN analysis, through the development of plug-ins. On the other hand, another emerging trend regards the efficient and parallel implementation of the visualization engine that may provide high interactivity and near real-time response time, as in NAViGaTOR. From a technological point of view, open-source, free and extensible tools, like Cytoscape, guarantee a long term sustainability due to the largeness of the developers and users communities, and provide a great flexibility since new functions are continuously added by the developer community through new plug-ins, but the emerging parallel, often closed-source tools like NAViGaTOR, can offer near real-time response time also in the analysis of very huge PINs. PMID:23368786

Scientific Benefits of Space Science Models Archiving at Community Coordinated Modeling Center

NASA Technical Reports Server (NTRS)

Kuznetsova, Maria M.; Berrios, David; Chulaki, Anna; Hesse, Michael; MacNeice, Peter J.; Maddox, Marlo M.; Pulkkinen, Antti; Rastaetter, Lutz; Taktakishvili, Aleksandre

2009-01-01

The Community Coordinated Modeling Center (CCMC) hosts a set of state-of-the-art space science models ranging from the solar atmosphere to the Earth's upper atmosphere. CCMC provides a web-based Run-on-Request system, by which the interested scientist can request simulations for a broad range of space science problems. To allow the models to be driven by data relevant to particular events CCMC developed a tool that automatically downloads data from data archives and transform them to required formats. CCMC also provides a tailored web-based visualization interface for the model output, as well as the capability to download the simulation output in portable format. CCMC offers a variety of visualization and output analysis tools to aid scientists in interpretation of simulation results. During eight years since the Run-on-request system became available the CCMC archived the results of almost 3000 runs that are covering significant space weather events and time intervals of interest identified by the community. The simulation results archived at CCMC also include a library of general purpose runs with modeled conditions that are used for education and research. Archiving results of simulations performed in support of several Modeling Challenges helps to evaluate the progress in space weather modeling over time. We will highlight the scientific benefits of CCMC space science model archive and discuss plans for further development of advanced methods to interact with simulation results.

Benefits of a Unified LaSRS++ Simulation for NAS-Wide and High-Fidelity Modeling

NASA Technical Reports Server (NTRS)

Glaab, Patricia; Madden, Michael

2014-01-01

The LaSRS++ high-fidelity vehicle simulation was extended in 2012 to support a NAS-wide simulation mode. Since the initial proof-of-concept, the LaSRS++ NAS-wide simulation is maturing into a research-ready tool. A primary benefit of this new capability is the consolidation of the two modeling paradigms under a single framework to save cost, facilitate iterative concept testing between the two tools, and to promote communication and model sharing between user communities at Langley. Specific benefits of each type of modeling are discussed along with the expected benefits of the unified framework. Current capability details of the LaSRS++ NAS-wide simulations are provided, including the visualization tool, live data interface, trajectory generators, terminal routing for arrivals and departures, maneuvering, re-routing, navigation, winds, and turbulence. The plan for future development is also described.

VISUAL3D - An EIT network on visualization of geomodels

NASA Astrophysics Data System (ADS)

Bauer, Tobias

2017-04-01

When it comes to interpretation of data and understanding of deep geological structures and bodies at different scales then modelling tools and modelling experience is vital for deep exploration. Geomodelling provides a platform for integration of different types of data, including new kinds of information (e.g., new improved measuring methods). EIT Raw Materials, initiated by the EIT (European Institute of Innovation and Technology) and funded by the European Commission, is the largest and strongest consortium in the raw materials sector worldwide. The VISUAL3D network of infrastructure is an initiative by EIT Raw Materials and aims at bringing together partners with 3D-4D-visualisation infrastructure and 3D-4D-modelling experience. The recently formed network collaboration interlinks hardware, software and expert knowledge in modelling visualization and output. A special focus will be the linking of research, education and industry and integrating multi-disciplinary data and to visualize the data in three and four dimensions. By aiding network collaborations we aim at improving the combination of geomodels with differing file formats and data characteristics. This will create an increased competency in modelling visualization and the ability to interchange and communicate models more easily. By combining knowledge and experience in geomodelling with expertise in Virtual Reality visualization partners of EIT Raw Materials but also external parties will have the possibility to visualize, analyze and validate their geomodels in immersive VR-environments. The current network combines partners from universities, research institutes, geological surveys and industry with a strong background in geological 3D-modelling and 3D visualization and comprises: Luleå University of Technology, Geological Survey of Finland, Geological Survey of Denmark and Greenland, TUBA Freiberg, Uppsala University, Geological Survey of France, RWTH Aachen, DMT, KGHM Cuprum, Boliden, Montan Universität Leoben, Slovenian National Building and Civil Engineering Institute, Tallinn University of Technology and Turku University. The infrastructure within the network comprises different types of capturing and visualization hardware, ranging from high resolution cubes, VR walls, VR goggle solutions, high resolution photogrammetry, UAVs, lidar-scanners, and many more.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keefer, Donald A.; Shaffer, Eric G.; Storsved, Brynne

