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

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.

A Visual Tool for Computer Supported Learning: The Robot Motion Planning Example

ERIC Educational Resources Information Center

Elnagar, Ashraf; Lulu, Leena

2007-01-01

We introduce an effective computer aided learning visual tool (CALVT) to teach graph-based applications. We present the robot motion planning problem as an example of such applications. The proposed tool can be used to simulate and/or further to implement practical systems in different areas of computer science such as graphics, computational…

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

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.

IViPP: A Tool for Visualization in Particle Physics

NASA Astrophysics Data System (ADS)

Tran, Hieu; Skiba, Elizabeth; Baldwin, Doug

2011-10-01

Experiments and simulations in physics generate a lot of data; visualization is helpful to prepare that data for analysis. IViPP (Interactive Visualizations in Particle Physics) is an interactive computer program that visualizes results of particle physics simulations or experiments. IViPP can handle data from different simulators, such as SRIM or MCNP. It can display relevant geometry and measured scalar data; it can do simple selection from the visualized data. In order to be an effective visualization tool, IViPP must have a software architecture that can flexibly adapt to new data sources and display styles. It must be able to display complicated geometry and measured data with a high dynamic range. We therefore organize it in a highly modular structure, we develop libraries to describe geometry algorithmically, use rendering algorithms running on the powerful GPU to display 3-D geometry at interactive rates, and we represent scalar values in a visual form of scientific notation that shows both mantissa and exponent. This work was supported in part by the US Department of Energy through the Laboratory for Laser Energetics (LLE), with special thanks to Craig Sangster at LLE.

OpenGl Visualization Tool and Library Version: 1.0

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

2010-06-22

GLVis is an OpenGL tool for visualization of finite element meshes and functions. When started without any options, GLVis starts a server, which waits for a socket connections and visualizes any recieved data. This way the results of simulations on a remote (parallel) machine can be visualized on the lical user desktop. GLVis can also be used to visualize a mesh with or without a finite element function (solution). It can run a batch sequence of commands (GLVis scripts), or display previously saved socket streams.

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.

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.

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.

Interactive Exploration of Cosmological Dark-Matter Simulation Data.

PubMed

Scherzinger, Aaron; Brix, Tobias; Drees, Dominik; Volker, Andreas; Radkov, Kiril; Santalidis, Niko; Fieguth, Alexander; Hinrichs, Klaus H

2017-01-01

The winning entry of the 2015 IEEE Scientific Visualization Contest, this article describes a visualization tool for cosmological data resulting from dark-matter simulations. The proposed system helps users explore all aspects of the data at once and receive more detailed information about structures of interest at any time. Moreover, novel methods for visualizing and interactively exploring dark-matter halo substructures are proposed.

CTViz: A tool for the visualization of transport in nanocomposites.

PubMed

Beach, Benjamin; Brown, Joshua; Tarlton, Taylor; Derosa, Pedro A

2016-05-01

A visualization tool (CTViz) for charge transport processes in 3-D hybrid materials (nanocomposites) was developed, inspired by the need for a graphical application to assist in code debugging and data presentation of an existing in-house code. As the simulation code grew, troubleshooting problems grew increasingly difficult without an effective way to visualize 3-D samples and charge transport in those samples. CTViz is able to produce publication and presentation quality visuals of the simulation box, as well as static and animated visuals of the paths of individual carriers through the sample. CTViz was designed to provide a high degree of flexibility in the visualization of the data. A feature that characterizes this tool is the use of shade and transparency levels to highlight important details in the morphology or in the transport paths by hiding or dimming elements of little relevance to the current view. This is fundamental for the visualization of 3-D systems with complex structures. The code presented here provides these required capabilities, but has gone beyond the original design and could be used as is or easily adapted for the visualization of other particulate transport where transport occurs on discrete paths. Copyright © 2016 Elsevier Inc. All rights reserved.

pV3-Gold Visualization Environment for Computer Simulations

NASA Technical Reports Server (NTRS)

Babrauckas, Theresa L.

1997-01-01

A new visualization environment, pV3-Gold, can be used during and after a computer simulation to extract and visualize the physical features in the results. This environment, which is an extension of the pV3 visualization environment developed at the Massachusetts Institute of Technology with guidance and support by researchers at the NASA Lewis Research Center, features many tools that allow users to display data in various ways.

Systems Analysis and Integration | Transportation Research | NREL

Science.gov Websites

data visualization displayed on a wall. Using a suite of simulation and analysis tools, NREL evaluates savings and reduce emissions. Pictured here, engineers discuss the 3D results of a vehicle simulation vehicles, and other alternative fuel vehicles. Using a suite of simulation and analysis tools, NREL

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

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...

Case Studies of Software Development Tools for Parallel Architectures

DTIC Science & Technology

1993-06-01

Simulation ............................................. 29 4.7.3 Visualization...autonomous entities, each with its own state and set of behaviors, as in simulation , tracking, or Battle Management. Because C2 applications are often... simulation , that is used to help the developer solve the problems. The new tool/problem solution matrix is structured in terms of the software development

Echo simulator with novel training and competency testing tools.

PubMed

Sheehan, Florence H; Otto, Catherine M; Freeman, Rosario V

2013-01-01

We developed and validated an echo simulator with three novel tools that facilitate training and enable quantitative and objective measurement of psychomotor as well as cognitive skill. First, the trainee can see original patient images - not synthetic or simulated images - that morph in real time as the mock transducer is manipulated on the mannequin. Second, augmented reality is used for Visual Guidance, a tool that assists the trainee in scanning by displaying the target organ in 3-dimensions (3D) together with the location of the current view plane and the plane of the anatomically correct view. Third, we introduce Image Matching, a tool that leverages the aptitude of the human brain for recognizing similarities and differences to help trainees learn to perform visual assessment of ultrasound images. Psychomotor competence is measured in terms of the view plane angle error. The construct validity of the simulator for competency testing was established by demonstrating its ability to discriminate novices vs. experts.

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.

Fuzzy-based simulation of real color blindness.

PubMed

Lee, Jinmi; dos Santos, Wellington P

2010-01-01

About 8% of men are affected by color blindness. That population is at a disadvantage since they cannot perceive a substantial amount of the visual information. This work presents two computational tools developed to assist color blind people. The first one tests color blindness and assess its severity. The second tool is based on Fuzzy Logic, and implements a method proposed to simulate real red and green color blindness in order to generate synthetic cases of color vision disturbance in a statistically significant amount. Our purpose is to develop correction tools and obtain a deeper understanding of the accessibility problems faced by people with chromatic visual impairment.

Tools and procedures for visualization of proteins and other biomolecules.

PubMed

Pan, Lurong; Aller, Stephen G

2015-04-01

Protein, peptides, and nucleic acids are biomolecules that drive biological processes in living organisms. An enormous amount of structural data for a large number of these biomolecules has been described with atomic precision in the form of structural "snapshots" that are freely available in public repositories. These snapshots can help explain how the biomolecules function, the nature of interactions between multi-molecular complexes, and even how small-molecule drugs can modulate the biomolecules for clinical benefits. Furthermore, these structural snapshots serve as inputs for sophisticated computer simulations to turn the biomolecules into moving, "breathing" molecular machines for understanding their dynamic properties in real-time computer simulations. In order for the researcher to take advantage of such a wealth of structural data, it is necessary to gain competency in the use of computer molecular visualization tools for exploring the structures and visualizing three-dimensional spatial representations. Here, we present protocols for using two common visualization tools--the Web-based Jmol and the stand-alone PyMOL package--as well as a few examples of other popular tools. Copyright © 2015 John Wiley & Sons, Inc.

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

Visual Programming: A Programming Tool for Increasing Mathematics Achivement

ERIC Educational Resources Information Center

Swanier, Cheryl A.; Seals, Cheryl D.; Billionniere, Elodie V.

2009-01-01

This paper aims to address the need of increasing student achievement in mathematics using a visual programming language such as Scratch. This visual programming language facilitates creating an environment where students in K-12 education can develop mathematical simulations while learning a visual programming language at the same time.…

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.

Information visualization of the minority game

NASA Astrophysics Data System (ADS)

Jiang, W.; Herbert, R. D.; Webber, R.

2008-02-01

Many dynamical systems produce large quantities of data. How can the system be understood from the output data? Often people are simply overwhelmed by the data. Traditional tools such as tables and plots are often not adequate, and new techniques are needed to help people to analyze the system. In this paper, we propose the use of two spacefilling visualization tools to examine the output from a complex agent-based financial model. We measure the effectiveness and performance of these tools through usability experiments. Based on the experimental results, we develop two new visualization techniques that combine the advantages and discard the disadvantages of the information visualization tools. The model we use is an evolutionary version of the Minority Game which simulates a financial market.

Virtual Observatories for Space Physics Observations and Simulations: New Routes to Efficient Access and Visualization

NASA Technical Reports Server (NTRS)

Roberts, Aaron

2005-01-01

New tools for data access and visualization promise to make the analysis of space plasma data both more efficient and more powerful, especially for answering questions about the global structure and dynamics of the Sun-Earth system. We will show how new existing tools (particularly the Virtual Space Physics Observatory-VSPO-and the Visual System for Browsing, Analysis and Retrieval of Data-ViSBARD; look for the acronyms in Google) already provide rapid access to such information as spacecraft orbits, browse plots, and detailed data, as well as visualizations that can quickly unite our view of multispacecraft observations. We will show movies illustrating multispacecraft observations of the solar wind and magnetosphere during a magnetic storm, and of simulations of 3 0-spacecraft observations derived from MHD simulations of the magnetosphere sampled along likely trajectories of the spacecraft for the MagCon mission. An important issue remaining to be solved is how best to integrate simulation data and services into the Virtual Observatory environment, and this talk will hopefully stimulate further discussion along these lines.

Visualization for Molecular Dynamics Simulation of Gas and Metal Surface Interaction

NASA Astrophysics Data System (ADS)

Puzyrkov, D.; Polyakov, S.; Podryga, V.

2016-02-01

The development of methods, algorithms and applications for visualization of molecular dynamics simulation outputs is discussed. The visual analysis of the results of such calculations is a complex and actual problem especially in case of the large scale simulations. To solve this challenging task it is necessary to decide on: 1) what data parameters to render, 2) what type of visualization to choose, 3) what development tools to use. In the present work an attempt to answer these questions was made. For visualization it was offered to draw particles in the corresponding 3D coordinates and also their velocity vectors, trajectories and volume density in the form of isosurfaces or fog. We tested the way of post-processing and visualization based on the Python language with use of additional libraries. Also parallel software was developed that allows processing large volumes of data in the 3D regions of the examined system. This software gives the opportunity to achieve desired results that are obtained in parallel with the calculations, and at the end to collect discrete received frames into a video file. The software package "Enthought Mayavi2" was used as the tool for visualization. This visualization application gave us the opportunity to study the interaction of a gas with a metal surface and to closely observe the adsorption effect.

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.

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.

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.

PAVA: Physiological and Anatomical Visual Analytics for Mapping of Tissue-Specific Concentration and Time-Course Data

EPA Science Inventory

We describe the development and implementation of a Physiological and Anatomical Visual Analytics tool (PAVA), a web browser-based application, used to visualize experimental/simulated chemical time-course data (dosimetry), epidemiological data and Physiologically-Annotated Data ...

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

ERIC Educational Resources Information Center

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…

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.

Comparisons of Kinematics and Dynamics Simulation Software Tools

NASA Technical Reports Server (NTRS)

Shiue, Yeu-Sheng Paul

2002-01-01

Kinematic and dynamic analyses for moving bodies are essential to system engineers and designers in the process of design and validations. 3D visualization and motion simulation plus finite element analysis (FEA) give engineers a better way to present ideas and results. Marshall Space Flight Center (MSFC) system engineering researchers are currently using IGRIP from DELMIA Inc. as a kinematic simulation tool for discrete bodies motion simulations. Although IGRIP is an excellent tool for kinematic simulation with some dynamic analysis capabilities in robotic control, explorations of other alternatives with more powerful dynamic analysis and FEA capabilities are necessary. Kinematics analysis will only examine the displacement, velocity, and acceleration of the mechanism without considering effects from masses of components. With dynamic analysis and FEA, effects such as the forces or torques at the joint due to mass and inertia of components can be identified. With keen market competition, ALGOR Mechanical Event Simulation (MES), MSC visualNastran 4D, Unigraphics Motion+, and Pro/MECHANICA were chosen for explorations. In this study, comparisons between software tools were presented in terms of following categories: graphical user interface (GUI), import capability, tutorial availability, ease of use, kinematic simulation capability, dynamic simulation capability, FEA capability, graphical output, technical support, and cost. Propulsion Test Article (PTA) with Fastrac engine model exported from IGRIP and an office chair mechanism were used as examples for simulations.

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

Visualization in simulation tools: requirements and a tool specification to support the teaching of dynamic biological processes.

PubMed

Jørgensen, Katarina M; Haddow, Pauline C

2011-08-01

Simulation tools are playing an increasingly important role behind advances in the field of systems biology. However, the current generation of biological science students has either little or no experience with such tools. As such, this educational glitch is limiting both the potential use of such tools as well as the potential for tighter cooperation between the designers and users. Although some simulation tool producers encourage their use in teaching, little attempt has hitherto been made to analyze and discuss their suitability as an educational tool for noncomputing science students. In general, today's simulation tools assume that the user has a stronger mathematical and computing background than that which is found in most biological science curricula, thus making the introduction of such tools a considerable pedagogical challenge. This paper provides an evaluation of the pedagogical attributes of existing simulation tools for cell signal transduction based on Cognitive Load theory. Further, design recommendations for an improved educational simulation tool are provided. The study is based on simulation tools for cell signal transduction. However, the discussions are relevant to a broader biological simulation tool set.

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.

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.

Dynamic simulation of the effect of soft toric contact lenses movement on retinal image quality.

PubMed

Niu, Yafei; Sarver, Edwin J; Stevenson, Scott B; Marsack, Jason D; Parker, Katrina E; Applegate, Raymond A

2008-04-01

To report the development of a tool designed to dynamically simulate the effect of soft toric contact lens movement on retinal image quality, initial findings on three eyes, and the next steps to be taken to improve the utility of the tool. Three eyes of two subjects wearing soft toric contact lenses were cyclopleged with 1% cyclopentolate and 2.5% phenylephrine. Four hundred wavefront aberration measurements over a 5-mm pupil were recorded during soft contact lens wear at 30 Hz using a complete ophthalmic analysis system aberrometer. Each wavefront error measurement was input into Visual Optics Laboratory (version 7.15, Sarver and Associates, Inc.) to generate a retinal simulation of a high contrast log MAR visual acuity chart. The individual simulations were combined into a single dynamic movie using a custom MatLab PsychToolbox program. Visual acuity was measured for each eye reading the movie with best cycloplegic spectacle correction through a 3-mm artificial pupil to minimize the influence of the eyes' uncorrected aberrations. Comparison of the simulated acuity was made to values recorded while the subject read unaberrated charts with contact lenses through a 5-mm artificial pupil. For one study eye, average acuity was the same as the natural contact lens viewing condition. For the other two study eyes visual acuity of the best simulation was more than one line worse than natural viewing conditions. Dynamic simulation of retinal image quality, although not yet perfect, is a promising technique for visually illustrating the optical effects on image quality because of the movements of alignment-sensitive corrections.

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.

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.

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.

Automated Extraction of Flow Features

NASA Technical Reports Server (NTRS)

Dorney, Suzanne (Technical Monitor); Haimes, Robert

2005-01-01

Computational Fluid Dynamics (CFD) simulations are routinely performed as part of the design process of most fluid handling devices. In order to efficiently and effectively use the results of a CFD simulation, visualization tools are often used. These tools are used in all stages of the CFD simulation including pre-processing, interim-processing, and post-processing, to interpret the results. Each of these stages requires visualization tools that allow one to examine the geometry of the device, as well as the partial or final results of the simulation. An engineer will typically generate a series of contour and vector plots to better understand the physics of how the fluid is interacting with the physical device. Of particular interest are detecting features such as shocks, re-circulation zones, and vortices (which will highlight areas of stress and loss). As the demand for CFD analyses continues to increase the need for automated feature extraction capabilities has become vital. In the past, feature extraction and identification were interesting concepts, but not required in understanding the physics of a steady flow field. This is because the results of the more traditional tools like; isc-surface, cuts and streamlines, were more interactive and easily abstracted so they could be represented to the investigator. These tools worked and properly conveyed the collected information at the expense of a great deal of interaction. For unsteady flow-fields, the investigator does not have the luxury of spending time scanning only one "snapshot" of the simulation. Automated assistance is required in pointing out areas of potential interest contained within the flow. This must not require a heavy compute burden (the visualization should not significantly slow down the solution procedure for co-processing environments). Methods must be developed to abstract the feature of interest and display it in a manner that physically makes sense.

Automated Extraction of Flow Features

NASA Technical Reports Server (NTRS)

Dorney, Suzanne (Technical Monitor); Haimes, Robert

2004-01-01

Computational Fluid Dynamics (CFD) simulations are routinely performed as part of the design process of most fluid handling devices. In order to efficiently and effectively use the results of a CFD simulation, visualization tools are often used. These tools are used in all stages of the CFD simulation including pre-processing, interim-processing, and post-processing, to interpret the results. Each of these stages requires visualization tools that allow one to examine the geometry of the device, as well as the partial or final results of the simulation. An engineer will typically generate a series of contour and vector plots to better understand the physics of how the fluid is interacting with the physical device. Of particular interest are detecting features such as shocks, recirculation zones, and vortices (which will highlight areas of stress and loss). As the demand for CFD analyses continues to increase the need for automated feature extraction capabilities has become vital. In the past, feature extraction and identification were interesting concepts, but not required in understanding the physics of a steady flow field. This is because the results of the more traditional tools like; iso-surface, cuts and streamlines, were more interactive and easily abstracted so they could be represented to the investigator. These tools worked and properly conveyed the collected information at the expense of a great deal of interaction. For unsteady flow-fields, the investigator does not have the luxury of spending time scanning only one "snapshot" of the simulation. Automated assistance is required in pointing out areas of potential interest contained within the flow. This must not require a heavy compute burden (the visualization should not significantly slow down the solution procedure for (co-processing environments). Methods must be developed to abstract the feature of interest and display it in a manner that physically makes sense.

Investigation of roughing machining simulation by using visual basic programming in NX CAM system

NASA Astrophysics Data System (ADS)

Hafiz Mohamad, Mohamad; Nafis Osman Zahid, Muhammed

2018-03-01

This paper outlines a simulation study to investigate the characteristic of roughing machining simulation in 4th axis milling processes by utilizing visual basic programming in NX CAM systems. The selection and optimization of cutting orientation in rough milling operation is critical in 4th axis machining. The main purpose of roughing operation is to approximately shape the machined parts into finished form by removing the bulk of material from workpieces. In this paper, the simulations are executed by manipulating a set of different cutting orientation to generate estimated volume removed from the machine parts. The cutting orientation with high volume removal is denoted as an optimum value and chosen to execute a roughing operation. In order to run the simulation, customized software is developed to assist the routines. Operations build-up instructions in NX CAM interface are translated into programming codes via advanced tool available in the Visual Basic Studio. The codes is customized and equipped with decision making tools to run and control the simulations. It permits the integration with any independent program files to execute specific operations. This paper aims to discuss about the simulation program and identifies optimum cutting orientations for roughing processes. The output of this study will broaden up the simulation routines performed in NX CAM systems.

Visualization of simulated urban spaces: inferring parameterized generation of streets, parcels, and aerial imagery.

PubMed

Vanegas, Carlos A; Aliaga, Daniel G; Benes, Bedrich; Waddell, Paul

2009-01-01

Urban simulation models and their visualization are used to help regional planning agencies evaluate alternative transportation investments, land use regulations, and environmental protection policies. Typical urban simulations provide spatially distributed data about number of inhabitants, land prices, traffic, and other variables. In this article, we build on a synergy of urban simulation, urban visualization, and computer graphics to automatically infer an urban layout for any time step of the simulation sequence. In addition to standard visualization tools, our method gathers data of the original street network, parcels, and aerial imagery and uses the available simulation results to infer changes to the original urban layout and produce a new and plausible layout for the simulation results. In contrast with previous work, our approach automatically updates the layout based on changes in the simulation data and thus can scale to a large simulation over many years. The method in this article offers a substantial step forward in building integrated visualization and behavioral simulation systems for use in community visioning, planning, and policy analysis. We demonstrate our method on several real cases using a 200 GB database for a 16,300 km2 area surrounding Seattle.

Supply Chain Simulator: A Scenario-Based Educational Tool to Enhance Student Learning

ERIC Educational Resources Information Center

Siddiqui, Atiq; Khan, Mehmood; Akhtar, Sohail

2008-01-01

Simulation-based educational products are excellent set of illustrative tools that proffer features like visualization of the dynamic behavior of a real system, etc. Such products have great efficacy in education and are known to be one of the first-rate student centered learning methodologies. These products allow students to practice skills such…

Fuels planning: science synthesis and integration; forest structure and fire hazard fact sheet 03: visualizing forest structure and fuels

Treesearch

Rocky Mountain Research Station USDA Forest Service

2004-01-01

The software described in this fact sheet provides managers with tools for visualizing forest and fuels information. Computer-based landscape simulations can help visualize stand and landscape conditions and the effects of different management treatments and fuel changes over time. These visualizations can assist forest planning by considering a range of management...

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

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

Analysis procedures and subjective flight results of a simulator validation and cue fidelity experiment

NASA Technical Reports Server (NTRS)

Carr, Peter C.; Mckissick, Burnell T.

1988-01-01

A joint experiment to investigate simulator validation and cue fidelity was conducted by the Dryden Flight Research Facility of NASA Ames Research Center (Ames-Dryden) and NASA Langley Research Center. The primary objective was to validate the use of a closed-loop pilot-vehicle mathematical model as an analytical tool for optimizing the tradeoff between simulator fidelity requirements and simulator cost. The validation process includes comparing model predictions with simulation and flight test results to evaluate various hypotheses for differences in motion and visual cues and information transfer. A group of five pilots flew air-to-air tracking maneuvers in the Langley differential maneuvering simulator and visual motion simulator and in an F-14 aircraft at Ames-Dryden. The simulators used motion and visual cueing devices including a g-seat, a helmet loader, wide field-of-view horizon, and a motion base platform.

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.

VOLCWORKS: A suite for optimization of hazards mapping

NASA Astrophysics Data System (ADS)

Delgado Granados, H.; Ramírez Guzmán, R.; Villareal Benítez, J. L.; García Sánchez, T.

2012-04-01

Making hazards maps is a process linking basic science, applied science and engineering for the benefit of the society. The methodologies for hazards maps' construction have evolved enormously together with the tools that allow the forecasting of the behavior of the materials produced by different eruptive processes. However, in spite of the development of tools and evolution of methodologies, the utility of hazards maps has not changed: prevention and mitigation of volcanic disasters. Integration of different tools for simulation of different processes for a single volcano is a challenge to be solved using software tools including processing, simulation and visualization techniques, and data structures in order to build up a suit that helps in the construction process starting from the integration of the geological data, simulations and simplification of the output to design a hazards/scenario map. Scientific visualization is a powerful tool to explore and gain insight into complex data from instruments and simulations. The workflow from data collection, quality control and preparation for simulations, to achieve visual and appropriate presentation is a process that is usually disconnected, using in most of the cases different applications for each of the needed processes, because it requires many tools that are not built for the solution of a specific problem, or were developed by research groups to solve particular tasks, but disconnected. In volcanology, due to its complexity, groups typically examine only one aspect of the phenomenon: ash dispersal, laharic flows, pyroclastic flows, lava flows, and ballistic projectile ejection, among others. However, when studying the hazards associated to the activity of a volcano, it is important to analyze all the processes comprehensively, especially for communication of results to the end users: decision makers and planners. In order to solve this problem and connect different parts of a workflow we are developing the suite VOLCWORKS, whose principle is to have a flexible-implementation architecture allowing rapid development of software to the extent specified by the needs including calculations, routines, or algorithms, both new and through redesign of available software in the volcanological community, but especially allowing to include new knowledge, models or software transferring them to software modules. The design is component-oriented platform, which allows incorporating particular solutions (routines, simulations, etc.), which can be concatenated for integration or highlighting information. The platform includes a graphical interface with capabilities for working in different visual environments that can be focused to the particular work of different types of users (researchers, lecturers, students, etc.). This platform aims to integrate simulation and visualization phases, incorporating proven tools (now isolated). VOLCWORKS can be used under different operating systems (Windows, Linux and Mac OS) and fit the context of use automatically and at runtime: in both tasks and their sequence, such as utilization of hardware resources (CPU, GPU, special monitors, etc.). The application has the ability to run on a laptop or even in a virtual reality room with access to supercomputers.

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

Distributed Observer Network

NASA Technical Reports Server (NTRS)

2008-01-01

NASA s advanced visual simulations are essential for analyses associated with life cycle planning, design, training, testing, operations, and evaluation. Kennedy Space Center, in particular, uses simulations for ground services and space exploration planning in an effort to reduce risk and costs while improving safety and performance. However, it has been difficult to circulate and share the results of simulation tools among the field centers, and distance and travel expenses have made timely collaboration even harder. In response, NASA joined with Valador Inc. to develop the Distributed Observer Network (DON), a collaborative environment that leverages game technology to bring 3-D simulations to conventional desktop and laptop computers. DON enables teams of engineers working on design and operations to view and collaborate on 3-D representations of data generated by authoritative tools. DON takes models and telemetry from these sources and, using commercial game engine technology, displays the simulation results in a 3-D visual environment. Multiple widely dispersed users, working individually or in groups, can view and analyze simulation results on desktop and laptop computers in real time.

Visual simulations of forest wildlife habitat structure, change, and landscape context in New England

Treesearch

Richard M. DeGraaf; Anna M. Lester; Mariko Yamasaki; William B. Leak

2007-01-01

Visualization is a powerful tool for depicting projections of forest structure and landscape conditions, for communicating habitat management practices, and for providing a landscape context to private landowners and to those concerned with public land management. Recent advances in visualization technology, especially in graphics quality, ease of use, and relative...

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.

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.

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.

Objective Assessment of Laparoscopic Force and Psychomotor Skills in a Novel Virtual Reality-Based Haptic Simulator.

PubMed

Prasad, M S Raghu; Manivannan, Muniyandi; Manoharan, Govindan; Chandramohan, S M

2016-01-01

Most of the commercially available virtual reality-based laparoscopic simulators do not effectively evaluate combined psychomotor and force-based laparoscopic skills. Consequently, the lack of training on these critical skills leads to intraoperative errors. To assess the effectiveness of the novel virtual reality-based simulator, this study analyzed the combined psychomotor (i.e., motion or movement) and force skills of residents and expert surgeons. The study also examined the effectiveness of real-time visual force feedback and tool motion during training. Bimanual fundamental (i.e., probing, pulling, sweeping, grasping, and twisting) and complex tasks (i.e., tissue dissection) were evaluated. In both tasks, visual feedback on applied force and tool motion were provided. The skills of the participants while performing the early tasks were assessed with and without visual feedback. Participants performed 5 repetitions of fundamental and complex tasks. Reaction force and instrument acceleration were used as metrics. Surgical Gastroenterology, Government Stanley Medical College and Hospital; Institute of Surgical Gastroenterology, Madras Medical College and Rajiv Gandhi Government General Hospital. Residents (N = 25; postgraduates and surgeons with <2 years of laparoscopic surgery) and expert surgeons (N = 25; surgeons with >4 and ≤10 years of laparoscopic surgery). Residents applied large forces compared with expert surgeons and performed abrupt tool movements (p < 0.001). However, visual + haptic feedback improved the performance of residents (p < 0.001). In complex tasks, visual + haptic feedback did not influence the applied force of expert surgeons, but influenced their tool motion (p < 0.001). Furthermore, in complex tissue sweeping task, expert surgeons applied more force, but were within the tissue damage limits. In both groups, exertion of large forces and abrupt tool motion were observed during grasping, probing or pulling, and tissue sweeping maneuvers (p < 0.001). Modern day curriculum-based training should evaluate the skills of residents with robust force and psychomotor-based exercises for proficient laparoscopy. Visual feedback on force and motion during training has the potential to enhance the learning curve of residents. Copyright © 2016 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

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.

VIPER: Virtual Intelligent Planetary Exploration Rover

NASA Technical Reports Server (NTRS)

Edwards, Laurence; Flueckiger, Lorenzo; Nguyen, Laurent; Washington, Richard

2001-01-01

Simulation and visualization of rover behavior are critical capabilities for scientists and rover operators to construct, test, and validate plans for commanding a remote rover. The VIPER system links these capabilities. using a high-fidelity virtual-reality (VR) environment. a kinematically accurate simulator, and a flexible plan executive to allow users to simulate and visualize possible execution outcomes of a plan under development. This work is part of a larger vision of a science-centered rover control environment, where a scientist may inspect and explore the environment via VR tools, specify science goals, and visualize the expected and actual behavior of the remote rover. The VIPER system is constructed from three generic systems, linked together via a minimal amount of customization into the integrated system. The complete system points out the power of combining plan execution, simulation, and visualization for envisioning rover behavior; it also demonstrates the utility of developing generic technologies. which can be combined in novel and useful ways.

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.

Remote visual analysis of large turbulence databases at multiple scales

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

Pulido, Jesus; Livescu, Daniel; Kanov, Kalin

The remote analysis and visualization of raw large turbulence datasets is challenging. Current accurate direct numerical simulations (DNS) of turbulent flows generate datasets with billions of points per time-step and several thousand time-steps per simulation. Until recently, the analysis and visualization of such datasets was restricted to scientists with access to large supercomputers. The public Johns Hopkins Turbulence database simplifies access to multi-terabyte turbulence datasets and facilitates the computation of statistics and extraction of features through the use of commodity hardware. In this paper, we present a framework designed around wavelet-based compression for high-speed visualization of large datasets and methodsmore » supporting multi-resolution analysis of turbulence. By integrating common technologies, this framework enables remote access to tools available on supercomputers and over 230 terabytes of DNS data over the Web. Finally, the database toolset is expanded by providing access to exploratory data analysis tools, such as wavelet decomposition capabilities and coherent feature extraction.« less

Remote visual analysis of large turbulence databases at multiple scales

DOE PAGES

Pulido, Jesus; Livescu, Daniel; Kanov, Kalin; ...

2018-06-15

The remote analysis and visualization of raw large turbulence datasets is challenging. Current accurate direct numerical simulations (DNS) of turbulent flows generate datasets with billions of points per time-step and several thousand time-steps per simulation. Until recently, the analysis and visualization of such datasets was restricted to scientists with access to large supercomputers. The public Johns Hopkins Turbulence database simplifies access to multi-terabyte turbulence datasets and facilitates the computation of statistics and extraction of features through the use of commodity hardware. In this paper, we present a framework designed around wavelet-based compression for high-speed visualization of large datasets and methodsmore » supporting multi-resolution analysis of turbulence. By integrating common technologies, this framework enables remote access to tools available on supercomputers and over 230 terabytes of DNS data over the Web. Finally, the database toolset is expanded by providing access to exploratory data analysis tools, such as wavelet decomposition capabilities and coherent feature extraction.« less

Simulation and visualization of fundamental optics phenomenon by LabVIEW

NASA Astrophysics Data System (ADS)

Lyu, Bohan

2017-08-01

Most instructors teach complex phenomenon by equation and static illustration without interactive multimedia. Students usually memorize phenomenon by taking note. However, only note or complex formula can not make user visualize the phenomenon of the photonics system. LabVIEW is a good tool for in automatic measurement. However, the simplicity of coding in LabVIEW makes it not only suit for automatic measurement, but also suitable for simulation and visualization of fundamental optics phenomenon. In this paper, five simple optics phenomenon will be discuss and simulation with LabVIEW. They are Snell's Law, Hermite-Gaussian beam transverse mode, square and circular aperture diffraction, polarization wave and Poincare sphere, and finally Fabry-Perrot etalon in spectrum domain.

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.

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

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.

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.

Linking Automated Data Analysis and Visualization with Applications in Developmental Biology and High-Energy Physics

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

Ruebel, Oliver

2009-11-20

Knowledge discovery from large and complex collections of today's scientific datasets is a challenging task. With the ability to measure and simulate more processes at increasingly finer spatial and temporal scales, the increasing number of data dimensions and data objects is presenting tremendous challenges for data analysis and effective data exploration methods and tools. Researchers are overwhelmed with data and standard tools are often insufficient to enable effective data analysis and knowledge discovery. The main objective of this thesis is to provide important new capabilities to accelerate scientific knowledge discovery form large, complex, and multivariate scientific data. The research coveredmore » in this thesis addresses these scientific challenges using a combination of scientific visualization, information visualization, automated data analysis, and other enabling technologies, such as efficient data management. The effectiveness of the proposed analysis methods is demonstrated via applications in two distinct scientific research fields, namely developmental biology and high-energy physics.Advances in microscopy, image analysis, and embryo registration enable for the first time measurement of gene expression at cellular resolution for entire organisms. Analysis of high-dimensional spatial gene expression datasets is a challenging task. By integrating data clustering and visualization, analysis of complex, time-varying, spatial gene expression patterns and their formation becomes possible. The analysis framework MATLAB and the visualization have been integrated, making advanced analysis tools accessible to biologist and enabling bioinformatic researchers to directly integrate their analysis with the visualization. Laser wakefield particle accelerators (LWFAs) promise to be a new compact source of high-energy particles and radiation, with wide applications ranging from medicine to physics. To gain insight into the complex physical processes of particle acceleration, physicists model LWFAs computationally. The datasets produced by LWFA simulations are (i) extremely large, (ii) of varying spatial and temporal resolution, (iii) heterogeneous, and (iv) high-dimensional, making analysis and knowledge discovery from complex LWFA simulation data a challenging task. To address these challenges this thesis describes the integration of the visualization system VisIt and the state-of-the-art index/query system FastBit, enabling interactive visual exploration of extremely large three-dimensional particle datasets. Researchers are especially interested in beams of high-energy particles formed during the course of a simulation. This thesis describes novel methods for automatic detection and analysis of particle beams enabling a more accurate and efficient data analysis process. By integrating these automated analysis methods with visualization, this research enables more accurate, efficient, and effective analysis of LWFA simulation data than previously possible.« less

Real simulation tools in introductory courses: packaging and repurposing our research code.

NASA Astrophysics Data System (ADS)

Heagy, L. J.; Cockett, R.; Kang, S.; Oldenburg, D.

2015-12-01

Numerical simulations are an important tool for scientific research and applications in industry. They provide a means to experiment with physics in a tangible, visual way, often providing insights into the problem. Over the last two years, we have been developing course and laboratory materials for an undergraduate geophysics course primarily taken by non-geophysics majors, including engineers and geologists. Our aim is to provide the students with resources to build intuition about geophysical techniques, promote curiosity driven exploration, and help them develop the skills necessary to communicate across disciplines. Using open-source resources and our existing research code, we have built modules around simulations, with supporting content to give student interactive tools for exploration into the impacts of input parameters and visualization of the resulting fields, fluxes and data for a variety of problems in applied geophysics, including magnetics, seismic, electromagnetics, and direct current resistivity. The content provides context for the problems, along with exercises that are aimed at getting students to experiment and ask 'what if...?' questions. In this presentation, we will discuss our approach for designing the structure of the simulation-based modules, the resources we have used, challenges we have encountered, general feedback from students and instructors, as well as our goals and roadmap for future improvement. We hope that our experiences and approach will be beneficial to other instructors who aim to put simulation tools in the hands of students.

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.

The change in critical technologies for computational physics

NASA Technical Reports Server (NTRS)

Watson, Val

1990-01-01

It is noted that the types of technology required for computational physics are changing as the field matures. Emphasis has shifted from computer technology to algorithm technology and, finally, to visual analysis technology as areas of critical research for this field. High-performance graphical workstations tied to a supercommunicator with high-speed communications along with the development of especially tailored visualization software has enabled analysis of highly complex fluid-dynamics simulations. Particular reference is made here to the development of visual analysis tools at NASA's Numerical Aerodynamics Simulation Facility. The next technology which this field requires is one that would eliminate visual clutter by extracting key features of simulations of physics and technology in order to create displays that clearly portray these key features. Research in the tuning of visual displays to human cognitive abilities is proposed. The immediate transfer of technology to all levels of computers, specifically the inclusion of visualization primitives in basic software developments for all work stations and PCs, is recommended.

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.

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

A breakthrough for experiencing and understanding simulated physics

NASA Technical Reports Server (NTRS)

Watson, Val

1988-01-01

The use of computer simulation in physics research is discussed, focusing on improvements to graphic workstations. Simulation capabilities and applications of enhanced visualization tools are outlined. The elements of an ideal computer simulation are presented and the potential for improving various simulation elements is examined. The interface between the human and the computer and simulation models are considered. Recommendations are made for changes in computer simulation practices and applications of simulation technology in education.

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.

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.

Biological Visualization, Imaging and Simulation(Bio-VIS) at NASA Ames Research Center: Developing New Software and Technology for Astronaut Training and Biology Research in Space

NASA Technical Reports Server (NTRS)

Smith, Jeffrey

2003-01-01

The Bio- Visualization, Imaging and Simulation (BioVIS) Technology Center at NASA's Ames Research Center is dedicated to developing and applying advanced visualization, computation and simulation technologies to support NASA Space Life Sciences research and the objectives of the Fundamental Biology Program. Research ranges from high resolution 3D cell imaging and structure analysis, virtual environment simulation of fine sensory-motor tasks, computational neuroscience and biophysics to biomedical/clinical applications. Computer simulation research focuses on the development of advanced computational tools for astronaut training and education. Virtual Reality (VR) and Virtual Environment (VE) simulation systems have become important training tools in many fields from flight simulation to, more recently, surgical simulation. The type and quality of training provided by these computer-based tools ranges widely, but the value of real-time VE computer simulation as a method of preparing individuals for real-world tasks is well established. Astronauts routinely use VE systems for various training tasks, including Space Shuttle landings, robot arm manipulations and extravehicular activities (space walks). Currently, there are no VE systems to train astronauts for basic and applied research experiments which are an important part of many missions. The Virtual Glovebox (VGX) is a prototype VE system for real-time physically-based simulation of the Life Sciences Glovebox where astronauts will perform many complex tasks supporting research experiments aboard the International Space Station. The VGX consists of a physical display system utilizing duel LCD projectors and circular polarization to produce a desktop-sized 3D virtual workspace. Physically-based modeling tools (Arachi Inc.) provide real-time collision detection, rigid body dynamics, physical properties and force-based controls for objects. The human-computer interface consists of two magnetic tracking devices (Ascention Inc.) attached to instrumented gloves (Immersion Inc.) which co-locate the user's hands with hand/forearm representations in the virtual workspace. Force-feedback is possible in a work volume defined by a Phantom Desktop device (SensAble inc.). Graphics are written in OpenGL. The system runs on a 2.2 GHz Pentium 4 PC. The prototype VGX provides astronauts and support personnel with a real-time physically-based VE system to simulate basic research tasks both on Earth and in the microgravity of Space. The immersive virtual environment of the VGX also makes it a useful tool for virtual engineering applications including CAD development, procedure design and simulation of human-system systems in a desktop-sized work volume.

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

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.

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

Development of a 3-D Nuclear Event Visualization Program Using Unity

NASA Astrophysics Data System (ADS)

Kuhn, Victoria

2017-09-01

Simulations have become increasingly important for science and there is an increasing emphasis on the visualization of simulations within a Virtual Reality (VR) environment. Our group is exploring this capability as a visualization tool not just for those curious about science, but also for educational purposes for K-12 students. Using data collected in 3-D by a Time Projection Chamber (TPC), we are able to visualize nuclear and cosmic events. The Unity game engine was used to recreate the TPC to visualize these events and construct a VR application. The methods used to create these simulations will be presented along with an example of a simulation. I will also present on the development and testing of this program, which I carried out this past summer at MSU as part of an REU program. We used data from the S πRIT TPC, but the software can be applied to other 3-D detectors. This work is supported by the U.S. Department of Energy under Grant Nos. DE-SC0014530, DE-NA0002923 and US NSF under Grant No. PHY-1565546.

Identifying secondary-school students' difficulties when reading visual representations displayed in physics simulations

NASA Astrophysics Data System (ADS)

López, Víctor; Pintó, Roser

2017-07-01

Computer simulations are often considered effective educational tools, since their visual and communicative power enable students to better understand physical systems and phenomena. However, previous studies have found that when students read visual representations some reading difficulties can arise, especially when these are complex or dynamic representations. We have analyzed how secondary-school students read the visual representations displayed in two PhET simulations (one addressing the friction-heating at microscopic level, and the other addressing the electromagnetic induction), and different typologies of reading difficulties have been identified: when reading the compositional structure of the representation, when giving appropriate relevance and semantic meaning to each visual element, and also when dealing with multiple representations and dynamic information. All students experienced at least one of these difficulties, and very similar difficulties appeared in the two groups of students, despite the different scientific content of the simulations. In conclusion, visualisation does not imply a full comprehension of the content of scientific simulations per se, and an effective reading process requires a set of reading skills, previous knowledge, attention, and external supports. Science teachers should bear in mind these issues in order to help students read images to take benefit of their educational potential.

Analyzing and Visualizing Cosmological Simulations with ParaView

NASA Astrophysics Data System (ADS)

Woodring, Jonathan; Heitmann, Katrin; Ahrens, James; Fasel, Patricia; Hsu, Chung-Hsing; Habib, Salman; Pope, Adrian

2011-07-01

The advent of large cosmological sky surveys—ushering in the era of precision cosmology—has been accompanied by ever larger cosmological simulations. The analysis of these simulations, which currently encompass tens of billions of particles and up to a trillion particles in the near future, is often as daunting as carrying out the simulations in the first place. Therefore, the development of very efficient analysis tools combining qualitative and quantitative capabilities is a matter of some urgency. In this paper, we introduce new analysis features implemented within ParaView, a fully parallel, open-source visualization toolkit, to analyze large N-body simulations. A major aspect of ParaView is that it can live and operate on the same machines and utilize the same parallel power as the simulation codes themselves. In addition, data movement is in a serious bottleneck now and will become even more of an issue in the future; an interactive visualization and analysis tool that can handle data in situ is fast becoming essential. The new features in ParaView include particle readers and a very efficient halo finder that identifies friends-of-friends halos and determines common halo properties, including spherical overdensity properties. In combination with many other functionalities already existing within ParaView, such as histogram routines or interfaces to programming languages like Python, this enhanced version enables fast, interactive, and convenient analyses of large cosmological simulations. In addition, development paths are available for future extensions.

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.

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.

Publicly Releasing a Large Simulation Dataset with NDS Labs

NASA Astrophysics Data System (ADS)

Goldbaum, Nathan

2016-03-01

Optimally, all publicly funded research should be accompanied by the tools, code, and data necessary to fully reproduce the analysis performed in journal articles describing the research. This ideal can be difficult to attain, particularly when dealing with large (>10 TB) simulation datasets. In this lightning talk, we describe the process of publicly releasing a large simulation dataset to accompany the submission of a journal article. The simulation was performed using Enzo, an open source, community-developed N-body/hydrodynamics code and was analyzed using a wide range of community- developed tools in the scientific Python ecosystem. Although the simulation was performed and analyzed using an ecosystem of sustainably developed tools, we enable sustainable science using our data by making it publicly available. Combining the data release with the NDS Labs infrastructure allows a substantial amount of added value, including web-based access to analysis and visualization using the yt analysis package through an IPython notebook interface. In addition, we are able to accompany the paper submission to the arXiv preprint server with links to the raw simulation data as well as interactive real-time data visualizations that readers can explore on their own or share with colleagues during journal club discussions. It is our hope that the value added by these services will substantially increase the impact and readership of the paper.

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.

BioVEC: a program for biomolecule visualization with ellipsoidal coarse-graining.

PubMed

Abrahamsson, Erik; Plotkin, Steven S

2009-09-01

Biomolecule Visualization with Ellipsoidal Coarse-graining (BioVEC) is a tool for visualizing molecular dynamics simulation data while allowing coarse-grained residues to be rendered as ellipsoids. BioVEC reads in configuration files, which may be output from molecular dynamics simulations that include orientation output in either quaternion or ANISOU format, and can render frames of the trajectory in several common image formats for subsequent concatenation into a movie file. The BioVEC program is written in C++, uses the OpenGL API for rendering, and is open source. It is lightweight, allows for user-defined settings for and texture, and runs on either Windows or Linux platforms.

High-power graphic computers for visual simulation: a real-time--rendering revolution

NASA Technical Reports Server (NTRS)

Kaiser, M. K.

1996-01-01

Advances in high-end graphics computers in the past decade have made it possible to render visual scenes of incredible complexity and realism in real time. These new capabilities make it possible to manipulate and investigate the interactions of observers with their visual world in ways once only dreamed of. This paper reviews how these developments have affected two preexisting domains of behavioral research (flight simulation and motion perception) and have created a new domain (virtual environment research) which provides tools and challenges for the perceptual psychologist. Finally, the current limitations of these technologies are considered, with an eye toward how perceptual psychologist might shape future developments.

A boxplot for circular data.

PubMed

Buttarazzi, Davide; Pandolfo, Giuseppe; Porzio, Giovanni C

2018-05-21

The box-and-whiskers plot is an extraordinary graphical tool that provides a quick visual summary of an observed distribution. In spite of its many extensions, a really suitable boxplot to display circular data is not yet available. Thanks to its simplicity and strong visual impact, such a tool would be especially useful in all fields where circular measures arise: biometrics, astronomy, environmetrics, Earth sciences, to cite just a few. For this reason, in line with Tukey's original idea, a Tukey-like circular boxplot is introduced. Several simulated and real datasets arising in biology are used to illustrate the proposed graphical tool. © 2018, The International Biometric Society.

Physics-based interactive volume manipulation for sharing surgical process.

PubMed

Nakao, Megumi; Minato, Kotaro

2010-05-01

This paper presents a new set of techniques by which surgeons can interactively manipulate patient-specific volumetric models for sharing surgical process. To handle physical interaction between the surgical tools and organs, we propose a simple surface-constraint-based manipulation algorithm to consistently simulate common surgical manipulations such as grasping, holding and retraction. Our computation model is capable of simulating soft-tissue deformation and incision in real time. We also present visualization techniques in order to rapidly visualize time-varying, volumetric information on the deformed image. This paper demonstrates the success of the proposed methods in enabling the simulation of surgical processes, and the ways in which this simulation facilitates preoperative planning and rehearsal.

MAGIC: Model and Graphic Information Converter

NASA Technical Reports Server (NTRS)

Herbert, W. C.

2009-01-01

MAGIC is a software tool capable of converting highly detailed 3D models from an open, standard format, VRML 2.0/97, into the proprietary DTS file format used by the Torque Game Engine from GarageGames. MAGIC is used to convert 3D simulations from authoritative sources into the data needed to run the simulations in NASA's Distributed Observer Network. The Distributed Observer Network (DON) is a simulation presentation tool built by NASA to facilitate the simulation sharing requirements of the Data Presentation and Visualization effort within the Constellation Program. DON is built on top of the Torque Game Engine (TGE) and has chosen TGE's Dynamix Three Space (DTS) file format to represent 3D objects within simulations.

Novel Scientific Visualization Interfaces for Interactive Information Visualization and Sharing

NASA Astrophysics Data System (ADS)

Demir, I.; Krajewski, W. F.

2012-12-01

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 in the Iowa Flood Information System (IFIS), developed within the light of these challenges. The IFIS is a web-based platform developed by the Iowa Flood Center (IFC) to provide access to and visualization of flood inundation maps, real-time flood conditions, flood forecasts both short-term and seasonal, and other flood-related data for communities in Iowa. The key element of the system's architecture is the notion of community. Locations of the communities, those near streams and rivers, define basin boundaries. The IFIS provides community-centric watershed and river characteristics, weather (rainfall) conditions, and streamflow data and visualization tools. Interactive interfaces allow access to inundation maps for different stage and return period values, and flooding scenarios with contributions from multiple rivers. Real-time and historical data of water levels, gauge heights, and rainfall conditions are available in the IFIS. 2D and 3D interactive visualizations in the IFIS make the data more understandable to general public. Users are able to filter data sources for their communities and selected rivers. The data and information on IFIS is also accessible through web services and mobile applications. The IFIS is optimized for various browsers and screen sizes to provide access through multiple platforms including tablets and mobile devices. Multiple view modes in the IFIS accommodate different user types from general public to researchers and decision makers by providing different level of tools and details. River view mode allows users to visualize data from multiple IFC bridge sensors and USGS stream gauges to follow flooding condition along a river. The IFIS will help communities make better-informed decisions on the occurrence of floods, and will alert communities in advance to help minimize damage of floods.

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.

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.

Visual Data-Analytics of Large-Scale Parallel Discrete-Event Simulations

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

Ross, Caitlin; Carothers, Christopher D.; Mubarak, Misbah

Parallel discrete-event simulation (PDES) is an important tool in the codesign of extreme-scale systems because PDES provides a cost-effective way to evaluate designs of highperformance computing systems. Optimistic synchronization algorithms for PDES, such as Time Warp, allow events to be processed without global synchronization among the processing elements. A rollback mechanism is provided when events are processed out of timestamp order. Although optimistic synchronization protocols enable the scalability of large-scale PDES, the performance of the simulations must be tuned to reduce the number of rollbacks and provide an improved simulation runtime. To enable efficient large-scale optimistic simulations, one has tomore » gain insight into the factors that affect the rollback behavior and simulation performance. We developed a tool for ROSS model developers that gives them detailed metrics on the performance of their large-scale optimistic simulations at varying levels of simulation granularity. Model developers can use this information for parameter tuning of optimistic simulations in order to achieve better runtime and fewer rollbacks. In this work, we instrument the ROSS optimistic PDES framework to gather detailed statistics about the simulation engine. We have also developed an interactive visualization interface that uses the data collected by the ROSS instrumentation to understand the underlying behavior of the simulation engine. The interface connects real time to virtual time in the simulation and provides the ability to view simulation data at different granularities. We demonstrate the usefulness of our framework by performing a visual analysis of the dragonfly network topology model provided by the CODES simulation framework built on top of ROSS. The instrumentation needs to minimize overhead in order to accurately collect data about the simulation performance. To ensure that the instrumentation does not introduce unnecessary overhead, we perform a scaling study that compares instrumented ROSS simulations with their noninstrumented counterparts in order to determine the amount of perturbation when running at different simulation scales.« less

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.

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.

3D Feature Extraction for Unstructured Grids

NASA Technical Reports Server (NTRS)

Silver, Deborah

1996-01-01

Visualization techniques provide tools that help scientists identify observed phenomena in scientific simulation. To be useful, these tools must allow the user to extract regions, classify and visualize them, abstract them for simplified representations, and track their evolution. Object Segmentation provides a technique to extract and quantify regions of interest within these massive datasets. This article explores basic algorithms to extract coherent amorphous regions from two-dimensional and three-dimensional scalar unstructured grids. The techniques are applied to datasets from Computational Fluid Dynamics and those from Finite Element Analysis.

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

Evaluating the Interactive Learning Tool Simreal+ for Visualizing and Simulating Mathematical Concepts

ERIC Educational Resources Information Center

Hadjerrouit, Said

2015-01-01

This research study aims at evaluating the suitability of SimReal+ for effective use in teacher education. SimReal+ was originally developed to teach mathematics in universities, but it is has been recently improved to include school mathematics. The basic idea of SimReal+ is that the visualization of mathematical concepts is a powerful technique…

The Effect of Color Choice on Learner Interpretation of a Cosmology Visualization

ERIC Educational Resources Information Center

Buck, Zoe

2013-01-01

As we turn more and more to high-end computing to understand the Universe at cosmological scales, dynamic visualizations of simulations will take on a vital role as perceptual and cognitive tools. In collaboration with the Adler Planetarium and University of California High-Performance AstroComputing Center (UC-HiPACC), I am interested in better…

Remote Visualization and Remote Collaboration On Computational Fluid Dynamics

NASA Technical Reports Server (NTRS)

Watson, Val; Lasinski, T. A. (Technical Monitor)

1995-01-01

A new technology has been developed for remote visualization that provides remote, 3D, high resolution, dynamic, interactive viewing of scientific data (such as fluid dynamics simulations or measurements). Based on this technology, some World Wide Web sites on the Internet are providing fluid dynamics data for educational or testing purposes. This technology is also being used for remote collaboration in joint university, industry, and NASA projects in computational fluid dynamics and wind tunnel testing. Previously, remote visualization of dynamic data was done using video format (transmitting pixel information) such as video conferencing or MPEG movies on the Internet. The concept for this new technology is to send the raw data (e.g., grids, vectors, and scalars) along with viewing scripts over the Internet and have the pixels generated by a visualization tool running on the viewer's local workstation. The visualization tool that is currently used is FAST (Flow Analysis Software Toolkit).

POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations

PubMed Central

Porollo, Aleksey; Meller, Jaroslaw

2010-01-01

Molecular simulations offer important mechanistic and functional clues in studies of proteins and other macromolecules. However, interpreting the results of such simulations increasingly requires tools that can combine information from multiple structural databases and other web resources, and provide highly integrated and versatile analysis tools. Here, we present a new web server that integrates high-quality animation of molecular motion (MM) with structural and functional analysis of macromolecules. The new tool, dubbed POLYVIEW-MM, enables animation of trajectories generated by molecular dynamics and related simulation techniques, as well as visualization of alternative conformers, e.g. obtained as a result of protein structure prediction methods or small molecule docking. To facilitate structural analysis, POLYVIEW-MM combines interactive view and analysis of conformational changes using Jmol and its tailored extensions, publication quality animation using PyMol, and customizable 2D summary plots that provide an overview of MM, e.g. in terms of changes in secondary structure states and relative solvent accessibility of individual residues in proteins. Furthermore, POLYVIEW-MM integrates visualization with various structural annotations, including automated mapping of known inter-action sites from structural homologs, mapping of cavities and ligand binding sites, transmembrane regions and protein domains. URL: http://polyview.cchmc.org/conform.html. PMID:20504857

From printed color to image appearance: tool for advertising assessment

NASA Astrophysics Data System (ADS)

Bonanomi, Cristian; Marini, Daniele; Rizzi, Alessandro

2012-07-01

We present a methodology to calculate the color appearance of advertising billboards set in indoor and outdoor environments, printed on different types of paper support and viewed under different illuminations. The aim is to simulate the visual appearance of an image printed on a specific support, observed in a certain context and illuminated with a specific source of light. Knowing in advance the visual rendering of an image in different conditions can avoid problems related to its visualization. The proposed method applies a sequence of transformations to convert a four channels image (CMYK) into a spectral one, considering the paper support, then it simulates the chosen illumination, and finally computes an estimation of the appearance.

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.

Virtual Collaborative Simulation Environment for Integrated Product and Process Development

NASA Technical Reports Server (NTRS)

Gulli, Michael A.

1997-01-01

Deneb Robotics is a leader in the development of commercially available, leading edge three- dimensional simulation software tools for virtual prototyping,, simulation-based design, manufacturing process simulation, and factory floor simulation and training applications. Deneb has developed and commercially released a preliminary Virtual Collaborative Engineering (VCE) capability for Integrated Product and Process Development (IPPD). This capability allows distributed, real-time visualization and evaluation of design concepts, manufacturing processes, and total factory and enterprises in one seamless simulation environment.

Instrumental resolution of the chopper spectrometer 4SEASONS evaluated by Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Kajimoto, Ryoichi; Sato, Kentaro; Inamura, Yasuhiro; Fujita, Masaki

2018-05-01

We performed simulations of the resolution function of the 4SEASONS spectrometer at J-PARC by using the Monte Carlo simulation package McStas. The simulations showed reasonably good agreement with analytical calculations of energy and momentum resolutions by using a simplified description. We implemented new functionalities in Utsusemi, the standard data analysis tool used in 4SEASONS, to enable visualization of the simulated resolution function and predict its shape for specific experimental configurations.

Method of simulation and visualization of FDG metabolism based on VHP image

NASA Astrophysics Data System (ADS)

Cui, Yunfeng; Bai, Jing

2005-04-01

FDG ([18F] 2-fluoro-2-deoxy-D-glucose) is the typical tracer used in clinical PET (positron emission tomography) studies. The FDG-PET is an important imaging tool for early diagnosis and treatment of malignant tumor and functional disease. The main purpose of this work is to propose a method that represents FDG metabolism in human body through the simulation and visualization of 18F distribution process dynamically based on the segmented VHP (Visible Human Project) image dataset. First, the plasma time-activity curve (PTAC) and the tissues time-activity curves (TTAC) are obtained from the previous studies and the literatures. According to the obtained PTAC and TTACs, a set of corresponding values are assigned to the segmented VHP image, Thus a set of dynamic images are derived to show the 18F distribution in the concerned tissues for the predetermined sampling schedule. Finally, the simulated FDG distribution images are visualized in 3D and 2D formats, respectively, incorporated with principal interaction functions. As compared with original PET image, our visualization result presents higher resolution because of the high resolution of VHP image data, and show the distribution process of 18F dynamically. The results of our work can be used in education and related research as well as a tool for the PET operator to design their PET experiment program.

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

PRODIGEN: visualizing the probability landscape of stochastic gene regulatory networks in state and time space.

PubMed

Ma, Chihua; Luciani, Timothy; Terebus, Anna; Liang, Jie; Marai, G Elisabeta

2017-02-15

Visualizing the complex probability landscape of stochastic gene regulatory networks can further biologists' understanding of phenotypic behavior associated with specific genes. We present PRODIGEN (PRObability DIstribution of GEne Networks), a web-based visual analysis tool for the systematic exploration of probability distributions over simulation time and state space in such networks. PRODIGEN was designed in collaboration with bioinformaticians who research stochastic gene networks. The analysis tool combines in a novel way existing, expanded, and new visual encodings to capture the time-varying characteristics of probability distributions: spaghetti plots over one dimensional projection, heatmaps of distributions over 2D projections, enhanced with overlaid time curves to display temporal changes, and novel individual glyphs of state information corresponding to particular peaks. We demonstrate the effectiveness of the tool through two case studies on the computed probabilistic landscape of a gene regulatory network and of a toggle-switch network. Domain expert feedback indicates that our visual approach can help biologists: 1) visualize probabilities of stable states, 2) explore the temporal probability distributions, and 3) discover small peaks in the probability landscape that have potential relation to specific diseases.

TU-A-17A-02: In Memoriam of Ben Galkin: Virtual Tools for Validation of X-Ray Breast Imaging Systems

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

Myers, K; Bakic, P; Abbey, C

2014-06-15

This symposium will explore simulation methods for the preclinical evaluation of novel 3D and 4D x-ray breast imaging systems – the subject of AAPM taskgroup TG234. Given the complex design of modern imaging systems, simulations offer significant advantages over long and costly clinical studies in terms of reproducibility, reduced radiation exposures, a known reference standard, and the capability for studying patient and disease subpopulations through appropriate choice of simulation parameters. Our focus will be on testing the realism of software anthropomorphic phantoms and virtual clinical trials tools developed for the optimization and validation of breast imaging systems. The symposium willmore » review the stateof- the-science, as well as the advantages and limitations of various approaches to testing realism of phantoms and simulated breast images. Approaches based upon the visual assessment of synthetic breast images by expert observers will be contrasted with approaches based upon comparing statistical properties between synthetic and clinical images. The role of observer models in the assessment of realism will be considered. Finally, an industry perspective will be presented, summarizing the role and importance of virtual tools and simulation methods in product development. The challenges and conditions that must be satisfied in order for computational modeling and simulation to play a significantly increased role in the design and evaluation of novel breast imaging systems will be addressed. Learning Objectives: Review the state-of-the science in testing realism of software anthropomorphic phantoms and virtual clinical trials tools; Compare approaches based upon the visual assessment by expert observers vs. the analysis of statistical properties of synthetic images; Discuss the role of observer models in the assessment of realism; Summarize the industry perspective to virtual methods for breast imaging.« less

Distributed Observer Network

NASA Technical Reports Server (NTRS)

Conroy, Michael; Mazzone, Rebecca; Little, William; Elfrey, Priscilla; Mann, David; Mabie, Kevin; Cuddy, Thomas; Loundermon, Mario; Spiker, Stephen; McArthur, Frank;

MO-E-18C-04: Advanced Computer Simulation and Visualization Tools for Enhanced Understanding of Core Medical Physics Concepts

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

Naqvi, S

2014-06-15

Purpose: Most medical physics programs emphasize proficiency in routine clinical calculations and QA. The formulaic aspect of these calculations and prescriptive nature of measurement protocols obviate the need to frequently apply basic physical principles, which, therefore, gradually decay away from memory. E.g. few students appreciate the role of electron transport in photon dose, making it difficult to understand key concepts such as dose buildup, electronic disequilibrium effects and Bragg-Gray theory. These conceptual deficiencies manifest when the physicist encounters a new system, requiring knowledge beyond routine activities. Methods: Two interactive computer simulation tools are developed to facilitate deeper learning of physicalmore » principles. One is a Monte Carlo code written with a strong educational aspect. The code can “label” regions and interactions to highlight specific aspects of the physics, e.g., certain regions can be designated as “starters” or “crossers,” and any interaction type can be turned on and off. Full 3D tracks with specific portions highlighted further enhance the visualization of radiation transport problems. The second code calculates and displays trajectories of a collection electrons under arbitrary space/time dependent Lorentz force using relativistic kinematics. Results: Using the Monte Carlo code, the student can interactively study photon and electron transport through visualization of dose components, particle tracks, and interaction types. The code can, for instance, be used to study kerma-dose relationship, explore electronic disequilibrium near interfaces, or visualize kernels by using interaction forcing. The electromagnetic simulator enables the student to explore accelerating mechanisms and particle optics in devices such as cyclotrons and linacs. Conclusion: The proposed tools are designed to enhance understanding of abstract concepts by highlighting various aspects of the physics. The simulations serve as virtual experiments that give deeper and long lasting understanding of core principles. The student can then make sound judgements in novel situations encountered beyond routine clinical activities.« less

Interactive Tools for Measuring Visual Scanning Performance and Reaction Time

PubMed Central

Seeanner, Julia; Hennessy, Sarah; Manganelli, Joseph; Crisler, Matthew; Rosopa, Patrick; Jenkins, Casey; Anderson, Michael; Drouin, Nathalie; Belle, Leah; Truesdail, Constance; Tanner, Stephanie

2017-01-01

Occupational therapists are constantly searching for engaging, high-technology interactive tasks that provide immediate feedback to evaluate and train clients with visual scanning deficits. This study examined the relationship between two tools: the VISION COACH™ interactive light board and the Functional Object Detection© (FOD) Advanced driving simulator scenario. Fifty-four healthy drivers, ages 21–66 yr, were divided into three age groups. Participants performed braking response and visual target (E) detection tasks of the FOD Advanced driving scenario, followed by two sets of three trials using the VISION COACH Full Field 60 task. Results showed no significant effect of age on FOD Advanced performance but a significant effect of age on VISION COACH performance. Correlations showed that participants’ performance on both braking and E detection tasks were significantly positively correlated with performance on the VISION COACH (.37 < r < .40, p < .01). These tools provide new options for therapists. PMID:28218598

ViSimpl: Multi-View Visual Analysis of Brain Simulation Data

PubMed Central

Galindo, Sergio E.; Toharia, Pablo; Robles, Oscar D.; Pastor, Luis

2016-01-01

After decades of independent morphological and functional brain research, a key point in neuroscience nowadays is to understand the combined relationships between the structure of the brain and its components and their dynamics on multiple scales, ranging from circuits of neurons at micro or mesoscale to brain regions at macroscale. With such a goal in mind, there is a vast amount of research focusing on modeling and simulating activity within neuronal structures, and these simulations generate large and complex datasets which have to be analyzed in order to gain the desired insight. In such context, this paper presents ViSimpl, which integrates a set of visualization and interaction tools that provide a semantic view of brain data with the aim of improving its analysis procedures. ViSimpl provides 3D particle-based rendering that allows visualizing simulation data with their associated spatial and temporal information, enhancing the knowledge extraction process. It also provides abstract representations of the time-varying magnitudes supporting different data aggregation and disaggregation operations and giving also focus and context clues. In addition, ViSimpl tools provide synchronized playback control of the simulation being analyzed. Finally, ViSimpl allows performing selection and filtering operations relying on an application called NeuroScheme. All these views are loosely coupled and can be used independently, but they can also work together as linked views, both in centralized and distributed computing environments, enhancing the data exploration and analysis procedures. PMID:27774062

ViSimpl: Multi-View Visual Analysis of Brain Simulation Data.

PubMed

Galindo, Sergio E; Toharia, Pablo; Robles, Oscar D; Pastor, Luis

2016-01-01

After decades of independent morphological and functional brain research, a key point in neuroscience nowadays is to understand the combined relationships between the structure of the brain and its components and their dynamics on multiple scales, ranging from circuits of neurons at micro or mesoscale to brain regions at macroscale. With such a goal in mind, there is a vast amount of research focusing on modeling and simulating activity within neuronal structures, and these simulations generate large and complex datasets which have to be analyzed in order to gain the desired insight. In such context, this paper presents ViSimpl, which integrates a set of visualization and interaction tools that provide a semantic view of brain data with the aim of improving its analysis procedures. ViSimpl provides 3D particle-based rendering that allows visualizing simulation data with their associated spatial and temporal information, enhancing the knowledge extraction process. It also provides abstract representations of the time-varying magnitudes supporting different data aggregation and disaggregation operations and giving also focus and context clues. In addition, ViSimpl tools provide synchronized playback control of the simulation being analyzed. Finally, ViSimpl allows performing selection and filtering operations relying on an application called NeuroScheme. All these views are loosely coupled and can be used independently, but they can also work together as linked views, both in centralized and distributed computing environments, enhancing the data exploration and analysis procedures.

An Integrated Software Package to Enable Predictive Simulation Capabilities

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

Chen, Yousu; Fitzhenry, Erin B.; Jin, Shuangshuang

The power grid is increasing in complexity due to the deployment of smart grid technologies. Such technologies vastly increase the size and complexity of power grid systems for simulation and modeling. This increasing complexity necessitates not only the use of high-performance-computing (HPC) techniques, but a smooth, well-integrated interplay between HPC applications. This paper presents a new integrated software package that integrates HPC applications and a web-based visualization tool based on a middleware framework. This framework can support the data communication between different applications. Case studies with a large power system demonstrate the predictive capability brought by the integrated software package,more » as well as the better situational awareness provided by the web-based visualization tool in a live mode. Test results validate the effectiveness and usability of the integrated software package.« less

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.

A Lunar Surface Operations Simulator

NASA Technical Reports Server (NTRS)

Nayar, H.; Balaram, J.; Cameron, J.; Jain, A.; Lim, C.; Mukherjee, R.; Peters, S.; Pomerantz, M.; Reder, L.; Shakkottai, P.;

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.

A Bubble Chamber Simulator: A New Tool for the Physics Classroom

ERIC Educational Resources Information Center

Gagnon, Michel

2011-01-01

Mainly used in the 1960s, bubble chambers played a major role in particle physics. Now replaced with modern electronic detectors, we believe they remain an important didactic tool to introduce particle physics as they provide visual, appealing and insightful pictures. Sadly, this rare type of detector is mostly accessible through open-door events…

SAFAS: Unifying Form and Structure through Interactive 3D Simulation

ERIC Educational Resources Information Center

Polys, Nicholas F.; Bacim, Felipe; Setareh, Mehdi; Jones, Brett D.

2015-01-01

There has been a significant gap between the tools used for the design of a building's architectural form and those that evaluate the structural physics of that form. Seeking to bring the perspectives of visual design and structural engineering closer together, we developed and evaluated a design tool for students and practitioners to explore the…

Accomplishments and challenges of surgical simulation.

PubMed

Satava, R M

2001-03-01

For nearly a decade, advanced computer technologies have created extraordinary educational tools using three-dimensional (3D) visualization and virtual reality. Pioneering efforts in surgical simulation with these tools have resulted in a first generation of simulators for surgical technical skills. Accomplishments include simulations with 3D models of anatomy for practice of surgical tasks, initial assessment of student performance in technical skills, and awareness by professional societies of potential in surgical education and certification. However, enormous challenges remain, which include improvement of technical fidelity, standardization of accurate metrics for performance evaluation, integration of simulators into a robust educational curriculum, stringent evaluation of simulators for effectiveness and value added to surgical training, determination of simulation application to certification of surgical technical skills, and a business model to implement and disseminate simulation successfully throughout the medical education community. This review looks at the historical progress of surgical simulators, their accomplishments, and the challenges that remain.

Planning, Implementation and Optimization of Future space Missions using an Immersive Visualization Environement (IVE) Machine

NASA Astrophysics Data System (ADS)

Harris, E.

Planning, Implementation and Optimization of Future Space Missions using an Immersive Visualization Environment (IVE) Machine E. N. Harris, Lockheed Martin Space Systems, Denver, CO and George.W. Morgenthaler, U. of Colorado at Boulder History: A team of 3-D engineering visualization experts at the Lockheed Martin Space Systems Company have developed innovative virtual prototyping simulation solutions for ground processing and real-time visualization of design and planning of aerospace missions over the past 6 years. At the University of Colorado, a team of 3-D visualization experts are developing the science of 3-D visualization and immersive visualization at the newly founded BP Center for Visualization, which began operations in October, 2001. (See IAF/IAA-01-13.2.09, "The Use of 3-D Immersive Visualization Environments (IVEs) to Plan Space Missions," G. A. Dorn and G. W. Morgenthaler.) Progressing from Today's 3-D Engineering Simulations to Tomorrow's 3-D IVE Mission Planning, Simulation and Optimization Techniques: 3-D (IVEs) and visualization simulation tools can be combined for efficient planning and design engineering of future aerospace exploration and commercial missions. This technology is currently being developed and will be demonstrated by Lockheed Martin in the (IVE) at the BP Center using virtual simulation for clearance checks, collision detection, ergonomics and reach-ability analyses to develop fabrication and processing flows for spacecraft and launch vehicle ground support operations and to optimize mission architecture and vehicle design subject to realistic constraints. Demonstrations: Immediate aerospace applications to be demonstrated include developing streamlined processing flows for Reusable Space Transportation Systems and Atlas Launch Vehicle operations and Mars Polar Lander visual work instructions. Long-range goals include future international human and robotic space exploration missions such as the development of a Mars Reconnaissance Orbiter and Lunar Base construction scenarios. Innovative solutions utilizing Immersive Visualization provide the key to streamlining the mission planning and optimizing engineering design phases of future aerospace missions.

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.

Analytical evaluation of two motion washout techniques

NASA Technical Reports Server (NTRS)

Young, L. R.

1977-01-01

Practical tools were developed which extend the state of the art of moving base flight simulation for research and training purposes. The use of visual and vestibular cues to minimize the actual motion of the simulator itself was a primary consideration. The investigation consisted of optimum programming of motion cues based on a physiological model of the vestibular system to yield 'ideal washout logic' for any given simulator constraints.

6 DOF Nonlinear AUV Simulation Toolbox

DTIC Science & Technology

1997-01-01

is to supply a flexible 3D -simulation platform for motion visualization, in-lab debugging and testing of mission-specific strategies as well as those...Explorer are modular designed [Smith] in order to cut time and cost for vehicle recontlguration. A flexible 3D -simulation platform is desired to... 3D models. Current implemented modules include a nonlinear dynamic model for the OEX, shared memory and semaphore manager tools, shared memory monitor

Consistent design schematics for biological systems: standardization of representation in biological engineering

PubMed Central

Matsuoka, Yukiko; Ghosh, Samik; Kitano, Hiroaki

2009-01-01

The discovery by design paradigm driving research in synthetic biology entails the engineering of de novo biological constructs with well-characterized input–output behaviours and interfaces. The construction of biological circuits requires iterative phases of design, simulation and assembly, leading to the fabrication of a biological device. In order to represent engineered models in a consistent visual format and further simulating them in silico, standardization of representation and model formalism is imperative. In this article, we review different efforts for standardization, particularly standards for graphical visualization and simulation/annotation schemata adopted in systems biology. We identify the importance of integrating the different standardization efforts and provide insights into potential avenues for developing a common framework for model visualization, simulation and sharing across various tools. We envision that such a synergistic approach would lead to the development of global, standardized schemata in biology, empowering deeper understanding of molecular mechanisms as well as engineering of novel biological systems. PMID:19493898

ChemVoyage: A Web-Based, Simulated Learning Environment with Scaffolding and Linking Visualization to Conceptualization

ERIC Educational Resources Information Center

McRae, Christopher; Karuso, Peter; Liu, Fei

2012-01-01

The Web is now a standard tool for information access and dissemination in higher education. The prospect of Web-based, simulated learning platforms and technologies, however, remains underexplored. We have developed a Web-based tutorial program (ChemVoyage) for a third-year organic chemistry class on the topic of pericyclic reactions to…

Pedagogy-Based-Technology and Chemistry Students' Performance in Higher Institutions: A Case of Debre Berhan University

ERIC Educational Resources Information Center

Demissie, Tesfaye; Ochonogor, Chukunoye E.; Engida, Temechegn

2011-01-01

Many students have difficulty in learning abstract and complex lessons of chemistry. This study investigated how students develop their understandings of abstract and complex lessons in chemistry with the aid of visualizing tools: animation, simulation and video that allow them to build clear concepts. Animation, simulation and video enable…

Technology transfer of operator-in-the-loop simulation

NASA Technical Reports Server (NTRS)

Yae, K. H.; Lin, H. C.; Lin, T. C.; Frisch, H. P.

1994-01-01

The technology developed for operator-in-the-loop simulation in space teleoperation has been applied to Caterpillar's backhoe, wheel loader, and off-highway truck. On an SGI workstation, the simulation integrates computer modeling of kinematics and dynamics, real-time computational and visualization, and an interface with the operator through the operator's console. The console is interfaced with the workstation through an IBM-PC in which the operator's commands were digitized and sent through an RS-232 serial port. The simulation gave visual feedback adequate for the operator in the loop, with the camera's field of vision projected on a large screen in multiple view windows. The view control can emulate either stationary or moving cameras. This simulator created an innovative engineering design environment by integrating computer software and hardware with the human operator's interactions. The backhoe simulation has been adopted by Caterpillar in building a virtual reality tool for backhoe design.

compuGUT: An in silico platform for simulating intestinal fermentation

NASA Astrophysics Data System (ADS)

Moorthy, Arun S.; Eberl, Hermann J.

The microbiota inhabiting the colon and its effect on health is a topic of significant interest. In this paper, we describe the compuGUT - a simulation tool developed to assist in exploring interactions between intestinal microbiota and their environment. The primary numerical machinery is implemented in C, and the accessory scripts for loading and visualization are prepared in bash (LINUX) and R. SUNDIALS libraries are employed for numerical integration, and googleVis API for interactive visualization. Supplementary material includes a concise description of the underlying mathematical model, and detailed characterization of numerical errors and computing times associated with implementation parameters.

Conversion of NIMROD simulation results for graphical analysis using VisIt

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

Romero-Talamas, C A

Software routines developed to prepare NIMROD [C. R. Sovinec et al., J. Comp. Phys. 195, 355 (2004)] results for three-dimensional visualization from simulations of the Sustained Spheromak Physics Experiment (SSPX ) [E. B. Hooper et al., Nucl. Fusion 39, 863 (1999)] are presented here. The visualization is done by first converting the NIMROD output to a format known as legacy VTK and then loading it to VisIt, a graphical analysis tool that includes three-dimensional rendering and various mathematical operations for large data sets. Sample images obtained from the processing of NIMROD data with VisIt are included.

The LatHyS database for planetary plasma environment investigations: Overview and a case study of data/model comparisons

NASA Astrophysics Data System (ADS)

Modolo, R.; Hess, S.; Génot, V.; Leclercq, L.; Leblanc, F.; Chaufray, J.-Y.; Weill, P.; Gangloff, M.; Fedorov, A.; Budnik, E.; Bouchemit, M.; Steckiewicz, M.; André, N.; Beigbeder, L.; Popescu, D.; Toniutti, J.-P.; Al-Ubaidi, T.; Khodachenko, M.; Brain, D.; Curry, S.; Jakosky, B.; Holmström, M.

2018-01-01

We present the Latmos Hybrid Simulation (LatHyS) database, which is dedicated to the investigations of planetary plasma environment. Simulation results of several planetary objects (Mars, Mercury, Ganymede) are available in an online catalogue. The full description of the simulations and their results is compliant with a data model developped in the framework of the FP7 IMPEx project. The catalogue is interfaced with VO-visualization tools such AMDA, 3DView, TOPCAT, CLweb or the IMPEx portal. Web services ensure the possibilities of accessing and extracting simulated quantities/data. We illustrate the interoperability between the simulation database and VO-tools using a detailed science case that focuses on a three-dimensional representation of the solar wind interaction with the Martian upper atmosphere, combining MAVEN and Mars Express observations and simulation results.

The force pyramid: a spatial analysis of force application during virtual reality brain tumor resection.

PubMed

Azarnoush, Hamed; Siar, Samaneh; Sawaya, Robin; Zhrani, Gmaan Al; Winkler-Schwartz, Alexander; Alotaibi, Fahad Eid; Bugdadi, Abdulgadir; Bajunaid, Khalid; Marwa, Ibrahim; Sabbagh, Abdulrahman Jafar; Del Maestro, Rolando F

2017-07-01

OBJECTIVE Virtual reality simulators allow development of novel methods to analyze neurosurgical performance. The concept of a force pyramid is introduced as a Tier 3 metric with the ability to provide visual and spatial analysis of 3D force application by any instrument used during simulated tumor resection. This study was designed to answer 3 questions: 1) Do study groups have distinct force pyramids? 2) Do handedness and ergonomics influence force pyramid structure? 3) Are force pyramids dependent on the visual and haptic characteristics of simulated tumors? METHODS Using a virtual reality simulator, NeuroVR (formerly NeuroTouch), ultrasonic aspirator force application was continually assessed during resection of simulated brain tumors by neurosurgeons, residents, and medical students. The participants performed simulated resections of 18 simulated brain tumors with different visual and haptic characteristics. The raw data, namely, coordinates of the instrument tip as well as contact force values, were collected by the simulator. To provide a visual and qualitative spatial analysis of forces, the authors created a graph, called a force pyramid, representing force sum along the z-coordinate for different xy coordinates of the tool tip. RESULTS Sixteen neurosurgeons, 15 residents, and 84 medical students participated in the study. Neurosurgeon, resident and medical student groups displayed easily distinguishable 3D "force pyramid fingerprints." Neurosurgeons had the lowest force pyramids, indicating application of the lowest forces, followed by resident and medical student groups. Handedness, ergonomics, and visual and haptic tumor characteristics resulted in distinct well-defined 3D force pyramid patterns. CONCLUSIONS Force pyramid fingerprints provide 3D spatial assessment displays of instrument force application during simulated tumor resection. Neurosurgeon force utilization and ergonomic data form a basis for understanding and modulating resident force application and improving patient safety during tumor resection.

Astroinformatics in the Age of LSST: Analyzing the Summer 2012 Data Release

NASA Astrophysics Data System (ADS)

Borne, Kirk D.; De Lee, N. M.; Stassun, K.; Paegert, M.; Cargile, P.; Burger, D.; Bloom, J. S.; Richards, J.

2013-01-01

The Large Synoptic Survey Telescope (LSST) will image the visible southern sky every three nights. This multi-band, multi-epoch survey will produce a torrent of data, which traditional methods of object-by-object data analysis will not be able to accommodate. Thus the need for new astroinformatics tools to visualize, simulate, mine, and analyze this quantity of data. The Berkeley Center for Time-Domain Informatics (CTDI) is building the informatics infrastructure for generic light curve classification, including the innovation of new algorithms for feature generation and machine learning. The CTDI portal (http://dotastro.org) contains one of the largest collections of public light curves, with visualization and exploration tools. The group has also published the first calibrated probabilistic classification catalog of 50k variable stars along with a data exploration portal called http://bigmacc.info. Twice a year, the LSST collaboration releases simulated LSST data, in order to aid software development. This poster also showcases a suite of new tools from the Vanderbilt Initiative in Data-instensive Astrophysics (VIDA), designed to take advantage of these large data sets. VIDA's Filtergraph interactive web tool allows one to instantly create an interactive data portal for fast, real-time visualization of large data sets. Filtergraph enables quick selection of interesting objects by easily filtering on many different columns, 2-D and 3-D representations, and on-the-fly arithmetic calculations on the data. It also makes sharing the data and the tool with collaborators very easy. The EB/RRL Factory is a neural-network based variable star classifier, which is designed to quickly identify variable stars in a variety of classes from LSST light curve data (currently tuned to Eclipsing Binaries and RR Lyrae stars), and to provide likelihood-based orbital elements or stellar parameters as appropriate. Finally the LCsimulator software allows one to create simulated light curves of multiple types of variable stars based on an LSST cadence.

Simulation and evaluation of the Sh-2F helicopter in a shipboard environment using the interchangeable cab system

NASA Technical Reports Server (NTRS)

Paulk, C. H., Jr.; Astill, D. L.; Donley, S. T.

1983-01-01

The operation of the SH-2F helicopter from the decks of small ships in adverse weather was simulated using a large amplitude vertical motion simulator, a wide angle computer generated imagery visual system, and an interchangeable cab (ICAB). The simulation facility, the mathematical programs, and the validation method used to ensure simulation fidelity are described. The results show the simulator to be a useful tool in simulating the ship-landing problem. Characteristics of the ICAB system and ways in which the simulation can be improved are presented.

Fluid Simulation in the Movies: Navier and Stokes Must Be Circulating in Their Graves

NASA Astrophysics Data System (ADS)

Tessendorf, Jerry

2010-11-01

Fluid simulations based on the Incompressible Navier-Stokes equations are commonplace computer graphics tools in the visual effects industry. These simulations mostly come from custom C++ code written by the visual effects companies. Their significant impact in films was recognized in 2008 with Academy Awards to four visual effects companies for their technical achievement. However artists are not fluid dynamicists, and fluid dynamics simulations are expensive to use in a deadline-driven production environment. As a result, the simulation algorithms are modified to limit the computational resources, adapt them to production workflow, and to respect the client's vision of the film plot. Eulerian solvers on fixed rectangular grids use a mix of momentum solvers, including Semi-Lagrangian, FLIP, and QUICK. Incompressibility is enforced with FFT, Conjugate Gradient, and Multigrid methods. For liquids, a levelset field tracks the free surface. Smooth Particle Hydrodynamics is also used, and is part of a hybrid Eulerian-SPH liquid simulator. Artists use all of them in a mix and match fashion to control the appearance of the simulation. Specially designed forces and boundary conditions control the flow. The simulation can be an input to artistically driven procedural particle simulations that enhance the flow with more detail and drama. Post-simulation processing increases the visual detail beyond the grid resolution. Ultimately, iterative simulation methods that fit naturally in the production workflow are extremely desirable but not yet successful. Results from some efforts for iterative methods are shown, and other approaches motivated by the history of production are proposed.

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 high-quality high-fidelity visualization of the September 11 attack on the World Trade Center.

PubMed

Rosen, Paul; Popescu, Voicu; Hoffmann, Christoph; Irfanoglu, Ayhan

2008-01-01

In this application paper, we describe the efforts of a multidisciplinary team towards producing a visualization of the September 11 Attack on the North Tower of New York's World Trade Center. The visualization was designed to meet two requirements. First, the visualization had to depict the impact with high fidelity, by closely following the laws of physics. Second, the visualization had to be eloquent to a nonexpert user. This was achieved by first designing and computing a finite-element analysis (FEA) simulation of the impact between the aircraft and the top 20 stories of the building, and then by visualizing the FEA results with a state-of-the-art commercial animation system. The visualization was enabled by an automatic translator that converts the simulation data into an animation system 3D scene. We built upon a previously developed translator. The translator was substantially extended to enable and control visualization of fire and of disintegrating elements, to better scale with the number of nodes and number of states, to handle beam elements with complex profiles, and to handle smoothed particle hydrodynamics liquid representation. The resulting translator is a powerful automatic and scalable tool for high-quality visualization of FEA results.

Simulation Assessment Validation Environment (SAVE). Software User’s Manual

DTIC Science & Technology

2000-09-01

requirements and decisions are made. The integration is leveraging work from other DoD organizations so that high -end results are attainable much faster than...planning through the modeling and simulation data capture and visualization process. The planners can complete the manufacturing process plan with a high ...technologies. This tool is also used to perform “ high level” factory process simulation prior to full CAD model development and help define feasible

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.

Simulation System for Training in Laparoscopic Surgery

NASA Technical Reports Server (NTRS)

Basdogan, Cagatay; Ho, Chih-Hao

2003-01-01

A computer-based simulation system creates a visual and haptic virtual environment for training a medical practitioner in laparoscopic surgery. Heretofore, it has been common practice to perform training in partial laparoscopic surgical procedures by use of a laparoscopic training box that encloses a pair of laparoscopic tools, objects to be manipulated by the tools, and an endoscopic video camera. However, the surgical procedures simulated by use of a training box are usually poor imitations of the actual ones. The present computer-based system improves training by presenting a more realistic simulated environment to the trainee. The system includes a computer monitor that displays a real-time image of the affected interior region of the patient, showing laparoscopic instruments interacting with organs and tissues, as would be viewed by use of an endoscopic video camera and displayed to a surgeon during a laparoscopic operation. The system also includes laparoscopic tools that the trainee manipulates while observing the image on the computer monitor (see figure). The instrumentation on the tools consists of (1) position and orientation sensors that provide input data for the simulation and (2) actuators that provide force feedback to simulate the contact forces between the tools and tissues. The simulation software includes components that model the geometries of surgical tools, components that model the geometries and physical behaviors of soft tissues, and components that detect collisions between them. Using the measured positions and orientations of the tools, the software detects whether they are in contact with tissues. In the event of contact, the deformations of the tissues and contact forces are computed by use of the geometric and physical models. The image on the computer screen shows tissues deformed accordingly, while the actuators apply the corresponding forces to the distal ends of the tools. For the purpose of demonstration, the system has been set up to simulate the insertion of a flexible catheter in a bile duct. [As thus configured, the system can also be used to simulate other endoscopic procedures (e.g., bronchoscopy and colonoscopy) that include the insertion of flexible tubes into flexible ducts.] A hybrid approach has been followed in developing the software for real-time simulation of the visual and haptic interactions (1) between forceps and the catheter, (2) between the forceps and the duct, and (3) between the catheter and the duct. The deformations of the duct are simulated by finite-element and modalanalysis procedures, using only the most significant vibration modes of the duct for computing deformations and interaction forces. The catheter is modeled as a set of virtual particles uniformly distributed along the center line of the catheter and connected to each other via linear and torsional springs and damping elements. The interactions between the forceps and the duct as well as the catheter are simulated by use of a ray-based haptic-interaction- simulating technique in which the forceps are modeled as connected line segments.

VISUAL-SEVEIF, a tool for integrating fire behavior simulation and economic evaluation of the impact of Wildfires

Treesearch

Francisco Rodríguez y Silva; Juan Ramón Molina Martínez; Miguel Ángel Herrera Machuca; Jesús Mª Rodríguez Leal

2013-01-01

Progress made in recent years in fire science, particularly as applied to forest fire protection, coupled with the increased power offered by mathematical processors integrated into computers, has led to important developments in the field of dynamic and static simulation of forest fires. Furthermore, and similarly, econometric models applied to economic...

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.