A free software application, RVA, has been developed as a plugin to the US DOE-funded ParaView visualization package, to provide support in the visualization and analysis of complex reservoirs being managed using multi-fluid EOR techniques. RVA, for Reservoir Visualization and Analysis, was developed as an open-source plugin to the 64 bit Windows version of ParaView 3.14. RVA was developed at the University of Illinois at Urbana-Champaign, with contributions from the Illinois State Geological Survey, Department of Computer Science and National Center for Supercomputing Applications. RVA was designed to utilize and enhance the state-of-the-art visualization capabilities within ParaView, readily allowing jointmore » visualization of geologic framework and reservoir fluid simulation model results. Particular emphasis was placed on enabling visualization and analysis of simulation results highlighting multiple fluid phases, multiple properties for each fluid phase (including flow lines), multiple geologic models and multiple time steps. Additional advanced functionality was provided through the development of custom code to implement data mining capabilities. The built-in functionality of ParaView provides the capacity to process and visualize data sets ranging from small models on local desktop systems to extremely large models created and stored on remote supercomputers. The RVA plugin that we developed and the associated User Manual provide improved functionality through new software tools, and instruction in the use of ParaView-RVA, targeted to petroleum engineers and geologists in industry and research. The RVA web site (http://rva.cs.illinois.edu) provides an overview of functions, and the development web site (https://github.com/shaffer1/RVA) provides ready access to the source code, compiled binaries, user manual, and a suite of demonstration data sets. Key functionality has been included to support a range of reservoirs visualization and analysis needs, including: sophisticated connectivity analysis, cross sections through simulation results between selected wells, simplified volumetric calculations, global vertical exaggeration adjustments, ingestion of UTChem simulation results, ingestion of Isatis geostatistical framework models, interrogation of joint geologic and reservoir modeling results, joint visualization and analysis of well history files, location-targeted visualization, advanced correlation analysis, visualization of flow paths, and creation of static images and animations highlighting targeted reservoir features.« less

RVA: A Plugin for ParaView 3.14

DOE Office of Scientific and Technical Information (OSTI.GOV)

2015-09-04

RVA is a plugin developed for the 64-bit Windows version of the ParaView 3.14 visualization package. RVA is designed to provide support in the visualization and analysis of complex reservoirs being managed using multi-fluid EOR techniques. RVA, for Reservoir Visualization and Analysis, was developed at the University of Illinois at Urbana-Champaign, with contributions from the Illinois State Geological Survey, Department of Computer Science and National Center for Supercomputing Applications. RVA was designed to utilize and enhance the state-of-the-art visualization capabilities within ParaView, readily allowing joint visualization of geologic framework and reservoir fluid simulation model results. Particular emphasis was placed onmore » enabling visualization and analysis of simulation results highlighting multiple fluid phases, multiple properties for each fluid phase (including flow lines), multiple geologic models and multiple time steps. Additional advanced functionality was provided through the development of custom code to implement data mining capabilities. The built-in functionality of ParaView provides the capacity to process and visualize data sets ranging from small models on local desktop systems to extremely large models created and stored on remote supercomputers. The RVA plugin that we developed and the associated User Manual provide improved functionality through new software tools, and instruction in the use of ParaView-RVA, targeted to petroleum engineers and geologists in industry and research. The RVA web site (http://rva.cs.illinois.edu) provides an overview of functions, and the development web site (https://github.com/shaffer1/RVA) provides ready access to the source code, compiled binaries, user manual, and a suite of demonstration data sets. Key functionality has been included to support a range of reservoirs visualization and analysis needs, including: sophisticated connectivity analysis, cross sections through simulation results between selected wells, simplified volumetric calculations, global vertical exaggeration adjustments, ingestion of UTChem simulation results, ingestion of Isatis geostatistical framework models, interrogation of joint geologic and reservoir modeling results, joint visualization and analysis of well history files, location-targeted visualization, advanced correlation analysis, visualization of flow paths, and creation of static images and animations highlighting targeted reservoir features.« less

MSX-3D: a tool to validate 3D protein models using mass spectrometry.

PubMed

Heymann, Michaël; Paramelle, David; Subra, Gilles; Forest, Eric; Martinez, Jean; Geourjon, Christophe; Deléage, Gilbert

2008-12-01

The technique of chemical cross-linking followed by mass spectrometry has proven to bring valuable information about the protein structure and interactions between proteic subunits. It is an effective and efficient way to experimentally investigate some aspects of a protein structure when NMR and X-ray crystallography data are lacking. We introduce MSX-3D, a tool specifically geared to validate protein models using mass spectrometry. In addition to classical peptides identifications, it allows an interactive 3D visualization of the distance constraints derived from a cross-linking experiment. Freely available at http://proteomics-pbil.ibcp.fr

Web-based access, aggregation, and visualization of future climate projections with emphasis on agricultural assessments

NASA Astrophysics Data System (ADS)

Villoria, Nelson B.; Elliott, Joshua; Müller, Christoph; Shin, Jaewoo; Zhao, Lan; Song, Carol

2018-01-01

Access to climate and spatial datasets by non-specialists is restricted by technical barriers involving hardware, software and data formats. We discuss an open-source online tool that facilitates downloading the climate data from the global circulation models used by the Inter-Sectoral Impacts Model Intercomparison Project. The tool also offers temporal and spatial aggregation capabilities for incorporating future climate scenarios in applications where spatial aggregation is important. We hope that streamlined access to these data facilitates analysis of climate related issues while considering the uncertainties derived from future climate projections and temporal aggregation choices.