A Lyapunov Function Based Remedial Action Screening Tool Using Real-Time Data

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

Mitra, Joydeep; Ben-Idris, Mohammed; Faruque, Omar

This report summarizes the outcome of a research project that comprised the development of a Lyapunov function based remedial action screening tool using real-time data (L-RAS). The L-RAS is an advanced computational tool that is intended to assist system operators in making real-time redispatch decisions to preserve power grid stability. The tool relies on screening contingencies using a homotopy method based on Lyapunov functions to avoid, to the extent possible, the use of time domain simulations. This enables transient stability evaluation at real-time speed without the use of massively parallel computational resources. The project combined the following components. 1. Developmentmore » of a methodology for contingency screening using a homotopy method based on Lyapunov functions and real-time data. 2. Development of a methodology for recommending remedial actions based on the screening results. 3. Development of a visualization and operator interaction interface. 4. Testing of screening tool, validation of control actions, and demonstration of project outcomes on a representative real system simulated on a Real-Time Digital Simulator (RTDS) cluster. The project was led by Michigan State University (MSU), where the theoretical models including homotopy-based screening, trajectory correction using real-time data, and remedial action were developed and implemented in the form of research-grade software. Los Alamos National Laboratory (LANL) contributed to the development of energy margin sensitivity dynamics, which constituted a part of the remedial action portfolio. Florida State University (FSU) and Southern California Edison (SCE) developed a model of the SCE system that was implemented on FSU's RTDS cluster to simulate real-time data that was streamed over the internet to MSU where the L-RAS tool was executed and remedial actions were communicated back to FSU to execute stabilizing controls on the simulated system. LCG Consulting developed the visualization and operator interaction interface, based on specifications provided by MSU. The project was performed from October 2012 to December 2016, at the end of which the L-RAS tool, as described above, was completed and demonstrated. The project resulted in the following innovations and contributions: (a) the L-RAS software prototype, tested on a simulated system, vetted by utility personnel, and potentially ready for wider testing and commercialization; (b) an RTDS-based test bed that can be used for future research in the field; (c) a suite of breakthrough theoretical contributions to the field of power system stability and control; and (d) a new tool for visualization of power system stability margins. While detailed descriptions of the development and implementation of the various project components have been provided in the quarterly reports, this final report provides an overview of the complete project, and is demonstrated using public domain test systems commonly used in the literature. The SCE system, and demonstrations thereon, are not included in this report due to Critical Energy Infrastructure Information (CEII) restrictions.« less

Review: visual analytics of climate networks

NASA Astrophysics Data System (ADS)

Nocke, T.; Buschmann, S.; Donges, J. F.; Marwan, N.; Schulz, H.-J.; Tominski, C.

2015-09-01

Network analysis has become an important approach in studying complex spatiotemporal behaviour within geophysical observation and simulation data. This new field produces increasing numbers of large geo-referenced networks to be analysed. Particular focus lies currently on the network analysis of the complex statistical interrelationship structure within climatological fields. The standard procedure for such network analyses is the extraction of network measures in combination with static standard visualisation methods. Existing interactive visualisation methods and tools for geo-referenced network exploration are often either not known to the analyst or their potential is not fully exploited. To fill this gap, we illustrate how interactive visual analytics methods in combination with geovisualisation can be tailored for visual climate network investigation. Therefore, the paper provides a problem analysis relating the multiple visualisation challenges to a survey undertaken with network analysts from the research fields of climate and complex systems science. Then, as an overview for the interested practitioner, we review the state-of-the-art in climate network visualisation and provide an overview of existing tools. As a further contribution, we introduce the visual network analytics tools CGV and GTX, providing tailored solutions for climate network analysis, including alternative geographic projections, edge bundling, and 3-D network support. Using these tools, the paper illustrates the application potentials of visual analytics for climate networks based on several use cases including examples from global, regional, and multi-layered climate networks.

Review: visual analytics of climate networks

NASA Astrophysics Data System (ADS)

Nocke, T.; Buschmann, S.; Donges, J. F.; Marwan, N.; Schulz, H.-J.; Tominski, C.

2015-04-01

Network analysis has become an important approach in studying complex spatiotemporal behaviour within geophysical observation and simulation data. This new field produces increasing amounts of large geo-referenced networks to be analysed. Particular focus lies currently on the network analysis of the complex statistical interrelationship structure within climatological fields. The standard procedure for such network analyses is the extraction of network measures in combination with static standard visualisation methods. Existing interactive visualisation methods and tools for geo-referenced network exploration are often either not known to the analyst or their potential is not fully exploited. To fill this gap, we illustrate how interactive visual analytics methods in combination with geovisualisation can be tailored for visual climate network investigation. Therefore, the paper provides a problem analysis, relating the multiple visualisation challenges with a survey undertaken with network analysts from the research fields of climate and complex systems science. Then, as an overview for the interested practitioner, we review the state-of-the-art in climate network visualisation and provide an overview of existing tools. As a further contribution, we introduce the visual network analytics tools CGV and GTX, providing tailored solutions for climate network analysis, including alternative geographic projections, edge bundling, and 3-D network support. Using these tools, the paper illustrates the application potentials of visual analytics for climate networks based on several use cases including examples from global, regional, and multi-layered climate networks.

Ethylene glycol revisited: Molecular dynamics simulations and visualization of the liquid and its hydrogen-bond network☆

PubMed Central

Kaiser, Alexander; Ismailova, Oksana; Koskela, Antti; Huber, Stefan E.; Ritter, Marcel; Cosenza, Biagio; Benger, Werner; Nazmutdinov, Renat; Probst, Michael

2014-01-01

Molecular dynamics simulations of liquid ethylene glycol described by the OPLS-AA force field were performed to gain insight into its hydrogen-bond structure. We use the population correlation function as a statistical measure for the hydrogen-bond lifetime. In an attempt to understand the complicated hydrogen-bonding, we developed new molecular visualization tools within the Vish Visualization shell and used it to visualize the life of each individual hydrogen-bond. With this tool hydrogen-bond formation and breaking as well as clustering and chain formation in hydrogen-bonded liquids can be observed directly. Liquid ethylene glycol at room temperature does not show significant clustering or chain building. The hydrogen-bonds break often due to the rotational and vibrational motions of the molecules leading to an H-bond half-life time of approximately 1.5 ps. However, most of the H-bonds are reformed again so that after 50 ps only 40% of these H-bonds are irreversibly broken due to diffusional motion. This hydrogen-bond half-life time due to diffusional motion is 80.3 ps. The work was preceded by a careful check of various OPLS-based force fields used in the literature. It was found that they lead to quite different angular and H-bond distributions. PMID:24748697

The design of real time infrared image generation software based on Creator and Vega

NASA Astrophysics Data System (ADS)

Wang, Rui-feng; Wu, Wei-dong; Huo, Jun-xiu

2013-09-01

Considering the requirement of high reality and real-time quality dynamic infrared image of an infrared image simulation, a method to design real-time infrared image simulation application on the platform of VC++ is proposed. This is based on visual simulation software Creator and Vega. The functions of Creator are introduced simply, and the main features of Vega developing environment are analyzed. The methods of infrared modeling and background are offered, the designing flow chart of the developing process of IR image real-time generation software and the functions of TMM Tool and MAT Tool and sensor module are explained, at the same time, the real-time of software is designed.

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.

PROTERAN: animated terrain evolution for visual analysis of patterns in protein folding trajectory.

PubMed

Zhou, Ruhong; Parida, Laxmi; Kapila, Kush; Mudur, Sudhir

2007-01-01

The mechanism of protein folding remains largely a mystery in molecular biology, despite the enormous effort from many groups in the past decades. Currently, the protein folding mechanism is often characterized by calculating the free energy landscape versus various reaction coordinates such as the fraction of native contacts, the radius of gyration and so on. In this paper, we present an integrated approach towards understanding the folding process via visual analysis of patterns of these reaction coordinates. The three disparate processes (1) protein folding simulation, (2) pattern elicitation and (3) visualization of patterns, work in tandem. Thus as the protein folds, the changing landscape in the pattern space can be viewed via the visualization tool, PROTERAN, a program we developed for this purpose. We first present an incremental (on-line) trie-based pattern discovery algorithm to elicit the patterns and then describe the terrain metaphor based visualization tool. Using two example small proteins, a beta-hairpin and a designed protein Trp-cage, we next demonstrate that this combined pattern discovery and visualization approach extracts crucial information about protein folding intermediates and mechanism.

FAST: A multi-processed environment for visualization of computational fluid dynamics

NASA Technical Reports Server (NTRS)

Bancroft, Gordon V.; Merritt, Fergus J.; Plessel, Todd C.; Kelaita, Paul G.; Mccabe, R. Kevin

1991-01-01

Three-dimensional, unsteady, multi-zoned fluid dynamics simulations over full scale aircraft are typical of the problems being investigated at NASA Ames' Numerical Aerodynamic Simulation (NAS) facility on CRAY2 and CRAY-YMP supercomputers. With multiple processor workstations available in the 10-30 Mflop range, we feel that these new developments in scientific computing warrant a new approach to the design and implementation of analysis tools. These larger, more complex problems create a need for new visualization techniques not possible with the existing software or systems available as of this writing. The visualization techniques will change as the supercomputing environment, and hence the scientific methods employed, evolves even further. The Flow Analysis Software Toolkit (FAST), an implementation of a software system for fluid mechanics analysis, is discussed.

Creating executable architectures using Visual Simulation Objects (VSO)

NASA Astrophysics Data System (ADS)

Woodring, John W.; Comiskey, John B.; Petrov, Orlin M.; Woodring, Brian L.

2005-05-01

Investigations have been performed to identify a methodology for creating executable models of architectures and simulations of architecture that lead to an understanding of their dynamic properties. Colored Petri Nets (CPNs) are used to describe architecture because of their strong mathematical foundations, the existence of techniques for their verification and graph theory"s well-established history of success in modern science. CPNs have been extended to interoperate with legacy simulations via a High Level Architecture (HLA) compliant interface. It has also been demonstrated that an architecture created as a CPN can be integrated with Department of Defense Architecture Framework products to ensure consistency between static and dynamic descriptions. A computer-aided tool, Visual Simulation Objects (VSO), which aids analysts in specifying, composing and executing architectures, has been developed to verify the methodology and as a prototype commercial product.

The Development of Dispatcher Training Simulator in a Thermal Energy Generation System

NASA Astrophysics Data System (ADS)

Hakim, D. L.; Abdullah, A. G.; Mulyadi, Y.; Hasan, B.

2018-01-01

A dispatcher training simulator (DTS) is a real-time Human Machine Interface (HMI)-based control tool that is able to visualize industrial control system processes. The present study was aimed at developing a simulator tool for boilers in a thermal power station. The DTS prototype was designed using technical data of thermal power station boilers in Indonesia. It was then designed and implemented in Wonderware Intouch 10. The resulting simulator came with component drawing, animation, control display, alarm system, real-time trend, historical trend. This application used 26 tagnames and was equipped with a security system. The test showed that the principles of real-time control worked well. It is expected that this research could significantly contribute to the development of thermal power station, particularly in terms of its application as a training simulator for beginning dispatchers.

A web portal for hydrodynamical, cosmological simulations

NASA Astrophysics Data System (ADS)

Ragagnin, A.; Dolag, K.; Biffi, V.; Cadolle Bel, M.; Hammer, N. J.; Krukau, A.; Petkova, M.; Steinborn, D.

2017-07-01

This article describes a data centre hosting a web portal for accessing and sharing the output of large, cosmological, hydro-dynamical simulations with a broad scientific community. It also allows users to receive related scientific data products by directly processing the raw simulation data on a remote computing cluster. The data centre has a multi-layer structure: a web portal, a job control layer, a computing cluster and a HPC storage system. The outer layer enables users to choose an object from the simulations. Objects can be selected by visually inspecting 2D maps of the simulation data, by performing highly compounded and elaborated queries or graphically by plotting arbitrary combinations of properties. The user can run analysis tools on a chosen object. These services allow users to run analysis tools on the raw simulation data. The job control layer is responsible for handling and performing the analysis jobs, which are executed on a computing cluster. The innermost layer is formed by a HPC storage system which hosts the large, raw simulation data. The following services are available for the users: (I) CLUSTERINSPECT visualizes properties of member galaxies of a selected galaxy cluster; (II) SIMCUT returns the raw data of a sub-volume around a selected object from a simulation, containing all the original, hydro-dynamical quantities; (III) SMAC creates idealized 2D maps of various, physical quantities and observables of a selected object; (IV) PHOX generates virtual X-ray observations with specifications of various current and upcoming instruments.

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.

Interactive Tools for Measuring Visual Scanning Performance and Reaction Time.

PubMed

Brooks, Johnell; Seeanner, Julia; Hennessy, Sarah; Manganelli, Joseph; Crisler, Matthew; Rosopa, Patrick; Jenkins, Casey; Anderson, Michael; Drouin, Nathalie; Belle, Leah; Truesdail, Constance; Tanner, Stephanie

Occupational therapists are constantly searching for engaging, high-technology interactive tasks that provide immediate feedback to evaluate and train clients with visual scanning deficits. This study examined the relationship between two tools: the VISION COACH™ interactive light board and the Functional Object Detection © (FOD) Advanced driving simulator scenario. Fifty-four healthy drivers, ages 21-66 yr, were divided into three age groups. Participants performed braking response and visual target (E) detection tasks of the FOD Advanced driving scenario, followed by two sets of three trials using the VISION COACH Full Field 60 task. Results showed no significant effect of age on FOD Advanced performance but a significant effect of age on VISION COACH performance. Correlations showed that participants' performance on both braking and E detection tasks were significantly positively correlated with performance on the VISION COACH (.37 < r < .40, p < .01). These tools provide new options for therapists. Copyright © 2017 by the American Occupational Therapy Association, Inc.

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.

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.

Practises to identify and prevent adverse aircraft-and-rotorcraft-pilot couplings-A ground simulator perspective

NASA Astrophysics Data System (ADS)

Pavel, Marilena D.; Jump, Michael; Masarati, Pierangelo; Zaichik, Larisa; Dang-Vu, Binh; Smaili, Hafid; Quaranta, Giuseppe; Stroosma, Olaf; Yilmaz, Deniz; Johnes, Michael; Gennaretti, Massimmo; Ionita, Achim

2015-08-01

The aviation community relies heavily on flight simulators as a fundamental tool for research, pilot training and development of any new aircraft design. The goal of the present paper is to provide a review on how effective ground simulation is as an assessment tool for unmasking adverse Aircraft-and-Rotorcraft Pilot Couplings (APC/RPC). Although it is generally believed that simulators are not reliable in revealing the existence of A/RPC tendencies, the paper demonstrates that a proper selection of high-gain tasks combined with appropriate motion and visual cueing can reveal negative features of a particular aircraft that may lead to A/RPC. The paper discusses new methods for real-time A/RPC detection that can be used as a tool for unmasking adverse A/RPC. Although flight simulators will not achieve the level of reality of in-flight testing, exposing A/RPC tendencies in the simulator may be the only convenient safe place to evaluate the wide range of conditions that could produce hazardous A/RPC events.

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.

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...

Overcoming the Critical Shortage of STEM - Prepared Secondary Students Through Modeling and Simulation

NASA Technical Reports Server (NTRS)

Spencer, Thomas; Berry, Brandon

2012-01-01

In developing understanding of technological systems - modeling and simulation tools aid significantly in the learning and visualization processes. In design courses we sketch , extrude, shape, refine and animate with virtual tools in 3D. Final designs are built using a 3D printer. Aspiring architects create spaces with realistic materials and lighting schemes rendered on model surfaces to create breathtaking walk-throughs of virtual spaces. Digital Electronics students design systems that address real-world needs. Designs are simulated in virtual circuits to provide proof of concept before physical construction. This vastly increases students' ability to design and build complex systems. We find students using modeling and simulation in the learning process, assimilate information at a much faster pace and engage more deeply in learning. As Pre-Engineering educators within the Career and Technical Education program at our school division's Technology Academy our task is to help learners in their quest to develop deep understanding of complex technological systems in a variety of engineering disciplines. Today's young learners have vast opportunities to learn with tools that many of us only dreamed about a decade or so ago when we were engaged in engineering and other technical studies. Today's learner paints with a virtual brush - scenes that can aid significantly in the learning and visualization processes. Modeling and simulation systems have become the new standard tool set in the technical classroom [1-5]. Modeling and simulation systems are now applied as feedback loops in the learning environment. Much of the study of behavior change through the use of feedback loops can be attributed to Stanford Psychologist Alfred Bandura. "Drawing on several education experiments involving children, Bandura observed that giving individuals a clear goal and a means to evaluate their progress toward that goal greatly increased the likelihood that they would achieve it."

Evaluating role of interactive visualization tool in improving students' conceptual understanding of chemical equilibrium

NASA Astrophysics Data System (ADS)

Sampath Kumar, Bharath

The purpose of this study is to examine the role of partnering visualization tool such as simulation towards development of student's concrete conceptual understanding of chemical equilibrium. Students find chemistry concepts abstract, especially at the microscopic level. Chemical equilibrium is one such topic. While research studies have explored effectiveness of low tech instructional strategies such as analogies, jigsaw, cooperative learning, and using modeling blocks, fewer studies have explored the use of visualization tool such as simulations in the context of dynamic chemical equilibrium. Research studies have identified key reasons behind misconceptions such as lack of systematic understanding of foundational chemistry concepts, failure to recognize the system is dynamic, solving numerical problems on chemical equilibrium in an algorithmic fashion, erroneous application Le Chatelier's principle (LCP) etc. Kress et al. (2001) suggested that external representation in the form of visualization is more than a tool for learning, because it enables learners to make meanings or express their ideas which cannot be readily done so through a verbal representation alone. Mixed method study design was used towards data collection. The qualitative portion of the study is aimed towards understanding the change in student's mental model before and after the intervention. A quantitative instrument was developed based on common areas of misconceptions identified by research studies. A pilot study was conducted prior to the actual study to obtain feedback from students on the quantitative instrument and the simulation. Participants for the pilot study were sampled from a single general chemistry class. Following the pilot study, the research study was conducted with a total of 27 students (N=15 in experimental group and N=12 in control group). Prior to participating in the study, students have completed their midterm test on the topic of chemical equilibrium. Qualitative interviews pre and post revealed students' mental model or thought process towards chemical equilibrium. Simulations used in the study were developed using the SCRATCH software platform. In order to test the effect of visualization tool on students' conceptual understanding of chemical equilibrium, an ANCOVA analysis was conducted. Results from a one-factor ANCOVA showed posttest scores were significantly higher for the experimental group (Mpostadj. = 7.27 SDpost = 1.387) relative to the control group (Mpostadj. = 2.67, SDpost = 1.371) after adjusting for pretest scores, F (1,24) = 71.82, MSE = 1.497, p = 0.03, eta 2p = 0.75, d = 3.33. Cohen's d was converted to an attenuated effect size d* using the procedure outlined in Thompson (2006). The adjusted (for pretest scores) group mean difference estimate without measure error correction for the posttest scores and the pretest scores was 4.2 with a Cohen's d = 3.04. An alternate approach reported in Cho and Preacher (2015) was used to determine effect size. The adjusted (for pretest scores) group mean difference estimate with measurement error correction only for the posttest scores (but not with measurement error correction for the pretest scores) was 4.99 with a Cohen's d = 3.61. Finally, the adjusted (for pretest scores) group mean difference estimate with measurement error correction for both pretest and posttest scores was 4.23 with a Cohen's d = 3.07. From a quantitative perspective, these effect size indicate a strong relationship between the experimental intervention provided and students' conceptual understanding of chemical equilibrium concepts. That is, those students who received the experimental intervention had exceptionally higher. KEYWORDS: Chemical Equilibrium, Visualization, Alternate Conceptions, Ontological Shift. Simulations.

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.

Trend-Centric Motion Visualization: Designing and Applying a New Strategy for Analyzing Scientific Motion Collections.

PubMed

Schroeder, David; Korsakov, Fedor; Knipe, Carissa Mai-Ping; Thorson, Lauren; Ellingson, Arin M; Nuckley, David; Carlis, John; Keefe, Daniel F

2014-12-01

In biomechanics studies, researchers collect, via experiments or simulations, datasets with hundreds or thousands of trials, each describing the same type of motion (e.g., a neck flexion-extension exercise) but under different conditions (e.g., different patients, different disease states, pre- and post-treatment). Analyzing similarities and differences across all of the trials in these collections is a major challenge. Visualizing a single trial at a time does not work, and the typical alternative of juxtaposing multiple trials in a single visual display leads to complex, difficult-to-interpret visualizations. We address this problem via a new strategy that organizes the analysis around motion trends rather than trials. This new strategy matches the cognitive approach that scientists would like to take when analyzing motion collections. We introduce several technical innovations making trend-centric motion visualization possible. First, an algorithm detects a motion collection's trends via time-dependent clustering. Second, a 2D graphical technique visualizes how trials leave and join trends. Third, a 3D graphical technique, using a median 3D motion plus a visual variance indicator, visualizes the biomechanics of the set of trials within each trend. These innovations are combined to create an interactive exploratory visualization tool, which we designed through an iterative process in collaboration with both domain scientists and a traditionally-trained graphic designer. We report on insights generated during this design process and demonstrate the tool's effectiveness via a validation study with synthetic data and feedback from expert musculoskeletal biomechanics researchers who used the tool to analyze the effects of disc degeneration on human spinal kinematics.

Using parallel computing for the display and simulation of the space debris environment

NASA Astrophysics Data System (ADS)

Möckel, M.; Wiedemann, C.; Flegel, S.; Gelhaus, J.; Vörsmann, P.; Klinkrad, H.; Krag, H.

2011-07-01

Parallelism is becoming the leading paradigm in today's computer architectures. In order to take full advantage of this development, new algorithms have to be specifically designed for parallel execution while many old ones have to be upgraded accordingly. One field in which parallel computing has been firmly established for many years is computer graphics. Calculating and displaying three-dimensional computer generated imagery in real time requires complex numerical operations to be performed at high speed on a large number of objects. Since most of these objects can be processed independently, parallel computing is applicable in this field. Modern graphics processing units (GPUs) have become capable of performing millions of matrix and vector operations per second on multiple objects simultaneously. As a side project, a software tool is currently being developed at the Institute of Aerospace Systems that provides an animated, three-dimensional visualization of both actual and simulated space debris objects. Due to the nature of these objects it is possible to process them individually and independently from each other. Therefore, an analytical orbit propagation algorithm has been implemented to run on a GPU. By taking advantage of all its processing power a huge performance increase, compared to its CPU-based counterpart, could be achieved. For several years efforts have been made to harness this computing power for applications other than computer graphics. Software tools for the simulation of space debris are among those that could profit from embracing parallelism. With recently emerged software development tools such as OpenCL it is possible to transfer the new algorithms used in the visualization outside the field of computer graphics and implement them, for example, into the space debris simulation environment. This way they can make use of parallel hardware such as GPUs and Multi-Core-CPUs for faster computation. In this paper the visualization software will be introduced, including a comparison between the serial and the parallel method of orbit propagation. Ways of how to use the benefits of the latter method for space debris simulation will be discussed. An introduction to OpenCL will be given as well as an exemplary algorithm from the field of space debris simulation.

Using parallel computing for the display and simulation of the space debris environment

NASA Astrophysics Data System (ADS)

Moeckel, Marek; Wiedemann, Carsten; Flegel, Sven Kevin; Gelhaus, Johannes; Klinkrad, Heiner; Krag, Holger; Voersmann, Peter

Parallelism is becoming the leading paradigm in today's computer architectures. In order to take full advantage of this development, new algorithms have to be specifically designed for parallel execution while many old ones have to be upgraded accordingly. One field in which parallel computing has been firmly established for many years is computer graphics. Calculating and displaying three-dimensional computer generated imagery in real time requires complex numerical operations to be performed at high speed on a large number of objects. Since most of these objects can be processed independently, parallel computing is applicable in this field. Modern graphics processing units (GPUs) have become capable of performing millions of matrix and vector operations per second on multiple objects simultaneously. As a side project, a software tool is currently being developed at the Institute of Aerospace Systems that provides an animated, three-dimensional visualization of both actual and simulated space debris objects. Due to the nature of these objects it is possible to process them individually and independently from each other. Therefore, an analytical orbit propagation algorithm has been implemented to run on a GPU. By taking advantage of all its processing power a huge performance increase, compared to its CPU-based counterpart, could be achieved. For several years efforts have been made to harness this computing power for applications other than computer graphics. Software tools for the simulation of space debris are among those that could profit from embracing parallelism. With recently emerged software development tools such as OpenCL it is possible to transfer the new algorithms used in the visualization outside the field of computer graphics and implement them, for example, into the space debris simulation environment. This way they can make use of parallel hardware such as GPUs and Multi-Core-CPUs for faster computation. In this paper the visualization software will be introduced, including a comparison between the serial and the parallel method of orbit propagation. Ways of how to use the benefits of the latter method for space debris simulation will be discussed. An introduction of OpenCL will be given as well as an exemplary algorithm from the field of space debris simulation.

Collision detection and modeling of rigid and deformable objects in laparoscopic simulator

NASA Astrophysics Data System (ADS)

Dy, Mary-Clare; Tagawa, Kazuyoshi; Tanaka, Hiromi T.; Komori, Masaru

2015-03-01

Laparoscopic simulators are viable alternatives for surgical training and rehearsal. Haptic devices can also be incorporated with virtual reality simulators to provide additional cues to the users. However, to provide realistic feedback, the haptic device must be updated by 1kHz. On the other hand, realistic visual cues, that is, the collision detection and deformation between interacting objects must be rendered at least 30 fps. Our current laparoscopic simulator detects the collision between a point on the tool tip, and on the organ surfaces, in which haptic devices are attached on actual tool tips for realistic tool manipulation. The triangular-mesh organ model is rendered using a mass spring deformation model, or finite element method-based models. In this paper, we investigated multi-point-based collision detection on the rigid tool rods. Based on the preliminary results, we propose a method to improve the collision detection scheme, and speed up the organ deformation reaction. We discuss our proposal for an efficient method to compute simultaneous multiple collision between rigid (laparoscopic tools) and deformable (organs) objects, and perform the subsequent collision response, with haptic feedback, in real-time.

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.

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.

The Hyperwall

NASA Technical Reports Server (NTRS)

Biegel, Bryan A. (Technical Monitor); Sandstrom, Timothy A.; Henze, Chris; Levit, Creon

2003-01-01

This paper presents the hyperwall, a visualization cluster that uses coordinated visualizations for interactive exploration of multidimensional data and simulations. The system strongly leverages the human eye-brain system with a generous 7x7 array offlat panel LCD screens powered by a beowulf clustel: With each screen backed by a workstation class PC, graphic and compute intensive applications can be applied to a broad range of data. Navigational tools are presented that allow for investigation of high dimensional spaces.

Design of UAV-Embedded Microphone Array System for Sound Source Localization in Outdoor Environments †

PubMed Central

Hoshiba, Kotaro; Washizaki, Kai; Wakabayashi, Mizuho; Ishiki, Takahiro; Bando, Yoshiaki; Gabriel, Daniel; Nakadai, Kazuhiro; Okuno, Hiroshi G.

2017-01-01

In search and rescue activities, unmanned aerial vehicles (UAV) should exploit sound information to compensate for poor visual information. This paper describes the design and implementation of a UAV-embedded microphone array system for sound source localization in outdoor environments. Four critical development problems included water-resistance of the microphone array, efficiency in assembling, reliability of wireless communication, and sufficiency of visualization tools for operators. To solve these problems, we developed a spherical microphone array system (SMAS) consisting of a microphone array, a stable wireless network communication system, and intuitive visualization tools. The performance of SMAS was evaluated with simulated data and a demonstration in the field. Results confirmed that the SMAS provides highly accurate localization, water resistance, prompt assembly, stable wireless communication, and intuitive information for observers and operators. PMID:29099790

Design of UAV-Embedded Microphone Array System for Sound Source Localization in Outdoor Environments.

PubMed

Hoshiba, Kotaro; Washizaki, Kai; Wakabayashi, Mizuho; Ishiki, Takahiro; Kumon, Makoto; Bando, Yoshiaki; Gabriel, Daniel; Nakadai, Kazuhiro; Okuno, Hiroshi G

2017-11-03

In search and rescue activities, unmanned aerial vehicles (UAV) should exploit sound information to compensate for poor visual information. This paper describes the design and implementation of a UAV-embedded microphone array system for sound source localization in outdoor environments. Four critical development problems included water-resistance of the microphone array, efficiency in assembling, reliability of wireless communication, and sufficiency of visualization tools for operators. To solve these problems, we developed a spherical microphone array system (SMAS) consisting of a microphone array, a stable wireless network communication system, and intuitive visualization tools. The performance of SMAS was evaluated with simulated data and a demonstration in the field. Results confirmed that the SMAS provides highly accurate localization, water resistance, prompt assembly, stable wireless communication, and intuitive information for observers and operators.

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.

Transforming GIS data into functional road models for large-scale traffic simulation.

PubMed

Wilkie, David; Sewall, Jason; Lin, Ming C

2012-06-01

There exists a vast amount of geographic information system (GIS) data that model road networks around the world as polylines with attributes. In this form, the data are insufficient for applications such as simulation and 3D visualization-tools which will grow in power and demand as sensor data become more pervasive and as governments try to optimize their existing physical infrastructure. In this paper, we propose an efficient method for enhancing a road map from a GIS database to create a geometrically and topologically consistent 3D model to be used in real-time traffic simulation, interactive visualization of virtual worlds, and autonomous vehicle navigation. The resulting representation provides important road features for traffic simulations, including ramps, highways, overpasses, legal merge zones, and intersections with arbitrary states, and it is independent of the simulation methodologies. We test the 3D models of road networks generated by our algorithm on real-time traffic simulation using both macroscopic and microscopic techniques.

SOCR Motion Charts: An Efficient, Open-Source, Interactive and Dynamic Applet for Visualizing Longitudinal Multivariate Data

PubMed Central

Al-Aziz, Jameel; Christou, Nicolas; Dinov, Ivo D.

2011-01-01

The amount, complexity and provenance of data have dramatically increased in the past five years. Visualization of observed and simulated data is a critical component of any social, environmental, biomedical or scientific quest. Dynamic, exploratory and interactive visualization of multivariate data, without preprocessing by dimensionality reduction, remains a nearly insurmountable challenge. The Statistics Online Computational Resource (www.SOCR.ucla.edu) provides portable online aids for probability and statistics education, technology-based instruction and statistical computing. We have developed a new Java-based infrastructure, SOCR Motion Charts, for discovery-based exploratory analysis of multivariate data. This interactive data visualization tool enables the visualization of high-dimensional longitudinal data. SOCR Motion Charts allows mapping of ordinal, nominal and quantitative variables onto time, 2D axes, size, colors, glyphs and appearance characteristics, which facilitates the interactive display of multidimensional data. We validated this new visualization paradigm using several publicly available multivariate datasets including Ice-Thickness, Housing Prices, Consumer Price Index, and California Ozone Data. SOCR Motion Charts is designed using object-oriented programming, implemented as a Java Web-applet and is available to the entire community on the web at www.socr.ucla.edu/SOCR_MotionCharts. It can be used as an instructional tool for rendering and interrogating high-dimensional data in the classroom, as well as a research tool for exploratory data analysis. PMID:21479108

Virtual reality training and assessment in laparoscopic rectum surgery.

PubMed

Pan, Jun J; Chang, Jian; Yang, Xiaosong; Liang, Hui; Zhang, Jian J; Qureshi, Tahseen; Howell, Robert; Hickish, Tamas

2015-06-01

Virtual-reality (VR) based simulation techniques offer an efficient and low cost alternative to conventional surgery training. This article describes a VR training and assessment system in laparoscopic rectum surgery. To give a realistic visual performance of interaction between membrane tissue and surgery tools, a generalized cylinder based collision detection and a multi-layer mass-spring model are presented. A dynamic assessment model is also designed for hierarchy training evaluation. With this simulator, trainees can operate on the virtual rectum with both visual and haptic sensation feedback simultaneously. The system also offers surgeons instructions in real time when improper manipulation happens. The simulator has been tested and evaluated by ten subjects. This prototype system has been verified by colorectal surgeons through a pilot study. They believe the visual performance and the tactile feedback are realistic. It exhibits the potential to effectively improve the surgical skills of trainee surgeons and significantly shorten their learning curve. Copyright © 2014 John Wiley & Sons, Ltd.

A collaborative visual analytics suite for protein folding research.

PubMed

Harvey, William; Park, In-Hee; Rübel, Oliver; Pascucci, Valerio; Bremer, Peer-Timo; Li, Chenglong; Wang, Yusu

2014-09-01

Molecular dynamics (MD) simulation is a crucial tool for understanding principles behind important biochemical processes such as protein folding and molecular interaction. With the rapidly increasing power of modern computers, large-scale MD simulation experiments can be performed regularly, generating huge amounts of MD data. An important question is how to analyze and interpret such massive and complex data. One of the (many) challenges involved in analyzing MD simulation data computationally is the high-dimensionality of such data. Given a massive collection of molecular conformations, researchers typically need to rely on their expertise and prior domain knowledge in order to retrieve certain conformations of interest. It is not easy to make and test hypotheses as the data set as a whole is somewhat "invisible" due to its high dimensionality. In other words, it is hard to directly access and examine individual conformations from a sea of molecular structures, and to further explore the entire data set. There is also no easy and convenient way to obtain a global view of the data or its various modalities of biochemical information. To this end, we present an interactive, collaborative visual analytics tool for exploring massive, high-dimensional molecular dynamics simulation data sets. The most important utility of our tool is to provide a platform where researchers can easily and effectively navigate through the otherwise "invisible" simulation data sets, exploring and examining molecular conformations both as a whole and at individual levels. The visualization is based on the concept of a topological landscape, which is a 2D terrain metaphor preserving certain topological and geometric properties of the high dimensional protein energy landscape. In addition to facilitating easy exploration of conformations, this 2D terrain metaphor also provides a platform where researchers can visualize and analyze various properties (such as contact density) overlayed on the top of the 2D terrain. Finally, the software provides a collaborative environment where multiple researchers can assemble observations and biochemical events into storyboards and share them in real time over the Internet via a client-server architecture. The software is written in Scala and runs on the cross-platform Java Virtual Machine. Binaries and source code are available at http://www.aylasoftware.org and have been released under the GNU General Public License. Copyright © 2014 Elsevier Inc. All rights reserved.

Simbrain 3.0: A flexible, visually-oriented neural network simulator.

PubMed

Tosi, Zachary; Yoshimi, Jeffrey

2016-11-01

Simbrain 3.0 is a software package for neural network design and analysis, which emphasizes flexibility (arbitrarily complex networks can be built using a suite of basic components) and a visually rich, intuitive interface. These features support both students and professionals. Students can study all of the major classes of neural networks in a familiar graphical setting, and can easily modify simulations, experimenting with networks and immediately seeing the results of their interventions. With the 3.0 release, Simbrain supports models on the order of thousands of neurons and a million synapses. This allows the same features that support education to support research professionals, who can now use the tool to quickly design, run, and analyze the behavior of large, highly customizable simulations. Copyright © 2016 Elsevier Ltd. All rights reserved.

High-Performance Agent-Based Modeling Applied to Vocal Fold Inflammation and Repair.

PubMed

Seekhao, Nuttiiya; Shung, Caroline; JaJa, Joseph; Mongeau, Luc; Li-Jessen, Nicole Y K

2018-01-01

Fast and accurate computational biology models offer the prospect of accelerating the development of personalized medicine. A tool capable of estimating treatment success can help prevent unnecessary and costly treatments and potential harmful side effects. A novel high-performance Agent-Based Model (ABM) was adopted to simulate and visualize multi-scale complex biological processes arising in vocal fold inflammation and repair. The computational scheme was designed to organize the 3D ABM sub-tasks to fully utilize the resources available on current heterogeneous platforms consisting of multi-core CPUs and many-core GPUs. Subtasks are further parallelized and convolution-based diffusion is used to enhance the performance of the ABM simulation. The scheme was implemented using a client-server protocol allowing the results of each iteration to be analyzed and visualized on the server (i.e., in-situ ) while the simulation is running on the same server. The resulting simulation and visualization software enables users to interact with and steer the course of the simulation in real-time as needed. This high-resolution 3D ABM framework was used for a case study of surgical vocal fold injury and repair. The new framework is capable of completing the simulation, visualization and remote result delivery in under 7 s per iteration, where each iteration of the simulation represents 30 min in the real world. The case study model was simulated at the physiological scale of a human vocal fold. This simulation tracks 17 million biological cells as well as a total of 1.7 billion signaling chemical and structural protein data points. The visualization component processes and renders all simulated biological cells and 154 million signaling chemical data points. The proposed high-performance 3D ABM was verified through comparisons with empirical vocal fold data. Representative trends of biomarker predictions in surgically injured vocal folds were observed.

High-Performance Agent-Based Modeling Applied to Vocal Fold Inflammation and Repair

PubMed Central

Seekhao, Nuttiiya; Shung, Caroline; JaJa, Joseph; Mongeau, Luc; Li-Jessen, Nicole Y. K.

2018-01-01

Fast and accurate computational biology models offer the prospect of accelerating the development of personalized medicine. A tool capable of estimating treatment success can help prevent unnecessary and costly treatments and potential harmful side effects. A novel high-performance Agent-Based Model (ABM) was adopted to simulate and visualize multi-scale complex biological processes arising in vocal fold inflammation and repair. The computational scheme was designed to organize the 3D ABM sub-tasks to fully utilize the resources available on current heterogeneous platforms consisting of multi-core CPUs and many-core GPUs. Subtasks are further parallelized and convolution-based diffusion is used to enhance the performance of the ABM simulation. The scheme was implemented using a client-server protocol allowing the results of each iteration to be analyzed and visualized on the server (i.e., in-situ) while the simulation is running on the same server. The resulting simulation and visualization software enables users to interact with and steer the course of the simulation in real-time as needed. This high-resolution 3D ABM framework was used for a case study of surgical vocal fold injury and repair. The new framework is capable of completing the simulation, visualization and remote result delivery in under 7 s per iteration, where each iteration of the simulation represents 30 min in the real world. The case study model was simulated at the physiological scale of a human vocal fold. This simulation tracks 17 million biological cells as well as a total of 1.7 billion signaling chemical and structural protein data points. The visualization component processes and renders all simulated biological cells and 154 million signaling chemical data points. The proposed high-performance 3D ABM was verified through comparisons with empirical vocal fold data. Representative trends of biomarker predictions in surgically injured vocal folds were observed. PMID:29706894

PRANAS: A New Platform for Retinal Analysis and Simulation.

PubMed

Cessac, Bruno; Kornprobst, Pierre; Kraria, Selim; Nasser, Hassan; Pamplona, Daniela; Portelli, Geoffrey; Viéville, Thierry

2017-01-01

The retina encodes visual scenes by trains of action potentials that are sent to the brain via the optic nerve. In this paper, we describe a new free access user-end software allowing to better understand this coding. It is called PRANAS (https://pranas.inria.fr), standing for Platform for Retinal ANalysis And Simulation. PRANAS targets neuroscientists and modelers by providing a unique set of retina-related tools. PRANAS integrates a retina simulator allowing large scale simulations while keeping a strong biological plausibility and a toolbox for the analysis of spike train population statistics. The statistical method (entropy maximization under constraints) takes into account both spatial and temporal correlations as constraints, allowing to analyze the effects of memory on statistics. PRANAS also integrates a tool computing and representing in 3D (time-space) receptive fields. All these tools are accessible through a friendly graphical user interface. The most CPU-costly of them have been implemented to run in parallel.

Case studies on design, simulation and visualization of control and measurement applications using REX control system

NASA Astrophysics Data System (ADS)

Ozana, Stepan; Pies, Martin; Docekal, Tomas

2016-06-01

REX Control System is a professional advanced tool for design and implementation of complex control systems that belongs to softPLC category. It covers the entire process starting from simulation of functionality of the application before deployment, through implementation on real-time target, towards analysis, diagnostics and visualization. Basically it consists of two parts: the development tools and the runtime system. It is also compatible with Simulink environment, and the way of implementation of control algorithm is very similar. The control scheme is finally compiled (using RexDraw utility) and uploaded into a chosen real-time target (using RexView utility). There is a wide variety of hardware platforms and real-time operating systems supported by REX Control System such as for example Windows Embedded, Linux, Linux/Xenomai deployed on SBC, IPC, PAC, Raspberry Pi and others with many I/O interfaces. It is modern system designed both for measurement and control applications, offering a lot of additional functions concerning data archiving, visualization based on HTML5, and communication standards. The paper will sum up possibilities of its use in educational process, focused on control of case studies of physical models with classical and advanced control algorithms.

Simulated color: a diagnostic tool for skin lesions like port-wine stain

NASA Astrophysics Data System (ADS)

Randeberg, Lise L.; Svaasand, Lars O.

2001-05-01

A device independent method for skin color visualization has been developed. Colors reconstructed from a reflectance spectrum are presented on a computer screen by sRGB (standard Red Green Blue) color coordinates. The colors are presented as adjacent patches surrounded by a medium grey border. CIELAB color coordinates and CIE (International Commission on Illumination) color difference (Delta) E are computed. The change in skin color due to a change in average blood content or scattering properties in dermis is investigated. This is done by analytical simulations based on the diffusion approximation. It is found that an 11% change in average blood content and a 15% change in scattering properties will give a visible color change. A supposed visibility limit for (Delta) E is given. This value is based on experimental testing and the known properties of the human visual system. This limit value can be used as a tool to determine when to terminate laser treatment of port- wine stain due to low treatment response, i.e. low (Delta) E between treatments. The visualization method presented seems promising for medical applications as port-wine stain diagnostics. The method gives good possibilities for electronic transfer of data between clinics because it is device independent.

Framework and algorithms for illustrative visualizations of time-varying flows on unstructured meshes

DOE PAGES

Rattner, Alexander S.; Guillen, Donna Post; Joshi, Alark; ...

2016-03-17

Photo- and physically realistic techniques are often insufficient for visualization of fluid flow simulations, especially for 3D and time-varying studies. Substantial research effort has been dedicated to the development of non-photorealistic and illustration-inspired visualization techniques for compact and intuitive presentation of such complex datasets. However, a great deal of work has been reproduced in this field, as many research groups have developed specialized visualization software. Additionally, interoperability between illustrative visualization software is limited due to diverse processing and rendering architectures employed in different studies. In this investigation, a framework for illustrative visualization is proposed, and implemented in MarmotViz, a ParaViewmore » plug-in, enabling its use on a variety of computing platforms with various data file formats and mesh geometries. Region-of-interest identification and feature-tracking algorithms incorporated into this tool are described. Implementations of multiple illustrative effect algorithms are also presented to demonstrate the use and flexibility of this framework. Here, by providing an integrated framework for illustrative visualization of CFD data, MarmotViz can serve as a valuable asset for the interpretation of simulations of ever-growing scale.« less

Physically Based Virtual Surgery Planning and Simulation Tools for Personal Health Care Systems

NASA Astrophysics Data System (ADS)

Dogan, Firat; Atilgan, Yasemin

The virtual surgery planning and simulation tools have gained a great deal of importance in the last decade in a consequence of increasing capacities at the information technology level. The modern hardware architectures, large scale database systems, grid based computer networks, agile development processes, better 3D visualization and all the other strong aspects of the information technology brings necessary instruments into almost every desk. The last decade’s special software and sophisticated super computer environments are now serving to individual needs inside “tiny smart boxes” for reasonable prices. However, resistance to learning new computerized environments, insufficient training and all the other old habits prevents effective utilization of IT resources by the specialists of the health sector. In this paper, all the aspects of the former and current developments in surgery planning and simulation related tools are presented, future directions and expectations are investigated for better electronic health care systems.

Visualization in mechanics: the dynamics of an unbalanced roller

NASA Astrophysics Data System (ADS)

Cumber, Peter S.

2017-04-01

It is well known that mechanical engineering students often find mechanics a difficult area to grasp. This article describes a system of equations describing the motion of a balanced and an unbalanced roller constrained by a pivot arm. A wide range of dynamics can be simulated with the model. The equations of motion are embedded in a graphical user interface for its numerical solution in MATLAB. This allows a student's focus to be on the influence of different parameters on the system dynamics. The simulation tool can be used as a dynamics demonstrator in a lecture or as an educational tool driven by the imagination of the student. By way of demonstration the simulation tool has been applied to a range of roller-pivot arm configurations. In addition, approximations to the equations of motion are explored and a second-order model is shown to be accurate for a limited range of parameters.

MeshVoro: A Three-Dimensional Voronoi Mesh Building Tool for the TOUGH Family of Codes

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

Freeman, C. M.; Boyle, K. L.; Reagan, M.

2013-09-30

Few tools exist for creating and visualizing complex three-dimensional simulation meshes, and these have limitations that restrict their application to particular geometries and circumstances. Mesh generation needs to trend toward ever more general applications. To that end, we have developed MeshVoro, a tool that is based on the Voro (Rycroft 2009) library and is capable of generating complex threedimensional Voronoi tessellation-based (unstructured) meshes for the solution of problems of flow and transport in subsurface geologic media that are addressed by the TOUGH (Pruess et al. 1999) family of codes. MeshVoro, which includes built-in data visualization routines, is a particularly usefulmore » tool because it extends the applicability of the TOUGH family of codes by enabling the scientifically robust and relatively easy discretization of systems with challenging 3D geometries. We describe several applications of MeshVoro. We illustrate the ability of the tool to straightforwardly transform a complex geological grid into a simulation mesh that conforms to the specifications of the TOUGH family of codes. We demonstrate how MeshVoro can describe complex system geometries with a relatively small number of grid blocks, and we construct meshes for geometries that would have been practically intractable with a standard Cartesian grid approach. We also discuss the limitations and appropriate applications of this new technology.« less

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

Usefulness of ERTS-1 satellite imagery as a data-gathering tool by resource managers in the Bureau of Land Management. [Arizona, California, Oregon, and Alaska

NASA Technical Reports Server (NTRS)

Bentley, R. G.

1974-01-01

ERTS-1 satellite imagery can be an effective data-gathering tool for resource managers. Techniques are developed which allow managers to visually analyze simulated color infrared composite images to map perennial and ephemeral (annual) plant communities. Tentative results indicate that ephemeral plant growth and development and potential to produce forage can be monitored.

Visualizing human communication in business process simulations

NASA Astrophysics Data System (ADS)

Groehn, Matti; Jalkanen, Janne; Haho, Paeivi; Nieminen, Marko; Smeds, Riitta

1999-03-01

In this paper a description of business process simulation is given. Crucial part in the simulation of business processes is the analysis of social contacts between the participants. We will introduce a tool to collect log data and how this log data can be effectively analyzed using two different kind of methods: discussion flow charts and self-organizing maps. Discussion flow charts revealed the communication patterns and self-organizing maps are a very effective way of clustering the participants into development groups.

Real-time simulation and visualization of volumetric brain deformation for image-guided neurosurgery

NASA Astrophysics Data System (ADS)

Ferrant, Matthieu; Nabavi, Arya; Macq, Benoit M. M.; Kikinis, Ron; Warfield, Simon K.

2001-05-01

During neurosurgery, the challenge for the neurosurgeon is to remove as much as possible of a tumor without destroying healthy tissue. This can be difficult because healthy and diseased tissue can have the same visual appearance. To this aim, and because the surgeon cannot see underneath the brain surface, image-guided neurosurgery systems are being increasingly used. However, during surgery, deformation of the brain occurs (due to brain shift and tumor resection), therefore causing errors in the surgical planning with respect to preoperative imaging. In our previous work, we developed software for capturing the deformation of the brain during neurosurgery. The software also allows preoperative data to be updated according to the intraoperative imaging so as to reflect the shape changes of the brain during surgery. Our goal in this paper was to rapidly visualize and characterize this deformation over the course of surgery with appropriate tools. Therefore, we developed tools allowing the doctor to visualize (in 2D and 3D) deformations, as well as the stress tensors characterizing the deformation along with the updated preoperative and intraoperative imaging during the course of surgery. Such tools significantly add to the value of intraoperative imaging and hence could improve surgical outcomes.

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.

Visual analysis of fluid dynamics at NASA's numerical aerodynamic simulation facility

NASA Technical Reports Server (NTRS)

Watson, Velvin R.

1991-01-01

A study aimed at describing and illustrating visualization tools used in Computational Fluid Dynamics (CFD) and indicating how these tools are likely to change by showing a projected resolution of the human computer interface is presented. The following are outlined using a graphically based test format: the revolution of human computer environments for CFD research; comparison of current environments; current environments with the ideal; predictions for the future CFD environments; what can be done to accelerate the improvements. The following comments are given: when acquiring visualization tools, potential rapid changes must be considered; environmental changes over the next ten years due to human computer interface cannot be fathomed; data flow packages such as AVS, apE, Explorer and Data Explorer are easy to learn and use for small problems, excellent for prototyping, but not so efficient for large problems; the approximation techniques used in visualization software must be appropriate for the data; it has become more cost effective to move jobs that fit on workstations and run only memory intensive jobs on the supercomputer; use of three dimensional skills will be maximized when the three dimensional environment is built in from the start.

Geographic Visualization of Power-Grid Dynamics

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

Sukumar, Sreenivas R.

2015-06-18

The visualization enables the simulation analyst to see changes in the frequency through time and space. With this technology, the analyst has a bird's eye view of the frequency at loads and generators as the simulated power system responds to the loss of a generator, spikes in load, and other contingencies. The significance of a contingency to the operation of an electrical power system depends critically on how the resulting tansients evolve in time and space. Consequently, these dynamic events can only be understood when seen in their proper geographic context. this understanding is indispensable to engineers working on themore » next generation of distributed sensing and control systems for the smart grid. By making possible a natural and intuitive presentation of dynamic behavior, our new visualization technology is a situational-awareness tool for power-system engineers.« less

Three-Dimensional Visualization with Large Data Sets: A Simulation of Spreading Cortical Depression in Human Brain

PubMed Central

Ertürk, Korhan Levent; Şengül, Gökhan

2012-01-01

We developed 3D simulation software of human organs/tissues; we developed a database to store the related data, a data management system to manage the created data, and a metadata system for the management of data. This approach provides two benefits: first of all the developed system does not require to keep the patient's/subject's medical images on the system, providing less memory usage. Besides the system also provides 3D simulation and modification options, which will help clinicians to use necessary tools for visualization and modification operations. The developed system is tested in a case study, in which a 3D human brain model is created and simulated from 2D MRI images of a human brain, and we extended the 3D model to include the spreading cortical depression (SCD) wave front, which is an electrical phoneme that is believed to cause the migraine. PMID:23258956

MEVA--An Interactive Visualization Application for Validation of Multifaceted Meteorological Data with Multiple 3D Devices.

PubMed

Helbig, Carolin; Bilke, Lars; Bauer, Hans-Stefan; Böttinger, Michael; Kolditz, Olaf

2015-01-01

To achieve more realistic simulations, meteorologists develop and use models with increasing spatial and temporal resolution. The analyzing, comparing, and visualizing of resulting simulations becomes more and more challenging due to the growing amounts and multifaceted character of the data. Various data sources, numerous variables and multiple simulations lead to a complex database. Although a variety of software exists suited for the visualization of meteorological data, none of them fulfills all of the typical domain-specific requirements: support for quasi-standard data formats and different grid types, standard visualization techniques for scalar and vector data, visualization of the context (e.g., topography) and other static data, support for multiple presentation devices used in modern sciences (e.g., virtual reality), a user-friendly interface, and suitability for cooperative work. Instead of attempting to develop yet another new visualization system to fulfill all possible needs in this application domain, our approach is to provide a flexible workflow that combines different existing state-of-the-art visualization software components in order to hide the complexity of 3D data visualization tools from the end user. To complete the workflow and to enable the domain scientists to interactively visualize their data without advanced skills in 3D visualization systems, we developed a lightweight custom visualization application (MEVA - multifaceted environmental data visualization application) that supports the most relevant visualization and interaction techniques and can be easily deployed. Specifically, our workflow combines a variety of different data abstraction methods provided by a state-of-the-art 3D visualization application with the interaction and presentation features of a computer-games engine. Our customized application includes solutions for the analysis of multirun data, specifically with respect to data uncertainty and differences between simulation runs. In an iterative development process, our easy-to-use application was developed in close cooperation with meteorologists and visualization experts. The usability of the application has been validated with user tests. We report on how this application supports the users to prove and disprove existing hypotheses and discover new insights. In addition, the application has been used at public events to communicate research results.

MEVA - An Interactive Visualization Application for Validation of Multifaceted Meteorological Data with Multiple 3D Devices

PubMed Central

Helbig, Carolin; Bilke, Lars; Bauer, Hans-Stefan; Böttinger, Michael; Kolditz, Olaf

2015-01-01

Background To achieve more realistic simulations, meteorologists develop and use models with increasing spatial and temporal resolution. The analyzing, comparing, and visualizing of resulting simulations becomes more and more challenging due to the growing amounts and multifaceted character of the data. Various data sources, numerous variables and multiple simulations lead to a complex database. Although a variety of software exists suited for the visualization of meteorological data, none of them fulfills all of the typical domain-specific requirements: support for quasi-standard data formats and different grid types, standard visualization techniques for scalar and vector data, visualization of the context (e.g., topography) and other static data, support for multiple presentation devices used in modern sciences (e.g., virtual reality), a user-friendly interface, and suitability for cooperative work. Methods and Results Instead of attempting to develop yet another new visualization system to fulfill all possible needs in this application domain, our approach is to provide a flexible workflow that combines different existing state-of-the-art visualization software components in order to hide the complexity of 3D data visualization tools from the end user. To complete the workflow and to enable the domain scientists to interactively visualize their data without advanced skills in 3D visualization systems, we developed a lightweight custom visualization application (MEVA - multifaceted environmental data visualization application) that supports the most relevant visualization and interaction techniques and can be easily deployed. Specifically, our workflow combines a variety of different data abstraction methods provided by a state-of-the-art 3D visualization application with the interaction and presentation features of a computer-games engine. Our customized application includes solutions for the analysis of multirun data, specifically with respect to data uncertainty and differences between simulation runs. In an iterative development process, our easy-to-use application was developed in close cooperation with meteorologists and visualization experts. The usability of the application has been validated with user tests. We report on how this application supports the users to prove and disprove existing hypotheses and discover new insights. In addition, the application has been used at public events to communicate research results. PMID:25915061

Validation of a low dose simulation technique for computed tomography images.

PubMed

Muenzel, Daniela; Koehler, Thomas; Brown, Kevin; Zabić, Stanislav; Fingerle, Alexander A; Waldt, Simone; Bendik, Edgar; Zahel, Tina; Schneider, Armin; Dobritz, Martin; Rummeny, Ernst J; Noël, Peter B

2014-01-01

Evaluation of a new software tool for generation of simulated low-dose computed tomography (CT) images from an original higher dose scan. Original CT scan data (100 mAs, 80 mAs, 60 mAs, 40 mAs, 20 mAs, 10 mAs; 100 kV) of a swine were acquired (approved by the regional governmental commission for animal protection). Simulations of CT acquisition with a lower dose (simulated 10-80 mAs) were calculated using a low-dose simulation algorithm. The simulations were compared to the originals of the same dose level with regard to density values and image noise. Four radiologists assessed the realistic visual appearance of the simulated images. Image characteristics of simulated low dose scans were similar to the originals. Mean overall discrepancy of image noise and CT values was -1.2% (range -9% to 3.2%) and -0.2% (range -8.2% to 3.2%), respectively, p>0.05. Confidence intervals of discrepancies ranged between 0.9-10.2 HU (noise) and 1.9-13.4 HU (CT values), without significant differences (p>0.05). Subjective observer evaluation of image appearance showed no visually detectable difference. Simulated low dose images showed excellent agreement with the originals concerning image noise, CT density values, and subjective assessment of the visual appearance of the simulated images. An authentic low-dose simulation opens up opportunity with regard to staff education, protocol optimization and introduction of new techniques.

Communication library for run-time visualization of distributed, asynchronous data

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

Rowlan, J.; Wightman, B.T.

1994-04-01

In this paper we present a method for collecting and visualizing data generated by a parallel computational simulation during run time. Data distributed across multiple processes is sent across parallel communication lines to a remote workstation, which sorts and queues the data for visualization. We have implemented our method in a set of tools called PORTAL (for Parallel aRchitecture data-TrAnsfer Library). The tools comprise generic routines for sending data from a parallel program (callable from either C or FORTRAN), a semi-parallel communication scheme currently built upon Unix Sockets, and a real-time connection to the scientific visualization program AVS. Our methodmore » is most valuable when used to examine large datasets that can be efficiently generated and do not need to be stored on disk. The PORTAL source libraries, detailed documentation, and a working example can be obtained by anonymous ftp from info.mcs.anl.gov from the file portal.tar.Z from the directory pub/portal.« less

Metadata Mapper: a web service for mapping data between independent visual analysis components, guided by perceptual rules

NASA Astrophysics Data System (ADS)

Rogowitz, Bernice E.; Matasci, Naim

2011-03-01

The explosion of online scientific data from experiments, simulations, and observations has given rise to an avalanche of algorithmic, visualization and imaging methods. There has also been enormous growth in the introduction of tools that provide interactive interfaces for exploring these data dynamically. Most systems, however, do not support the realtime exploration of patterns and relationships across tools and do not provide guidance on which colors, colormaps or visual metaphors will be most effective. In this paper, we introduce a general architecture for sharing metadata between applications and a "Metadata Mapper" component that allows the analyst to decide how metadata from one component should be represented in another, guided by perceptual rules. This system is designed to support "brushing [1]," in which highlighting a region of interest in one application automatically highlights corresponding values in another, allowing the scientist to develop insights from multiple sources. Our work builds on the component-based iPlant Cyberinfrastructure [2] and provides a general approach to supporting interactive, exploration across independent visualization and visual analysis components.

A Simple Evacuation Modeling and Simulation Tool for First Responders

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

Koch, Daniel B; Payne, Patricia W

2015-01-01

Although modeling and simulation of mass evacuations during a natural or man-made disaster is an on-going and vigorous area of study, tool adoption by front-line first responders is uneven. Some of the factors that account for this situation include cost and complexity of the software. For several years, Oak Ridge National Laboratory has been actively developing the free Incident Management Preparedness and Coordination Toolkit (IMPACT) to address these issues. One of the components of IMPACT is a multi-agent simulation module for area-based and path-based evacuations. The user interface is designed so that anyone familiar with typical computer drawing tools canmore » quickly author a geospatially-correct evacuation visualization suitable for table-top exercises. Since IMPACT is designed for use in the field where network communications may not be available, quick on-site evacuation alternatives can be evaluated to keep pace with a fluid threat situation. Realism is enhanced by incorporating collision avoidance into the simulation. Statistics are gathered as the simulation unfolds, including most importantly time-to-evacuate, to help first responders choose the best course of action.« less

Engineering visualization utilizing advanced animation

NASA Technical Reports Server (NTRS)

Sabionski, Gunter R.; Robinson, Thomas L., Jr.

1989-01-01

Engineering visualization is the use of computer graphics to depict engineering analysis and simulation in visual form from project planning through documentation. Graphics displays let engineers see data represented dynamically which permits the quick evaluation of results. The current state of graphics hardware and software generally allows the creation of two types of 3D graphics. The use of animated video as an engineering visualization tool is presented. The engineering, animation, and videography aspects of animated video production are each discussed. Specific issues include the integration of staffing expertise, hardware, software, and the various production processes. A detailed explanation of the animation process reveals the capabilities of this unique engineering visualization method. Automation of animation and video production processes are covered and future directions are proposed.

Visualization of the Eastern Renewable Generation Integration Study: Preprint

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

Gruchalla, Kenny; Novacheck, Joshua; Bloom, Aaron

The Eastern Renewable Generation Integration Study (ERGIS), explores the operational impacts of the wide spread adoption of wind and solar photovoltaics (PV) resources in the U.S. Eastern Interconnection and Quebec Interconnection (collectively, EI). In order to understand some of the economic and reliability challenges of managing hundreds of gigawatts of wind and PV generation, we developed state of the art tools, data, and models for simulating power system operations using hourly unit commitment and 5-minute economic dispatch over an entire year. Using NREL's high-performance computing capabilities and new methodologies to model operations, we found that the EI, as simulated withmore » evolutionary change in 2026, could balance the variability and uncertainty of wind and PV at a 5-minute level under a variety of conditions. A large-scale display and a combination of multiple coordinated views and small multiples were used to visually analyze the four large highly multivariate scenarios with high spatial and temporal resolutions. state of the art tools, data, and models for simulating power system operations using hourly unit commitment and 5-minute economic dispatch over an entire year. Using NRELs high-performance computing capabilities and new methodologies to model operations, we found that the EI, as simulated with evolutionary change in 2026, could balance the variability and uncertainty of wind and PV at a 5-minute level under a variety of conditions. A large-scale display and a combination of multiple coordinated views and small multiples were used to visually analyze the four large highly multivariate scenarios with high spatial and temporal resolutions.« less

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

Springmeyer, R R; Brugger, E; Cook, R

The Data group provides data analysis and visualization support to its customers. This consists primarily of the development and support of VisIt, a data analysis and visualization tool. Support ranges from answering questions about the tool, providing classes on how to use the tool, and performing data analysis and visualization for customers. The Information Management and Graphics Group supports and develops tools that enhance our ability to access, display, and understand large, complex data sets. Activities include applying visualization software for large scale data exploration; running video production labs on two networks; supporting graphics libraries and tools for end users;more » maintaining PowerWalls and assorted other displays; and developing software for searching and managing scientific data. Researchers in the Center for Applied Scientific Computing (CASC) work on various projects including the development of visualization techniques for large scale data exploration that are funded by the ASC program, among others. The researchers also have LDRD projects and collaborations with other lab researchers, academia, and industry. The IMG group is located in the Terascale Simulation Facility, home to Dawn, Atlas, BGL, and others, which includes both classified and unclassified visualization theaters, a visualization computer floor and deployment workshop, and video production labs. We continued to provide the traditional graphics group consulting and video production support. We maintained five PowerWalls and many other displays. We deployed a 576-node Opteron/IB cluster with 72 TB of memory providing a visualization production server on our classified network. We continue to support a 128-node Opteron/IB cluster providing a visualization production server for our unclassified systems and an older 256-node Opteron/IB cluster for the classified systems, as well as several smaller clusters to drive the PowerWalls. The visualization production systems includes NFS servers to provide dedicated storage for data analysis and visualization. The ASC projects have delivered new versions of visualization and scientific data management tools to end users and continue to refine them. VisIt had 4 releases during the past year, ending with VisIt 2.0. We released version 2.4 of Hopper, a Java application for managing and transferring files. This release included a graphical disk usage view which works on all types of connections and an aggregated copy feature for quickly transferring massive datasets quickly and efficiently to HPSS. We continue to use and develop Blockbuster and Telepath. Both the VisIt and IMG teams were engaged in a variety of movie production efforts during the past year in addition to the development tasks.« less

Flowgen: Flowchart-based documentation for C + + codes

NASA Astrophysics Data System (ADS)

Kosower, David A.; Lopez-Villarejo, J. J.

2015-11-01

We present the Flowgen tool, which generates flowcharts from annotated C + + source code. The tool generates a set of interconnected high-level UML activity diagrams, one for each function or method in the C + + sources. It provides a simple and visual overview of complex implementations of numerical algorithms. Flowgen is complementary to the widely-used Doxygen documentation tool. The ultimate aim is to render complex C + + computer codes accessible, and to enhance collaboration between programmers and algorithm or science specialists. We describe the tool and a proof-of-concept application to the VINCIA plug-in for simulating collisions at CERN's Large Hadron Collider.

Ultra-scale Visualization Climate Data Analysis Tools (UV-CDAT)

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

Williams, Dean N.; Silva, Claudio

2013-09-30

For the past three years, a large analysis and visualization effort—funded by the Department of Energy’s Office of Biological and Environmental Research (BER), the National Aeronautics and Space Administration (NASA), and the National Oceanic and Atmospheric Administration (NOAA)—has brought together a wide variety of industry-standard scientific computing libraries and applications to create Ultra-scale Visualization Climate Data Analysis Tools (UV-CDAT) to serve the global climate simulation and observational research communities. To support interactive analysis and visualization, all components connect through a provenance application–programming interface to capture meaningful history and workflow. Components can be loosely coupled into the framework for fast integrationmore » or tightly coupled for greater system functionality and communication with other components. The overarching goal of UV-CDAT is to provide a new paradigm for access to and analysis of massive, distributed scientific data collections by leveraging distributed data architectures located throughout the world. The UV-CDAT framework addresses challenges in analysis and visualization and incorporates new opportunities, including parallelism for better efficiency, higher speed, and more accurate scientific inferences. Today, it provides more than 600 users access to more analysis and visualization products than any other single source.« less

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.

Predicting SPE Fluxes: Coupled Simulations and Analysis Tools

NASA Astrophysics Data System (ADS)

Gorby, M.; Schwadron, N.; Linker, J.; Caplan, R. M.; Wijaya, J.; Downs, C.; Lionello, R.

2017-12-01

Presented here is a nuts-and-bolts look at the coupled framework of Predictive Science Inc's Magnetohydrodynamics Around a Sphere (MAS) code and the Energetic Particle Radiation Environment Module (EPREM). MAS simulated coronal mass ejection output from a variety of events can be selected as the MHD input to EPREM and a variety of parameters can be set to run against: bakground seed particle spectra, mean free path, perpendicular diffusion efficiency, etc.. A standard set of visualizations are produced as well as a library of analysis tools for deeper inquiries. All steps will be covered end-to-end as well as the framework's user interface and availability.

NeuroManager: a workflow analysis based simulation management engine for computational neuroscience

PubMed Central

Stockton, David B.; Santamaria, Fidel

2015-01-01

We developed NeuroManager, an object-oriented simulation management software engine for computational neuroscience. NeuroManager automates the workflow of simulation job submissions when using heterogeneous computational resources, simulators, and simulation tasks. The object-oriented approach (1) provides flexibility to adapt to a variety of neuroscience simulators, (2) simplifies the use of heterogeneous computational resources, from desktops to super computer clusters, and (3) improves tracking of simulator/simulation evolution. We implemented NeuroManager in MATLAB, a widely used engineering and scientific language, for its signal and image processing tools, prevalence in electrophysiology analysis, and increasing use in college Biology education. To design and develop NeuroManager we analyzed the workflow of simulation submission for a variety of simulators, operating systems, and computational resources, including the handling of input parameters, data, models, results, and analyses. This resulted in 22 stages of simulation submission workflow. The software incorporates progress notification, automatic organization, labeling, and time-stamping of data and results, and integrated access to MATLAB's analysis and visualization tools. NeuroManager provides users with the tools to automate daily tasks, and assists principal investigators in tracking and recreating the evolution of research projects performed by multiple people. Overall, NeuroManager provides the infrastructure needed to improve workflow, manage multiple simultaneous simulations, and maintain provenance of the potentially large amounts of data produced during the course of a research project. PMID:26528175

NeuroManager: a workflow analysis based simulation management engine for computational neuroscience.

PubMed

Stockton, David B; Santamaria, Fidel

2015-01-01

We developed NeuroManager, an object-oriented simulation management software engine for computational neuroscience. NeuroManager automates the workflow of simulation job submissions when using heterogeneous computational resources, simulators, and simulation tasks. The object-oriented approach (1) provides flexibility to adapt to a variety of neuroscience simulators, (2) simplifies the use of heterogeneous computational resources, from desktops to super computer clusters, and (3) improves tracking of simulator/simulation evolution. We implemented NeuroManager in MATLAB, a widely used engineering and scientific language, for its signal and image processing tools, prevalence in electrophysiology analysis, and increasing use in college Biology education. To design and develop NeuroManager we analyzed the workflow of simulation submission for a variety of simulators, operating systems, and computational resources, including the handling of input parameters, data, models, results, and analyses. This resulted in 22 stages of simulation submission workflow. The software incorporates progress notification, automatic organization, labeling, and time-stamping of data and results, and integrated access to MATLAB's analysis and visualization tools. NeuroManager provides users with the tools to automate daily tasks, and assists principal investigators in tracking and recreating the evolution of research projects performed by multiple people. Overall, NeuroManager provides the infrastructure needed to improve workflow, manage multiple simultaneous simulations, and maintain provenance of the potentially large amounts of data produced during the course of a research project.

Open the VALT™: Creation and application of a visually authentic learning tool.

PubMed

Ackland-Tilbrook, Vanessa; Warland, Jane

2015-05-01

This paper describes the process of creating and applying a Visually Authentic Learning Tool (VALT™) in an undergraduate midwifery program. The VALT was developed to facilitate learning in the topic "bleeding in pregnancy". The VALTs objective is to open the mind of the student to facilitate learning via the visual representation of authentic real life simulations designed to enhance and bring to life the written scenario. Students were asked for their feedback of the VALTs. A descriptive analysis was performed on the collated results to determine how the students rated the VALTS in terms of satisfaction and meeting their learning needs. Overall the students seemed to value the VALTs as they present an engaging and unique opportunity to promote learning whilst acknowledging and valuing different learning style within the student group. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

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.

Reconstruction, Enhancement, Visualization, and Ergonomic Assessment for Laparoscopic Surgery

DTIC Science & Technology

2007-02-01

support and upgrade of the REVEAL display system and tool suite in the University of Maryland Medical Center’s Simulation Center, (2) stereo video display...technology deployment, (3) stereo probe calibration benchmarks and support tools , (4) the production of research media, (5) baseline results from...endoscope can be used to generate a stereoscopic view for a surgeon, as with the DaVinci robot in use today. In order to use such an endoscope for

Tracking Blade Tip Vortices for Numerical Flow Simulations of Hovering Rotorcraft

NASA Technical Reports Server (NTRS)

Kao, David L.

2016-01-01

Blade tip vortices generated by a helicopter rotor blade are a major source of rotor noise and airframe vibration. This occurs when a vortex passes closely by, and interacts with, a rotor blade. The accurate prediction of Blade Vortex Interaction (BVI) continues to be a challenge for Computational Fluid Dynamics (CFD). Though considerable research has been devoted to BVI noise reduction and experimental techniques for measuring the blade tip vortices in a wind tunnel, there are only a handful of post-processing tools available for extracting vortex core lines from CFD simulation data. In order to calculate the vortex core radius, most of these tools require the user to manually select a vortex core to perform the calculation. Furthermore, none of them provide the capability to track the growth of a vortex core, which is a measure of how quickly the vortex diffuses over time. This paper introduces an automated approach for tracking the core growth of a blade tip vortex from CFD simulations of rotorcraft in hover. The proposed approach offers an effective method for the quantification and visualization of blade tip vortices in helicopter rotor wakes. Keywords: vortex core, feature extraction, CFD, numerical flow visualization

High fidelity simulations of infrared imagery with animated characters

NASA Astrophysics Data System (ADS)

Näsström, F.; Persson, A.; Bergström, D.; Berggren, J.; Hedström, J.; Allvar, J.; Karlsson, M.

2012-06-01

High fidelity simulations of IR signatures and imagery tend to be slow and do not have effective support for animation of characters. Simplified rendering methods based on computer graphics methods can be used to overcome these limitations. This paper presents a method to combine these tools and produce simulated high fidelity thermal IR data of animated people in terrain. Infrared signatures for human characters have been calculated using RadThermIR. To handle multiple character models, these calculations use a simplified material model for the anatomy and clothing. Weather and temperature conditions match the IR-texture used in the terrain model. The calculated signatures are applied to the animated 3D characters that, together with the terrain model, are used to produce high fidelity IR imagery of people or crowds. For high level animation control and crowd simulations, HLAS (High Level Animation System) has been developed. There are tools available to create and visualize skeleton based animations, but tools that allow control of the animated characters on a higher level, e.g. for crowd simulation, are usually expensive and closed source. We need the flexibility of HLAS to add animation into an HLA enabled sensor system simulation framework.

Forecasting and visualization of wildfires in a 3D geographical information system

NASA Astrophysics Data System (ADS)

Castrillón, M.; Jorge, P. A.; López, I. J.; Macías, A.; Martín, D.; Nebot, R. J.; Sabbagh, I.; Quintana, F. M.; Sánchez, J.; Sánchez, A. J.; Suárez, J. P.; Trujillo, A.

2011-03-01

This paper describes a wildfire forecasting application based on a 3D virtual environment and a fire simulation engine. A novel open-source framework is presented for the development of 3D graphics applications over large geographic areas, offering high performance 3D visualization and powerful interaction tools for the Geographic Information Systems (GIS) community. The application includes a remote module that allows simultaneous connections of several users for monitoring a real wildfire event. The system is able to make a realistic composition of what is really happening in the area of the wildfire with dynamic 3D objects and location of human and material resources in real time, providing a new perspective to analyze the wildfire information. The user is enabled to simulate and visualize the propagation of a fire on the terrain integrating at the same time spatial information on topography and vegetation types with weather and wind data. The application communicates with a remote web service that is in charge of the simulation task. The user may specify several parameters through a friendly interface before the application sends the information to the remote server responsible of carrying out the wildfire forecasting using the FARSITE simulation model. During the process, the server connects to different external resources to obtain up-to-date meteorological data. The client application implements a realistic 3D visualization of the fire evolution on the landscape. A Level Of Detail (LOD) strategy contributes to improve the performance of the visualization system.

Visual Computing Environment

NASA Technical Reports Server (NTRS)

Lawrence, Charles; Putt, Charles W.

1997-01-01

The Visual Computing Environment (VCE) is a NASA Lewis Research Center project to develop a framework for intercomponent and multidisciplinary computational simulations. Many current engineering analysis codes simulate various aspects of aircraft engine operation. For example, existing computational fluid dynamics (CFD) codes can model the airflow through individual engine components such as the inlet, compressor, combustor, turbine, or nozzle. Currently, these codes are run in isolation, making intercomponent and complete system simulations very difficult to perform. In addition, management and utilization of these engineering codes for coupled component simulations is a complex, laborious task, requiring substantial experience and effort. To facilitate multicomponent aircraft engine analysis, the CFD Research Corporation (CFDRC) is developing the VCE system. This system, which is part of NASA's Numerical Propulsion Simulation System (NPSS) program, can couple various engineering disciplines, such as CFD, structural analysis, and thermal analysis. The objectives of VCE are to (1) develop a visual computing environment for controlling the execution of individual simulation codes that are running in parallel and are distributed on heterogeneous host machines in a networked environment, (2) develop numerical coupling algorithms for interchanging boundary conditions between codes with arbitrary grid matching and different levels of dimensionality, (3) provide a graphical interface for simulation setup and control, and (4) provide tools for online visualization and plotting. VCE was designed to provide a distributed, object-oriented environment. Mechanisms are provided for creating and manipulating objects, such as grids, boundary conditions, and solution data. This environment includes parallel virtual machine (PVM) for distributed processing. Users can interactively select and couple any set of codes that have been modified to run in a parallel distributed fashion on a cluster of heterogeneous workstations. A scripting facility allows users to dictate the sequence of events that make up the particular simulation.

Living Liquid: Design and Evaluation of an Exploratory Visualization Tool for Museum Visitors.

PubMed

Ma, J; Liao, I; Ma, Kwan-Liu; Frazier, J

2012-12-01

Interactive visualizations can allow science museum visitors to explore new worlds by seeing and interacting with scientific data. However, designing interactive visualizations for informal learning environments, such as museums, presents several challenges. First, visualizations must engage visitors on a personal level. Second, visitors often lack the background to interpret visualizations of scientific data. Third, visitors have very limited time at individual exhibits in museums. This paper examines these design considerations through the iterative development and evaluation of an interactive exhibit as a visualization tool that gives museumgoers access to scientific data generated and used by researchers. The exhibit prototype, Living Liquid, encourages visitors to ask and answer their own questions while exploring the time-varying global distribution of simulated marine microbes using a touchscreen interface. Iterative development proceeded through three rounds of formative evaluations using think-aloud protocols and interviews, each round informing a key visualization design decision: (1) what to visualize to initiate inquiry, (2) how to link data at the microscopic scale to global patterns, and (3) how to include additional data that allows visitors to pursue their own questions. Data from visitor evaluations suggests that, when designing visualizations for public audiences, one should (1) avoid distracting visitors from data that they should explore, (2) incorporate background information into the visualization, (3) favor understandability over scientific accuracy, and (4) layer data accessibility to structure inquiry. Lessons learned from this case study add to our growing understanding of how to use visualizations to actively engage learners with scientific data.

Simulation validation of the XV-15 tilt-rotor research aircraft

NASA Technical Reports Server (NTRS)

Ferguson, S. W.; Hanson, G. D.; Churchill, G. B.

1984-01-01

The results of a simulation validation program of the XV-15 tilt-rotor research aircraft are detailed, covering such simulation aspects as the mathematical model, visual system, motion system, cab aural system, cab control loader system, pilot perceptual fidelity, and generic tilt rotor applications. Simulation validation was performed for the hover, low-speed, and sideward flight modes, with consideration of the in-ground rotor effect. Several deficiencies of the mathematical model and the simulation systems were identified in the course of the simulation validation project, and some were corrected. It is noted that NASA's Vertical Motion Simulator used in the program is an excellent tool for tilt-rotor and rotorcraft design, development, and pilot training.

A Visual Basic simulation software tool for performance analysis of a membrane-based advanced water treatment plant.

PubMed

Pal, P; Kumar, R; Srivastava, N; Chaudhuri, J

2014-02-01

A Visual Basic simulation software (WATTPPA) has been developed to analyse the performance of an advanced wastewater treatment plant. This user-friendly and menu-driven software is based on the dynamic mathematical model for an industrial wastewater treatment scheme that integrates chemical, biological and membrane-based unit operations. The software-predicted results corroborate very well with the experimental findings as indicated in the overall correlation coefficient of the order of 0.99. The software permits pre-analysis and manipulation of input data, helps in optimization and exhibits performance of an integrated plant visually on a graphical platform. It allows quick performance analysis of the whole system as well as the individual units. The software first of its kind in its domain and in the well-known Microsoft Excel environment is likely to be very useful in successful design, optimization and operation of an advanced hybrid treatment plant for hazardous wastewater.

New Hypervelocity Terminal Intercept Guidance Systems for Deflecting/Disrupting Hazardous Asteroids

NASA Astrophysics Data System (ADS)

Lyzhoft, Joshua Richard

Computational modeling and simulations of visual and infrared (IR) sensors are investigated for a new hypervelocity terminal guidance system of intercepting small asteroids (50 to 150 meters in diameter). Computational software tools for signal-to-noise ratio estimation of visual and IR sensors, estimation of minimum and maximum ranges of target detection, and GPU (Graphics Processing Units)-accelerated simulations of the IR-based terminal intercept guidance systems are developed. Scaled polyhedron models of known objects, such as the Rosetta mission's Comet 67P/C-G, NASA's OSIRIS-REx Bennu, and asteroid 433 Eros, are utilized in developing a GPU-based simulation tool for the IR-based terminal intercept guidance systems. A parallelized-ray tracing algorithm for simulating realistic surface-to-surface shadowing of irregular-shaped asteroids or comets is developed. Polyhedron solid-angle approximation is also considered. Using these computational models, digital image processing is investigated to determine single or multiple impact locations to assess the technical feasibility of new planetary defense mission concepts of utilizing a Hypervelocity Asteroid Intercept Vehicle (HAIV) or a Multiple Kinetic-energy Interceptor Vehicle (MKIV). Study results indicate that the IR-based guidance system outperforms the visual-based system in asteroid detection and tracking. When using an IR sensor, predicting impact locations from filtered images resulted in less jittery spacecraft control accelerations than conducting missions with a visual sensor. Infrared sensors have also the possibility to detect asteroids at greater distances, and if properly used, can aid in terminal phase guidance for proper impact location determination for the MKIV system. Emerging new topics of the Minimum Orbit Intersection Distance (MOID) estimation and the Full-Two-Body Problem (F2BP) formulation are also investigated to assess a potential near-Earth object collision risk and the proximity gravity effects of an irregular-shaped binary-asteroid target on a standoff nuclear explosion mission.

HyperPASS, a New Aeroassist Tool

NASA Technical Reports Server (NTRS)

Gates, Kristin; McRonald, Angus; Nock, Kerry

2005-01-01

A new software tool designed to perform aeroassist studies has been developed by Global Aerospace Corporation (GAC). The Hypersonic Planetary Aeroassist Simulation System (HyperPASS) [1] enables users to perform guided aerocapture, guided ballute aerocapture, aerobraking, orbit decay, or unguided entry simulations at any of six target bodies (Venus, Earth, Mars, Jupiter, Titan, or Neptune). HyperPASS is currently being used for trade studies to investigate (1) aerocapture performance with alternate aeroshell types, varying flight path angle and entry velocity, different gload and heating limits, and angle of attack and angle of bank variations; (2) variable, attached ballute geometry; (3) railgun launched projectile trajectories, and (4) preliminary orbit decay evolution. After completing a simulation, there are numerous visualization options in which data can be plotted, saved, or exported to various formats. Several analysis examples will be described.

Telecom Modeling with ChatterBell.

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

Jrad, Ahmad M.; Kelic, Andjelka

This document provides a description and user manual for the ChatterBell voice telecom modeling and simulation capability. The intended audience consists of network planners and practitioners who wish to use the tool to model a particular voice network and analyze its behavior under varying assumptions and possible failure conditions. ChatterBell is built on top of the N-SMART voice simulation and visualization suite that was developed through collaboration between Sandia National Laboratories and Bell Laboratories of Lucent Technologies. The new and improved modeling and simulation tool has been modified and modernized to incorporate the latest development in the telecom world includingmore » the widespread use of VoIP technology. In addition, ChatterBell provides new commands and modeling capabilities that were not available in the N-SMART application.« less

A Document Visualization Tool Customized to Explore DRDC Reports (Un outil de visualisation de document concu precisement pour explorer les rapports de RDDC)

DTIC Science & Technology

2011-08-01

context of flight simulators . ................................................................................................................... 14...particular area? Suppose a commander at CFB Shearwater wanted to find out more about how he/she can best deal with issues of pilots’ motion sickness...in the flight simulator on base. As a first step, one would enter, “motion sickness” as a query in HanDles, and get the relevant documents returned

A Guide for Developing Human-Robot Interaction Experiments in the Robotic Interactive Visualization and Experimentation Technology (RIVET) Simulation

DTIC Science & Technology

2016-05-01

research, Kunkler (2006) suggested that the similarities between computer simulation tools and robotic surgery systems (e.g., mechanized feedback...distribution is unlimited. 49 Davies B. A review of robotics in surgery . Proceedings of the Institution of Mechanical Engineers, Part H: Journal...ARL-TR-7683 ● MAY 2016 US Army Research Laboratory A Guide for Developing Human- Robot Interaction Experiments in the Robotic

A proposal for an open source graphical environment for simulating x-ray optics

NASA Astrophysics Data System (ADS)

Sanchez del Rio, Manuel; Rebuffi, Luca; Demsar, Janez; Canestrari, Niccolo; Chubar, Oleg

2014-09-01

A new graphic environment to drive X-ray optics simulation packages such as SHADOW and SRW is proposed. The aim is to simulate a virtual experiment, including the description of the electron beam and simulate the emitted radiation, the optics, the scattering by the sample and radiation detection. Python is chosen as common interaction language. The ingredients of the new application, a glossary of variables for optical component, the selection of visualization tools, and the integration of all these components in a high level workflow environment built on Orange are presented.

Predicting Airport Screening Officers' Visual Search Competency With a Rapid Assessment.

PubMed

Mitroff, Stephen R; Ericson, Justin M; Sharpe, Benjamin

2018-03-01

Objective The study's objective was to assess a new personnel selection and assessment tool for aviation security screeners. A mobile app was modified to create a tool, and the question was whether it could predict professional screeners' on-job performance. Background A variety of professions (airport security, radiology, the military, etc.) rely on visual search performance-being able to detect targets. Given the importance of such professions, it is necessary to maximize performance, and one means to do so is to select individuals who excel at visual search. A critical question is whether it is possible to predict search competency within a professional search environment. Method Professional searchers from the USA Transportation Security Administration (TSA) completed a rapid assessment on a tablet-based X-ray simulator (XRAY Screener, derived from the mobile technology app Airport Scanner; Kedlin Company). The assessment contained 72 trials that were simulated X-ray images of bags. Participants searched for prohibited items and tapped on them with their finger. Results Performance on the assessment significantly related to on-job performance measures for the TSA officers such that those who were better XRAY Screener performers were both more accurate and faster at the actual airport checkpoint. Conclusion XRAY Screener successfully predicted on-job performance for professional aviation security officers. While questions remain about the underlying cognitive mechanisms, this quick assessment was found to significantly predict on-job success for a task that relies on visual search performance. Application It may be possible to quickly assess an individual's visual search competency, which could help organizations select new hires and assess their current workforce.

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.

Validation of a Low Dose Simulation Technique for Computed Tomography Images

PubMed Central

Muenzel, Daniela; Koehler, Thomas; Brown, Kevin; Žabić, Stanislav; Fingerle, Alexander A.; Waldt, Simone; Bendik, Edgar; Zahel, Tina; Schneider, Armin; Dobritz, Martin; Rummeny, Ernst J.; Noël, Peter B.

2014-01-01

Purpose Evaluation of a new software tool for generation of simulated low-dose computed tomography (CT) images from an original higher dose scan. Materials and Methods Original CT scan data (100 mAs, 80 mAs, 60 mAs, 40 mAs, 20 mAs, 10 mAs; 100 kV) of a swine were acquired (approved by the regional governmental commission for animal protection). Simulations of CT acquisition with a lower dose (simulated 10–80 mAs) were calculated using a low-dose simulation algorithm. The simulations were compared to the originals of the same dose level with regard to density values and image noise. Four radiologists assessed the realistic visual appearance of the simulated images. Results Image characteristics of simulated low dose scans were similar to the originals. Mean overall discrepancy of image noise and CT values was −1.2% (range −9% to 3.2%) and −0.2% (range −8.2% to 3.2%), respectively, p>0.05. Confidence intervals of discrepancies ranged between 0.9–10.2 HU (noise) and 1.9–13.4 HU (CT values), without significant differences (p>0.05). Subjective observer evaluation of image appearance showed no visually detectable difference. Conclusion Simulated low dose images showed excellent agreement with the originals concerning image noise, CT density values, and subjective assessment of the visual appearance of the simulated images. An authentic low-dose simulation opens up opportunity with regard to staff education, protocol optimization and introduction of new techniques. PMID:25247422

A texture-based framework for improving CFD data visualization in a virtual environment

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

Bivins, Gerrick O'Ron

2005-01-01

In the field of computational fluid dynamics (CFD) accurate representations of fluid phenomena can be simulated hut require large amounts of data to represent the flow domain. Most datasets generated from a CFD simulation can be coarse, ~10,000 nodes or cells, or very fine with node counts on the order of 1,000,000. A typical dataset solution can also contain multiple solutions for each node, pertaining to various properties of the flow at a particular node. Scalar properties such as density, temperature, pressure, and velocity magnitude are properties that are typically calculated and stored in a dataset solution. Solutions are notmore » limited to just scalar properties. Vector quantities, such as velocity, are also often calculated and stored for a CFD simulation. Accessing all of this data efficiently during runtime is a key problem for visualization in an interactive application. Understanding simulation solutions requires a post-processing tool to convert the data into something more meaningful. Ideally, the application would present an interactive visual representation of the numerical data for any dataset that was simulated while maintaining the accuracy of the calculated solution. Most CFD applications currently sacrifice interactivity for accuracy, yielding highly detailed flow descriptions hut limiting interaction for investigating the field.« less

A texture-based frameowrk for improving CFD data visualization in a virtual environment

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

Bivins, Gerrick O'Ron

2005-01-01

In the field of computational fluid dynamics (CFD) accurate representations of fluid phenomena can be simulated but require large amounts of data to represent the flow domain. Most datasets generated from a CFD simulation can be coarse, ~ 10,000 nodes or cells, or very fine with node counts on the order of 1,000,000. A typical dataset solution can also contain multiple solutions for each node, pertaining to various properties of the flow at a particular node. Scalar properties such as density, temperature, pressure, and velocity magnitude are properties that are typically calculated and stored in a dataset solution. Solutions aremore » not limited to just scalar properties. Vector quantities, such as velocity, are also often calculated and stored for a CFD simulation. Accessing all of this data efficiently during runtime is a key problem for visualization in an interactive application. Understanding simulation solutions requires a post-processing tool to convert the data into something more meaningful. Ideally, the application would present an interactive visual representation of the numerical data for any dataset that was simulated while maintaining the accuracy of the calculated solution. Most CFD applications currently sacrifice interactivity for accuracy, yielding highly detailed flow descriptions but limiting interaction for investigating the field.« less

A tool for simulating parallel branch-and-bound methods

NASA Astrophysics Data System (ADS)

Golubeva, Yana; Orlov, Yury; Posypkin, Mikhail

2016-01-01

The Branch-and-Bound method is known as one of the most powerful but very resource consuming global optimization methods. Parallel and distributed computing can efficiently cope with this issue. The major difficulty in parallel B&B method is the need for dynamic load redistribution. Therefore design and study of load balancing algorithms is a separate and very important research topic. This paper presents a tool for simulating parallel Branchand-Bound method. The simulator allows one to run load balancing algorithms with various numbers of processors, sizes of the search tree, the characteristics of the supercomputer's interconnect thereby fostering deep study of load distribution strategies. The process of resolution of the optimization problem by B&B method is replaced by a stochastic branching process. Data exchanges are modeled using the concept of logical time. The user friendly graphical interface to the simulator provides efficient visualization and convenient performance analysis.