Firing-rate based network modeling of the dLGN circuit: Effects of cortical feedback on spatiotemporal response properties of relay cells.

PubMed

Mobarhan, Milad Hobbi; Halnes, Geir; Martínez-Cañada, Pablo; Hafting, Torkel; Fyhn, Marianne; Einevoll, Gaute T

2018-05-01

Visually evoked signals in the retina pass through the dorsal geniculate nucleus (dLGN) on the way to the visual cortex. This is however not a simple feedforward flow of information: there is a significant feedback from cortical cells back to both relay cells and interneurons in the dLGN. Despite four decades of experimental and theoretical studies, the functional role of this feedback is still debated. Here we use a firing-rate model, the extended difference-of-Gaussians (eDOG) model, to explore cortical feedback effects on visual responses of dLGN relay cells. For this model the responses are found by direct evaluation of two- or three-dimensional integrals allowing for fast and comprehensive studies of putative effects of different candidate organizations of the cortical feedback. Our analysis identifies a special mixed configuration of excitatory and inhibitory cortical feedback which seems to best account for available experimental data. This configuration consists of (i) a slow (long-delay) and spatially widespread inhibitory feedback, combined with (ii) a fast (short-delayed) and spatially narrow excitatory feedback, where (iii) the excitatory/inhibitory ON-ON connections are accompanied respectively by inhibitory/excitatory OFF-ON connections, i.e. following a phase-reversed arrangement. The recent development of optogenetic and pharmacogenetic methods has provided new tools for more precise manipulation and investigation of the thalamocortical circuit, in particular for mice. Such data will expectedly allow the eDOG model to be better constrained by data from specific animal model systems than has been possible until now for cat. We have therefore made the Python tool pyLGN which allows for easy adaptation of the eDOG model to new situations.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Demeure, I.M.

The research presented here is concerned with representation techniques and tools to support the design, prototyping, simulation, and evaluation of message-based parallel, distributed computations. The author describes ParaDiGM-Parallel, Distributed computation Graph Model-a visual representation technique for parallel, message-based distributed computations. ParaDiGM provides several views of a computation depending on the aspect of concern. It is made of two complementary submodels, the DCPG-Distributed Computing Precedence Graph-model, and the PAM-Process Architecture Model-model. DCPGs are precedence graphs used to express the functionality of a computation in terms of tasks, message-passing, and data. PAM graphs are used to represent the partitioning of a computationmore » into schedulable units or processes, and the pattern of communication among those units. There is a natural mapping between the two models. He illustrates the utility of ParaDiGM as a representation technique by applying it to various computations (e.g., an adaptive global optimization algorithm, the client-server model). ParaDiGM representations are concise. They can be used in documenting the design and the implementation of parallel, distributed computations, in describing such computations to colleagues, and in comparing and contrasting various implementations of the same computation. He then describes VISA-VISual Assistant, a software tool to support the design, prototyping, and simulation of message-based parallel, distributed computations. VISA is based on the ParaDiGM model. In particular, it supports the editing of ParaDiGM graphs to describe the computations of interest, and the animation of these graphs to provide visual feedback during simulations. The graphs are supplemented with various attributes, simulation parameters, and interpretations which are procedures that can be executed by VISA.« less

Using a visual programming language to bridge the cognitive gap between a novice's mental model and program code

NASA Astrophysics Data System (ADS)

Smith, Bryan J.

Current research suggests that many students do not know how to program very well at the conclusion of their introductory programming course. We believe that a reason novices have such difficulties learning programming is because engineering novices often learn through a lecture format where someone with programming knowledge lectures to novices, the novices attempt to absorb the content, and then reproduce it during exams. By primarily appealing to programming novices who prefer to understand visually, we research whether programming novices understand programming better if computer science concepts are presented using a visual programming language than if these programs are presented using a text-based programming language. This method builds upon previous research that suggests that most engineering students are visual learners, and we propose that using a flow-based visual programming language will address some of the most important and difficult topics to novices of programming. We use an existing flow-model tool, RAPTOR, to test this method, and share the program understanding results using this theory.

Genoviz Software Development Kit: Java tool kit for building genomics visualization applications.

PubMed

Helt, Gregg A; Nicol, John W; Erwin, Ed; Blossom, Eric; Blanchard, Steven G; Chervitz, Stephen A; Harmon, Cyrus; Loraine, Ann E

2009-08-25

Visualization software can expose previously undiscovered patterns in genomic data and advance biological science. The Genoviz Software Development Kit (SDK) is an open source, Java-based framework designed for rapid assembly of visualization software applications for genomics. The Genoviz SDK framework provides a mechanism for incorporating adaptive, dynamic zooming into applications, a desirable feature of genome viewers. Visualization capabilities of the Genoviz SDK include automated layout of features along genetic or genomic axes; support for user interactions with graphical elements (Glyphs) in a map; a variety of Glyph sub-classes that promote experimentation with new ways of representing data in graphical formats; and support for adaptive, semantic zooming, whereby objects change their appearance depending on zoom level and zooming rate adapts to the current scale. Freely available demonstration and production quality applications, including the Integrated Genome Browser, illustrate Genoviz SDK capabilities. Separation between graphics components and genomic data models makes it easy for developers to add visualization capability to pre-existing applications or build new applications using third-party data models. Source code, documentation, sample applications, and tutorials are available at http://genoviz.sourceforge.net/.