XIMPOL: a new x-ray polarimetry observation-simulation and analysis framework

NASA Astrophysics Data System (ADS)

Omodei, Nicola; Baldini, Luca; Pesce-Rollins, Melissa; di Lalla, Niccolò

2017-08-01

We present a new simulation framework, XIMPOL, based on the python programming language and the Scipy stack, specifically developed for X-ray polarimetric applications. XIMPOL is not tied to any specific mission or instrument design and is meant to produce fast and yet realistic observation-simulations, given as basic inputs: (i) an arbitrary source model including morphological, temporal, spectral and polarimetric information, and (ii) the response functions of the detector under study, i.e., the effective area, the energy dispersion, the point-spread function and the modulation factor. The format of the response files is OGIP compliant, and the framework has the capability of producing output files that can be directly fed into the standard visualization and analysis tools used by the X-ray community, including XSPEC which make it a useful tool not only for simulating physical systems, but also to develop and test end-to-end analysis chains.

Visualization resources for Iowa State University and the Iowa DOT : an automated design model to simulator converter.

DOT National Transportation Integrated Search

2012-11-01

This project developed an automatic conversion software tool that takes input a from an Iowa Department of Transportation (DOT) MicroStation three-dimensional (3D) design file and converts it into a form that can be used by the University of Iowas...

How Augmented Reality Enables Conceptual Understanding of Challenging Science Content

ERIC Educational Resources Information Center

Yoon, Susan; Anderson, Emma; Lin, Joyce; Elinich, Karen

2017-01-01

Research on learning about science has revealed that students often hold robust misconceptions about a number of scientific ideas. Digital simulation and dynamic visualization tools have helped to ameliorate these learning challenges by providing scaffolding to understand various aspects of the phenomenon. In this study we hypothesize that…

IMPLEMENTATION OF A CAPE-OPEN COMPLIANT PROCESS SIMULATOR USING MICROSOFT'S VISUAL STUDIO.NET AND THE .NET FRAMEWORK

EPA Science Inventory

The United States Environmental Protection Agency is developing a Computer
Aided Process Engineering (CAPE) software tool for the metal finishing
industry that helps users design efficient metal finishing processes that
are less polluting to the environment. Metal finish...

Risk Reduction and Training using Simulation Based Tools - 12180

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

Hall, Irin P.

2012-07-01

Process Modeling and Simulation (M and S) has been used for many years in manufacturing and similar domains, as part of an industrial engineer's tool box. Traditionally, however, this technique has been employed in small, isolated projects where models were created from scratch, often making it time and cost prohibitive. Newport News Shipbuilding (NNS) has recognized the value of this predictive technique and what it offers in terms of risk reduction, cost avoidance and on-schedule performance of highly complex work. To facilitate implementation, NNS has been maturing a process and the software to rapidly deploy and reuse M and Smore » based decision support tools in a variety of environments. Some examples of successful applications by NNS of this technique in the nuclear domain are a reactor refueling simulation based tool, a fuel handling facility simulation based tool and a tool for dynamic radiation exposure tracking. The next generation of M and S applications include expanding simulation based tools into immersive and interactive training. The applications discussed here take a tool box approach to creating simulation based decision support tools for maximum utility and return on investment. This approach involves creating a collection of simulation tools that can be used individually or integrated together for a larger application. The refueling simulation integrates with the fuel handling facility simulation to understand every aspect and dependency of the fuel handling evolutions. This approach translates nicely to other complex domains where real system experimentation is not feasible, such as nuclear fuel lifecycle and waste management. Similar concepts can also be applied to different types of simulation techniques. For example, a process simulation of liquid waste operations may be useful to streamline and plan operations, while a chemical model of the liquid waste composition is an important tool for making decisions with respect to waste disposition. Integrating these tools into a larger virtual system provides a tool for making larger strategic decisions. The key to integrating and creating these virtual environments is the software and the process used to build them. Although important steps in the direction of using simulation based tools for nuclear domain, the applications described here represent only a small cross section of possible benefits. The next generation of applications will, likely, focus on situational awareness and adaptive planning. Situational awareness refers to the ability to visualize in real time the state of operations. Some useful tools in this area are Geographic Information Systems (GIS), which help monitor and analyze geographically referenced information. Combined with such situational awareness capability, simulation tools can serve as the platform for adaptive planning tools. These are the tools that allow the decision maker to react to the changing environment in real time by synthesizing massive amounts of data into easily understood information. For the nuclear domains, this may mean creation of Virtual Nuclear Systems, from Virtual Waste Processing Plants to Virtual Nuclear Reactors. (authors)« less

Case studies on design, simulation and visualization of control and measurement applications using REX control system

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

Ozana, Stepan, E-mail: stepan.ozana@vsb.cz; Pies, Martin, E-mail: martin.pies@vsb.cz; Docekal, Tomas, E-mail: docekalt@email.cz

REX Control System is a professional advanced tool for design and implementation of complex control systems that belongs to softPLC category. It covers the entire process starting from simulation of functionality of the application before deployment, through implementation on real-time target, towards analysis, diagnostics and visualization. Basically it consists of two parts: the development tools and the runtime system. It is also compatible with Simulink environment, and the way of implementation of control algorithm is very similar. The control scheme is finally compiled (using RexDraw utility) and uploaded into a chosen real-time target (using RexView utility). There is a widemore » variety of hardware platforms and real-time operating systems supported by REX Control System such as for example Windows Embedded, Linux, Linux/Xenomai deployed on SBC, IPC, PAC, Raspberry Pi and others with many I/O interfaces. It is modern system designed both for measurement and control applications, offering a lot of additional functions concerning data archiving, visualization based on HTML5, and communication standards. The paper will sum up possibilities of its use in educational process, focused on control of case studies of physical models with classical and advanced control algorithms.« less

Visual acuity estimation from simulated images

NASA Astrophysics Data System (ADS)

Duncan, William J.

Simulated images can provide insight into the performance of optical systems, especially those with complicated features. Many modern solutions for presbyopia and cataracts feature sophisticated power geometries or diffractive elements. Some intraocular lenses (IOLs) arrive at multifocality through the use of a diffractive surface and multifocal contact lenses have a radially varying power profile. These type of elements induce simultaneous vision as well as affecting vision much differently than a monofocal ophthalmic appliance. With myriad multifocal ophthalmics available on the market it is difficult to compare or assess performance in ways that effect wearers of such appliances. Here we present software and algorithmic metrics that can be used to qualitatively and quantitatively compare ophthalmic element performance, with specific examples of bifocal intraocular lenses (IOLs) and multifocal contact lenses. We anticipate this study, methods, and results to serve as a starting point for more complex models of vision and visual acuity in a setting where modeling is advantageous. Generating simulated images of real- scene scenarios is useful for patients in assessing vision quality with a certain appliance. Visual acuity estimation can serve as an important tool for manufacturing and design of ophthalmic appliances.

In-Situ Visualization Experiments with ParaView Cinema in RAGE

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

Kares, Robert John

2015-10-15

A previous paper described some numerical experiments performed using the ParaView/Catalyst in-situ visualization infrastructure deployed in the Los Alamos RAGE radiation-hydrodynamics code to produce images from a running large scale 3D ICF simulation. One challenge of the in-situ approach apparent in these experiments was the difficulty of choosing parameters likes isosurface values for the visualizations to be produced from the running simulation without the benefit of prior knowledge of the simulation results and the resultant cost of recomputing in-situ generated images when parameters are chosen suboptimally. A proposed method of addressing this difficulty is to simply render multiple images atmore » runtime with a range of possible parameter values to produce a large database of images and to provide the user with a tool for managing the resulting database of imagery. Recently, ParaView/Catalyst has been extended to include such a capability via the so-called Cinema framework. Here I describe some initial experiments with the first delivery of Cinema and make some recommendations for future extensions of Cinema’s capabilities.« less

Data Cube Visualization with Blender

NASA Astrophysics Data System (ADS)

Kent, Brian R.; Gárate, Matías

2017-06-01

With the increasing data acquisition rates from observational and computational astrophysics, new tools are needed to study and visualize data. We present a methodology for rendering 3D data cubes using the open-source 3D software Blender. By importing processed observations and numerical simulations through the Voxel Data format, we are able use the Blender interface and Python API to create high-resolution animated visualizations. We review the methods for data import, animation, and camera movement, and present examples of this methodology. The 3D rendering of data cubes gives scientists the ability to create appealing displays that can be used for both scientific presentations as well as public outreach.

The dark side of photovoltaic — 3D simulation of glare assessing risk and discomfort

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

Rose, Thomas; Wollert, Alexander

2015-04-15

Photovoltaic (PV) systems form an important force in the implementation of renewable energies, but as we all know, the force has always its dark side. Besides efficiency considerations and discussions about architectures of power distribution networks, the increasing numbers of installations of PV systems for implementing renewable energies have secondary effects. PV systems can generate glare due to optical reflections and hence might be a serious concern. On the one hand, glare could affect safety, e.g. regarding traffic. On the other hand, glare is a constant source of discomfort in vicinities of PV systems. Hence, assessment of glare is decisivemore » for the success of renewable energies near municipalities and traffic zones for the success of solar power. Several courts decided on the change of PV systems and even on their de-installation because of glare effects. Thus, location-based assessments are required to limit potential reflections and to avoid risks for public infrastructure or discomfort of residents. The question arises on how to calculate reflections accurately according to the environment's topography. Our approach is founded in a 3D-based simulation methodology to calculate and visualize reflections based on the geometry of the environment of PV systems. This computational model is implemented by an interactive tool for simulation and visualization. Hence, project planners receive flexible assistance for adjusting the parameters of solar panels amid the planning process and in particular before the installation of a PV system. - Highlights: • Solar panels cause glare that impacts neighborhoods and traffic infrastructures. • Glare might cause disability and discomfort. • 3D environment for the calculation of glare • Interactive tool to simulate and visualize reflections • Impact assessment of solar power plant farms.« less

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

Applications of pilot scanning behavior to integrated display research

NASA Technical Reports Server (NTRS)

Waller, M. C.

1977-01-01

The oculometer is an electrooptical device designed to measure pilot scanning behavior during instrument approaches and landing operations. An overview of some results from a simulation study is presented to illustrate how information from the oculometer installed in a visual motion simulator, combined with measures of performance and control input data, can provide insight into the behavior and tactics of individual pilots during instrument approaches. Differences in measured behavior of the pilot subjects are pointed out; these differences become apparent in the way the pilots distribute their visual attention, in the amount of control activity, and in selected performance measures. Some of these measured differences have diagnostic implications, suggesting the use of the oculometer along with performance measures as a pilot training tool.

Evaluating methods to visualize patterns of genetic differentiation on a landscape.

PubMed

House, Geoffrey L; Hahn, Matthew W

2018-05-01

With advances in sequencing technology, research in the field of landscape genetics can now be conducted at unprecedented spatial and genomic scales. This has been especially evident when using sequence data to visualize patterns of genetic differentiation across a landscape due to demographic history, including changes in migration. Two recent model-based visualization methods that can highlight unusual patterns of genetic differentiation across a landscape, SpaceMix and EEMS, are increasingly used. While SpaceMix's model can infer long-distance migration, EEMS' model is more sensitive to short-distance changes in genetic differentiation, and it is unclear how these differences may affect their results in various situations. Here, we compare SpaceMix and EEMS side by side using landscape genetics simulations representing different migration scenarios. While both methods excel when patterns of simulated migration closely match their underlying models, they can produce either un-intuitive or misleading results when the simulated migration patterns match their models less well, and this may be difficult to assess in empirical data sets. We also introduce unbundled principal components (un-PC), a fast, model-free method to visualize patterns of genetic differentiation by combining principal components analysis (PCA), which is already used in many landscape genetics studies, with the locations of sampled individuals. Un-PC has characteristics of both SpaceMix and EEMS and works well with simulated and empirical data. Finally, we introduce msLandscape, a collection of tools that streamline the creation of customizable landscape-scale simulations using the popular coalescent simulator ms and conversion of the simulated data for use with un-PC, SpaceMix and EEMS. © 2017 John Wiley & Sons Ltd.

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

Influence of Immersive Human Scale Architectural Representation on Design Judgment

NASA Astrophysics Data System (ADS)

Elder, Rebecca L.

Unrealistic visual representation of architecture within our existing environments have lost all reference to the human senses. As a design tool, visual and auditory stimuli can be utilized to determine human's perception of design. This experiment renders varying building inputs within different sites, simulated with corresponding immersive visual and audio sensory cues. Introducing audio has been proven to influence the way a person perceives a space, yet most inhabitants rely strictly on their sense of vision to make design judgments. Though not as apparent, users prefer spaces that have a better quality of sound and comfort. Through a series of questions, we can begin to analyze whether a design is fit for both an acoustic and visual environment.

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

Visualization of particle interactions in granular media.

PubMed

Meier, Holger A; Schlemmer, Michael; Wagner, Christian; Kerren, Andreas; Hagen, Hans; Kuhl, Ellen; Steinmann, Paul

2008-01-01

Interaction between particles in so-called granular media, such as soil and sand, plays an important role in the context of geomechanical phenomena and numerous industrial applications. A two scale homogenization approach based on a micro and a macro scale level is briefly introduced in this paper. Computation of granular material in such a way gives a deeper insight into the context of discontinuous materials and at the same time reduces the computational costs. However, the description and the understanding of the phenomena in granular materials are not yet satisfactory. A sophisticated problem-specific visualization technique would significantly help to illustrate failure phenomena on the microscopic level. As main contribution, we present a novel 2D approach for the visualization of simulation data, based on the above outlined homogenization technique. Our visualization tool supports visualization on micro scale level as well as on macro scale level. The tool shows both aspects closely arranged in form of multiple coordinated views to give users the possibility to analyze the particle behavior effectively. A novel type of interactive rose diagrams was developed to represent the dynamic contact networks on the micro scale level in a condensed and efficient way.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.

PubMed

McGibbon, Robert T; Beauchamp, Kyle A; Harrigan, Matthew P; Klein, Christoph; Swails, Jason M; Hernández, Carlos X; Schwantes, Christian R; Wang, Lee-Ping; Lane, Thomas J; Pande, Vijay S

2015-10-20

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

PubMed Central

McGibbon, Robert T.; Beauchamp, Kyle A.; Harrigan, Matthew P.; Klein, Christoph; Swails, Jason M.; Hernández, Carlos X.; Schwantes, Christian R.; Wang, Lee-Ping; Lane, Thomas J.; Pande, Vijay S.

2015-01-01

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. PMID:26488642

Ranked centroid projection: a data visualization approach with self-organizing maps.

PubMed

Yen, G G; Wu, Z

2008-02-01

The self-organizing map (SOM) is an efficient tool for visualizing high-dimensional data. In this paper, the clustering and visualization capabilities of the SOM, especially in the analysis of textual data, i.e., document collections, are reviewed and further developed. A novel clustering and visualization approach based on the SOM is proposed for the task of text mining. The proposed approach first transforms the document space into a multidimensional vector space by means of document encoding. Afterwards, a growing hierarchical SOM (GHSOM) is trained and used as a baseline structure to automatically produce maps with various levels of detail. Following the GHSOM training, the new projection method, namely the ranked centroid projection (RCP), is applied to project the input vectors to a hierarchy of 2-D output maps. The RCP is used as a data analysis tool as well as a direct interface to the data. In a set of simulations, the proposed approach is applied to an illustrative data set and two real-world scientific document collections to demonstrate its applicability.

A computer graphics system for visualizing spacecraft in orbit

NASA Technical Reports Server (NTRS)

Eyles, Don E.

1989-01-01

To carry out unanticipated operations with resources already in space is part of the rationale for a permanently manned space station in Earth orbit. The astronauts aboard a space station will require an on-board, spatial display tool to assist the planning and rehearsal of upcoming operations. Such a tool can also help astronauts to monitor and control such operations as they occur, especially in cases where first-hand visibility is not possible. A computer graphics visualization system designed for such an application and currently implemented as part of a ground-based simulation is described. The visualization system presents to the user the spatial information available in the spacecraft's computers by drawing a dynamic picture containing the planet Earth, the Sun, a star field, and up to two spacecraft. The point of view within the picture can be controlled by the user to obtain a number of specific visualization functions. The elements of the display, the methods used to control the display's point of view, and some of the ways in which the system can be used are described.

Evaluating System Parameters on a Dragonfly using Simulation and Visualization

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

Bhatele, Abhinav; Jain, Nikhil; Livnat, Yarden

The dragon y topology is becoming a popular choice for build- ing high-radix, low-diameter networks with high-bandwidth links. Even with a powerful network, preliminary experi- ments on Edison at NERSC have shown that for communica- tion heavy applications, job interference and thus presumably job placement remains an important factor. In this paper, we explore the e ects of job placement, job sizes, parallel workloads and network con gurations on network through- put to better understand inter-job interference. We use a simulation tool called Damsel y to model the network be- havior of Edison and study the impact of various systemmore » parameters on network throughput. Parallel workloads based on ve representative communication patters are used and the simulation studies on up to 131,072 cores are aided by a new visualization of the dragon y network.« less

Unsteady, Cooled Turbine Simulation Using a PC-Linux Analysis System

NASA Technical Reports Server (NTRS)

List, Michael G.; Turner, Mark G.; Chen, Jen-Pimg; Remotigue, Michael G.; Veres, Joseph P.

2004-01-01

The fist stage of the high-pressure turbine (HPT) of the GE90 engine was simulated with a three-dimensional unsteady Navier-Sokes solver, MSU Turbo, which uses source terms to simulate the cooling flows. In addition to the solver, its pre-processor, GUMBO, and a post-processing and visualization tool, Turbomachinery Visual3 (TV3) were run in a Linux environment to carry out the simulation and analysis. The solver was run both with and without cooling. The introduction of cooling flow on the blade surfaces, case, and hub and its effects on both rotor-vane interaction as well the effects on the blades themselves were the principle motivations for this study. The studies of the cooling flow show the large amount of unsteadiness in the turbine and the corresponding hot streak migration phenomenon. This research on the GE90 turbomachinery has also led to a procedure for running unsteady, cooled turbine analysis on commodity PC's running the Linux operating system.

Simulation-Based Analysis of Reentry Dynamics for the Sharp Atmospheric Entry Vehicle

NASA Technical Reports Server (NTRS)

Tillier, Clemens Emmanuel

1998-01-01

This thesis describes the analysis of the reentry dynamics of a high-performance lifting atmospheric entry vehicle through numerical simulation tools. The vehicle, named SHARP, is currently being developed by the Thermal Protection Materials and Systems branch of NASA Ames Research Center, Moffett Field, California. The goal of this project is to provide insight into trajectory tradeoffs and vehicle dynamics using simulation tools that are powerful, flexible, user-friendly and inexpensive. Implemented Using MATLAB and SIMULINK, these tools are developed with an eye towards further use in the conceptual design of the SHARP vehicle's trajectory and flight control systems. A trajectory simulator is used to quantify the entry capabilities of the vehicle subject to various operational constraints. Using an aerodynamic database computed by NASA and a model of the earth, the simulator generates the vehicle trajectory in three-dimensional space based on aerodynamic angle inputs. Requirements for entry along the SHARP aerothermal performance constraint are evaluated for different control strategies. Effect of vehicle mass on entry parameters is investigated, and the cross range capability of the vehicle is evaluated. Trajectory results are presented and interpreted. A six degree of freedom simulator builds on the trajectory simulator and provides attitude simulation for future entry controls development. A Newtonian aerodynamic model including control surfaces and a mass model are developed. A visualization tool for interpreting simulation results is described. Control surfaces are roughly sized. A simple controller is developed to fly the vehicle along its aerothermal performance constraint using aerodynamic flaps for control. This end-to-end demonstration proves the suitability of the 6-DOF simulator for future flight control system development. Finally, issues surrounding real-time simulation with hardware in the loop are discussed.

EDITORIAL: Focus on Visualization in Physics FOCUS ON VISUALIZATION IN PHYSICS

NASA Astrophysics Data System (ADS)

Sanders, Barry C.; Senden, Tim; Springel, Volker

2008-12-01

Advances in physics are intimately connected with developments in a new technology, the telescope, precision clocks, even the computer all have heralded a shift in thinking. These landmark developments open new opportunities accelerating research and in turn new scientific directions. These technological drivers often correspond to new instruments, but equally might just as well flag a new mathematical tool, an algorithm or even means to visualize physics in a new way. Early on in this twenty-first century, scientific communities are just starting to explore the potential of digital visualization. Whether visualization is used to represent and communicate complex concepts, or to understand and interpret experimental data, or to visualize solutions to complex dynamical equations, the basic tools of visualization are shared in each of these applications and implementations. High-performance computing exemplifies the integration of visualization with leading research. Visualization is an indispensable tool for analyzing and interpreting complex three-dimensional dynamics as well as to diagnose numerical problems in intricate parallel calculation algorithms. The effectiveness of visualization arises by exploiting the unmatched capability of the human eye and visual cortex to process the large information content of images. In a brief glance, we recognize patterns or identify subtle features even in noisy data, something that is difficult or impossible to achieve with more traditional forms of data analysis. Importantly, visualizations guide the intuition of researchers and help to comprehend physical phenomena that lie far outside of direct experience. In fact, visualizations literally allow us to see what would otherwise remain completely invisible. For example, artificial imagery created to visualize the distribution of dark matter in the Universe has been instrumental to develop the notion of a cosmic web, and for helping to establish the current standard model of cosmology wherein this (in principle invisible) dark matter dominates the cosmic matter content. The advantages of visualization found for simulated data also hold for real world data as well. With the application of computerized acquisition many scientific disciplines are witnessing exponential growth rates of the volume of accumulated raw data, which often makes it daunting to condense the information into a manageable form, a challenge that can be addressed by modern visualization techniques. Such visualizations are also often an enticing way to communicate scientific results to the general public. This need for visualization is especially true in basic science, with its reliance on a benevolent and interested general public that drives the need for high-quality visualizations. Despite the widespread use of visualization, this technology has suffered from a lack of the unifying influence of shared common experiences. As with any emerging technology practitioners have often independently found solutions to similar problems. It is the aim of this focus issue to celebrate the importance of visualization, report on its growing use by the broad community of physicists, including biophysics, chemical physics, geophysics, astrophysics, and medical physics, and provide an opportunity for the diverse community of scientists using visualization to share work in one issue of a journal that itself is in the vanguard of supporting visualization and multimedia. A remarkable breadth and diversity of visualization in physics is to be found in this issue spanning fundamental aspects of relativity theory to computational fluid dynamics. The topics span length scales that are as small as quantum phenomena to the entire observable Universe. We have been impressed by the quality of the submissions and hope that this snap-shot will introduce, inform, motivate and maybe even help to unify visualization in physics. Readers are also directed to the December issue of Physics World which includes the following features highlighting work in this collection and other novel uses of visualization techniques: 'A feast of visualization' Physics World December 2008 pp 20 23 'Seeing the quantum world' by Barry Sanders Physics World December 2008 pp 24 27 'A picture of the cosmos' by Mark SubbaRao and Miguel Aragon-Calvo Physics World December 2008 pp 29 32 'Thinking outside the cube' by César A Hidalgo Physics World December 2008 pp 34 37 Focus on Visualization in Physics Contents Visualization of spiral and scroll waves in simulated and experimental cardiac tissue E M Cherry and F H Fenton Visualization of large scale structure from the Sloan Digital Sky Survey M U SubbaRao, M A Aragón-Calvo, H W Chen, J M Quashnock, A S Szalay and D G York How computers can help us in creating an intuitive access to relativity Hanns Ruder, Daniel Weiskopf, Hans-Peter Nollert and Thomas Müller Lagrangian particle tracking in three dimensions via single-camera in-line digital holography Jiang Lu, Jacob P Fugal, Hansen Nordsiek, Ewe Wei Saw, Raymond A Shaw and Weidong Yang Quantifying spatial heterogeneity from images Andrew E Pomerantz and Yi-Qiao Song Disaggregation and scientific visualization of earthscapes considering trends and spatial dependence structures S Grunwald Strength through structure: visualization and local assessment of the trabecular bone structure C Räth, R Monetti, J Bauer, I Sidorenko, D Müller, M Matsuura, E-M Lochmüller, P Zysset and F Eckstein Thermonuclear supernovae: a multi-scale astrophysical problem challenging numerical simulations and visualization F K Röpke and R Bruckschen Visualization needs and techniques for astrophysical simulations W Kapferer and T Riser Flow visualization and field line advection in computational fluid dynamics: application to magnetic fields and turbulent flows Pablo Mininni, Ed Lee, Alan Norton and John Clyne Splotch: visualizing cosmological simulations K Dolag, M Reinecke, C Gheller and S Imboden Visualizing a silicon quantum computer Barry C Sanders, Lloyd C L Hollenberg, Darran Edmundson and Andrew Edmundson Colliding galaxies, rotating neutron stars and merging black holes—visualizing high dimensional datasets on arbitrary meshes Werner Benger A low complexity visualization tool that helps to perform complex systems analysis M G Beiró, J I Alvarez-Hamelin and J R Busch Visualizing astrophysical N-body systems John Dubinski

Data Visualization Using Immersive Virtual Reality Tools

NASA Astrophysics Data System (ADS)

Cioc, Alexandru; Djorgovski, S. G.; Donalek, C.; Lawler, E.; Sauer, F.; Longo, G.

2013-01-01

The growing complexity of scientific data poses serious challenges for an effective visualization. Data sets, e.g., catalogs of objects detected in sky surveys, can have a very high dimensionality, ~ 100 - 1000. Visualizing such hyper-dimensional data parameter spaces is essentially impossible, but there are ways of visualizing up to ~ 10 dimensions in a pseudo-3D display. We have been experimenting with the emerging technologies of immersive virtual reality (VR) as a platform for a scientific, interactive, collaborative data visualization. Our initial experiments used the virtual world of Second Life, and more recently VR worlds based on its open source code, OpenSimulator. There we can visualize up to ~ 100,000 data points in ~ 7 - 8 dimensions (3 spatial and others encoded as shapes, colors, sizes, etc.), in an immersive virtual space where scientists can interact with their data and with each other. We are now developing a more scalable visualization environment using the popular (practically an emerging standard) Unity 3D Game Engine, coded using C#, JavaScript, and the Unity Scripting Language. This visualization tool can be used through a standard web browser, or a standalone browser of its own. Rather than merely plotting data points, the application creates interactive three-dimensional objects of various shapes, colors, and sizes, and of course the XYZ positions, encoding various dimensions of the parameter space, that can be associated interactively. Multiple users can navigate through this data space simultaneously, either with their own, independent vantage points, or with a shared view. At this stage ~ 100,000 data points can be easily visualized within seconds on a simple laptop. The displayed data points can contain linked information; e.g., upon a clicking on a data point, a webpage with additional information can be rendered within the 3D world. A range of functionalities has been already deployed, and more are being added. We expect to make this visualization tool freely available to the academic community within a few months, on an experimental (beta testing) basis.

Ovis: A Framework for Visual Analysis of Ocean Forecast Ensembles.

PubMed

Höllt, Thomas; Magdy, Ahmed; Zhan, Peng; Chen, Guoning; Gopalakrishnan, Ganesh; Hoteit, Ibrahim; Hansen, Charles D; Hadwiger, Markus

2014-08-01

We present a novel integrated visualization system that enables interactive visual analysis of ensemble simulations of the sea surface height that is used in ocean forecasting. The position of eddies can be derived directly from the sea surface height and our visualization approach enables their interactive exploration and analysis.The behavior of eddies is important in different application settings of which we present two in this paper. First, we show an application for interactive planning of placement as well as operation of off-shore structures using real-world ensemble simulation data of the Gulf of Mexico. Off-shore structures, such as those used for oil exploration, are vulnerable to hazards caused by eddies, and the oil and gas industry relies on ocean forecasts for efficient operations. We enable analysis of the spatial domain, as well as the temporal evolution, for planning the placement and operation of structures.Eddies are also important for marine life. They transport water over large distances and with it also heat and other physical properties as well as biological organisms. In the second application we present the usefulness of our tool, which could be used for planning the paths of autonomous underwater vehicles, so called gliders, for marine scientists to study simulation data of the largely unexplored Red Sea.

Proposal Tools for ASTRO-E

NASA Astrophysics Data System (ADS)

Mukai, K.; ASTRO-E Guest Observer Facility Team

1998-12-01

The XRS instrument on board ASTRO-E is expected to last about two years, before it runs out of cryogen. This leads us to place a particular emphasis on the technical aspects of the observing proposals to maximize the scientific return, more so than for missions/instruments with longer life times. In this talk, we will introduce the tools that we provide for you to write technically sound ASTRO-E XRS proposals. They include PIMMS/W3pimms and xspec/WebSpec for exposure time calculation, simaste for more detailed simulations (particularly of extended sources), and Wasabi, the Web-based observation visualization tool.

Picture this: The value of multiple visual representations for student learning of quantum concepts in general chemistry

NASA Astrophysics Data System (ADS)

Allen, Emily Christine

Mental models for scientific learning are often defined as, "cognitive tools situated between experiments and theories" (Duschl & Grandy, 2012). In learning, these cognitive tools are used to not only take in new information, but to help problem solve in new contexts. Nancy Nersessian (2008) describes a mental model as being "[loosely] characterized as a representation of a system with interactive parts with representations of those interactions. Models can be qualitative, quantitative, and/or simulative (mental, physical, computational)" (p. 63). If conceptual parts used by the students in science education are inaccurate, then the resulting model will not be useful. Students in college general chemistry courses are presented with multiple abstract topics and often struggle to fit these parts into complete models. This is especially true for topics that are founded on quantum concepts, such as atomic structure and molecular bonding taught in college general chemistry. The objectives of this study were focused on how students use visual tools introduced during instruction to reason with atomic and molecular structure, what misconceptions may be associated with these visual tools, and how visual modeling skills may be taught to support students' use of visual tools for reasoning. The research questions for this study follow from Gilbert's (2008) theory that experts use multiple representations when reasoning and modeling a system, and Kozma and Russell's (2005) theory of representational competence levels. This study finds that as students developed greater command of their understanding of abstract quantum concepts, they spontaneously provided additional representations to describe their more sophisticated models of atomic and molecular structure during interviews. This suggests that when visual modeling with multiple representations is taught, along with the limitations of the representations, it can assist students in the development of models for reasoning about abstract topics such as atomic and molecular structure. There is further gain if students' difficulties with these representations are targeted through the use additional instruction such as a workbook that requires the students to exercise their visual modeling skills.

Infusion of a Gaming Paradigm into Computer-Aided Engineering Design Tools

DTIC Science & Technology

2012-05-03

Virtual Test Bed (VTB), and the gaming tool, Unity3D . This hybrid gaming environment coupled a three-dimensional (3D) multibody vehicle system model...from Google Earth to the 3D visual front-end fabricated around Unity3D . The hybrid environment was sufficiently developed to support analyses of the...ndFr Cti3r4 G’OjrdFr ctior-2 The VTB simulation of the vehicle dynamics ran concurrently with and interacted with the gaming engine, Unity3D which

Modeling Airport Ground Operations using Discrete Event Simulation (DES) and X3D Visualization

DTIC Science & Technology

2008-03-01

scenes. It is written in open-source Java and XML using the Netbeans platform, which gave the features of being suitable as standalone applications...and as a plug-in module for the Netbeans integrated development environment (IDE). X3D Graphics is the tool used for the elaboration the creation of...process is shown in Figure 2. To 20 create a new event graph in Viskit, first, Viskit tool must be launched via Netbeans or from the executable

Multi-focused geospatial analysis using probes.

PubMed

Butkiewicz, Thomas; Dou, Wenwen; Wartell, Zachary; Ribarsky, William; Chang, Remco

2008-01-01

Traditional geospatial information visualizations often present views that restrict the user to a single perspective. When zoomed out, local trends and anomalies become suppressed and lost; when zoomed in for local inspection, spatial awareness and comparison between regions become limited. In our model, coordinated visualizations are integrated within individual probe interfaces, which depict the local data in user-defined regions-of-interest. Our probe concept can be incorporated into a variety of geospatial visualizations to empower users with the ability to observe, coordinate, and compare data across multiple local regions. It is especially useful when dealing with complex simulations or analyses where behavior in various localities differs from other localities and from the system as a whole. We illustrate the effectiveness of our technique over traditional interfaces by incorporating it within three existing geospatial visualization systems: an agent-based social simulation, a census data exploration tool, and an 3D GIS environment for analyzing urban change over time. In each case, the probe-based interaction enhances spatial awareness, improves inspection and comparison capabilities, expands the range of scopes, and facilitates collaboration among multiple users.

Spatial Cognition Support for Exploring the Design Mechanics of Building Structures

ERIC Educational Resources Information Center

Rudy, Margit; Hauck, Richard

2008-01-01

A web-based tool for visualizing the simulated structural behavior of building models was developed to support the teaching of structural design to architecture and engineering students by activating their spatial cognition capabilities. The main didactic issues involved establishing a consistent and complete three-dimensional vocabulary (3D)…

Simulating the Effects of Alternative Forest Management Strategies on Landscape Structure

Treesearch

Eric J. Gustafson; Thomas Crow

1996-01-01

Quantitative, spatial tools are needed to assess the long-term spatial consequences of alternative management strategies for land use planning and resource management. We constructed a timber harvest allocation model (HARVEST) that provides a visual and quantitative means to predict the spatial pattern of forest openings produced by alternative harvest strategies....

Education about Hallucinations Using an Internet Virtual Reality System: A Qualitative Survey

ERIC Educational Resources Information Center

Yellowlees, Peter M.; Cook, James N.

2006-01-01

Objective: The authors evaluate an Internet virtual reality technology as an education tool about the hallucinations of psychosis. Method: This is a pilot project using Second Life, an Internet-based virtual reality system, in which a virtual reality environment was constructed to simulate the auditory and visual hallucinations of two patients…

Emulation of rocket trajectory based on a six degree of freedom model

NASA Astrophysics Data System (ADS)

Zhang, Wenpeng; Li, Fan; Wu, Zhong; Li, Rong

2008-10-01

In this paper, a 6-DOF motion mathematical model is discussed. It is consisted of body dynamics and kinematics block, aero dynamics block and atmosphere block. Based on Simulink, the whole rocket trajectory mathematical model is developed. In this model, dynamic system simulation becomes easy and visual. The method of modularization design gives more convenience to transplant. At last, relevant data is given to be validated by Monte Carlo means. Simulation results show that the flight trajectory of the rocket can be simulated preferably by means of this model, and it also supplies a necessary simulating tool for the development of control system.

On the Treatment of Field Quantities and Elemental Continuity in FEM Solutions.

PubMed

Jallepalli, Ashok; Docampo-Sanchez, Julia; Ryan, Jennifer K; Haimes, Robert; Kirby, Robert M

2018-01-01

As the finite element method (FEM) and the finite volume method (FVM), both traditional and high-order variants, continue their proliferation into various applied engineering disciplines, it is important that the visualization techniques and corresponding data analysis tools that act on the results produced by these methods faithfully represent the underlying data. To state this in another way: the interpretation of data generated by simulation needs to be consistent with the numerical schemes that underpin the specific solver technology. As the verifiable visualization literature has demonstrated: visual artifacts produced by the introduction of either explicit or implicit data transformations, such as data resampling, can sometimes distort or even obfuscate key scientific features in the data. In this paper, we focus on the handling of elemental continuity, which is often only continuous or piecewise discontinuous, when visualizing primary or derived fields from FEM or FVM simulations. We demonstrate that traditional data handling and visualization of these fields introduce visual errors. In addition, we show how the use of the recently proposed line-SIAC filter provides a way of handling elemental continuity issues in an accuracy-conserving manner with the added benefit of casting the data in a smooth context even if the representation is element discontinuous.

Using the GeoFEST Faulted Region Simulation System

NASA Technical Reports Server (NTRS)

Parker, Jay W.; Lyzenga, Gregory A.; Donnellan, Andrea; Judd, Michele A.; Norton, Charles D.; Baker, Teresa; Tisdale, Edwin R.; Li, Peggy

2004-01-01

GeoFEST (the Geophysical Finite Element Simulation Tool) simulates stress evolution, fault slip and plastic/elastic processes in realistic materials, and so is suitable for earthquake cycle studies in regions such as Southern California. Many new capabilities and means of access for GeoFEST are now supported. New abilities include MPI-based cluster parallel computing using automatic PYRAMID/Parmetis-based mesh partitioning, automatic mesh generation for layered media with rectangular faults, and results visualization that is integrated with remote sensing data. The parallel GeoFEST application has been successfully run on over a half-dozen computers, including Intel Xeon clusters, Itanium II and Altix machines, and the Apple G5 cluster. It is not separately optimized for different machines, but relies on good domain partitioning for load-balance and low communication, and careful writing of the parallel diagonally preconditioned conjugate gradient solver to keep communication overhead low. Demonstrated thousand-step solutions for over a million finite elements on 64 processors require under three hours, and scaling tests show high efficiency when using more than (order of) 4000 elements per processor. The source code and documentation for GeoFEST is available at no cost from Open Channel Foundation. In addition GeoFEST may be used through a browser-based portal environment available to approved users. That environment includes semi-automated geometry creation and mesh generation tools, GeoFEST, and RIVA-based visualization tools that include the ability to generate a flyover animation showing deformations and topography. Work is in progress to support simulation of a region with several faults using 16 million elements, using a strain energy metric to adapt the mesh to faithfully represent the solution in a region of widely varying strain.

Reliability of regional climate simulations

NASA Astrophysics Data System (ADS)

Ahrens, W.; Block, A.; Böhm, U.; Hauffe, D.; Keuler, K.; Kücken, M.; Nocke, Th.

2003-04-01

Quantification of uncertainty becomes more and more a key issue for assessing the trustability of future climate scenarios. In addition to the mean conditions, climate impact modelers focus in particular on extremes. Before generating such scenarios using e.g. dynamic regional climate models, a careful validation of present-day simulations should be performed to determine the range of errors for the quantities of interest under recent conditions as a raw estimate of their uncertainty in the future. Often, multiple aspects shall be covered together, and the required simulation accuracy depends on the user's demand. In our approach, a massive parallel regional climate model shall be used on the one hand to generate "long-term" high-resolution climate scenarios for several decades, and on the other hand to provide very high-resolution ensemble simulations of future dry spells or heavy rainfall events. To diagnosis the model's performance for present-day simulations, we have recently developed and tested a first version of a validation and visualization chain for this model. It is, however, applicable in a much more general sense and could be used as a common test bed for any regional climate model aiming at this type of simulations. Depending on the user's interest, integrated quality measures can be derived for near-surface parameters using multivariate techniques and multidimensional distance measures in a first step. At this point, advanced visualization techniques have been developed and included to allow for visual data mining and to qualitatively identify dominating aspects and regularities. Univariate techniques that are especially designed to assess climatic aspects in terms of statistical properties can then be used to quantitatively diagnose the error contributions of the individual used parameters. Finally, a comprehensive in-depth diagnosis tool allows to investigate, why the model produces the obtained near-surface results to answer the question if the model performs well from the modeler's point of view. Examples will be presented for results obtained using this approach for assessing the risk of potential total agricultural yield loss under drought conditions in Northeast Brazil and for evaluating simulation results for a 10-year period for Europe. To support multi-run simulations and result evaluation, the model will be embedded into an already existing simulation environment that provides further postprocessing tools for sensitivity studies, behavioral analysis and Monte-Carlo simulations, but also for ensemble scenario analysis in one of the next steps.

Designs for Risk Evaluation and Management

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

The Designs for Risk Evaluation and Management (DREAM) tool was developed as part of the effort to quantify the risk of geologic storage of carbon dioxide (CO 2) under the U.S. Department of Energy's National Risk Assessment Partnership (NRAP). DREAM is an optimization tool created to identify optimal monitoring schemes that minimize the time to first detection of CO 2 leakage from a subsurface storage formation. DREAM acts as a post-processer on user-provided output from subsurface leakage simulations. While DREAM was developed for CO 2 leakage scenarios, it is applicable to any subsurface leakage simulation of the same output format.more » The DREAM tool is comprised of three main components: (1) a Java wizard used to configure and execute the simulations, (2) a visualization tool to view the domain space and optimization results, and (3) a plotting tool used to analyze the results. A secondary Java application is provided to aid users in converting common American Standard Code for Information Interchange (ASCII) output data to the standard DREAM hierarchical data format (HDF5). DREAM employs a simulated annealing approach that searches the solution space by iteratively mutating potential monitoring schemes built of various configurations of monitoring locations and leak detection parameters. This approach has proven to be orders of magnitude faster than an exhaustive search of the entire solution space. The user's manual illustrates the program graphical user interface (GUI), describes the tool inputs, and includes an example application.« less

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.

Validation of a novel technique for creating simulated radiographs using computed tomography datasets.

PubMed

Mendoza, Patricia; d'Anjou, Marc-André; Carmel, Eric N; Fournier, Eric; Mai, Wilfried; Alexander, Kate; Winter, Matthew D; Zwingenberger, Allison L; Thrall, Donald E; Theoret, Christine

2014-01-01

Understanding radiographic anatomy and the effects of varying patient and radiographic tube positioning on image quality can be a challenge for students. The purposes of this study were to develop and validate a novel technique for creating simulated radiographs using computed tomography (CT) datasets. A DICOM viewer (ORS Visual) plug-in was developed with the ability to move and deform cuboidal volumetric CT datasets, and to produce images simulating the effects of tube-patient-detector distance and angulation. Computed tomographic datasets were acquired from two dogs, one cat, and one horse. Simulated radiographs of different body parts (n = 9) were produced using different angles to mimic conventional projections, before actual digital radiographs were obtained using the same projections. These studies (n = 18) were then submitted to 10 board-certified radiologists who were asked to score visualization of anatomical landmarks, depiction of patient positioning, realism of distortion/magnification, and image quality. No significant differences between simulated and actual radiographs were found for anatomic structure visualization and patient positioning in the majority of body parts. For the assessment of radiographic realism, no significant differences were found between simulated and digital radiographs for canine pelvis, equine tarsus, and feline abdomen body parts. Overall, image quality and contrast resolution of simulated radiographs were considered satisfactory. Findings from the current study indicated that radiographs simulated using this new technique are comparable to actual digital radiographs. Further studies are needed to apply this technique in developing interactive tools for teaching radiographic anatomy and the effects of varying patient and tube positioning. © 2013 American College of Veterinary Radiology.

Immersive Molecular Visualization with Omnidirectional Stereoscopic Ray Tracing and Remote Rendering

PubMed Central

Stone, John E.; Sherman, William R.; Schulten, Klaus

2016-01-01

Immersive molecular visualization provides the viewer with intuitive perception of complex structures and spatial relationships that are of critical interest to structural biologists. The recent availability of commodity head mounted displays (HMDs) provides a compelling opportunity for widespread adoption of immersive visualization by molecular scientists, but HMDs pose additional challenges due to the need for low-latency, high-frame-rate rendering. State-of-the-art molecular dynamics simulations produce terabytes of data that can be impractical to transfer from remote supercomputers, necessitating routine use of remote visualization. Hardware-accelerated video encoding has profoundly increased frame rates and image resolution for remote visualization, however round-trip network latencies would cause simulator sickness when using HMDs. We present a novel two-phase rendering approach that overcomes network latencies with the combination of omnidirectional stereoscopic progressive ray tracing and high performance rasterization, and its implementation within VMD, a widely used molecular visualization and analysis tool. The new rendering approach enables immersive molecular visualization with rendering techniques such as shadows, ambient occlusion lighting, depth-of-field, and high quality transparency, that are particularly helpful for the study of large biomolecular complexes. We describe ray tracing algorithms that are used to optimize interactivity and quality, and we report key performance metrics of the system. The new techniques can also benefit many other application domains. PMID:27747138

Simulation of X-ray transient absorption for following vibrations in coherently ionized F2 molecules

NASA Astrophysics Data System (ADS)

Dutoi, Anthony D.; Leone, Stephen R.

2017-01-01

Femtosecond and attosecond X-ray transient absorption experiments are becoming increasingly sophisticated tools for probing nuclear dynamics. In this work, we explore and develop theoretical tools needed for interpretation of such spectra,in order to characterize the vibrational coherences that result from ionizing a molecule in a strong IR field. Ab initio data for F2 is combined with simulations of nuclear dynamics, in order to simulate time-resolved X-ray absorption spectra for vibrational wavepackets after coherent ionization at 0 K and at finite temperature. Dihalogens pose rather difficult electronic structure problems, and the issues encountered in this work will be reflective of those encountered with any core-valence excitation simulation when a bond is breaking. The simulations reveal a strong dependence of the X-ray absorption maximum on the locations of the vibrational wave packets. A Fourier transform of the simulated signal shows features at the overtone frequencies of both the neutral and the cation, which reflect spatial interferences of the vibrational eigenstates. This provides a direct path for implementing ultrafast X-ray spectroscopic methods to visualize coherent nuclear dynamics.