Automated Visual Cognitive Tasks for Recording Neural Activity Using a Floor Projection Maze

PubMed Central

Kent, Brendon W.; Yang, Fang-Chi; Burwell, Rebecca D.

2014-01-01

Neuropsychological tasks used in primates to investigate mechanisms of learning and memory are typically visually guided cognitive tasks. We have developed visual cognitive tasks for rats using the Floor Projection Maze1,2 that are optimized for visual abilities of rats permitting stronger comparisons of experimental findings with other species. In order to investigate neural correlates of learning and memory, we have integrated electrophysiological recordings into fully automated cognitive tasks on the Floor Projection Maze1,2. Behavioral software interfaced with an animal tracking system allows monitoring of the animal's behavior with precise control of image presentation and reward contingencies for better trained animals. Integration with an in vivo electrophysiological recording system enables examination of behavioral correlates of neural activity at selected epochs of a given cognitive task. We describe protocols for a model system that combines automated visual presentation of information to rodents and intracranial reward with electrophysiological approaches. Our model system offers a sophisticated set of tools as a framework for other cognitive tasks to better isolate and identify specific mechanisms contributing to particular cognitive processes. PMID:24638057

Developments to the Sylvan stand structure model to describe wood quality changes in southern bottomland hardwood forests because of forest management

Treesearch

Ian R. Scott

2009-01-01

Growth models can produce a wealth of detailed information that is often very difficult to perceive because it is frequently presented either as summary tables, stand view or landscape view visualizations. We have developed new tools for use with the Sylvan model (Larsen 1994) that allow the analysis of wood-quality changes as a consequence of forest management....

Stereoscopic vascular models of the head and neck: A computed tomography angiography visualization.

PubMed

Cui, Dongmei; Lynch, James C; Smith, Andrew D; Wilson, Timothy D; Lehman, Michael N

2016-01-01

Computer-assisted 3D models are used in some medical and allied health science schools; however, they are often limited to online use and 2D flat screen-based imaging. Few schools take advantage of 3D stereoscopic learning tools in anatomy education and clinically relevant anatomical variations when teaching anatomy. A new approach to teaching anatomy includes use of computed tomography angiography (CTA) images of the head and neck to create clinically relevant 3D stereoscopic virtual models. These high resolution images of the arteries can be used in unique and innovative ways to create 3D virtual models of the vasculature as a tool for teaching anatomy. Blood vessel 3D models are presented stereoscopically in a virtual reality environment, can be rotated 360° in all axes, and magnified according to need. In addition, flexible views of internal structures are possible. Images are displayed in a stereoscopic mode, and students view images in a small theater-like classroom while wearing polarized 3D glasses. Reconstructed 3D models enable students to visualize vascular structures with clinically relevant anatomical variations in the head and neck and appreciate spatial relationships among the blood vessels, the skull and the skin. © 2015 American Association of Anatomists.

Process Mining for Individualized Behavior Modeling Using Wireless Tracking in Nursing Homes

PubMed Central

Fernández-Llatas, Carlos; Benedi, José-Miguel; García-Gómez, Juan M.; Traver, Vicente

2013-01-01

The analysis of human behavior patterns is increasingly used for several research fields. The individualized modeling of behavior using classical techniques requires too much time and resources to be effective. A possible solution would be the use of pattern recognition techniques to automatically infer models to allow experts to understand individual behavior. However, traditional pattern recognition algorithms infer models that are not readily understood by human experts. This limits the capacity to benefit from the inferred models. Process mining technologies can infer models as workflows, specifically designed to be understood by experts, enabling them to detect specific behavior patterns in users. In this paper, the eMotiva process mining algorithms are presented. These algorithms filter, infer and visualize workflows. The workflows are inferred from the samples produced by an indoor location system that stores the location of a resident in a nursing home. The visualization tool is able to compare and highlight behavior patterns in order to facilitate expert understanding of human behavior. This tool was tested with nine real users that were monitored for a 25-week period. The results achieved suggest that the behavior of users is continuously evolving and changing and that this change can be measured, allowing for behavioral change detection. PMID:24225907

Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis

DOE PAGES

Pavlopoulos, Georgios A.; Paez-Espino, David; Kyrpides, Nikos C.; ...