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.

Ultrascale Visualization of Climate Data

NASA Technical Reports Server (NTRS)

Williams, Dean N.; Bremer, Timo; Doutriaux, Charles; Patchett, John; Williams, Sean; Shipman, Galen; Miller, Ross; Pugmire, David R.; Smith, Brian; Steed, Chad;

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.

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

Airport Viz - a 3D Tool to Enhance Security Operations

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

Koch, Daniel B

2006-01-01

In the summer of 2000, the National Safe Skies Alliance (NSSA) awarded a project to the Applied Visualization Center (AVC) at the University of Tennessee, Knoxville (UTK) to develop a 3D computer tool to assist the Federal Aviation Administration security group, now the Transportation Security Administration (TSA), in evaluating new equipment and procedures to improve airport checkpoint security. A preliminary tool was demonstrated at the 2001 International Aviation Security Technology Symposium. Since then, the AVC went on to construct numerous detection equipment models as well as models of several airports. Airport Viz has been distributed by the NSSA to amore » number of airports around the country which are able to incorporate their own CAD models into the software due to its unique open architecture. It provides a checkpoint design and passenger flow simulation function, a layout design and simulation tool for checked baggage and cargo screening, and a means to assist in the vulnerability assessment of airport access points for pedestrians and vehicles.« less

A Flexible Approach for the Statistical Visualization of Ensemble Data

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

Potter, K.; Wilson, A.; Bremer, P.

2009-09-29

Scientists are increasingly moving towards ensemble data sets to explore relationships present in dynamic systems. Ensemble data sets combine spatio-temporal simulation results generated using multiple numerical models, sampled input conditions and perturbed parameters. While ensemble data sets are a powerful tool for mitigating uncertainty, they pose significant visualization and analysis challenges due to their complexity. We present a collection of overview and statistical displays linked through a high level of interactivity to provide a framework for gaining key scientific insight into the distribution of the simulation results as well as the uncertainty associated with the data. In contrast to methodsmore » that present large amounts of diverse information in a single display, we argue that combining multiple linked statistical displays yields a clearer presentation of the data and facilitates a greater level of visual data analysis. We demonstrate this approach using driving problems from climate modeling and meteorology and discuss generalizations to other fields.« less

Evaluating the Efficacy of Wavelet Configurations on Turbulent-Flow Data

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

Li, Shaomeng; Gruchalla, Kenny; Potter, Kristin

2015-10-25

I/O is increasingly becoming a significant constraint for simulation codes and visualization tools on modern supercomputers. Data compression is an attractive workaround, and, in particular, wavelets provide a promising solution. However, wavelets can be applied in multiple configurations, and the variations in configuration impact accuracy, storage cost, and execution time. While the variation in these factors over wavelet configurations have been explored in image processing, they are not well understood for visualization and analysis of scientific data. To illuminate this issue, we evaluate multiple wavelet configurations on turbulent-flow data. Our approach is to repeat established analysis routines on uncompressed andmore » lossy-compressed versions of a data set, and then quantitatively compare their outcomes. Our findings show that accuracy varies greatly based on wavelet configuration, while storage cost and execution time vary less. Overall, our study provides new insights for simulation analysts and visualization experts, who need to make tradeoffs between accuracy, storage cost, and execution time.« less

Adaptive Optics Analysis of Visual Benefit with Higher-order Aberrations Correction of Human Eye - Poster Paper

NASA Astrophysics Data System (ADS)

Xue, Lixia; Dai, Yun; Rao, Xuejun; Wang, Cheng; Hu, Yiyun; Liu, Qian; Jiang, Wenhan

2008-01-01

Higher-order aberrations correction can improve visual performance of human eye to some extent. To evaluate how much visual benefit can be obtained with higher-order aberrations correction we developed an adaptive optics vision simulator (AOVS). Dynamic real time optimized modal compensation was used to implement various customized higher-order ocular aberrations correction strategies. The experimental results indicate that higher-order aberrations correction can improve visual performance of human eye comparing with only lower-order aberration correction but the improvement degree and higher-order aberration correction strategy are different from each individual. Some subjects can acquire great visual benefit when higher-order aberrations were corrected but some subjects acquire little visual benefit even though all higher-order aberrations were corrected. Therefore, relative to general lower-order aberrations correction strategy, customized higher-order aberrations correction strategy is needed to obtain optimal visual improvement for each individual. AOVS provides an effective tool for higher-order ocular aberrations optometry for customized ocular aberrations correction.

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.

Modeling RF-induced Plasma-Surface Interactions with VSim

NASA Astrophysics Data System (ADS)

Jenkins, Thomas G.; Smithe, David N.; Pankin, Alexei Y.; Roark, Christine M.; Stoltz, Peter H.; Zhou, Sean C.-D.; Kruger, Scott E.

2014-10-01

An overview of ongoing enhancements to the Plasma Discharge (PD) module of Tech-X's VSim software tool is presented. A sub-grid kinetic sheath model, developed for the accurate computation of sheath potentials near metal and dielectric-coated walls, enables the physical effects of DC and RF sheath dynamics to be included in macroscopic-scale plasma simulations that need not explicitly resolve sheath scale lengths. Sheath potential evolution, together with particle behavior near the sheath (e.g. sputtering), can thus be simulated in complex, experimentally relevant geometries. Simulations of RF sheath-enhanced impurity production near surfaces of the C-Mod field-aligned ICRF antenna are presented to illustrate the model; impurity mitigation techniques are also explored. Model extensions to capture the physics of secondary electron emission and of multispecies plasmas are summarized, together with a discussion of improved tools for plasma chemistry and IEDF/EEDF visualization and modeling. The latter tools are also highly relevant for commercial plasma processing applications. Ultimately, we aim to establish VSimPD as a robust, efficient computational tool for modeling fusion and industrial plasma processes. Supported by U.S. DoE SBIR Phase I/II Award DE-SC0009501.

FuelCalc: A Method for Estimating Fuel Characteristics

Treesearch

Elizabeth Reinhardt; Duncan Lutes; Joe Scott

2006-01-01

This paper describes the FuelCalc computer program. FuelCalc is a tool to compute surface and canopy fuel loads and characteristics from inventory data, to support fuel treatment decisions by simulating effects of a wide range of silvicultural treatments on surface fuels and canopy fuels, and to provide linkages to stand visualization, fire behavior and fire effects...

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

SpectraPlot.com: Integrated spectroscopic modeling of atomic and molecular gases

NASA Astrophysics Data System (ADS)

Goldenstein, Christopher S.; Miller, Victor A.; Mitchell Spearrin, R.; Strand, Christopher L.

2017-10-01

SpectraPlot is a web-based application for simulating spectra of atomic and molecular gases. At the time this manuscript was written, SpectraPlot consisted of four primary tools for calculating: (1) atomic and molecular absorption spectra, (2) atomic and molecular emission spectra, (3) transition linestrengths, and (4) blackbody emission spectra. These tools currently employ the NIST ASD, HITRAN2012, and HITEMP2010 databases to perform line-by-line simulations of spectra. SpectraPlot employs a modular, integrated architecture, enabling multiple simulations across multiple databases and/or thermodynamic conditions to be visualized in an interactive plot window. The primary objective of this paper is to describe the architecture and spectroscopic models employed by SpectraPlot in order to provide its users with the knowledge required to understand the capabilities and limitations of simulations performed using SpectraPlot. Further, this manuscript discusses the accuracy of several underlying approximations used to decrease computational time, in particular, the use of far-wing cutoff criteria.

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.

Concept of Operations Visualization in Support of Ares I Production

NASA Technical Reports Server (NTRS)

Chilton, James H.; Smith, Daid Alan

2008-01-01

Boeing was selected in 2007 to manufacture Ares I Upper Stage and Instrument Unit according to NASA's design which would require the use of the latest manufacturing and integration processes to meet NASA budget and schedule targets. Past production experience has established that the majority of the life cycle cost is established during the initial design process. Concept of Operations (CONOPs) visualizations/simulations help to reduce life cycle cost during the early design stage. Production and operation visualizations can reduce tooling, factory capacity, safety, and build process risks while spreading program support across government, academic, media and public constituencies. The NASA/Boeing production visualization (DELMIA; Digital Enterprise Lean Manufacturing Interactive Application) promotes timely, concurrent and collaborative producibility analysis (Boeing)while supporting Upper Stage Design Cycles (NASA). The DELMIA CONOPs visualization reduced overall Upper Stage production flow time at the manufacturing facility by over 100 man-days to 312.5 man-days and helped to identify technical access issues. The NASA/Boeing Interactive Concept of Operations (ICON) provides interactive access to Ares using real mission parameters, allows users to configure the mission which encourages ownership and identifies areas for improvement, allows mission operations or spacecraft detail to be added as needed, and provides an effective, low coast advocacy, outreach and education tool.

Visualization of the Invisible, Explanation of the Unknown, Ruggedization of the Unstable: Sensitivity Analysis, Virtual Tryout and Robust Design through Systematic Stochastic Simulation

NASA Astrophysics Data System (ADS)

Zwickl, Titus; Carleer, Bart; Kubli, Waldemar

2005-08-01

In the past decade, sheet metal forming simulation became a well established tool to predict the formability of parts. In the automotive industry, this has enabled significant reduction in the cost and time for vehicle design and development, and has helped to improve the quality and performance of vehicle parts. However, production stoppages for troubleshooting and unplanned die maintenance, as well as production quality fluctuations continue to plague manufacturing cost and time. The focus therefore has shifted in recent times beyond mere feasibility to robustness of the product and process being engineered. Ensuring robustness is the next big challenge for the virtual tryout / simulation technology. We introduce new methods, based on systematic stochastic simulations, to visualize the behavior of the part during the whole forming process — in simulation as well as in production. Sensitivity analysis explains the response of the part to changes in influencing parameters. Virtual tryout allows quick exploration of changed designs and conditions. Robust design and manufacturing guarantees quality and process capability for the production process. While conventional simulations helped to reduce development time and cost by ensuring feasible processes, robustness engineering tools have the potential for far greater cost and time savings. Through examples we illustrate how expected and unexpected behavior of deep drawing parts may be tracked down, identified and assigned to the influential parameters. With this knowledge, defects can be eliminated or springback can be compensated e.g.; the response of the part to uncontrollable noise can be predicted and minimized. The newly introduced methods enable more reliable and predictable stamping processes in general.

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.

Adaptation of G-TAG Software for Validating Touch-and-Go Comet Surface Sampling Design Methodology

NASA Technical Reports Server (NTRS)

Mandic, Milan; Acikmese, Behcet; Blackmore, Lars

2011-01-01

The G-TAG software tool was developed under the R&TD on Integrated Autonomous Guidance, Navigation, and Control for Comet Sample Return, and represents a novel, multi-body dynamics simulation software tool for studying TAG sampling. The G-TAG multi-body simulation tool provides a simulation environment in which a Touch-and-Go (TAG) sampling event can be extensively tested. TAG sampling requires the spacecraft to descend to the surface, contact the surface with a sampling collection device, and then to ascend to a safe altitude. The TAG event lasts only a few seconds but is mission-critical with potentially high risk. Consequently, there is a need for the TAG event to be well characterized and studied by simulation and analysis in order for the proposal teams to converge on a reliable spacecraft design. This adaptation of the G-TAG tool was developed to support the Comet Odyssey proposal effort, and is specifically focused to address comet sample return missions. In this application, the spacecraft descends to and samples from the surface of a comet. Performance of the spacecraft during TAG is assessed based on survivability and sample collection performance. For the adaptation of the G-TAG simulation tool to comet scenarios, models are developed that accurately describe the properties of the spacecraft, approach trajectories, and descent velocities, as well as the models of the external forces and torques acting on the spacecraft. The adapted models of the spacecraft, descent profiles, and external sampling forces/torques were more sophisticated and customized for comets than those available in the basic G-TAG simulation tool. Scenarios implemented include the study of variations in requirements, spacecraft design (size, locations, etc. of the spacecraft components), and the environment (surface properties, slope, disturbances, etc.). The simulations, along with their visual representations using G-View, contributed to the Comet Odyssey New Frontiers proposal effort by indicating problems and/or benefits of different approaches and designs.

TESSIM: a simulator for the Athena-X-IFU

NASA Astrophysics Data System (ADS)

Wilms, J.; Smith, S. J.; Peille, P.; Ceballos, M. T.; Cobo, B.; Dauser, T.; Brand, T.; den Hartog, R. H.; Bandler, S. R.; de Plaa, J.; den Herder, J.-W. A.

2016-07-01

We present the design of tessim, a simulator for the physics of transition edge sensors developed in the framework of the Athena end to end simulation effort. Designed to represent the general behavior of transition edge sensors and to provide input for engineering and science studies for Athena, tessim implements a numerical solution of the linearized equations describing these devices. The simulation includes a model for the relevant noise sources and several implementations of possible trigger algorithms. Input and output of the software are standard FITS- files which can be visualized and processed using standard X-ray astronomical tool packages. Tessim is freely available as part of the SIXTE package (http://www.sternwarte.uni-erlangen.de/research/sixte/).

TESSIM: A Simulator for the Athena-X-IFU

NASA Technical Reports Server (NTRS)

Wilms, J.; Smith, S. J.; Peille, P.; Ceballos, M. T.; Cobo, B.; Dauser, T.; Brand, T.; Den Hartog, R. H.; Bandler, S. R.; De Plaa, J.;

Parallel Processing of Numerical Tsunami Simulations on a High Performance Cluster based on the GDAL Library

NASA Astrophysics Data System (ADS)

Schroeder, Matthias; Jankowski, Cedric; Hammitzsch, Martin; Wächter, Joachim

2014-05-01

Thousands of numerical tsunami simulations allow the computation of inundation and run-up along the coast for vulnerable areas over the time. A so-called Matching Scenario Database (MSDB) [1] contains this large number of simulations in text file format. In order to visualize these wave propagations the scenarios have to be reprocessed automatically. In the TRIDEC project funded by the seventh Framework Programme of the European Union a Virtual Scenario Database (VSDB) and a Matching Scenario Database (MSDB) were established amongst others by the working group of the University of Bologna (UniBo) [1]. One part of TRIDEC was the developing of a new generation of a Decision Support System (DSS) for tsunami Early Warning Systems (TEWS) [2]. A working group of the GFZ German Research Centre for Geosciences was responsible for developing the Command and Control User Interface (CCUI) as central software application which support operator activities, incident management and message disseminations. For the integration and visualization in the CCUI, the numerical tsunami simulations from MSDB must be converted into the shapefiles format. The usage of shapefiles enables a much easier integration into standard Geographic Information Systems (GIS). Since also the CCUI is based on two widely used open source products (GeoTools library and uDig), whereby the integration of shapefiles is provided by these libraries a priori. In this case, for an example area around the Western Iberian margin several thousand tsunami variations were processed. Due to the mass of data only a program-controlled process was conceivable. In order to optimize the computing efforts and operating time the use of an existing GFZ High Performance Computing Cluster (HPC) had been chosen. Thus, a geospatial software was sought after that is capable for parallel processing. The FOSS tool Geospatial Data Abstraction Library (GDAL/OGR) was used to match the coordinates with the wave heights and generates the different shapefiles for certain time steps. The shapefiles contain afterwards lines for visualizing the isochrones of the wave propagation and moreover, data about the maximum wave height and the Estimated Time of Arrival (ETA) at the coast. Our contribution shows the entire workflow and the visualizing results of the-processing for the example region Western Iberian ocean margin. [1] Armigliato A., Pagnoni G., Zaniboni F, Tinti S. (2013), Database of tsunami scenario simulations for Western Iberia: a tool for the TRIDEC Project Decision Support System for tsunami early warning, Vol. 15, EGU2013-5567, EGU General Assembly 2013, Vienna (Austria). [2] Löwe, P., Wächter, J., Hammitzsch, M., Lendholt, M., Häner, R. (2013): The Evolution of Service-oriented Disaster Early Warning Systems in the TRIDEC Project, 23rd International Ocean and Polar Engineering Conference - ISOPE-2013, Anchorage (USA).

Image jitter enhances visual performance when spatial resolution is impaired.

PubMed

Watson, Lynne M; Strang, Niall C; Scobie, Fraser; Love, Gordon D; Seidel, Dirk; Manahilov, Velitchko

2012-09-06

Visibility of low-spatial frequency stimuli improves when their contrast is modulated at 5 to 10 Hz compared with stationary stimuli. Therefore, temporal modulations of visual objects could enhance the performance of low vision patients who primarily perceive images of low-spatial frequency content. We investigated the effect of retinal-image jitter on word recognition speed and facial emotion recognition in subjects with central visual impairment. Word recognition speed and accuracy of facial emotion discrimination were measured in volunteers with AMD under stationary and jittering conditions. Computer-driven and optoelectronic approaches were used to induce retinal-image jitter with duration of 100 or 166 ms and amplitude within the range of 0.5 to 2.6° visual angle. Word recognition speed was also measured for participants with simulated (Bangerter filters) visual impairment. Text jittering markedly enhanced word recognition speed for people with severe visual loss (101 ± 25%), while for those with moderate visual impairment, this effect was weaker (19 ± 9%). The ability of low vision patients to discriminate the facial emotions of jittering images improved by a factor of 2. A prototype of optoelectronic jitter goggles produced similar improvement in facial emotion discrimination. Word recognition speed in participants with simulated visual impairment was enhanced for interjitter intervals over 100 ms and reduced for shorter intervals. Results suggest that retinal-image jitter with optimal frequency and amplitude is an effective strategy for enhancing visual information processing in the absence of spatial detail. These findings will enable the development of novel tools to improve the quality of life of low vision patients.

Processing infrared images of aircraft lapjoints

NASA Technical Reports Server (NTRS)

Syed, Hazari; Winfree, William P.; Cramer, K. E.

1992-01-01

Techniques for processing IR images of aging aircraft lapjoint data are discussed. Attention is given to a technique for detecting disbonds in aircraft lapjoints which clearly delineates the disbonded region from the bonded regions. The technique is weak on unpainted aircraft skin surfaces, but can be overridden by using a self-adhering contact sheet. Neural network analysis on raw temperature data has been shown to be an effective tool for visualization of images. Numerical simulation results show the above processing technique to be an effective tool in delineating the disbonds.

Teaching strategies for using projected images to develop conceptual understanding: Exploring discussion practices in computer simulation and static image-based lessons

NASA Astrophysics Data System (ADS)

Price, Norman T.

The availability and sophistication of visual display images, such as simulations, for use in science classrooms has increased exponentially however, it can be difficult for teachers to use these images to encourage and engage active student thinking. There is a need to describe flexible discussion strategies that use visual media to engage active thinking. This mixed methods study analyzes teacher behavior in lessons using visual media about the particulate model of matter that were taught by three experienced middle school teachers. Each teacher taught one half of their students with lessons using static overheads and taught the other half with lessons using a projected dynamic simulation. The quantitative analysis of pre-post data found significant gain differences between the two image mode conditions, suggesting that the students who were assigned to the simulation condition learned more than students who were assigned to the overhead condition. Open coding was used to identify a set of eight image-based teaching strategies that teachers were using with visual displays. Fixed codes for this set of image-based discussion strategies were then developed and used to analyze video and transcripts of whole class discussions from 12 lessons. The image-based discussion strategies were refined over time in a set of three in-depth 2x2 comparative case studies of two teachers teaching one lesson topic with two image display modes. The comparative case study data suggest that the simulation mode may have offered greater affordances than the overhead mode for planning and enacting discussions. The 12 discussions were also coded for overall teacher student interaction patterns, such as presentation, IRE, and IRF. When teachers moved during a lesson from using no image to using either image mode, some teachers were observed asking more questions when the image was displayed while others asked many fewer questions. The changes in teacher student interaction patterns suggest that teachers vary on whether they consider the displayed image as a "tool-for-telling" and a "tool-for-asking." The study attempts to provide new descriptions of strategies teachers use to orchestrate image-based discussions designed to promote student engagement and reasoning in lessons with conceptual goals.

Topographica: Building and Analyzing Map-Level Simulations from Python, C/C++, MATLAB, NEST, or NEURON Components

PubMed Central

Bednar, James A.

2008-01-01

Many neural regions are arranged into two-dimensional topographic maps, such as the retinotopic maps in mammalian visual cortex. Computational simulations have led to valuable insights about how cortical topography develops and functions, but further progress has been hindered by the lack of appropriate tools. It has been particularly difficult to bridge across levels of detail, because simulators are typically geared to a specific level, while interfacing between simulators has been a major technical challenge. In this paper, we show that the Python-based Topographica simulator makes it straightforward to build systems that cross levels of analysis, as well as providing a common framework for evaluating and comparing models implemented in other simulators. These results rely on the general-purpose abstractions around which Topographica is designed, along with the Python interfaces becoming available for many simulators. In particular, we present a detailed, general-purpose example of how to wrap an external spiking PyNN/NEST simulation as a Topographica component using only a dozen lines of Python code, making it possible to use any of the extensive input presentation, analysis, and plotting tools of Topographica. Additional examples show how to interface easily with models in other types of simulators. Researchers simulating topographic maps externally should consider using Topographica's analysis tools (such as preference map, receptive field, or tuning curve measurement) to compare results consistently, and for connecting models at different levels. This seamless interoperability will help neuroscientists and computational scientists to work together to understand how neurons in topographic maps organize and operate. PMID:19352443

Visualization of Octree Adaptive Mesh Refinement (AMR) in Astrophysical Simulations

NASA Astrophysics Data System (ADS)

Labadens, M.; Chapon, D.; Pomaréde, D.; Teyssier, R.

2012-09-01

Computer simulations are important in current cosmological research. Those simulations run in parallel on thousands of processors, and produce huge amount of data. Adaptive mesh refinement is used to reduce the computing cost while keeping good numerical accuracy in regions of interest. RAMSES is a cosmological code developed by the Commissariat à l'énergie atomique et aux énergies alternatives (English: Atomic Energy and Alternative Energies Commission) which uses Octree adaptive mesh refinement. Compared to grid based AMR, the Octree AMR has the advantage to fit very precisely the adaptive resolution of the grid to the local problem complexity. However, this specific octree data type need some specific software to be visualized, as generic visualization tools works on Cartesian grid data type. This is why the PYMSES software has been also developed by our team. It relies on the python scripting language to ensure a modular and easy access to explore those specific data. In order to take advantage of the High Performance Computer which runs the RAMSES simulation, it also uses MPI and multiprocessing to run some parallel code. We would like to present with more details our PYMSES software with some performance benchmarks. PYMSES has currently two visualization techniques which work directly on the AMR. The first one is a splatting technique, and the second one is a custom ray tracing technique. Both have their own advantages and drawbacks. We have also compared two parallel programming techniques with the python multiprocessing library versus the use of MPI run. The load balancing strategy has to be smartly defined in order to achieve a good speed up in our computation. Results obtained with this software are illustrated in the context of a massive, 9000-processor parallel simulation of a Milky Way-like galaxy.

Analysis of visual quality improvements provided by known tools for HDR content

NASA Astrophysics Data System (ADS)

Kim, Jaehwan; Alshina, Elena; Lee, JongSeok; Park, Youngo; Choi, Kwang Pyo

2016-09-01

In this paper, the visual quality of different solutions for high dynamic range (HDR) compression using MPEG test contents is analyzed. We also simulate the method for an efficient HDR compression which is based on statistical property of the signal. The method is compliant with HEVC specification and also easily compatible with other alternative methods which might require HEVC specification changes. It was subjectively tested on commercial TVs and compared with alternative solutions for HDR coding. Subjective visual quality tests were performed using SUHD TVs model which is SAMSUNG JS9500 with maximum luminance up to 1000nit in test. The solution that is based on statistical property shows not only improvement of objective performance but improvement of visual quality compared to other HDR solutions, while it is compatible with HEVC specification.

Graphical Tests for Power Comparison of Competing Designs.

PubMed

Hofmann, H; Follett, L; Majumder, M; Cook, D

2012-12-01

Lineups have been established as tools for visual testing similar to standard statistical inference tests, allowing us to evaluate the validity of graphical findings in an objective manner. In simulation studies lineups have been shown as being efficient: the power of visual tests is comparable to classical tests while being much less stringent in terms of distributional assumptions made. This makes lineups versatile, yet powerful, tools in situations where conditions for regular statistical tests are not or cannot be met. In this paper we introduce lineups as a tool for evaluating the power of competing graphical designs. We highlight some of the theoretical properties and then show results from two studies evaluating competing designs: both studies are designed to go to the limits of our perceptual abilities to highlight differences between designs. We use both accuracy and speed of evaluation as measures of a successful design. The first study compares the choice of coordinate system: polar versus cartesian coordinates. The results show strong support in favor of cartesian coordinates in finding fast and accurate answers to spotting patterns. The second study is aimed at finding shift differences between distributions. Both studies are motivated by data problems that we have recently encountered, and explore using simulated data to evaluate the plot designs under controlled conditions. Amazon Mechanical Turk (MTurk) is used to conduct the studies. The lineups provide an effective mechanism for objectively evaluating plot designs.

Planning, implementation and optimization of future space missions using an immersive visualization environment (IVE) machine

NASA Astrophysics Data System (ADS)

Nathan Harris, E.; Morgenthaler, George W.

2004-07-01

Beginning in 1995, a team of 3-D engineering visualization experts assembled at the Lockheed Martin Space Systems Company and began to develop innovative virtual prototyping simulation tools for performing ground processing and real-time visualization of design and planning of aerospace missions. At the University of Colorado, a team of 3-D visualization experts also began developing the science of 3-D visualization and immersive visualization at the newly founded British Petroleum (BP) Center for visualization, which began operations in October, 2001. BP acquired ARCO in the year 2000 and awarded the 3-D flexible IVE developed by ARCO (beginning in 1990) to the University of Colorado, CU, the winner in a competition among 6 Universities. CU then hired Dr. G. Dorn, the leader of the ARCO team as Center Director, and the other experts to apply 3-D immersive visualization to aerospace and to other University Research fields, while continuing research on surface interpretation of seismic data and 3-D volumes. This paper recounts further progress and outlines plans in Aerospace applications at Lockheed Martin and CU.

Ranking of Business Process Simulation Software Tools with DEX/QQ Hierarchical Decision Model.

PubMed

Damij, Nadja; Boškoski, Pavle; Bohanec, Marko; Mileva Boshkoska, Biljana

2016-01-01

The omnipresent need for optimisation requires constant improvements of companies' business processes (BPs). Minimising the risk of inappropriate BP being implemented is usually performed by simulating the newly developed BP under various initial conditions and "what-if" scenarios. An effectual business process simulations software (BPSS) is a prerequisite for accurate analysis of an BP. Characterisation of an BPSS tool is a challenging task due to the complex selection criteria that includes quality of visual aspects, simulation capabilities, statistical facilities, quality reporting etc. Under such circumstances, making an optimal decision is challenging. Therefore, various decision support models are employed aiding the BPSS tool selection. The currently established decision support models are either proprietary or comprise only a limited subset of criteria, which affects their accuracy. Addressing this issue, this paper proposes a new hierarchical decision support model for ranking of BPSS based on their technical characteristics by employing DEX and qualitative to quantitative (QQ) methodology. Consequently, the decision expert feeds the required information in a systematic and user friendly manner. There are three significant contributions of the proposed approach. Firstly, the proposed hierarchical model is easily extendible for adding new criteria in the hierarchical structure. Secondly, a fully operational decision support system (DSS) tool that implements the proposed hierarchical model is presented. Finally, the effectiveness of the proposed hierarchical model is assessed by comparing the resulting rankings of BPSS with respect to currently available results.

Linking Simulation with Formal Verification and Modeling of Wireless Sensor Network in TLA+

NASA Astrophysics Data System (ADS)

Martyna, Jerzy

In this paper, we present the results of the simulation of a wireless sensor network based on the flooding technique and SPIN protocols. The wireless sensor network was specified and verified by means of the TLA+ specification language [1]. For a model of wireless sensor network built this way simulation was carried with the help of specially constructed software tools. The obtained results allow us to predict the behaviour of the wireless sensor network in various topologies and spatial densities. Visualization of the output data enable precise examination of some phenomenas in wireless sensor networks, such as a hidden terminal, etc.

Perceptual evaluation of visual alerts in surveillance videos

NASA Astrophysics Data System (ADS)

Rogowitz, Bernice E.; Topkara, Mercan; Pfeiffer, William; Hampapur, Arun

2015-03-01

Visual alerts are commonly used in video monitoring and surveillance systems to mark events, presumably making them more salient to human observers. Surprisingly, the effectiveness of computer-generated alerts in improving human performance has not been widely studied. To address this gap, we have developed a tool for simulating different alert parameters in a realistic visual monitoring situation, and have measured human detection performance under conditions that emulated different set-points in a surveillance algorithm. In the High-Sensitivity condition, the simulated alerts identified 100% of the events with many false alarms. In the Lower-Sensitivity condition, the simulated alerts correctly identified 70% of the targets, with fewer false alarms. In the control condition, no simulated alerts were provided. To explore the effects of learning, subjects performed these tasks in three sessions, on separate days, in a counterbalanced, within subject design. We explore these results within the context of cognitive models of human attention and learning. We found that human observers were more likely to respond to events when marked by a visual alert. Learning played a major role in the two alert conditions. In the first session, observers generated almost twice as many False Alarms as in the No-Alert condition, as the observers responded pre-attentively to the computer-generated false alarms. However, this rate dropped equally dramatically in later sessions, as observers learned to discount the false cues. Highest observer Precision, Hits/(Hits + False Alarms), was achieved in the High Sensitivity condition, but only after training. The successful evaluation of surveillance systems depends on understanding human attention and performance.

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.

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

3rd Annual Earth System Grid Federation and 3rd Annual Earth System Grid Federation and Ultrascale Visualization Climate Data Analysis Tools Face-to-Face Meeting Report December 2013

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

Williams, Dean N.

The climate and weather data science community gathered December 3–5, 2013, at Lawrence Livermore National Laboratory, in Livermore, California, for the third annual Earth System Grid Federation (ESGF) and Ultra-scale Visualization Climate Data Analysis Tools (UV-CDAT) Face-to-Face (F2F) Meeting, which was 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 UV-CDAT are global collaborations designed to develop a new generation of open-source software infrastructure that provides distributed access and analysis to observed andmore » simulated data from the climate and weather communities. The tools and infrastructure developed under these international multi-agency collaborations are critical to understanding extreme weather conditions and long-term climate change, while the F2F meetings help to build a stronger climate and weather data science community and stronger federated software infrastructure. The 2013 F2F meeting determined requirements for existing and impending national and international community projects; enhancements needed for data distribution, analysis, and visualization infrastructure; and standards and resources needed for better collaborations.« less

PACS-based interface for 3D anatomical structure visualization and surgical planning

NASA Astrophysics Data System (ADS)

Koehl, Christophe; Soler, Luc; Marescaux, Jacques

2002-05-01

The interpretation of radiological image is routine but it remains a rather difficult task for physicians. It requires complex mental processes, that permit translation from 2D slices into 3D localization and volume determination of visible diseases. An easier and more extensive visualization and exploitation of medical images can be reached through the use of computer-based systems that provide real help from patient admission to post-operative followup. In this way, we have developed a 3D visualization interface linked to a PACS database that allows manipulation and interaction on virtual organs delineated from CT-scan or MRI. This software provides the 3D real-time surface rendering of anatomical structures, an accurate evaluation of volumes and distances and the improvement of radiological image analysis and exam annotation through a negatoscope tool. It also provides a tool for surgical planning allowing the positioning of an interactive laparoscopic instrument and the organ resection. The software system could revolutionize the field of computerized imaging technology. Indeed, it provides a handy and portable tool for pre-operative and intra-operative analysis of anatomy and pathology in various medical fields. This constitutes the first step of the future development of augmented reality and surgical simulation systems.

Collaborative Visualization for Large-Scale Accelerator Electromagnetic Modeling (Final Report)

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

William J. Schroeder

2011-11-13

This report contains the comprehensive summary of the work performed on the SBIR Phase II, Collaborative Visualization for Large-Scale Accelerator Electromagnetic Modeling at Kitware Inc. in collaboration with Stanford Linear Accelerator Center (SLAC). The goal of the work was to develop collaborative visualization tools for large-scale data as illustrated in the figure below. The solutions we proposed address the typical problems faced by geographicallyand organizationally-separated research and engineering teams, who produce large data (either through simulation or experimental measurement) and wish to work together to analyze and understand their data. Because the data is large, we expect that it cannotmore » be easily transported to each team member's work site, and that the visualization server must reside near the data. Further, we also expect that each work site has heterogeneous resources: some with large computing clients, tiled (or large) displays and high bandwidth; others sites as simple as a team member on a laptop computer. Our solution is based on the open-source, widely used ParaView large-data visualization application. We extended this tool to support multiple collaborative clients who may locally visualize data, and then periodically rejoin and synchronize with the group to discuss their findings. Options for managing session control, adding annotation, and defining the visualization pipeline, among others, were incorporated. We also developed and deployed a Web visualization framework based on ParaView that enables the Web browser to act as a participating client in a collaborative session. The ParaView Web Visualization framework leverages various Web technologies including WebGL, JavaScript, Java and Flash to enable interactive 3D visualization over the web using ParaView as the visualization server. We steered the development of this technology by teaming with the SLAC National Accelerator Laboratory. SLAC has a computationally-intensive problem important to the nations scientific progress as described shortly. Further, SLAC researchers routinely generate massive amounts of data, and frequently collaborate with other researchers located around the world. Thus SLAC is an ideal teammate through which to develop, test and deploy this technology. The nature of the datasets generated by simulations performed at SLAC presented unique visualization challenges especially when dealing with higher-order elements that were addressed during this Phase II. During this Phase II, we have developed a strong platform for collaborative visualization based on ParaView. We have developed and deployed a ParaView Web Visualization framework that can be used for effective collaboration over the Web. Collaborating and visualizing over the Web presents the community with unique opportunities for sharing and accessing visualization and HPC resources that hitherto with either inaccessible or difficult to use. The technology we developed in here will alleviate both these issues as it becomes widely deployed and adopted.« less

Visual Data Exploration and Analysis - Report on the Visualization Breakout Session of the SCaLeS Workshop

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

Bethel, E. Wes; Frank, Randy; Fulcomer, Sam

Scientific visualization is the transformation of abstract information into images, and it plays an integral role in the scientific process by facilitating insight into observed or simulated phenomena. Visualization as a discipline spans many research areas from computer science, cognitive psychology and even art. Yet the most successful visualization applications are created when close synergistic interactions with domain scientists are part of the algorithmic design and implementation process, leading to visual representations with clear scientific meaning. Visualization is used to explore, to debug, to gain understanding, and as an analysis tool. Visualization is literally everywhere--images are present in this report,more » on television, on the web, in books and magazines--the common theme is the ability to present information visually that is rapidly assimilated by human observers, and transformed into understanding or insight. As an indispensable part a modern science laboratory, visualization is akin to the biologist's microscope or the electrical engineer's oscilloscope. Whereas the microscope is limited to small specimens or use of optics to focus light, the power of scientific visualization is virtually limitless: visualization provides the means to examine data that can be at galactic or atomic scales, or at any size in between. Unlike the traditional scientific tools for visual inspection, visualization offers the means to ''see the unseeable.'' Trends in demographics or changes in levels of atmospheric CO{sub 2} as a function of greenhouse gas emissions are familiar examples of such unseeable phenomena. Over time, visualization techniques evolve in response to scientific need. Each scientific discipline has its ''own language,'' verbal and visual, used for communication. The visual language for depicting electrical circuits is much different than the visual language for depicting theoretical molecules or trends in the stock market. There is no ''one visualization too'' that can serve as a panacea for all science disciplines. Instead, visualization researchers work hand in hand with domain scientists as part of the scientific research process to define, create, adapt and refine software that ''speaks the visual language'' of each scientific domain.« less

Review of hardware-in-the-loop simulation and its prospects in the automotive area

NASA Astrophysics Data System (ADS)

Fathy, Hosam K.; Filipi, Zoran S.; Hagena, Jonathan; Stein, Jeffrey L.

2006-05-01

Hardware-in-the-loop (HIL) simulation is rapidly evolving from a control prototyping tool to a system modeling, simulation, and synthesis paradigm synergistically combining many advantages of both physical and virtual prototyping. This paper provides a brief overview of the key enablers and numerous applications of HIL simulation, focusing on its metamorphosis from a control validation tool into a system development paradigm. It then describes a state-of-the art engine-in-the-loop (EIL) simulation facility that highlights the use of HIL simulation for the system-level experimental evaluation of powertrain interactions and development of strategies for clean and efficient propulsion. The facility comprises a real diesel engine coupled to accurate real-time driver, driveline, and vehicle models through a highly responsive dynamometer. This enables the verification of both performance and fuel economy predictions of different conventional and hybrid powertrains. Furthermore, the facility can both replicate the highly dynamic interactions occurring within a real powertrain and measure their influence on transient emissions and visual signature through state-of-the-art instruments. The viability of this facility for integrated powertrain system development is demonstrated through a case study exploring the development of advanced High Mobility Multipurpose Wheeled Vehicle (HMMWV) powertrains.

Simulated Prosthetic Vision: The Benefits of Computer-Based Object Recognition and Localization.

PubMed

Macé, Marc J-M; Guivarch, Valérian; Denis, Grégoire; Jouffrais, Christophe

2015-07-01

Clinical trials with blind patients implanted with a visual neuroprosthesis showed that even the simplest tasks were difficult to perform with the limited vision restored with current implants. Simulated prosthetic vision (SPV) is a powerful tool to investigate the putative functions of the upcoming generations of visual neuroprostheses. Recent studies based on SPV showed that several generations of implants will be required before usable vision is restored. However, none of these studies relied on advanced image processing. High-level image processing could significantly reduce the amount of information required to perform visual tasks and help restore visuomotor behaviors, even with current low-resolution implants. In this study, we simulated a prosthetic vision device based on object localization in the scene. We evaluated the usability of this device for object recognition, localization, and reaching. We showed that a very low number of electrodes (e.g., nine) are sufficient to restore visually guided reaching movements with fair timing (10 s) and high accuracy. In addition, performance, both in terms of accuracy and speed, was comparable with 9 and 100 electrodes. Extraction of high level information (object recognition and localization) from video images could drastically enhance the usability of current visual neuroprosthesis. We suggest that this method-that is, localization of targets of interest in the scene-may restore various visuomotor behaviors. This method could prove functional on current low-resolution implants. The main limitation resides in the reliability of the vision algorithms, which are improving rapidly. Copyright © 2015 International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

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.

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

Simulating Earthquakes for Science and Society: New Earthquake Visualizations Ideal for Use in Science Communication

NASA Astrophysics Data System (ADS)

de Groot, R. M.; Benthien, M. L.

2006-12-01

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 have gained visibility via television news coverage in Southern California. These types of visualizations are becoming pervasive in the teaching and learning of concepts related to earth science. 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). Earthquakes are ideal candidates for visualization products: they cannot be predicted, are completed in a matter of seconds, occur deep in the earth, and the time between events can be on a geologic time scale. For example, the southern part of the San Andreas fault has not seen a major earthquake since about 1690, setting the stage for an earthquake as large as magnitude 7.7 -- the "big one." Since no one has experienced such an earthquake, visualizations can help people understand the scale of such an event. Accordingly, SCEC has developed a revolutionary simulation of this earthquake, with breathtaking visualizations that are now being distributed. 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.

Trend-Centric Motion Visualization: Designing and Applying a new Strategy for Analyzing Scientific Motion Collections

PubMed Central

Schroeder, David; Korsakov, Fedor; Knipe, Carissa Mai-Ping; Thorson, Lauren; Ellingson, Arin M.; Nuckley, David; Carlis, John; Keefe, Daniel F

2017-01-01

In biomechanics studies, researchers collect, via experiments or simulations, datasets with hundreds or thousands of trials, each describing the same type of motion (e.g., a neck flexion-extension exercise) but under different conditions (e.g., different patients, different disease states, pre- and post-treatment). Analyzing similarities and differences across all of the trials in these collections is a major challenge. Visualizing a single trial at a time does not work, and the typical alternative of juxtaposing multiple trials in a single visual display leads to complex, difficult-to-interpret visualizations. We address this problem via a new strategy that organizes the analysis around motion trends rather than trials. This new strategy matches the cognitive approach that scientists would like to take when analyzing motion collections. We introduce several technical innovations making trend-centric motion visualization possible. First, an algorithm detects a motion collection’s trends via time-dependent clustering. Second, a 2D graphical technique visualizes how trials leave and join trends. Third, a 3D graphical technique, using a median 3D motion plus a visual variance indicator, visualizes the biomechanics of the set of trials within each trend. These innovations are combined to create an interactive exploratory visualization tool, which we designed through an iterative process in collaboration with both domain scientists and a traditionally-trained graphic designer. We report on insights generated during this design process and demonstrate the tool’s effectiveness via a validation study with synthetic data and feedback from expert musculoskeletal biomechanics researchers who used the tool to analyze the effects of disc degeneration on human spinal kinematics. PMID:26356978

SimLabel: a graphical user interface to simulate continuous wave EPR spectra from site-directed spin labeling experiments.

PubMed

Etienne, E; Le Breton, N; Martinho, M; Mileo, E; Belle, V

2017-08-01

Site-directed spin labeling (SDSL) combined with continuous wave electron paramagnetic resonance (cw EPR) spectroscopy is a powerful technique to reveal, at the residue level, structural transitions in proteins. SDSL-EPR is based on the selective grafting of a paramagnetic label on the protein under study, followed by cw EPR analysis. To extract valuable quantitative information from SDSL-EPR spectra and thus give reliable interpretation on biological system dynamics, numerical simulations of the spectra are required. Such spectral simulations can be carried out by coding in MATLAB using functions from the EasySpin toolbox. For non-expert users of MATLAB, this could be a complex task or even impede the use of such simulation tool. We developed a graphical user interface called SimLabel dedicated to run cw EPR spectra simulations particularly coming from SDSL-EPR experiments. Simlabel provides an intuitive way to visualize, simulate, and fit such cw EPR spectra. An example of SDSL-EPR spectra simulation concerning the study of an intrinsically disordered region undergoing a local induced folding is described and discussed. We believe that this new tool will help the users to rapidly obtain reliable simulated spectra and hence facilitate the interpretation of their results. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

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.

Akuna: An Open Source User Environment for Managing Subsurface Simulation Workflows

NASA Astrophysics Data System (ADS)

Freedman, V. L.; Agarwal, D.; Bensema, K.; Finsterle, S.; Gable, C. W.; Keating, E. H.; Krishnan, H.; Lansing, C.; Moeglein, W.; Pau, G. S. H.; Porter, E.; Scheibe, T. D.

2014-12-01

The U.S. Department of Energy (DOE) is investing in development of a numerical modeling toolset called ASCEM (Advanced Simulation Capability for Environmental Management) to support modeling analyses at legacy waste sites. ASCEM is an open source and modular computing framework that incorporates new advances and tools for predicting contaminant fate and transport in natural and engineered systems. The ASCEM toolset includes both a Platform with Integrated Toolsets (called Akuna) and a High-Performance Computing multi-process simulator (called Amanzi). The focus of this presentation is on Akuna, an open-source user environment that manages subsurface simulation workflows and associated data and metadata. In this presentation, key elements of Akuna are demonstrated, which includes toolsets for model setup, database management, sensitivity analysis, parameter estimation, uncertainty quantification, and visualization of both model setup and simulation results. A key component of the workflow is in the automated job launching and monitoring capabilities, which allow a user to submit and monitor simulation runs on high-performance, parallel computers. Visualization of large outputs can also be performed without moving data back to local resources. These capabilities make high-performance computing accessible to the users who might not be familiar with batch queue systems and usage protocols on different supercomputers and clusters.

Transparency and Documentation in Simulations of Infectious Disease Outbreaks: Towards Evidence-Based Public Health Decisions and Communications

NASA Astrophysics Data System (ADS)

Ekberg, Joakim; Timpka, Toomas; Morin, Magnus; Jenvald, Johan; Nyce, James M.; Gursky, Elin A.; Eriksson, Henrik

Computer simulations have emerged as important tools in the preparation for outbreaks of infectious disease. To support the collaborative planning and responding to the outbreaks, reports from simulations need to be transparent (accessible) with regard to the underlying parametric settings. This paper presents a design for generation of simulation reports where the background settings used in the simulation models are automatically visualized. We extended the ontology-management system Protégé to tag different settings into categories, and included these in report generation in parallel to the simulation outcomes. The report generator takes advantage of an XSLT specification and collects the documentation of the particular simulation settings into abridged XMLs including also summarized results. We conclude that even though inclusion of critical background settings in reports may not increase the accuracy of infectious disease simulations, it can prevent misunderstandings and less than optimal public health decisions.