2017-07-18

Gene expression, signal transduction, protein/chemical interactions, biomedical literature cooccurrences, and other concepts are often captured in biological network representations where nodes represent a certain bioentity and edges the connections between them. While many tools to manipulate, visualize, and interactively explore such networks already exist, only few of them can scale up and follow today’s indisputable information growth. In this review, we shortly list a catalog of available network visualization tools and, from a user-experience point of view, we identify four candidate tools suitable for larger-scale network analysis, visualization, and exploration. Lastly, we comment on their strengths and their weaknesses andmore » empirically discuss their scalability, user friendliness, and postvisualization capabilities.« less

Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pavlopoulos, Georgios A.; Paez-Espino, David; Kyrpides, Nikos C.

Gene expression, signal transduction, protein/chemical interactions, biomedical literature cooccurrences, and other concepts are often captured in biological network representations where nodes represent a certain bioentity and edges the connections between them. While many tools to manipulate, visualize, and interactively explore such networks already exist, only few of them can scale up and follow today’s indisputable information growth. In this review, we shortly list a catalog of available network visualization tools and, from a user-experience point of view, we identify four candidate tools suitable for larger-scale network analysis, visualization, and exploration. Lastly, we comment on their strengths and their weaknesses andmore » empirically discuss their scalability, user friendliness, and postvisualization capabilities.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Fangyan; Zhang, Song; Chung Wong, Pak

Effectively visualizing large graphs and capturing the statistical properties are two challenging tasks. To aid in these two tasks, many sampling approaches for graph simplification have been proposed, falling into three categories: node sampling, edge sampling, and traversal-based sampling. It is still unknown which approach is the best. We evaluate commonly used graph sampling methods through a combined visual and statistical comparison of graphs sampled at various rates. We conduct our evaluation on three graph models: random graphs, small-world graphs, and scale-free graphs. Initial results indicate that the effectiveness of a sampling method is dependent on the graph model, themore » size of the graph, and the desired statistical property. This benchmark study can be used as a guideline in choosing the appropriate method for a particular graph sampling task, and the results presented can be incorporated into graph visualization and analysis tools.« less

Using Self-Organizing Neural Network Map Combined with Ward's Clustering Algorithm for Visualization of Students' Cognitive Structural Models about Aliveness Concept

PubMed Central

Ugulu, Ilker; Aydin, Halil

2016-01-01

We propose an approach to clustering and visualization of students' cognitive structural models. We use the self-organizing map (SOM) combined with Ward's clustering to conduct cluster analysis. In the study carried out on 100 subjects, a conceptual understanding test consisting of open-ended questions was used as a data collection tool. The results of analyses indicated that students constructed the aliveness concept by associating it predominantly with human. Motion appeared as the most frequently associated term with the aliveness concept. The results suggest that the aliveness concept has been constructed using anthropocentric and animistic cognitive structures. In the next step, we used the data obtained from the conceptual understanding test for training the SOM. Consequently, we propose a visualization method about cognitive structure of the aliveness concept. PMID:26819579

ClimatePipes: User-Friendly Data Access, Manipulation, Analysis & Visualization of Community Climate Models

NASA Astrophysics Data System (ADS)

Chaudhary, A.; DeMarle, D.; Burnett, B.; Harris, C.; Silva, W.; Osmari, D.; Geveci, B.; Silva, C.; Doutriaux, C.; Williams, D. N.

2013-12-01

The impact of climate change will resonate through a broad range of fields including public health, infrastructure, water resources, and many others. Long-term coordinated planning, funding, and action are required for climate change adaptation and mitigation. Unfortunately, widespread use of climate data (simulated and observed) in non-climate science communities is impeded by factors such as large data size, lack of adequate metadata, poor documentation, and lack of sufficient computational and visualization resources. We present ClimatePipes to address many of these challenges by creating an open source platform that provides state-of-the-art, user-friendly data access, analysis, and visualization for climate and other relevant geospatial datasets, making the climate data available to non-researchers, decision-makers, and other stakeholders. The overarching goals of ClimatePipes are: - Enable users to explore real-world questions related to climate change. - Provide tools for data access, analysis, and visualization. - Facilitate collaboration by enabling users to share datasets, workflows, and visualization. ClimatePipes uses a web-based application platform for its widespread support on mainstream operating systems, ease-of-use, and inherent collaboration support. The front-end of ClimatePipes uses HTML5 (WebGL, Canvas2D, CSS3) to deliver state-of-the-art visualization and to provide a best-in-class user experience. The back-end of the ClimatePipes is built around Python using the Visualization Toolkit (VTK, http://vtk.org), Climate Data Analysis Tools (CDAT, http://uv-cdat.llnl.gov), and other climate and geospatial data processing tools such as GDAL and PROJ4. ClimatePipes web-interface to query and access data from remote sources (such as ESGF). Shown in the figure is climate data layer from ESGF on top of map data layer from OpenStreetMap. The ClimatePipes workflow editor provides flexibility and fine grained control, and uses the VisTrails (http://www.vistrails.org) workflow engine in the backend.

Stereoscopic Vascular Models of the Head and Neck: A Computed Tomography Angiography Visualization

ERIC Educational Resources Information Center

Cui, Dongmei; Lynch, James C.; Smith, Andrew D.; Wilson, Timothy D.; Lehman, Michael N.

2016-01-01

Computer-assisted 3D models are used in some medical and allied health science schools; however, they are often limited to online use and 2D flat screen-based imaging. Few schools take advantage of 3D stereoscopic learning tools in anatomy education and clinically relevant anatomical variations when teaching anatomy. A new approach to teaching…

Logic Modeling in Quantitative Systems Pharmacology

PubMed Central

Traynard, Pauline; Tobalina, Luis; Eduati, Federica; Calzone, Laurence

2017-01-01

Here we present logic modeling as an approach to understand deregulation of signal transduction in disease and to characterize a drug's mode of action. We discuss how to build a logic model from the literature and experimental data and how to analyze the resulting model to obtain insights of relevance for systems pharmacology. Our workflow uses the free tools OmniPath (network reconstruction from the literature), CellNOpt (model fit to experimental data), MaBoSS (model analysis), and Cytoscape (visualization). PMID:28681552

A web-based data visualization tool for the MIMIC-II database.

PubMed

Lee, Joon; Ribey, Evan; Wallace, James R

2016-02-04

Although MIMIC-II, a public intensive care database, has been recognized as an invaluable resource for many medical researchers worldwide, becoming a proficient MIMIC-II researcher requires knowledge of SQL programming and an understanding of the MIMIC-II database schema. These are challenging requirements especially for health researchers and clinicians who may have limited computer proficiency. In order to overcome this challenge, our objective was to create an interactive, web-based MIMIC-II data visualization tool that first-time MIMIC-II users can easily use to explore the database. The tool offers two main features: Explore and Compare. The Explore feature enables the user to select a patient cohort within MIMIC-II and visualize the distributions of various administrative, demographic, and clinical variables within the selected cohort. The Compare feature enables the user to select two patient cohorts and visually compare them with respect to a variety of variables. The tool is also helpful to experienced MIMIC-II researchers who can use it to substantially accelerate the cumbersome and time-consuming steps of writing SQL queries and manually visualizing extracted data. Any interested researcher can use the MIMIC-II data visualization tool for free to quickly and conveniently conduct a preliminary investigation on MIMIC-II with a few mouse clicks. Researchers can also use the tool to learn the characteristics of the MIMIC-II patients. Since it is still impossible to conduct multivariable regression inside the tool, future work includes adding analytics capabilities. Also, the next version of the tool will aim to utilize MIMIC-III which contains more data.

The development of a virtual 3D model of the renal corpuscle from serial histological sections for E-learning environments.

PubMed

Roth, Jeremy A; Wilson, Timothy D; Sandig, Martin

2015-01-01

Histology is a core subject in the anatomical sciences where learners are challenged to interpret two-dimensional (2D) information (gained from histological sections) to extrapolate and understand the three-dimensional (3D) morphology of cells, tissues, and organs. In gross anatomical education 3D models and learning tools have been associated with improved learning outcomes, but similar tools have not been created for histology education to visualize complex cellular structure-function relationships. This study outlines steps in creating a virtual 3D model of the renal corpuscle from serial, semi-thin, histological sections obtained from epoxy resin-embedded kidney tissue. The virtual renal corpuscle model was generated by digital segmentation to identify: Bowman's capsule, nuclei of epithelial cells in the parietal capsule, afferent arteriole, efferent arteriole, proximal convoluted tubule, distal convoluted tubule, glomerular capillaries, podocyte nuclei, nuclei of extraglomerular mesangial cells, nuclei of epithelial cells of the macula densa in the distal convoluted tubule. In addition to the imported images of the original sections the software generates, and allows for visualization of, images of virtual sections generated in any desired orientation, thus serving as a "virtual microtome". These sections can be viewed separately or with the 3D model in transparency. This approach allows for the development of interactive e-learning tools designed to enhance histology education of microscopic structures with complex cellular interrelationships. Future studies will focus on testing the efficacy of interactive virtual 3D models for histology education. © 2015 American Association of Anatomists.

Screening for hearing, visual and dual sensory impairment in older adults using behavioural cues: a validation study.

PubMed

Roets-Merken, Lieve M; Zuidema, Sytse U; Vernooij-Dassen, Myrra J F J; Kempen, Gertrudis I J M

2014-11-01

This study investigated the psychometric properties of the Severe Dual Sensory Loss screening tool, a tool designed to help nurses and care assistants to identify hearing, visual and dual sensory impairment in older adults. Construct validity of the Severe Dual Sensory Loss screening tool was evaluated using Crohnbach's alpha and factor analysis. Interrater reliability was calculated using Kappa statistics. To evaluate the predictive validity, sensitivity and specificity were calculated by comparison with the criterion standard assessment for hearing and vision. The criterion used for hearing impairment was a hearing loss of ≥40 decibel measured by pure-tone audiometry, and the criterion for visual impairment was a visual acuity of ≤0.3 diopter or a visual field of ≤0.3°. Feasibility was evaluated by the time needed to fill in the screening tool and the clarity of the instruction and items. Prevalence of dual sensory impairment was calculated. A total of 56 older adults receiving aged care and 12 of their nurses and care assistants participated in the study. Crohnbach's alpha was 0.81 for the hearing subscale and 0.84 for the visual subscale. Factor analysis showed two constructs for hearing and two for vision. Kappa was 0.71 for the hearing subscale and 0.74 for the visual subscale. The predictive validity showed a sensitivity of 0.71 and a specificity of 0.72 for the hearing subscale; and a sensitivity of 0.69 and a specificity of 0.78 for the visual subscale. The optimum cut-off point for each subscale was score 1. The nurses and care assistants reported that the Severe Dual Sensory Loss screening tool was easy to use. The prevalence of hearing and vision impairment was 55% and 29%, respectively, and that of dual sensory impairment was 20%. The Severe Dual Sensory Loss screening tool was compared with the criterion standards for hearing and visual impairment and was found a valid and reliable tool, enabling nurses and care assistants to identify hearing, visual and dual sensory impairment among older adults. Copyright © 2014 Elsevier Ltd. All rights reserved.