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.

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.

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.

iMatTOUGH: An open-source Matlab-based graphical user interface for pre- and post-processing of TOUGH2 and iTOUGH2 models

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

Tran, Anh Phuong; Dafflon, Baptiste; Hubbard, Susan

TOUGH2 and iTOUGH2 are powerful models that simulate the heat and fluid flows in porous and fracture media, and perform parameter estimation, sensitivity analysis and uncertainty propagation analysis. However, setting up the input files is not only tedious, but error prone, and processing output files is time consuming. Here, we present an open source Matlab-based tool (iMatTOUGH) that supports the generation of all necessary inputs for both TOUGH2 and iTOUGH2 and visualize their outputs. The tool links the inputs of TOUGH2 and iTOUGH2, making sure the two input files are consistent. It supports the generation of rectangular computational mesh, i.e.,more » it automatically generates the elements and connections as well as their properties as required by TOUGH2. The tool also allows the specification of initial and time-dependent boundary conditions for better subsurface heat and water flow simulations. The effectiveness of the tool is illustrated by an example that uses TOUGH2 and iTOUGH2 to estimate soil hydrological and thermal properties from soil temperature data and simulate the heat and water flows at the Rifle site in Colorado.« less

Reducing the Schizophrenia Stigma: A New Approach Based on Augmented Reality

PubMed Central

Silva, Rafael D. de C.; Albuquerque, Saulo G. C.; Muniz, Artur de V.; Filho, Pedro P. Rebouças; Ribeiro, Sidarta

2017-01-01

Schizophrenia is a chronic mental disease that usually manifests psychotic symptoms and affects an individual's functionality. The stigma related to this disease is a serious obstacle for an adequate approach to its treatment. Stigma can, for example, delay the start of treatment, and it creates difficulties in interpersonal and professional relationships. This work proposes a new tool based on augmented reality to reduce the stigma related to schizophrenia. The tool is capable of simulating the psychotic symptoms typical of schizophrenia and simulates sense perception changes in order to create an immersive experience capable of generating pathological experiences of a patient with schizophrenia. The integration into the proposed environment occurs through immersion glasses and an embedded camera. Audio and visual effects can also be applied in real time. To validate the proposed environment, medical students experienced the virtual environment and then answered three questionnaires to assess (i) stigmas related to schizophrenia, (ii) the efficiency and effectiveness of the tool, and, finally (iii) stigma after simulation. The analysis of the questionnaires showed that the proposed model is a robust tool and quite realistic and, thus, very promising in reducing stigma associated with schizophrenia by instilling in the observer a greater comprehension of any person during an schizophrenic outbreak, whether a patient or a family member. PMID:29317860

iMatTOUGH: An open-source Matlab-based graphical user interface for pre- and post-processing of TOUGH2 and iTOUGH2 models

DOE PAGES

Tran, Anh Phuong; Dafflon, Baptiste; Hubbard, Susan

2016-04-01

TOUGH2 and iTOUGH2 are powerful models that simulate the heat and fluid flows in porous and fracture media, and perform parameter estimation, sensitivity analysis and uncertainty propagation analysis. However, setting up the input files is not only tedious, but error prone, and processing output files is time consuming. Here, we present an open source Matlab-based tool (iMatTOUGH) that supports the generation of all necessary inputs for both TOUGH2 and iTOUGH2 and visualize their outputs. The tool links the inputs of TOUGH2 and iTOUGH2, making sure the two input files are consistent. It supports the generation of rectangular computational mesh, i.e.,more » it automatically generates the elements and connections as well as their properties as required by TOUGH2. The tool also allows the specification of initial and time-dependent boundary conditions for better subsurface heat and water flow simulations. The effectiveness of the tool is illustrated by an example that uses TOUGH2 and iTOUGH2 to estimate soil hydrological and thermal properties from soil temperature data and simulate the heat and water flows at the Rifle site in Colorado.« less

VisIVO: A Tool for the Virtual Observatory and Grid Environment

NASA Astrophysics Data System (ADS)

Becciani, U.; Comparato, M.; Costa, A.; Larsson, B.; Gheller, C.; Pasian, F.; Smareglia, R.

2007-10-01

We present the new features of VisIVO, software for the visualization and analysis of astrophysical data which can be retrieved from the Virtual Observatory framework and used for cosmological simulations running both on Windows and GNU/Linux platforms. VisIVO is VO standards compliant and supports the most important astronomical data formats such as FITS, HDF5 and VOTables. It is free software and can be downloaded from the web site http://visivo.cineca.it. VisIVO can interoperate with other astronomical VO compliant tools through PLASTIC (PLatform for AStronomical Tool InterConnection). This feature allows VisIVO to share data with many other astronomical packages to further analyze the loaded data.

gadfly: A pandas-based Framework for Analyzing GADGET Simulation Data

NASA Astrophysics Data System (ADS)

Hummel, Jacob A.

2016-11-01

We present the first public release (v0.1) of the open-source gadget Dataframe Library: gadfly. The aim of this package is to leverage the capabilities of the broader python scientific computing ecosystem by providing tools for analyzing simulation data from the astrophysical simulation codes gadget and gizmo using pandas, a thoroughly documented, open-source library providing high-performance, easy-to-use data structures that is quickly becoming the standard for data analysis in python. Gadfly is a framework for analyzing particle-based simulation data stored in the HDF5 format using pandas DataFrames. The package enables efficient memory management, includes utilities for unit handling, coordinate transformations, and parallel batch processing, and provides highly optimized routines for visualizing smoothed-particle hydrodynamics data sets.

Investigating grounded conceptualization: motor system state-dependence facilitates familiarity judgments of novel tools.

PubMed

Matheson, Heath E; Familiar, Ariana M; Thompson-Schill, Sharon L

2018-03-02

Theories of embodied cognition propose that we recognize tools in part by reactivating sensorimotor representations of tool use in a process of simulation. If motor simulations play a causal role in tool recognition then performing a concurrent motor task should differentially modulate recognition of experienced vs. non-experienced tools. We sought to test the hypothesis that an incompatible concurrent motor task modulates conceptual processing of learned vs. non-learned objects by directly manipulating the embodied experience of participants. We trained one group to use a set of novel, 3-D printed tools under the pretense that they were preparing for an archeological expedition to Mars (manipulation group); we trained a second group to report declarative information about how the tools are stored (storage group). With this design, familiarity and visual attention to different object parts was similar for both groups, though their qualitative interactions differed. After learning, participants made familiarity judgments of auditorily presented tool names while performing a concurrent motor task or simply sitting at rest. We showed that familiarity judgments were facilitated by motor state-dependence; specifically, in the manipulation group, familiarity was facilitated by a concurrent motor task, whereas in the spatial group familiarity was facilitated while sitting at rest. These results are the first to directly show that manipulation experience differentially modulates conceptual processing of familiar vs. unfamiliar objects, suggesting that embodied representations contribute to recognizing tools.

NETIMIS: Dynamic Simulation of Health Economics Outcomes Using Big Data.

PubMed

Johnson, Owen A; Hall, Peter S; Hulme, Claire

2016-02-01

Many healthcare organizations are now making good use of electronic health record (EHR) systems to record clinical information about their patients and the details of their healthcare. Electronic data in EHRs is generated by people engaged in complex processes within complex environments, and their human input, albeit shaped by computer systems, is compromised by many human factors. These data are potentially valuable to health economists and outcomes researchers but are sufficiently large and complex enough to be considered part of the new frontier of 'big data'. This paper describes emerging methods that draw together data mining, process modelling, activity-based costing and dynamic simulation models. Our research infrastructure includes safe links to Leeds hospital's EHRs with 3 million secondary and tertiary care patients. We created a multidisciplinary team of health economists, clinical specialists, and data and computer scientists, and developed a dynamic simulation tool called NETIMIS (Network Tools for Intervention Modelling with Intelligent Simulation; http://www.netimis.com ) suitable for visualization of both human-designed and data-mined processes which can then be used for 'what-if' analysis by stakeholders interested in costing, designing and evaluating healthcare interventions. We present two examples of model development to illustrate how dynamic simulation can be informed by big data from an EHR. We found the tool provided a focal point for multidisciplinary team work to help them iteratively and collaboratively 'deep dive' into big data.

Scalable isosurface visualization of massive datasets on commodity off-the-shelf clusters

PubMed Central

Bajaj, Chandrajit

2009-01-01

Tomographic imaging and computer simulations are increasingly yielding massive datasets. Interactive and exploratory visualizations have rapidly become indispensable tools to study large volumetric imaging and simulation data. Our scalable isosurface visualization framework on commodity off-the-shelf clusters is an end-to-end parallel and progressive platform, from initial data access to the final display. Interactive browsing of extracted isosurfaces is made possible by using parallel isosurface extraction, and rendering in conjunction with a new specialized piece of image compositing hardware called Metabuffer. In this paper, we focus on the back end scalability by introducing a fully parallel and out-of-core isosurface extraction algorithm. It achieves scalability by using both parallel and out-of-core processing and parallel disks. It statically partitions the volume data to parallel disks with a balanced workload spectrum, and builds I/O-optimal external interval trees to minimize the number of I/O operations of loading large data from disk. We also describe an isosurface compression scheme that is efficient for progress extraction, transmission and storage of isosurfaces. PMID:19756231

How mutation alters the evolutionary dynamics of cooperation on networks

NASA Astrophysics Data System (ADS)

Ichinose, Genki; Satotani, Yoshiki; Sayama, Hiroki

2018-05-01

Cooperation is ubiquitous at every level of living organisms. It is known that spatial (network) structure is a viable mechanism for cooperation to evolve. A recently proposed numerical metric, average gradient of selection (AGoS), a useful tool for interpreting and visualizing evolutionary dynamics on networks, allows simulation results to be visualized on a one-dimensional phase space. However, stochastic mutation of strategies was not considered in the analysis of AGoS. Here we extend AGoS so that it can analyze the evolution of cooperation where mutation may alter strategies of individuals on networks. We show that our extended AGoS correctly visualizes the final states of cooperation with mutation in the individual-based simulations. Our analyses revealed that mutation always has a negative effect on the evolution of cooperation regardless of the payoff functions, fraction of cooperators, and network structures. Moreover, we found that scale-free networks are the most vulnerable to mutation and thus the dynamics of cooperation are altered from bistability to coexistence on those networks, undergoing an imperfect pitchfork bifurcation.

Digital fabrication of multi-material biomedical objects.

PubMed

Cheung, H H; Choi, S H

2009-12-01

This paper describes a multi-material virtual prototyping (MMVP) system for modelling and digital fabrication of discrete and functionally graded multi-material objects for biomedical applications. The MMVP system consists of a DMMVP module, an FGMVP module and a virtual reality (VR) simulation module. The DMMVP module is used to model discrete multi-material (DMM) objects, while the FGMVP module is for functionally graded multi-material (FGM) objects. The VR simulation module integrates these two modules to perform digital fabrication of multi-material objects, which can be subsequently visualized and analysed in a virtual environment to optimize MMLM processes for fabrication of product prototypes. Using the MMVP system, two biomedical objects, including a DMM human spine and an FGM intervertebral disc spacer are modelled and digitally fabricated for visualization and analysis in a VR environment. These studies show that the MMVP system is a practical tool for modelling, visualization, and subsequent fabrication of biomedical objects of discrete and functionally graded multi-materials for biomedical applications. The system may be adapted to control MMLM machines with appropriate hardware for physical fabrication of biomedical objects.

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.

Paleomagnetism.org: An online multi-platform open source environment for paleomagnetic data analysis

NASA Astrophysics Data System (ADS)

Koymans, Mathijs R.; Langereis, Cor G.; Pastor-Galán, Daniel; van Hinsbergen, Douwe J. J.

2016-08-01

This contribution provides an overview of Paleomagnetism.org, an open-source, multi-platform online environment for paleomagnetic data analysis. Paleomagnetism.org provides an interactive environment where paleomagnetic data can be interpreted, evaluated, visualized, and exported. The Paleomagnetism.org application is split in to an interpretation portal, a statistics portal, and a portal for miscellaneous paleomagnetic tools. In the interpretation portal, principle component analysis can be performed on visualized demagnetization diagrams. Interpreted directions and great circles can be combined to find great circle solutions. These directions can be used in the statistics portal, or exported as data and figures. The tools in the statistics portal cover standard Fisher statistics for directions and VGPs, including other statistical parameters used as reliability criteria. Other available tools include an eigenvector approach foldtest, two reversal test including a Monte Carlo simulation on mean directions, and a coordinate bootstrap on the original data. An implementation is included for the detection and correction of inclination shallowing in sediments following TK03.GAD. Finally we provide a module to visualize VGPs and expected paleolatitudes, declinations, and inclinations relative to widely used global apparent polar wander path models in coordinates of major continent-bearing plates. The tools in the miscellaneous portal include a net tectonic rotation (NTR) analysis to restore a body to its paleo-vertical and a bootstrapped oroclinal test using linear regressive techniques, including a modified foldtest around a vertical axis. Paleomagnetism.org provides an integrated approach for researchers to work with visualized (e.g. hemisphere projections, Zijderveld diagrams) paleomagnetic data. The application constructs a custom exportable file that can be shared freely and included in public databases. This exported file contains all data and can later be imported to the application by other researchers. The accessibility and simplicity through which paleomagnetic data can be interpreted, analyzed, visualized, and shared makes Paleomagnetism.org of interest to the community.

A system to simulate and reproduce audio-visual environments for spatial hearing research.

PubMed

Seeber, Bernhard U; Kerber, Stefan; Hafter, Ervin R

2010-02-01

The article reports the experience gained from two implementations of the "Simulated Open-Field Environment" (SOFE), a setup that allows sounds to be played at calibrated levels over a wide frequency range from multiple loudspeakers in an anechoic chamber. Playing sounds from loudspeakers in the free-field has the advantage that each participant listens with their own ears, and individual characteristics of the ears are captured in the sound they hear. This makes an easy and accurate comparison between various listeners with and without hearing devices possible. The SOFE uses custom calibration software to assure individual equalization of each loudspeaker. Room simulation software creates the spatio-temporal reflection pattern of sound sources in rooms which is played via the SOFE loudspeakers. The sound playback system is complemented by a video projection facility which can be used to collect or give feedback or to study auditory-visual interaction. The article discusses acoustical and technical requirements for accurate sound playback against the specific needs in hearing research. An introduction to software concepts is given which allow easy, high-level control of the setup and thus fast experimental development, turning the SOFE into a "Swiss army knife" tool for auditory, spatial hearing and audio-visual research. Crown Copyright 2009. Published by Elsevier B.V. All rights reserved.

A System to Simulate and Reproduce Audio-Visual Environments for Spatial Hearing Research

PubMed Central

Seeber, Bernhard U.; Kerber, Stefan; Hafter, Ervin R.

2009-01-01

The article reports the experience gained from two implementations of the “Simulated Open-Field Environment” (SOFE), a setup that allows sounds to be played at calibrated levels over a wide frequency range from multiple loudspeakers in an anechoic chamber. Playing sounds from loudspeakers in the free-field has the advantage that each participant listens with their own ears, and individual characteristics of the ears are captured in the sound they hear. This makes an easy and accurate comparison between various listeners with and without hearing devices possible. The SOFE uses custom calibration software to assure individual equalization of each loudspeaker. Room simulation software creates the spatio-temporal reflection pattern of sound sources in rooms which is played via the SOFE loudspeakers. The sound playback system is complemented by a video projection facility which can be used to collect or give feedback or to study auditory-visual interaction. The article discusses acoustical and technical requirements for accurate sound playback against the specific needs in hearing research. An introduction to software concepts is given which allow easy, high-level control of the setup and thus fast experimental development, turning the SOFE into a “Swiss army knife” tool for auditory, spatial hearing and audio-visual research. PMID:19909802

Full-physics 3D heterogeneous simulations of electromagnetic induction fields on level and deformed sea ice

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

Samluk, Jesse P.; Geiger, Cathleen A.; Weiss, Chester J.

In this article we explore simulated responses of electromagnetic (EM) signals relative to in situ field surveys and quantify the effects that different values of conductivity in sea ice have on the EM fields. We compute EM responses of ice types with a three-dimensional (3-D) finite-volume discretization of Maxwell's equations and present 2-D sliced visualizations of their associated EM fields at discrete frequencies. Several interesting observations result: First, since the simulator computes the fields everywhere, each gridcell acts as a receiver within the model volume, and captures the complete, coupled interactions between air, snow, sea ice and sea water asmore » a function of their conductivity; second, visualizations demonstrate how 1-D approximations near deformed ice features are violated. But the most important new finding is that changes in conductivity affect EM field response by modifying the magnitude and spatial patterns (i.e. footprint size and shape) of current density and magnetic fields. These effects are demonstrated through a visual feature we define as 'null lines'. Null line shape is affected by changes in conductivity near material boundaries as well as transmitter location. Our results encourage the use of null lines as a planning tool for better ground-truth field measurements near deformed ice types.« less

Engaging Undergraduate Math Majors in Geoscience Research using Interactive Simulations and Computer Art

NASA Astrophysics Data System (ADS)

Matott, L. S.; Hymiak, B.; Reslink, C. F.; Baxter, C.; Aziz, S.

2012-12-01

As part of the NSF-sponsored 'URGE (Undergraduate Research Group Experiences) to Compute' program, Dr. Matott has been collaborating with talented Math majors to explore the design of cost-effective systems to safeguard groundwater supplies from contaminated sites. Such activity is aided by a combination of groundwater modeling, simulation-based optimization, and high-performance computing - disciplines largely unfamiliar to the students at the outset of the program. To help train and engage the students, a number of interactive and graphical software packages were utilized. Examples include: (1) a tutorial for exploring the behavior of evolutionary algorithms and other heuristic optimizers commonly used in simulation-based optimization; (2) an interactive groundwater modeling package for exploring alternative pump-and-treat containment scenarios at a contaminated site in Billings, Montana; (3) the R software package for visualizing various concepts related to subsurface hydrology; and (4) a job visualization tool for exploring the behavior of numerical experiments run on a large distributed computing cluster. Further engagement and excitement in the program was fostered by entering (and winning) a computer art competition run by the Coalition for Academic Scientific Computation (CASC). The winning submission visualizes an exhaustively mapped optimization cost surface and dramatically illustrates the phenomena of artificial minima - valley locations that correspond to designs whose costs are only partially optimal.

Full-physics 3D heterogeneous simulations of electromagnetic induction fields on level and deformed sea ice

DOE PAGES

Samluk, Jesse P.; Geiger, Cathleen A.; Weiss, Chester J.; ...

2015-10-01

In this article we explore simulated responses of electromagnetic (EM) signals relative to in situ field surveys and quantify the effects that different values of conductivity in sea ice have on the EM fields. We compute EM responses of ice types with a three-dimensional (3-D) finite-volume discretization of Maxwell's equations and present 2-D sliced visualizations of their associated EM fields at discrete frequencies. Several interesting observations result: First, since the simulator computes the fields everywhere, each gridcell acts as a receiver within the model volume, and captures the complete, coupled interactions between air, snow, sea ice and sea water asmore » a function of their conductivity; second, visualizations demonstrate how 1-D approximations near deformed ice features are violated. But the most important new finding is that changes in conductivity affect EM field response by modifying the magnitude and spatial patterns (i.e. footprint size and shape) of current density and magnetic fields. These effects are demonstrated through a visual feature we define as 'null lines'. Null line shape is affected by changes in conductivity near material boundaries as well as transmitter location. Our results encourage the use of null lines as a planning tool for better ground-truth field measurements near deformed ice types.« less

Development and evaluation of a connective tissue phantom model for subsurface visualization of cancers requiring wide local excision

NASA Astrophysics Data System (ADS)

Samkoe, Kimberley S.; Bates, Brent D.; Tselepidakis, Niki N.; DSouza, Alisha V.; Gunn, Jason R.; Ramkumar, Dipak B.; Paulsen, Keith D.; Pogue, Brian W.; Henderson, Eric R.

2017-12-01

Wide local excision (WLE) of tumors with negative margins remains a challenge because surgeons cannot directly visualize the mass. Fluorescence-guided surgery (FGS) may improve surgical accuracy; however, conventional methods with direct surface tumor visualization are not immediately applicable, and properties of tissues surrounding the cancer must be considered. We developed a phantom model for sarcoma resection with the near-infrared fluorophore IRDye 800CW and used it to iteratively define the properties of connective tissues that typically surround sarcoma tumors. We then tested the ability of a blinded surgeon to resect fluorescent tumor-simulating inclusions with ˜1-cm margins using predetermined target fluorescence intensities and a Solaris open-air fluorescence imaging system. In connective tissue-simulating phantoms, fluorescence intensity decreased with increasing blood concentration and increased with increasing intralipid concentrations. Fluorescent inclusions could be resolved at ≥1-cm depth in all inclusion concentrations and sizes tested. When inclusion depth was held constant, fluorescence intensity decreased with decreasing volume. Using targeted fluorescence intensities, a blinded surgeon was able to successfully excise inclusions with ˜1-cm margins from fat- and muscle-simulating phantoms with inclusion-to-background contrast ratios as low as 2∶1. Indirect, subsurface FGS is a promising tool for surgical resection of cancers requiring WLE.

A Simulation Study of Acoustic-Assisted Tracking of Whales for Mark-Recapture Surveys

PubMed Central

Peel, David; Miller, Brian S.; Kelly, Natalie; Dawson, Steve; Slooten, Elisabeth; Double, Michael C.

2014-01-01

Collecting enough data to obtain reasonable abundance estimates of whales is often difficult, particularly when studying rare species. Passive acoustics can be used to detect whale sounds and are increasingly used to estimate whale abundance. Much of the existing effort centres on the use of acoustics to estimate abundance directly, e.g. analysing detections in a distance sampling framework. Here, we focus on acoustics as a tool incorporated within mark-recapture surveys. In this context, acoustic tools are used to detect and track whales, which are then photographed or biopsied to provide data for mark-recapture analyses. The purpose of incorporating acoustics is to increase the encounter rate beyond using visual searching only. While this general approach is not new, its utility is rarely quantified. This paper predicts the “acoustically-assisted” encounter rate using a discrete-time individual-based simulation of whales and survey vessel. We validate the simulation framework using existing data from studies of sperm whales. We then use the framework to predict potential encounter rates in a study of Antarctic blue whales. We also investigate the effects of a number of the key parameters on encounter rate. Mean encounter rates from the simulation of sperm whales matched well with empirical data. Variance of encounter rate, however, was underestimated. The simulation of Antarctic blue whales found that passive acoustics should provide a 1.7–3.0 fold increase in encounter rate over visual-only methods. Encounter rate was most sensitive to acoustic detection range, followed by vocalisation rate. During survey planning and design, some indication of the relationship between expected sample size and effort is paramount; this simulation framework can be used to predict encounter rates and establish this relationship. For a case in point, the simulation framework indicates unequivocally that real-time acoustic tracking should be considered for quantifying the abundance of Antarctic blue whales via mark-recapture methods. PMID:24827919

A simulation study of acoustic-assisted tracking of whales for mark-recapture surveys.

PubMed

Peel, David; Miller, Brian S; Kelly, Natalie; Dawson, Steve; Slooten, Elisabeth; Double, Michael C

2014-01-01

Collecting enough data to obtain reasonable abundance estimates of whales is often difficult, particularly when studying rare species. Passive acoustics can be used to detect whale sounds and are increasingly used to estimate whale abundance. Much of the existing effort centres on the use of acoustics to estimate abundance directly, e.g. analysing detections in a distance sampling framework. Here, we focus on acoustics as a tool incorporated within mark-recapture surveys. In this context, acoustic tools are used to detect and track whales, which are then photographed or biopsied to provide data for mark-recapture analyses. The purpose of incorporating acoustics is to increase the encounter rate beyond using visual searching only. While this general approach is not new, its utility is rarely quantified. This paper predicts the "acoustically-assisted" encounter rate using a discrete-time individual-based simulation of whales and survey vessel. We validate the simulation framework using existing data from studies of sperm whales. We then use the framework to predict potential encounter rates in a study of Antarctic blue whales. We also investigate the effects of a number of the key parameters on encounter rate. Mean encounter rates from the simulation of sperm whales matched well with empirical data. Variance of encounter rate, however, was underestimated. The simulation of Antarctic blue whales found that passive acoustics should provide a 1.7-3.0 fold increase in encounter rate over visual-only methods. Encounter rate was most sensitive to acoustic detection range, followed by vocalisation rate. During survey planning and design, some indication of the relationship between expected sample size and effort is paramount; this simulation framework can be used to predict encounter rates and establish this relationship. For a case in point, the simulation framework indicates unequivocally that real-time acoustic tracking should be considered for quantifying the abundance of Antarctic blue whales via mark-recapture methods.

The SCEC Community Modeling Environment(SCEC/CME): A Collaboratory for Seismic Hazard Analysis

NASA Astrophysics Data System (ADS)

Maechling, P. J.; Jordan, T. H.; Minster, J. B.; Moore, R.; Kesselman, C.

2005-12-01

The SCEC Community Modeling Environment (SCEC/CME) Project is an NSF-supported Geosciences/IT partnership that is actively developing an advanced information infrastructure for system-level earthquake science in Southern California. This partnership includes SCEC, USC's Information Sciences Institute (ISI), the San Diego Supercomputer Center (SDSC), the Incorporated Institutions for Research in Seismology (IRIS), and the U.S. Geological Survey. The goal of the SCEC/CME is to develop seismological applications and information technology (IT) infrastructure to support the development of Seismic Hazard Analysis (SHA) programs and other geophysical simulations. The SHA application programs developed on the Project include a Probabilistic Seismic Hazard Analysis system called OpenSHA. OpenSHA computational elements that are currently available include a collection of attenuation relationships, and several Earthquake Rupture Forecasts (ERFs). Geophysicists in the collaboration have also developed Anelastic Wave Models (AWMs) using both finite-difference and finite-element approaches. Earthquake simulations using these codes have been run for a variety of earthquake sources. Rupture Dynamic Model (RDM) codes have also been developed that simulate friction-based fault slip. The SCEC/CME collaboration has also developed IT software and hardware infrastructure to support the development, execution, and analysis of these SHA programs. To support computationally expensive simulations, we have constructed a grid-based scientific workflow system. Using the SCEC grid, project collaborators can submit computations from the SCEC/CME servers to High Performance Computers at USC and TeraGrid High Performance Computing Centers. Data generated and archived by the SCEC/CME is stored in a digital library system, the Storage Resource Broker (SRB). This system provides a robust and secure system for maintaining the association between the data seta and their metadata. To provide an easy-to-use system for constructing SHA computations, a browser-based workflow assembly web portal has been developed. Users can compose complex SHA calculations, specifying SCEC/CME data sets as inputs to calculations, and calling SCEC/CME computational programs to process the data and the output. Knowledge-based software tools have been implemented that utilize ontological descriptions of SHA software and data can validate workflows created with this pathway assembly tool. Data visualization software developed by the collaboration supports analysis and validation of data sets. Several programs have been developed to visualize SCEC/CME data including GMT-based map making software for PSHA codes, 4D wavefield propagation visualization software based on OpenGL, and 3D Geowall-based visualization of earthquakes, faults, and seismic wave propagation. The SCEC/CME Project also helps to sponsor the SCEC UseIT Intern program. The UseIT Intern Program provides research opportunities in both Geosciences and Information Technology to undergraduate students in a variety of fields. The UseIT group has developed a 3D data visualization tool, called SCEC-VDO, as a part of this undergraduate research program.

STARE CubeSat Communications Testing, Simulation and Analysis

DTIC Science & Technology

2012-09-01

26  Figure 24.  STK MC3 Ground Station Locations ................................................... 31  x THIS PAGE INTENTIONALLY LEFT BLANK xi...Refinement of Ephemeris STK Satellite Tool Kit VPN Virtual Private Network xiv THIS PAGE INTENTIONALLY LEFT BLANK xv ACKNOWLEDGMENTS This...the radio itself. Using a signal attenuator to decrease signal strength by 10 dB increments, and a spectrum analyzer to see a visual representation

Simulations of Carnival Rides and Rube Goldberg Machines for the Visualization of Concepts of Statics and Dynamics

ERIC Educational Resources Information Center

Howard, William; Williams, Richard; Yao, Jason

2010-01-01

Solid modeling is widely used as a teaching tool in summer activities with high school students. The addition of motion analysis allows concepts from statics and dynamics to be introduced to students in both qualitative and quantitative ways. Two sets of solid modeling projects--carnival rides and Rube Goldberg machines--are shown to allow the…

Visual Purple, the Next Generation Crisis Management Decision Training Tool

DTIC Science & Technology

2001-09-01

talents of professional Hollywood screenwriters during the scripting and writing process of the simulations. Additionally, cinematic techniques learned...cultural, and language experts for research development. Additionally, GTA provides country specific support in script writing and cinematic resources as...The result is an entirely new dimension of realism that traditional exercises often fail to capture. The scenario requires the participant to make the

Analysis of post-mining excavations as places for municipal waste

NASA Astrophysics Data System (ADS)

Górniak-Zimroz, Justyna

2018-01-01

Waste management planning is an interdisciplinary task covering a wide range of issues including costs, legal requirements, spatial planning, environmental protection, geography, demographics, and techniques used in collecting, transporting, processing and disposing of waste. Designing and analyzing this issue is difficult and requires the use of advanced analysis methods and tools available in GIS geographic information systems containing readily available graphical and descriptive databases, data analysis tools providing expert decision support while selecting the best-designed alternative, and simulation models that allow the user to simulate many variants of waste management together with graphical visualization of the results of performed analyzes. As part of the research study, there have been works undertaken concerning the use of multi-criteria data analysis in waste management in areas located in southwestern Poland. These works have proposed the inclusion in waste management of post-mining excavations as places for the final or temporary collection of waste assessed in terms of their suitability with the tools available in GIS systems.

RF Models for Plasma-Surface Interactions in VSim

NASA Astrophysics Data System (ADS)

Jenkins, Thomas G.; Smithe, D. N.; Pankin, A. Y.; Roark, C. M.; Zhou, C. D.; Stoltz, P. H.; Kruger, S. E.

2014-10-01

An overview of ongoing enhancements to the Plasma Discharge (PD) module of Tech-X's VSim software tool is presented. A sub-grid kinetic sheath model, developed for the accurate computation of sheath potentials near metal and dielectric-coated walls, enables the physical effects of DC and RF sheath physics to be included in macroscopic-scale plasma simulations that need not explicitly resolve sheath scale lengths. Sheath potential evolution, together with particle behavior near the sheath, can thus be simulated in complex geometries. Generalizations of the model to include sputtering, secondary electron emission, and effects from multiple ion species and background magnetic fields are summarized; related numerical results are also presented. In addition, improved tools for plasma chemistry and IEDF/EEDF visualization and modeling are discussed, as well as our initial efforts toward the development of hybrid fluid/kinetic transition capabilities within VSim. Ultimately, we aim to establish VSimPD as a robust, efficient computational tool for modeling industrial plasma processes. Supported by US DoE SBIR-I/II Award DE-SC0009501.

OpenKIM - Building a Knowledgebase of Interatomic Models

NASA Astrophysics Data System (ADS)

Bierbaum, Matthew; Tadmor, Ellad; Elliott, Ryan; Wennblom, Trevor; Alemi, Alexander; Chen, Yan-Jiun; Karls, Daniel; Ludvik, Adam; Sethna, James

2014-03-01

The Knowledgebase of Interatomic Models (KIM) is an effort by the computational materials community to provide a standard interface for the development, characterization, and use of interatomic potentials. The KIM project has developed an API between simulation codes and interatomic models written in several different languages including C, Fortran, and Python. This interface is already supported in popular simulation environments such as LAMMPS and ASE, giving quick access to over a hundred compatible potentials that have been contributed so far. To compare and characterize models, we have developed a computational processing pipeline which automatically runs a series of tests for each model in the system, such as phonon dispersion relations and elastic constant calculations. To view the data from these tests, we created a rich set of interactive visualization tools located online. Finally, we created a Web repository to store and share these potentials, tests, and visualizations which can be found at https://openkim.org along with futher information.

Java 3D Interactive Visualization for Astrophysics

NASA Astrophysics Data System (ADS)

Chae, K.; Edirisinghe, D.; Lingerfelt, E. J.; Guidry, M. W.

2003-05-01

We are developing a series of interactive 3D visualization tools that employ the Java 3D API. We have applied this approach initially to a simple 3-dimensional galaxy collision model (restricted 3-body approximation), with quite satisfactory results. Running either as an applet under Web browser control, or as a Java standalone application, this program permits real-time zooming, panning, and 3-dimensional rotation of the galaxy collision simulation under user mouse and keyboard control. We shall also discuss applications of this technology to 3-dimensional visualization for other problems of astrophysical interest such as neutron star mergers and the time evolution of element/energy production networks in X-ray bursts. *Managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725.

The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.

PubMed

Treangen, Todd J; Ondov, Brian D; Koren, Sergey; Phillippy, Adam M

2014-01-01

Whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods are limited in their ability to perform sequence comparisons of multiple sequences simultaneously. Here we present the Harvest suite of core-genome alignment and visualization tools for the rapid and simultaneous analysis of thousands of intraspecific microbial strains. Harvest includes Parsnp, a fast core-genome multi-aligner, and Gingr, a dynamic visual platform. Together they provide interactive core-genome alignments, variant calls, recombination detection, and phylogenetic trees. Using simulated and real data we demonstrate that our approach exhibits unrivaled speed while maintaining the accuracy of existing methods. The Harvest suite is open-source and freely available from: http://github.com/marbl/harvest.

High speed digital holographic interferometry for hypersonic flow visualization

NASA Astrophysics Data System (ADS)

Hegde, G. M.; Jagdeesh, G.; Reddy, K. P. J.

2013-06-01

Optical imaging techniques have played a major role in understanding the flow dynamics of varieties of fluid flows, particularly in the study of hypersonic flows. Schlieren and shadowgraph techniques have been the flow diagnostic tools for the investigation of compressible flows since more than a century. However these techniques provide only the qualitative information about the flow field. Other optical techniques such as holographic interferometry and laser induced fluorescence (LIF) have been used extensively for extracting quantitative information about the high speed flows. In this paper we present the application of digital holographic interferometry (DHI) technique integrated with short duration hypersonic shock tunnel facility having 1 ms test time, for quantitative flow visualization. Dynamics of the flow fields in hypersonic/supersonic speeds around different test models is visualized with DHI using a high-speed digital camera (0.2 million fps). These visualization results are compared with schlieren visualization and CFD simulation results. Fringe analysis is carried out to estimate the density of the flow field.

Telearch - Integrated visual simulation environment for collaborative virtual archaeology.

NASA Astrophysics Data System (ADS)

Kurillo, Gregorij; Forte, Maurizio

Archaeologists collect vast amounts of digital data around the world; however, they lack tools for integration and collaborative interaction to support reconstruction and interpretation process. TeleArch software is aimed to integrate different data sources and provide real-time interaction tools for remote collaboration of geographically distributed scholars inside a shared virtual environment. The framework also includes audio, 2D and 3D video streaming technology to facilitate remote presence of users. In this paper, we present several experimental case studies to demonstrate the integration and interaction with 3D models and geographical information system (GIS) data in this collaborative environment.

Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data

PubMed Central

Kyoda, Koji; Tohsato, Yukako; Ho, Kenneth H. L.; Onami, Shuichi

2015-01-01

Motivation: Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. Results: We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. Availability and implementation: A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. Contact: sonami@riken.jp Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:25414366

Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data.

PubMed

Kyoda, Koji; Tohsato, Yukako; Ho, Kenneth H L; Onami, Shuichi

2015-04-01

Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Open-source web-enabled data management, analyses, and visualization of very large data in geosciences using Jupyter, Apache Spark, and community tools

NASA Astrophysics Data System (ADS)

Chaudhary, A.

2017-12-01

Current simulation models and sensors are producing high-resolution, high-velocity data in geosciences domain. Knowledge discovery from these complex and large size datasets require tools that are capable of handling very large data and providing interactive data analytics features to researchers. To this end, Kitware and its collaborators are producing open-source tools GeoNotebook, GeoJS, Gaia, and Minerva for geosciences that are using hardware accelerated graphics and advancements in parallel and distributed processing (Celery and Apache Spark) and can be loosely coupled to solve real-world use-cases. GeoNotebook (https://github.com/OpenGeoscience/geonotebook) is co-developed by Kitware and NASA-Ames and is an extension to the Jupyter Notebook. It provides interactive visualization and python-based analysis of geospatial data and depending the backend (KTile or GeoPySpark) can handle data sizes of Hundreds of Gigabytes to Terabytes. GeoNotebook uses GeoJS (https://github.com/OpenGeoscience/geojs) to render very large geospatial data on the map using WebGL and Canvas2D API. GeoJS is more than just a GIS library as users can create scientific plots such as vector and contour and can embed InfoVis plots using D3.js. GeoJS aims for high-performance visualization and interactive data exploration of scientific and geospatial location aware datasets and supports features such as Point, Line, Polygon, and advanced features such as Pixelmap, Contour, Heatmap, and Choropleth. Our another open-source tool Minerva ((https://github.com/kitware/minerva) is a geospatial application that is built on top of open-source web-based data management system Girder (https://github.com/girder/girder) which provides an ability to access data from HDFS or Amazon S3 buckets and provides capabilities to perform visualization and analyses on geosciences data in a web environment using GDAL and GeoPandas wrapped in a unified API provided by Gaia (https://github.com/OpenDataAnalytics/gaia). In this presentation, we will discuss core features of each of these tools and will present lessons learned on handling large data in the context of data management, analyses and visualization.

Create and Publish a Hierarchical Progressive Survey (HiPS)

NASA Astrophysics Data System (ADS)

Fernique, P.; Boch, T.; Pineau, F.; Oberto, A.

2014-05-01

Since 2009, the CDS promotes a method for visualizing based on the HEALPix sky tessellation. This method, called “Hierarchical Progressive Survey" or HiPS, allows one to display a survey progressively. It is particularly suited for all-sky surveys or deep fields. This visualization method is now integrated in several applications, notably Aladin, the SiTools/MIZAR CNES framework, and the recent HTML5 “Aladin Lite". Also, more than one hundred surveys are already available in this view mode. In this article, we will present the progress concerning this method and its recent adaptation to the astronomical catalogs such as the GAIA simulation.

Designsafe-Ci a Cyberinfrastructure for Natural Hazard Simulation and Data

NASA Astrophysics Data System (ADS)

Dawson, C.; Rathje, E.; Stanzione, D.; Padgett, J.; Pinelli, J. P.

2017-12-01

DesignSafe is the web-based research platform of the Natural Hazards Engineering Research Infrastructure (NHERI) network that provides the computational tools needed to manage and analyze critical data for natural hazards research, with wind and storm surge related hazards being a primary focus. One of the simulation tools under DesignSafe is the Advanced Circulation (ADCIRC) model, a coastal ocean model used in storm surge analysis. ADCIRC is an unstructured, finite element model with high resolution capabilities for studying storm surge impacts, and has long been used in storm surge hind-casting and forecasting. In this talk, we will demonstrate the use of ADCIRC within the DesignSafe platform and its use for forecasting Hurricane Harvey. We will also demonstrate how to analyze, visualize and archive critical storm surge related data within DesignSafe.

Quantitative petri net model of gene regulated metabolic networks in the cell.

PubMed

Chen, Ming; Hofestädt, Ralf

2011-01-01

A method to exploit hybrid Petri nets (HPN) for quantitatively modeling and simulating gene regulated metabolic networks is demonstrated. A global kinetic modeling strategy and Petri net modeling algorithm are applied to perform the bioprocess functioning and model analysis. With the model, the interrelations between pathway analysis and metabolic control mechanism are outlined. Diagrammatical results of the dynamics of metabolites are simulated and observed by implementing a HPN tool, Visual Object Net ++. An explanation of the observed behavior of the urea cycle is proposed to indicate possibilities for metabolic engineering and medical care. Finally, the perspective of Petri nets on modeling and simulation of metabolic networks is discussed.

Web service tools in the era of forest fire management and elimination

NASA Astrophysics Data System (ADS)

Poursanidis, Dimitris; Kochilakis, Giorgos; Chrysoulakis, Nektarios; Varella, Vasiliki; Kotroni, Vassiliki; Eftychidis, Giorgos; Lagouvardos, Kostas

2014-10-01

Wildfires in forests and forested areas in South Europe, North America, Central Asia and Australia are a diachronic threat with crucial ecological, economic and social impacts. Last decade the frequency, the magnitude and the intensity of fires have increased even more because of the climate change. An efficient response to such disasters requires an effective planning, with an early detection system of the ignition area and an accurate prediction of fire propagation to support the rapid response mechanisms. For this reason, information systems able to predict and visualize the behavior of fires, are valuable tools for fire fighting. Such systems, able also to perform simulations that evaluate the fire development scenarios, based on weather conditions, become valuable Decision Support Tools for fire mitigation planning. A Web-based Information System (WIS) developed in the framework of the FLIRE (Floods and fire risk assessment and management) project, a LIFE+ co-funded by the European Commission research, is presented in this study. The FLIRE WIS use forest fuel maps which have been developed by using generalized fuel maps, satellite data and in-situ observations. Furthermore, it leverages data from meteorological stations and weather forecast from numerical models to feed the fire propagation model with the necessary for the simulations inputs and to visualize the model's results for user defined time periods and steps. The user has real-time access to FLIRE WIS via any web browser from any platform (PC, Laptop, Tablet, Smartphone).

Pilots' visual scan patterns and situation awareness in flight operations.

PubMed

Yu, Chung-San; Wang, Eric Min-Yang; Li, Wen-Chin; Braithwaite, Graham

2014-07-01

Situation awareness (SA) is considered an essential prerequisite for safe flying. If the impact of visual scanning patterns on a pilot's situation awareness could be identified in flight operations, then eye-tracking tools could be integrated with flight simulators to improve training efficiency. Participating in this research were 18 qualified, mission-ready fighter pilots. The equipment included high-fidelity and fixed-base type flight simulators and mobile head-mounted eye-tracking devices to record a subject's eye movements and SA while performing air-to-surface tasks. There were significant differences in pilots' percentage of fixation in three operating phases: preparation (M = 46.09, SD = 14.79), aiming (M = 24.24, SD = 11.03), and release and break-away (M = 33.98, SD = 14.46). Also, there were significant differences in pilots' pupil sizes, which were largest in the aiming phase (M = 27,621, SD = 6390.8), followed by release and break-away (M = 27,173, SD = 5830.46), then preparation (M = 25,710, SD = 6078.79), which was the smallest. Furthermore, pilots with better SA performance showed lower perceived workload (M = 30.60, SD = 17.86), and pilots with poor SA performance showed higher perceived workload (M = 60.77, SD = 12.72). Pilots' percentage of fixation and average fixation duration among five different areas of interest showed significant differences as well. Eye-tracking devices can aid in capturing pilots' visual scan patterns and SA performance, unlike traditional flight simulators. Therefore, integrating eye-tracking devices into the simulator may be a useful method for promoting SA training in flight operations, and can provide in-depth understanding of the mechanism of visual scan patterns and information processing to improve training effectiveness in aviation.