Designing and Validation a Visual Fatigue Questionnaire for Video Display Terminals Operators

PubMed Central

Rajabi-Vardanjani, Hassan; Habibi, Ehsanollah; Pourabdian, Siyamak; Dehghan, Habibollah; Maracy, Mohammad Reza

2014-01-01

Background: Along with the rapid growth of technology its related tools such as computer, monitors and video display terminals (VDTs) grow as well. Based on the studies, the most common complaint reported is of the VDT users. Methods: This study attempts to design a proper tool to assess the visual fatigue of the VDT users. First draft of the questionnaire was prepared after a thorough study on the books, papers and similar questionnaires. The validity and reliability of the questionnaire was confirmed using the content validity index (CVI) beside that of the Cronbach's Coefficient Alpha. Then, a cross-sectional study was carried out on 248 of the VDT users in different professions. A theoretical model with four categories of symptoms of visual fatigue was derived from the previous studies and questionnaires. Having used the AMOS16 software, the construct validity of the questionnaire was evaluated using the confirmatory factor analysis. The correlation co-efficiency of the internal domains was calculated using the SPSS 11.5 software. To assess the quality check index and determining the visual fatigue levels, visual fatigue of the VDT users was measured by the questionnaire and visual fatigue meter (VFM) device. Cut-off points were identified by receiver operating characteristic curves. Results: CVI and reliability co-efficiency were both equal to 0.75. Model fit indices including root mean of squared error approximation, goodness of fit index and adjusted goodness of fit index were obtained 0.026, 0.96 and 0.92 respectfully. The correlation between the results measured with the questionnaire and VFM-90.1 device was −0.87. Cut-off points of the questionnaire were 0.65, 2.36 and 3.88. The confirmed questionnaire consists of four main areas: Eye strain (4 questions), visual impairment (5 questions) and the surface impairment of the eye (3 questions) and the out of eye problems (3 questions). Conclusions: The visual fatigue questionnaire contains 15 questions and has a very remarkable validity and reliability. Using this questionnaire and its findings, one will be able to identify, assess and finally prevent the effective factors of VDT users’ visual fatigue. PMID:25104995

A Haptic-Enhanced System for Molecular Sensing

NASA Astrophysics Data System (ADS)

Comai, Sara; Mazza, Davide

The science of haptics has received an enormous attention in the last decade. One of the major application trends of haptics technology is data visualization and training. In this paper, we present a haptically-enhanced system for manipulation and tactile exploration of molecules.The geometrical models of molecules is extracted either from theoretical or empirical data using file formats widely adopted in chemical and biological fields. The addition of information computed with computational chemistry tools, allows users to feel the interaction forces between an explored molecule and a charge associated to the haptic device, and to visualize a huge amount of numerical data in a more comprehensible way. The developed tool can be used either for teaching or research purposes due to its high reliance on both theoretical and experimental data.

Vortex filament method as a tool for computational visualization of quantum turbulence

PubMed Central

Hänninen, Risto; Baggaley, Andrew W.

2014-01-01

The vortex filament model has become a standard and powerful tool to visualize the motion of quantized vortices in helium superfluids. In this article, we present an overview of the method and highlight its impact in aiding our understanding of quantum turbulence, particularly superfluid helium. We present an analysis of the structure and arrangement of quantized vortices. Our results are in agreement with previous studies showing that under certain conditions, vortices form coherent bundles, which allows for classical vortex stretching, giving quantum turbulence a classical nature. We also offer an explanation for the differences between the observed properties of counterflow and pure superflow turbulence in a pipe. Finally, we suggest a mechanism for the generation of coherent structures in the presence of normal fluid shear. PMID:24704873

cellPACK: A Virtual Mesoscope to Model and Visualize Structural Systems Biology

PubMed Central

Johnson, Graham T.; Autin, Ludovic; Al-Alusi, Mostafa; Goodsell, David S.; Sanner, Michel F.; Olson, Arthur J.

2014-01-01

cellPACK assembles computational models of the biological mesoscale, an intermediate scale (10−7–10−8m) between molecular and cellular biology. cellPACK’s modular architecture unites existing and novel packing algorithms to generate, visualize and analyze comprehensive 3D models of complex biological environments that integrate data from multiple experimental systems biology and structural biology sources. cellPACK is currently available as open source code, with tools for validation of models and with recipes and models for five biological systems: blood plasma, cytoplasm, synaptic vesicles, HIV and a mycoplasma cell. We have applied cellPACK to model distributions of HIV envelope protein to test several hypotheses for consistency with experimental observations. Biologists, educators, and outreach specialists can interact with cellPACK models, develop new recipes and perform packing experiments through scripting and graphical user interfaces at http://cellPACK.org. PMID:25437435

Dose response explorer: an integrated open-source tool for exploring and modelling radiotherapy dose volume outcome relationships

NASA Astrophysics Data System (ADS)

El Naqa, I.; Suneja, G.; Lindsay, P. E.; Hope, A. J.; Alaly, J. R.; Vicic, M.; Bradley, J. D.; Apte, A.; Deasy, J. O.

2006-11-01

Radiotherapy treatment outcome models are a complicated function of treatment, clinical and biological factors. Our objective is to provide clinicians and scientists with an accurate, flexible and user-friendly software tool to explore radiotherapy outcomes data and build statistical tumour control or normal tissue complications models. The software tool, called the dose response explorer system (DREES), is based on Matlab, and uses a named-field structure array data type. DREES/Matlab in combination with another open-source tool (CERR) provides an environment for analysing treatment outcomes. DREES provides many radiotherapy outcome modelling features, including (1) fitting of analytical normal tissue complication probability (NTCP) and tumour control probability (TCP) models, (2) combined modelling of multiple dose-volume variables (e.g., mean dose, max dose, etc) and clinical factors (age, gender, stage, etc) using multi-term regression modelling, (3) manual or automated selection of logistic or actuarial model variables using bootstrap statistical resampling, (4) estimation of uncertainty in model parameters, (5) performance assessment of univariate and multivariate analyses using Spearman's rank correlation and chi-square statistics, boxplots, nomograms, Kaplan-Meier survival plots, and receiver operating characteristics curves, and (6) graphical capabilities to visualize NTCP or TCP prediction versus selected variable models using various plots. DREES provides clinical researchers with a tool customized for radiotherapy outcome modelling. DREES is freely distributed. We expect to continue developing DREES based on user feedback.

The Parallel System for Integrating Impact Models and Sectors (pSIMS)

NASA Technical Reports Server (NTRS)

Elliott, Joshua; Kelly, David; Chryssanthacopoulos, James; Glotter, Michael; Jhunjhnuwala, Kanika; Best, Neil; Wilde, Michael; Foster, Ian

2014-01-01

We present a framework for massively parallel climate impact simulations: the parallel System for Integrating Impact Models and Sectors (pSIMS). This framework comprises a) tools for ingesting and converting large amounts of data to a versatile datatype based on a common geospatial grid; b) tools for translating this datatype into custom formats for site-based models; c) a scalable parallel framework for performing large ensemble simulations, using any one of a number of different impacts models, on clusters, supercomputers, distributed grids, or clouds; d) tools and data standards for reformatting outputs to common datatypes for analysis and visualization; and e) methodologies for aggregating these datatypes to arbitrary spatial scales such as administrative and environmental demarcations. By automating many time-consuming and error-prone aspects of large-scale climate impacts studies, pSIMS accelerates computational research, encourages model intercomparison, and enhances reproducibility of simulation results. We present the pSIMS design and use example assessments to demonstrate its multi-model, multi-scale, and multi-sector versatility.

Data Model Management for Space Information Systems

NASA Technical Reports Server (NTRS)

Hughes, J. Steven; Crichton, Daniel J.; Ramirez, Paul; Mattmann, chris

2006-01-01

The Reference Architecture for Space Information Management (RASIM) suggests the separation of the data model from software components to promote the development of flexible information management systems. RASIM allows the data model to evolve independently from the software components and results in a robust implementation that remains viable as the domain changes. However, the development and management of data models within RASIM are difficult and time consuming tasks involving the choice of a notation, the capture of the model, its validation for consistency, and the export of the model for implementation. Current limitations to this approach include the lack of ability to capture comprehensive domain knowledge, the loss of significant modeling information during implementation, the lack of model visualization and documentation capabilities, and exports being limited to one or two schema types. The advent of the Semantic Web and its demand for sophisticated data models has addressed this situation by providing a new level of data model management in the form of ontology tools. In this paper we describe the use of a representative ontology tool to capture and manage a data model for a space information system. The resulting ontology is implementation independent. Novel on-line visualization and documentation capabilities are available automatically, and the ability to export to various schemas can be added through tool plug-ins. In addition, the ingestion of data instances into the ontology allows validation of the ontology and results in a domain knowledge base. Semantic browsers are easily configured for the knowledge base. For example the export of the knowledge base to RDF/XML and RDFS/XML and the use of open source metadata browsers provide ready-made user interfaces that support both text- and facet-based search. This paper will present the Planetary Data System (PDS) data model as a use case and describe the import of the data model into an ontology tool. We will also describe the current effort to provide interoperability with the European Space Agency (ESA)/Planetary Science Archive (PSA) which is critically dependent on a common data model.