Ranking of Business Process Simulation Software Tools with DEX/QQ Hierarchical Decision Model

PubMed Central

2016-01-01

The omnipresent need for optimisation requires constant improvements of companies’ business processes (BPs). Minimising the risk of inappropriate BP being implemented is usually performed by simulating the newly developed BP under various initial conditions and “what-if” scenarios. An effectual business process simulations software (BPSS) is a prerequisite for accurate analysis of an BP. Characterisation of an BPSS tool is a challenging task due to the complex selection criteria that includes quality of visual aspects, simulation capabilities, statistical facilities, quality reporting etc. Under such circumstances, making an optimal decision is challenging. Therefore, various decision support models are employed aiding the BPSS tool selection. The currently established decision support models are either proprietary or comprise only a limited subset of criteria, which affects their accuracy. Addressing this issue, this paper proposes a new hierarchical decision support model for ranking of BPSS based on their technical characteristics by employing DEX and qualitative to quantitative (QQ) methodology. Consequently, the decision expert feeds the required information in a systematic and user friendly manner. There are three significant contributions of the proposed approach. Firstly, the proposed hierarchical model is easily extendible for adding new criteria in the hierarchical structure. Secondly, a fully operational decision support system (DSS) tool that implements the proposed hierarchical model is presented. Finally, the effectiveness of the proposed hierarchical model is assessed by comparing the resulting rankings of BPSS with respect to currently available results. PMID:26871694

Modeling and simulation of offshore wind farm O&M processes

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

Joschko, Philip, E-mail: joschko@informatik.uni-hamburg.de; Widok, Andi H., E-mail: a.widok@htw-berlin.de; Appel, Susanne, E-mail: susanne.appel@hs-bremen.de

2015-04-15

This paper describes a holistic approach to operation and maintenance (O&M) processes in the domain of offshore wind farm power generation. The acquisition and process visualization is followed by a risk analysis of all relevant processes. Hereafter, a tool was designed, which is able to model the defined processes in a BPMN 2.0 notation, as well as connect and simulate them. Furthermore, the notation was enriched with new elements, representing other relevant factors that were, to date, only displayable with much higher effort. In that regard a variety of more complex situations were integrated, such as for example new processmore » interactions depending on different weather influences, in which case a stochastic weather generator was combined with the business simulation or other wind farm aspects important to the smooth running of the offshore wind farms. In addition, the choices for different methodologies, such as the simulation framework or the business process notation will be presented and elaborated depending on the impact they had on the development of the approach and the software solution. - Highlights: • Analysis of operation and maintenance processes of offshore wind farms • Process modeling with BPMN 2.0 • Domain-specific simulation tool.« less

Prediction of Thermal Transport Properties of Materials with Microstructural Complexity

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

Chen, Youping

This project aims at overcoming the major obstacle standing in the way of progress in dynamic multiscale simulation, which is the lack of a concurrent atomistic-continuum method that allows phonons, heat and defects to pass through the atomistic-continuum interface. The research has led to the development of a concurrent atomistic-continuum (CAC) methodology for multiscale simulations of materials microstructural, mechanical and thermal transport behavior. Its efficacy has been tested and demonstrated through simulations of dislocation dynamics and phonon transport coupled with microstructural evolution in a variety of materials and through providing visual evidences of the nature of phonon transport, such asmore » showing the propagation of heat pulses in single and polycrystalline solids is partially ballistic and partially diffusive. In addition to providing understanding on phonon scattering with phase interface and with grain boundaries, the research has contributed a multiscale simulation tool for understanding of the behavior of complex materials and has demonstrated the capability of the tool in simulating the dynamic, in situ experimental studies of nonequilibrium transient transport processes in material samples that are at length scales typically inaccessible by atomistically resolved methods.« less

Why Color Matters: The Effect of Visual Cues on Learner's Interpretation of Dark Matter in a Cosmology Visualization

NASA Astrophysics Data System (ADS)

Buck, Z.

2013-04-01

As we turn more and more to high-end computing to understand the Universe at cosmological scales, visualizations of simulations will take on a vital role as perceptual and cognitive tools. In collaboration with the Adler Planetarium and University of California High-Performance AstroComputing Center (UC-HiPACC), I am interested in better understanding the use of visualizations to mediate astronomy learning across formal and informal settings. The aspect of my research that I present here uses quantitative methods to investigate how learners are relying on color to interpret dark matter in a cosmology visualization. The concept of dark matter is vital to our current understanding of the Universe, and yet we do not know how to effectively present dark matter visually to support learning. I employ an alternative treatment post-test only experimental design, in which members of an equivalent sample are randomly assigned to one of three treatment groups, followed by treatment and a post-test. Results indicate significant correlation (p < .05) between the color of dark matter in the visualization and survey responses, implying that aesthetic variations like color can have a profound effect on audience interpretation of a cosmology visualization.

Teaching physics using Microsoft Excel

NASA Astrophysics Data System (ADS)

Uddin, Zaheer; Ahsanuddin, Muhammad; Khan, Danish Ahmed

2017-09-01

Excel is both ubiquitous and easily understandable. Most people from every walk of life know how to use MS office and Excel spreadsheets. Students are also familiar with spreadsheets. Most students know how to use spreadsheets for data analysis. Besides basic use of Excel, some important aspects of spreadsheets are highlighted in this article. MS Excel can be used to visualize effects of various parameters in a physical system. It can be used as a simulating tool; simulation of wind data has been done through spreadsheets in this study. Examples of Lissajous figures and a damped harmonic oscillator are presented in this article.

Observing system simulations using synthetic radiances and atmospheric retrievals derived for the AMSU and HIRS in a mesoscale model. [Advanced Microwave Sounding Unit

NASA Technical Reports Server (NTRS)

Diak, George R.; Huang, Hung-Lung; Kim, Dongsoo

1990-01-01

The paper addresses the concept of synthetic satellite imagery as a visualization and diagnostic tool for understanding satellite sensors of the future and to detail preliminary results on the quality of soundings from the current sensors. Preliminary results are presented on the quality of soundings from the combination of the High-Resolution Infrared Radiometer Sounder and the Advanced Microwave Sounding Unit. Results are also presented on the first Observing System Simulation Experiment using this data in a mesoscale numerical prediction model.

Rocinante, a virtual collaborative visualizer

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

McDonald, M.J.; Ice, L.G.

1996-12-31

With the goal of improving the ability of people around the world to share the development and use of intelligent systems, Sandia National Laboratories` Intelligent Systems and Robotics Center is developing new Virtual Collaborative Engineering (VCE) and Virtual Collaborative Control (VCC) technologies. A key area of VCE and VCC research is in shared visualization of virtual environments. This paper describes a Virtual Collaborative Visualizer (VCV), named Rocinante, that Sandia developed for VCE and VCC applications. Rocinante allows multiple participants to simultaneously view dynamic geometrically-defined environments. Each viewer can exclude extraneous detail or include additional information in the scene as desired.more » Shared information can be saved and later replayed in a stand-alone mode. Rocinante automatically scales visualization requirements with computer system capabilities. Models with 30,000 polygons and 4 Megabytes of texture display at 12 to 15 frames per second (fps) on an SGI Onyx and at 3 to 8 fps (without texture) on Indigo 2 Extreme computers. In its networked mode, Rocinante synchronizes its local geometric model with remote simulators and sensory systems by monitoring data transmitted through UDP packets. Rocinante`s scalability and performance make it an ideal VCC tool. Users throughout the country can monitor robot motions and the thinking behind their motion planners and simulators.« less

User Centered, Application Independent Visualization of National Airspace Data

NASA Technical Reports Server (NTRS)

Murphy, James R.; Hinton, Susan E.

2011-01-01

This paper describes an application independent software tool, IV4D, built to visualize animated and still 3D National Airspace System (NAS) data specifically for aeronautics engineers who research aggregate, as well as single, flight efficiencies and behavior. IV4D was origin ally developed in a joint effort between the National Aeronautics and Space Administration (NASA) and the Air Force Research Laboratory (A FRL) to support the visualization of air traffic data from the Airspa ce Concept Evaluation System (ACES) simulation program. The three mai n challenges tackled by IV4D developers were: 1) determining how to d istill multiple NASA data formats into a few minimal dataset types; 2 ) creating an environment, consisting of a user interface, heuristic algorithms, and retained metadata, that facilitates easy setup and fa st visualization; and 3) maximizing the user?s ability to utilize the extended range of visualization available with AFRL?s existing 3D te chnologies. IV4D is currently being used by air traffic management re searchers at NASA?s Ames and Langley Research Centers to support data visualizations.

MOST-visualization: software for producing automated textbook-style maps of genome-scale metabolic networks.

PubMed

Kelley, James J; Maor, Shay; Kim, Min Kyung; Lane, Anatoliy; Lun, Desmond S

2017-08-15

Visualization of metabolites, reactions and pathways in genome-scale metabolic networks (GEMs) can assist in understanding cellular metabolism. Three attributes are desirable in software used for visualizing GEMs: (i) automation, since GEMs can be quite large; (ii) production of understandable maps that provide ease in identification of pathways, reactions and metabolites; and (iii) visualization of the entire network to show how pathways are interconnected. No software currently exists for visualizing GEMs that satisfies all three characteristics, but MOST-Visualization, an extension of the software package MOST (Metabolic Optimization and Simulation Tool), satisfies (i), and by using a pre-drawn overview map of metabolism based on the Roche map satisfies (ii) and comes close to satisfying (iii). MOST is distributed for free on the GNU General Public License. The software and full documentation are available at http://most.ccib.rutgers.edu/. dslun@rutgers.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Dynamic Shade and Irradiance Simulation of Aquatic ...

EPA Pesticide Factsheets

Penumbra is a landscape shade and irradiance simulation model that simulates how solar energy spatially and temporally interacts within dynamic ecosystems such as riparian zones, forests, and other terrain that cast topological shadows. Direct and indirect solar energy accumulates across landscapes and is the main energy driver for increasing aquatic and landscape temperatures at both local and holistic scales. Landscape disturbances such as landuse change, clear cutting, and fire can cause significant variations in the resulting irradiance reaching particular locations. Penumbra can simulate solar angles and irradiance at definable temporal grains as low as one minute while simulating landscape shadowing up to an entire year. Landscapes can be represented at sub-meter resolutions with appropriate spatial data inputs, such as field data or elevation and surface object heights derived from light detection and ranging (LiDAR) data. This work describes Penumbra’s framework and methodology, external model integration capability, and appropriate model application for a variety of watershed restoration project types. First, an overview of Penumbra’s framework reveals what this model adds to the existing ecological modeling domain. Second, Penumbra’s stand-alone and integration modes are explained and demonstrated. Stand-alone modeling results are showcased within the 3-D visualization tool VISTAS (VISualizing Terrestrial-Aquatic Systems), which fluently summariz

Systematic analysis of signaling pathways using an integrative environment.

PubMed

Visvanathan, Mahesh; Breit, Marc; Pfeifer, Bernhard; Baumgartner, Christian; Modre-Osprian, Robert; Tilg, Bernhard

2007-01-01

Understanding the biological processes of signaling pathways as a whole system requires an integrative software environment that has comprehensive capabilities. The environment should include tools for pathway design, visualization, simulation and a knowledge base concerning signaling pathways as one. In this paper we introduce a new integrative environment for the systematic analysis of signaling pathways. This system includes environments for pathway design, visualization, simulation and a knowledge base that combines biological and modeling information concerning signaling pathways that provides the basic understanding of the biological system, its structure and functioning. The system is designed with a client-server architecture. It contains a pathway designing environment and a simulation environment as upper layers with a relational knowledge base as the underlying layer. The TNFa-mediated NF-kB signal trans-duction pathway model was designed and tested using our integrative framework. It was also useful to define the structure of the knowledge base. Sensitivity analysis of this specific pathway was performed providing simulation data. Then the model was extended showing promising initial results. The proposed system offers a holistic view of pathways containing biological and modeling data. It will help us to perform biological interpretation of the simulation results and thus contribute to a better understanding of the biological system for drug identification.

Iterating between Tools to Create and Edit Visualizations.

PubMed

Bigelow, Alex; Drucker, Steven; Fisher, Danyel; Meyer, Miriah

2017-01-01

A common workflow for visualization designers begins with a generative tool, like D3 or Processing, to create the initial visualization; and proceeds to a drawing tool, like Adobe Illustrator or Inkscape, for editing and cleaning. Unfortunately, this is typically a one-way process: once a visualization is exported from the generative tool into a drawing tool, it is difficult to make further, data-driven changes. In this paper, we propose a bridge model to allow designers to bring their work back from the drawing tool to re-edit in the generative tool. Our key insight is to recast this iteration challenge as a merge problem - similar to when two people are editing a document and changes between them need to reconciled. We also present a specific instantiation of this model, a tool called Hanpuku, which bridges between D3 scripts and Illustrator. We show several examples of visualizations that are iteratively created using Hanpuku in order to illustrate the flexibility of the approach. We further describe several hypothetical tools that bridge between other visualization tools to emphasize the generality of the model.

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.

Interactive investigations into planetary interiors

NASA Astrophysics Data System (ADS)

Rose, I.

2015-12-01

Many processes in Earth science are difficult to observe or visualize due to the large timescales and lengthscales over which they operate. The dynamics of planetary mantles are particularly challenging as we cannot even look at the rocks involved. As a result, much teaching material on mantle dynamics relies on static images and cartoons, many of which are decades old. Recent improvements in computing power and technology (largely driven by game and web development) have allowed for advances in real-time physics simulations and visualizations, but these have been slow to affect Earth science education.Here I demonstrate a teaching tool for mantle convection and seismology which solves the equations for conservation of mass, momentum, and energy in real time, allowing users make changes to the simulation and immediately see the effects. The user can ask and answer questions about what happens when they add heat in one place, or take it away from another place, or increase the temperature at the base of the mantle. They can also pause the simulation, and while it is paused, create and visualize seismic waves traveling through the mantle. These allow for investigations into and discussions about plate tectonics, earthquakes, hot spot volcanism, and planetary cooling.The simulation is rendered to the screen using OpenGL, and is cross-platform. It can be run as a native application for maximum performance, but it can also be embedded in a web browser for easy deployment and portability.

3D printing meets computational astrophysics: deciphering the structure of η Carinae's inner colliding winds

NASA Astrophysics Data System (ADS)

Madura, T. I.; Clementel, N.; Gull, T. R.; Kruip, C. J. H.; Paardekooper, J.-P.

2015-06-01

We present the first 3D prints of output from a supercomputer simulation of a complex astrophysical system, the colliding stellar winds in the massive (≳120 M⊙), highly eccentric (e ˜ 0.9) binary star system η Carinae. We demonstrate the methodology used to incorporate 3D interactive figures into a PDF (Portable Document Format) journal publication and the benefits of using 3D visualization and 3D printing as tools to analyse data from multidimensional numerical simulations. Using a consumer-grade 3D printer (MakerBot Replicator 2X), we successfully printed 3D smoothed particle hydrodynamics simulations of η Carinae's inner (r ˜ 110 au) wind-wind collision interface at multiple orbital phases. The 3D prints and visualizations reveal important, previously unknown `finger-like' structures at orbital phases shortly after periastron (φ ˜ 1.045) that protrude radially outwards from the spiral wind-wind collision region. We speculate that these fingers are related to instabilities (e.g. thin-shell, Rayleigh-Taylor) that arise at the interface between the radiatively cooled layer of dense post-shock primary-star wind and the fast (3000 km s-1), adiabatic post-shock companion-star wind. The success of our work and easy identification of previously unrecognized physical features highlight the important role 3D printing and interactive graphics can play in the visualization and understanding of complex 3D time-dependent numerical simulations of astrophysical phenomena.

Molecular Optical Simulation Environment (MOSE): A Platform for the Simulation of Light Propagation in Turbid Media

PubMed Central

Ren, Shenghan; Chen, Xueli; Wang, Hailong; Qu, Xiaochao; Wang, Ge; Liang, Jimin; Tian, Jie

2013-01-01

The study of light propagation in turbid media has attracted extensive attention in the field of biomedical optical molecular imaging. In this paper, we present a software platform for the simulation of light propagation in turbid media named the “Molecular Optical Simulation Environment (MOSE)”. Based on the gold standard of the Monte Carlo method, MOSE simulates light propagation both in tissues with complicated structures and through free-space. In particular, MOSE synthesizes realistic data for bioluminescence tomography (BLT), fluorescence molecular tomography (FMT), and diffuse optical tomography (DOT). The user-friendly interface and powerful visualization tools facilitate data analysis and system evaluation. As a major measure for resource sharing and reproducible research, MOSE aims to provide freeware for research and educational institutions, which can be downloaded at http://www.mosetm.net. PMID:23577215

Web-GIS-based SARS epidemic situation visualization

NASA Astrophysics Data System (ADS)

Lu, Xiaolin

2004-03-01

In order to research, perform statistical analysis and broadcast the information of SARS epidemic situation according to the relevant spatial position, this paper proposed a unified global visualization information platform for SARS epidemic situation based on Web-GIS and scientific virtualization technology. To setup the unified global visual information platform, the architecture of Web-GIS based interoperable information system is adopted to enable public report SARS virus information to health cure center visually by using the web visualization technology. A GIS java applet is used to visualize the relationship between spatial graphical data and virus distribution, and other web based graphics figures such as curves, bars, maps and multi-dimensional figures are used to visualize the relationship between SARS virus tendency with time, patient number or locations. The platform is designed to display the SARS information in real time, simulate visually for real epidemic situation and offer an analyzing tools for health department and the policy-making government department to support the decision-making for preventing against the SARS epidemic virus. It could be used to analyze the virus condition through visualized graphics interface, isolate the areas of virus source, and control the virus condition within shortest time. It could be applied to the visualization field of SARS preventing systems for SARS information broadcasting, data management, statistical analysis, and decision supporting.

Impacts of Fluid Dynamics Simulation in Study of Nasal Airflow Physiology and Pathophysiology in Realistic Human Three-Dimensional Nose Models

PubMed Central

Lee, Heow Peuh; Gordon, Bruce R.

2012-01-01

During the past decades, numerous computational fluid dynamics (CFD) studies, constructed from CT or MRI images, have simulated human nasal models. As compared to rhinomanometry and acoustic rhinometry, which provide quantitative information only of nasal airflow, resistance, and cross sectional areas, CFD enables additional measurements of airflow passing through the nasal cavity that help visualize the physiologic impact of alterations in intranasal structures. Therefore, it becomes possible to quantitatively measure, and visually appreciate, the airflow pattern (laminar or turbulent), velocity, pressure, wall shear stress, particle deposition, and temperature changes at different flow rates, in different parts of the nasal cavity. The effects of both existing anatomical factors, as well as post-operative changes, can be assessed. With recent improvements in CFD technology and computing power, there is a promising future for CFD to become a useful tool in planning, predicting, and evaluating outcomes of nasal surgery. This review discusses the possibilities and potential impacts, as well as technical limitations, of using CFD simulation to better understand nasal airflow physiology. PMID:23205221

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

SU-E-T-41: Analysis of GI Dose Variability Due to Intrafraction Setup Variance

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

Phillips, J; Wolfgang, J

2014-06-01

Purpose: Proton SBRT (stereotactic body radiation therapy) can be an effective modality for treatment of gastrointestinal tumors, but limited in practice due to sensitivity with respect to variation in the RPL (radiological path length). Small, intrafractional shifts in patient anatomy can lead to significant changes in the dose distribution. This study describes a tool designed to visualize uncertainties in radiological depth in patient CT's and aid in treatment plan design. Methods: This project utilizes the Shadie toolkit, a GPU-based framework that allows for real-time interactive calculations for volume visualization. Current SBRT simulation practice consists of a serial CT acquisition formore » the assessment of inter- and intra-fractional motion utilizing patient specific immobilization systems. Shadie was used to visualize potential uncertainties, including RPL variance and changes in gastric content. Input for this procedure consisted of two patient CT sets, contours of the desired organ, and a pre-calculated dose. In this study, we performed rigid registrations between sets of 4DCT's obtained from a patient with varying setup conditions. Custom visualizations are written by the user in Shadie, permitting one to create color-coded displays derived from a calculation along each ray. Results: Serial CT data acquired on subsequent days was analyzed for variation in RPB and gastric content. Specific shaders were created to visualize clinically relevant features, including RPL (radiological path length) integrated up to organs of interest. Using pre-calculated dose distributions and utilizing segmentation masks as additional input allowed us to further refine the display output from Shadie and create tools suitable for clinical usage. Conclusion: We have demonstrated a method to visualize potential uncertainty for intrafractional proton radiotherapy. We believe this software could prove a useful tool to guide those looking to design treatment plans least insensitive to motion for patients undergoing proton SBRT in the GI tract.« less

Spinoff 2013

NASA Technical Reports Server (NTRS)

2014-01-01

Topics covered include: Innovative Software Tools Measure Behavioral Alertness; Miniaturized, Portable Sensors Monitor Metabolic Health; Patient Simulators Train Emergency Caregivers; Solar Refrigerators Store Life-Saving Vaccines; Monitors Enable Medication Management in Patients' Homes; Handheld Diagnostic Device Delivers Quick Medical Readings; Experiments Result in Safer, Spin-Resistant Aircraft; Interfaces Visualize Data for Airline Safety, Efficiency; Data Mining Tools Make Flights Safer, More Efficient; NASA Standards Inform Comfortable Car Seats; Heat Shield Paves the Way for Commercial Space; Air Systems Provide Life Support to Miners; Coatings Preserve Metal, Stone, Tile, and Concrete; Robots Spur Software That Lends a Hand; Cloud-Based Data Sharing Connects Emergency Managers; Catalytic Converters Maintain Air Quality in Mines; NASA-Enhanced Water Bottles Filter Water on the Go; Brainwave Monitoring Software Improves Distracted Minds; Thermal Materials Protect Priceless, Personal Keepsakes; Home Air Purifiers Eradicate Harmful Pathogens; Thermal Materials Drive Professional Apparel Line; Radiant Barriers Save Energy in Buildings; Open Source Initiative Powers Real-Time Data Streams; Shuttle Engine Designs Revolutionize Solar Power; Procedure-Authoring Tool Improves Safety on Oil Rigs; Satellite Data Aid Monitoring of Nation's Forests; Mars Technologies Spawn Durable Wind Turbines; Programs Visualize Earth and Space for Interactive Education; Processor Units Reduce Satellite Construction Costs; Software Accelerates Computing Time for Complex Math; Simulation Tools Prevent Signal Interference on Spacecraft; Software Simplifies the Sharing of Numerical Models; Virtual Machine Language Controls Remote Devices; Micro-Accelerometers Monitor Equipment Health; Reactors Save Energy, Costs for Hydrogen Production; Cameras Monitor Spacecraft Integrity to Prevent Failures; Testing Devices Garner Data on Insulation Performance; Smart Sensors Gather Information for Machine Diagnostics; Oxygen Sensors Monitor Bioreactors and Ensure Health and Safety; Vision Algorithms Catch Defects in Screen Displays; and Deformable Mirrors Capture Exoplanet Data, Reflect Lasers.

Advanced helmet mounted display (AHMD)

NASA Astrophysics Data System (ADS)

Sisodia, Ashok; Bayer, Michael; Townley-Smith, Paul; Nash, Brian; Little, Jay; Cassarly, William; Gupta, Anurag

2007-04-01

Due to significantly increased U.S. military involvement in deterrent, observer, security, peacekeeping and combat roles around the world, the military expects significant future growth in the demand for deployable virtual reality trainers with networked simulation capability of the battle space visualization process. The use of HMD technology in simulated virtual environments has been initiated by the demand for more effective training tools. The AHMD overlays computer-generated data (symbology, synthetic imagery, enhanced imagery) augmented with actual and simulated visible environment. The AHMD can be used to support deployable reconfigurable training solutions as well as traditional simulation requirements, UAV augmented reality, air traffic control and Command, Control, Communications, Computers, Intelligence, Surveillance, and Reconnaissance (C4ISR) applications. This paper will describe the design improvements implemented for production of the AHMD System.

Visual Elements in Flight Simulation

DTIC Science & Technology

1975-07-01

control. In consequence, current efforts tc create appropriate visual simulations run the gamut from efforts toward almost complete replication of the...create appropriate visual simulations run the gamut from efforts to create appropriate visual simulations run the gamut from efforts toward almost

Evaluation of Game-Based Visualization Tools for Military Flight Simulation

DTIC Science & Technology

2014-02-01

pitch, and yaw) then converts this position to WGS84 geocentric coordinates to conform to DIS standards prior to broadcast. The position data of...each external entity is processed by X-Plane® directly in geocentric coordinates for out-the-window display. This interface then allows X- Plane® to...applied to each. Additionally, the XCITE software calculates entity locations in latitude, longitude, and altitude before converting to geocentric

Visual exploration and analysis of human-robot interaction rules

NASA Astrophysics Data System (ADS)

Zhang, Hui; Boyles, Michael J.

2013-01-01

We present a novel interaction paradigm for the visual exploration, manipulation and analysis of human-robot interaction (HRI) rules; our development is implemented using a visual programming interface and exploits key techniques drawn from both information visualization and visual data mining to facilitate the interaction design and knowledge discovery process. HRI is often concerned with manipulations of multi-modal signals, events, and commands that form various kinds of interaction rules. Depicting, manipulating and sharing such design-level information is a compelling challenge. Furthermore, the closed loop between HRI programming and knowledge discovery from empirical data is a relatively long cycle. This, in turn, makes design-level verification nearly impossible to perform in an earlier phase. In our work, we exploit a drag-and-drop user interface and visual languages to support depicting responsive behaviors from social participants when they interact with their partners. For our principal test case of gaze-contingent HRI interfaces, this permits us to program and debug the robots' responsive behaviors through a graphical data-flow chart editor. We exploit additional program manipulation interfaces to provide still further improvement to our programming experience: by simulating the interaction dynamics between a human and a robot behavior model, we allow the researchers to generate, trace and study the perception-action dynamics with a social interaction simulation to verify and refine their designs. Finally, we extend our visual manipulation environment with a visual data-mining tool that allows the user to investigate interesting phenomena such as joint attention and sequential behavioral patterns from multiple multi-modal data streams. We have created instances of HRI interfaces to evaluate and refine our development paradigm. As far as we are aware, this paper reports the first program manipulation paradigm that integrates visual programming interfaces, information visualization, and visual data mining methods to facilitate designing, comprehending, and evaluating HRI interfaces.

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.

Intuitive Visualization of Transient Flow: Towards a Full 3D Tool

NASA Astrophysics Data System (ADS)

Michel, Isabel; Schröder, Simon; Seidel, Torsten; König, Christoph

2015-04-01

Visualization of geoscientific data is a challenging task especially when targeting a non-professional audience. In particular, the graphical presentation of transient vector data can be a significant problem. With STRING Fraunhofer ITWM (Kaiserslautern, Germany) in collaboration with delta h Ingenieurgesellschaft mbH (Witten, Germany) developed a commercial software for intuitive 2D visualization of 3D flow problems. Through the intuitive character of the visualization experts can more easily transport their findings to non-professional audiences. In STRING pathlets moving with the flow provide an intuition of velocity and direction of both steady-state and transient flow fields. The visualization concept is based on the Lagrangian view of the flow which means that the pathlets' movement is along the direction given by pathlines. In order to capture every detail of the flow an advanced method for intelligent, time-dependent seeding of the pathlets is implemented based on ideas of the Finite Pointset Method (FPM) originally conceived at and continuously developed by Fraunhofer ITWM. Furthermore, by the same method pathlets are removed during the visualization to avoid visual cluttering. Additional scalar flow attributes, for example concentration or potential, can either be mapped directly to the pathlets or displayed in the background of the pathlets on the 2D visualization plane. The extensive capabilities of STRING are demonstrated with the help of different applications in groundwater modeling. We will discuss the strengths and current restrictions of STRING which have surfaced during daily use of the software, for example by delta h. Although the software focusses on the graphical presentation of flow data for non-professional audiences its intuitive visualization has also proven useful to experts when investigating details of flow fields. Due to the popular reception of STRING and its limitation to 2D, the need arises for the extension to a full 3D tool. Currently STRING can generate animations of single 2D cuts, either planar or curved surfaces, through 3D simulation domains. To provide a general tool for experts enabling also direct exploration and analysis of large 3D flow fields the software needs to be extended to intuitive as well as interactive visualizations of entire 3D flow domains. The current research concerning this project, which is funded by the Federal Ministry for Economic Affairs and Energy (Germany), is presented.

Validation of a novel virtual reality simulator for robotic surgery.

PubMed

Schreuder, Henk W R; Persson, Jan E U; Wolswijk, Richard G H; Ihse, Ingmar; Schijven, Marlies P; Verheijen, René H M

2014-01-01

With the increase in robotic-assisted laparoscopic surgery there is a concomitant rising demand for training methods. The objective was to establish face and construct validity of a novel virtual reality simulator (dV-Trainer, Mimic Technologies, Seattle, WA) for the use in training of robot-assisted surgery. A comparative cohort study was performed. Participants (n = 42) were divided into three groups according to their robotic experience. To determine construct validity, participants performed three different exercises twice. Performance parameters were measured. To determine face validity, participants filled in a questionnaire after completion of the exercises. Experts outperformed novices in most of the measured parameters. The most discriminative parameters were "time to complete" and "economy of motion" (P < 0.001). The training capacity of the simulator was rated 4.6 ± 0.5 SD on a 5-point Likert scale. The realism of the simulator in general, visual graphics, movements of instruments, interaction with objects, and the depth perception were all rated as being realistic. The simulator is considered to be a very useful training tool for residents and medical specialist starting with robotic surgery. Face and construct validity for the dV-Trainer could be established. The virtual reality simulator is a useful tool for training robotic surgery.

Validation of a Novel Virtual Reality Simulator for Robotic Surgery

PubMed Central

Schreuder, Henk W. R.; Persson, Jan E. U.; Wolswijk, Richard G. H.; Ihse, Ingmar; Schijven, Marlies P.; Verheijen, René H. M.

2014-01-01

Objective. With the increase in robotic-assisted laparoscopic surgery there is a concomitant rising demand for training methods. The objective was to establish face and construct validity of a novel virtual reality simulator (dV-Trainer, Mimic Technologies, Seattle, WA) for the use in training of robot-assisted surgery. Methods. A comparative cohort study was performed. Participants (n = 42) were divided into three groups according to their robotic experience. To determine construct validity, participants performed three different exercises twice. Performance parameters were measured. To determine face validity, participants filled in a questionnaire after completion of the exercises. Results. Experts outperformed novices in most of the measured parameters. The most discriminative parameters were “time to complete” and “economy of motion” (P < 0.001). The training capacity of the simulator was rated 4.6 ± 0.5 SD on a 5-point Likert scale. The realism of the simulator in general, visual graphics, movements of instruments, interaction with objects, and the depth perception were all rated as being realistic. The simulator is considered to be a very useful training tool for residents and medical specialist starting with robotic surgery. Conclusions. Face and construct validity for the dV-Trainer could be established. The virtual reality simulator is a useful tool for training robotic surgery. PMID:24600328

Peri-Elastodynamic Simulations of Guided Ultrasonic Waves in Plate-Like Structure with Surface Mounted PZT.

PubMed

Patra, Subir; Ahmed, Hossain; Banerjee, Sourav

2018-01-18

Peridynamic based elastodynamic computation tool named Peri-elastodynamics is proposed herein to simulate the three-dimensional (3D) Lamb wave modes in materials for the first time. Peri-elastodynamics is a nonlocal meshless approach which is a scale-independent generalized technique to visualize the acoustic and ultrasonic waves in plate-like structure, micro-electro-mechanical systems (MEMS) and nanodevices for their respective characterization. In this article, the characteristics of the fundamental Lamb wave modes are simulated in a sample plate-like structure. Lamb wave modes are generated using a surface mounted piezoelectric (PZT) transducer which is actuated from the top surface. The proposed generalized Peri-elastodynamics method is not only capable of simulating two dimensional (2D) in plane wave under plane strain condition formulated previously but also capable of accurately simulating the out of plane Symmetric and Antisymmetric Lamb wave modes in plate like structures in 3D. For structural health monitoring (SHM) of plate-like structures and nondestructive evaluation (NDE) of MEMS devices, it is necessary to simulate the 3D wave-damage interaction scenarios and visualize the different wave features due to damages. Hence, in addition, to simulating the guided ultrasonic wave modes in pristine material, Lamb waves were also simulated in a damaged plate. The accuracy of the proposed technique is verified by comparing the modes generated in the plate and the mode shapes across the thickness of the plate with theoretical wave analysis.

Virtual reality: teaching tool of the twenty-first century?

PubMed

Hoffman, H; Vu, D

1997-12-01

Virtual reality (VR) is gaining recognition for its enormous educational potential. While not yet in the mainstream of academic medical training, many prototype and first-generation VR applications are emerging, with target audiences ranging from first- and second-year medical students to residents in advanced clinical training. Visualization tools that take advantage of VR technologies are being designed to provide engaging and intuitive environments for learning visually and spatially complex topics such as human anatomy, biochemistry, and molecular biology. These applications present dynamic, three-dimensional views of structures and their spatial relationships, enabling users to move beyond "real-world" experiences by interacting with or altering virtual objects in ways that would otherwise be difficult or impossible. VR-based procedural and surgical simulations, often compared with flight simulators in aviation, hold significant promise for revolutionizing medical training. Already a wide range of simulations, representing diverse content areas and utilizing a variety of implementation strategies, are either under development or in their early implementation stages. These new systems promise to make broad-based training experiences available for students at all levels, without the risks and ethical concerns typically associated with using animal and human subjects. Medical students could acquire proficiency and gain confidence in the ability to perform a wide variety of techniques long before they need to use them clinically. Surgical residents could rehearse and refine operative procedures, using an unlimited pool of virtual patients manifesting a wide range of anatomic variations, traumatic wounds, and disease states. Those simulated encounters, in combination with existing opportunities to work with real patients, could increase the depth and breadth of learners' exposure to medical problems, ensure uniformity of training experiences, and enhance the acquisition of clinical skills.

A mixed-reality part-task trainer for subclavian venous access.

PubMed

Robinson, Albert R; Gravenstein, Nikolaus; Cooper, Lou Ann; Lizdas, David; Luria, Isaac; Lampotang, Samsun

2014-02-01

Mixed-reality (MR) procedural simulators combine virtual and physical components and visualization software that can be used for debriefing and offer an alternative to learn subclavian central venous access (SCVA). We present a SCVA MR simulator, a part-task trainer, which can assist in the training of medical personnel. Sixty-five participants were involved in the following: (1) a simulation trial 1; (2) a teaching intervention followed by trial 2 (with the simulator's visualization software); and (3) trial 3, a final simulation assessment. The main test parameters were time to complete SCVA and the SCVA score, a composite of efficiency and safety metrics generated by the simulator's scoring algorithm. Residents and faculty completed questionnaires presimulation and postsimulation that assessed their confidence in obtaining access and learner satisfaction questions, for example, realism of the simulator. The average SCVA score was improved by 24.5 (n=65). Repeated-measures analysis of variance showed significant reductions in average time (F=31.94, P<0.0001), number of attempts (F=10.56, P<0.0001), and score (F=18.59, P<0.0001). After the teaching intervention and practice with the MR simulator, the results no longer showed a difference in performance between the faculty and residents. On a 5-point scale (5=strongly agree), participants agreed that the SCVA simulator was realistic (M=4.3) and strongly agreed that it should be used as an educational tool (M=4.9). An SCVA mixed simulator offers a realistic representation of subclavian central venous access and offers new debriefing capabilities.

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…

'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.

TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD.

PubMed

Vermaas, Josh V; Hardy, David J; Stone, John E; Tajkhorshid, Emad; Kohlmeyer, Axel

2016-06-27

Molecular dynamics (MD) simulation engines use a variety of different approaches for modeling molecular systems with force fields that govern their dynamics and describe their topology. These different approaches introduce incompatibilities between engines, and previously published software bridges the gaps between many popular MD packages, such as between CHARMM and AMBER or GROMACS and LAMMPS. While there are many structure building tools available that generate topologies and structures in CHARMM format, only recently have mechanisms been developed to convert their results into GROMACS input. We present an approach to convert CHARMM-formatted topology and parameters into a format suitable for simulation with GROMACS by expanding the functionality of TopoTools, a plugin integrated within the widely used molecular visualization and analysis software VMD. The conversion process was diligently tested on a comprehensive set of biological molecules in vacuo. The resulting comparison between energy terms shows that the translation performed was lossless as the energies were unchanged for identical starting configurations. By applying the conversion process to conventional benchmark systems that mimic typical modestly sized MD systems, we explore the effect of the implementation choices made in CHARMM, NAMD, and GROMACS. The newly available automatic conversion capability breaks down barriers between simulation tools and user communities and allows users to easily compare simulation programs and leverage their unique features without the tedium of constructing a topology twice.

PlasmaPy: beginning a community developed Python package for plasma physics

NASA Astrophysics Data System (ADS)

Murphy, Nicholas A.; Huang, Yi-Min; PlasmaPy Collaboration

2016-10-01

In recent years, researchers in several disciplines have collaborated on community-developed open source Python packages such as Astropy, SunPy, and SpacePy. These packages provide core functionality, common frameworks for data analysis and visualization, and educational tools. We propose that our community begins the development of PlasmaPy: a new open source core Python package for plasma physics. PlasmaPy could include commonly used functions in plasma physics, easy-to-use plasma simulation codes, Grad-Shafranov solvers, eigenmode solvers, and tools to analyze both simulations and experiments. The development will include modern programming practices such as version control, embedding documentation in the code, unit tests, and avoiding premature optimization. We will describe early code development on PlasmaPy, and discuss plans moving forward. The success of PlasmaPy depends on active community involvement and a welcoming and inclusive environment, so anyone interested in joining this collaboration should contact the authors.

Update: Advancement of Contact Dynamics Modeling for Human Spaceflight Simulation Applications

NASA Technical Reports Server (NTRS)

Brain, Thomas A.; Kovel, Erik B.; MacLean, John R.; Quiocho, Leslie J.

2017-01-01

Pong is a new software tool developed at the NASA Johnson Space Center that advances interference-based geometric contact dynamics based on 3D graphics models. The Pong software consists of three parts: a set of scripts to extract geometric data from 3D graphics models, a contact dynamics engine that provides collision detection and force calculations based on the extracted geometric data, and a set of scripts for visualizing the dynamics response with the 3D graphics models. The contact dynamics engine can be linked with an external multibody dynamics engine to provide an integrated multibody contact dynamics simulation. This paper provides a detailed overview of Pong including the overall approach and modeling capabilities, which encompasses force generation from contact primitives and friction to computational performance. Two specific Pong-based examples of International Space Station applications are discussed, and the related verification and validation using this new tool are also addressed.

Validation of Hydrodynamic Load Models Using CFD for the OC4-DeepCwind Semisubmersible: Preprint

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

Benitz, M. A.; Schmidt, D. P.; Lackner, M. A.

Computational fluid dynamics (CFD) simulations were carried out on the OC4-DeepCwind semi-submersible to obtain a better understanding of how to set hydrodynamic coefficients for the structure when using an engineering tool such as FAST to model the system. The focus here was on the drag behavior and the effects of the free-surface, free-ends and multi-member arrangement of the semi-submersible structure. These effects are investigated through code-to-code comparisons and flow visualizations. The implications on mean load predictions from engineering tools are addressed. The work presented here suggests that selection of drag coefficients should take into consideration a variety of geometric factors.more » Furthermore, CFD simulations demonstrate large time-varying loads due to vortex shedding, which FAST's hydrodynamic module, HydroDyn, does not model. The implications of these oscillatory loads on the fatigue life needs to be addressed.« less

Automated Fluid Feature Extraction from Transient Simulations

NASA Technical Reports Server (NTRS)

Haimes, Robert

2000-01-01

In the past, feature extraction and identification were interesting concepts, but not required in understanding the physics of a steady flow field. This is because the results of the more traditional tools like iso-surfaces, cuts and streamlines, were more interactive and easily abstracted so they could be represented to the investigator. These tools worked and properly conveyed the collected information at the expense of a great deal of interaction. For unsteady flow-fields, the investigator does not have the luxury of spending time scanning only one 'snap-shot' of the simulation. Automated assistance is required in pointing out areas of potential interest contained within the flow. This must not require a heavy compute burden (the visualization should not significantly slow down the solution procedure for co-processing environments like pV3). And methods must be developed to abstract the feature and display it in a manner that physically makes sense.

Instrumentation, performance visualization, and debugging tools for multiprocessors

NASA Technical Reports Server (NTRS)

Yan, Jerry C.; Fineman, Charles E.; Hontalas, Philip J.

1991-01-01

The need for computing power has forced a migration from serial computation on a single processor to parallel processing on multiprocessor architectures. However, without effective means to monitor (and visualize) program execution, debugging, and tuning parallel programs becomes intractably difficult as program complexity increases with the number of processors. Research on performance evaluation tools for multiprocessors is being carried out at ARC. Besides investigating new techniques for instrumenting, monitoring, and presenting the state of parallel program execution in a coherent and user-friendly manner, prototypes of software tools are being incorporated into the run-time environments of various hardware testbeds to evaluate their impact on user productivity. Our current tool set, the Ames Instrumentation Systems (AIMS), incorporates features from various software systems developed in academia and industry. The execution of FORTRAN programs on the Intel iPSC/860 can be automatically instrumented and monitored. Performance data collected in this manner can be displayed graphically on workstations supporting X-Windows. We have successfully compared various parallel algorithms for computational fluid dynamics (CFD) applications in collaboration with scientists from the Numerical Aerodynamic Simulation Systems Division. By performing these comparisons, we show that performance monitors and debuggers such as AIMS are practical and can illuminate the complex dynamics that occur within parallel programs.

Development and evaluation of a connective tissue phantom model for subsurface visualization of cancers requiring wide local excision.

PubMed

Samkoe, Kimberley S; Bates, Brent D; Tselepidakis, Niki N; DSouza, Alisha V; Gunn, Jason R; Ramkumar, Dipak B; Paulsen, Keith D; Pogue, Brian W; Henderson, Eric R

2017-12-01

Wide local excision (WLE) of tumors with negative margins remains a challenge because surgeons cannot directly visualize the mass. Fluorescence-guided surgery (FGS) may improve surgical accuracy; however, conventional methods with direct surface tumor visualization are not immediately applicable, and properties of tissues surrounding the cancer must be considered. We developed a phantom model for sarcoma resection with the near-infrared fluorophore IRDye 800CW and used it to iteratively define the properties of connective tissues that typically surround sarcoma tumors. We then tested the ability of a blinded surgeon to resect fluorescent tumor-simulating inclusions with ∼1-cm margins using predetermined target fluorescence intensities and a Solaris open-air fluorescence imaging system. In connective tissue-simulating phantoms, fluorescence intensity decreased with increasing blood concentration and increased with increasing intralipid concentrations. Fluorescent inclusions could be resolved at ≥1-cm depth in all inclusion concentrations and sizes tested. When inclusion depth was held constant, fluorescence intensity decreased with decreasing volume. Using targeted fluorescence intensities, a blinded surgeon was able to successfully excise inclusions with ∼1-cm margins from fat- and muscle-simulating phantoms with inclusion-to-background contrast ratios as low as 2∶1. Indirect, subsurface FGS is a promising tool for surgical resection of cancers requiring WLE. (2017) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Characterization of hybrid lighting systems of the Electrical Engineering Building in the Industrial University of Santander

NASA Astrophysics Data System (ADS)

Galvis, D.; Exposito, C.; Osma, G.; Amado, L.; Ordóñez, G.

2016-07-01

This paper presents an analysis of hybrid lighting systems of Electrical Engineering Building in the Industrial University of Santander, which is a pilot of green building for warm- tropical conditions. Analysis of lighting performance of inner spaces is based on lighting curves obtained from characterization of daylighting systems of these spaces. A computation tool was made in Excel-Visual Basic to simulate the behaviour of artificial lighting system considering artificial control system, user behaviour and solar condition. Also, this tool allows to estimate the electrical energy consumption of the lighting system for a day, a month and a year.

Software Tools for Developing and Simulating the NASA LaRC CMF Motion Base

NASA Technical Reports Server (NTRS)

Bryant, Richard B., Jr.; Carrelli, David J.

2006-01-01

The NASA Langley Research Center (LaRC) Cockpit Motion Facility (CMF) motion base has provided many design and analysis challenges. In the process of addressing these challenges, a comprehensive suite of software tools was developed. The software tools development began with a detailed MATLAB/Simulink model of the motion base which was used primarily for safety loads prediction, design of the closed loop compensator and development of the motion base safety systems1. A Simulink model of the digital control law, from which a portion of the embedded code is directly generated, was later added to this model to form a closed loop system model. Concurrently, software that runs on a PC was created to display and record motion base parameters. It includes a user interface for controlling time history displays, strip chart displays, data storage, and initializing of function generators used during motion base testing. Finally, a software tool was developed for kinematic analysis and prediction of mechanical clearances for the motion system. These tools work together in an integrated package to support normal operations of the motion base, simulate the end to end operation of the motion base system providing facilities for software-in-the-loop testing, mechanical geometry and sensor data visualizations, and function generator setup and evaluation.

Changing learning with new interactive and media-rich instruction environments: virtual labs case study report.

PubMed

Huang, Camillan

2003-01-01

Technology has created a new dimension for visual teaching and learning with web-delivered interactive media. The Virtual Labs Project has embraced this technology with instructional design and evaluation methodologies behind the simPHYSIO suite of simulation-based, online interactive teaching modules in physiology for the Stanford students. In addition, simPHYSIO provides the convenience of anytime web-access and a modular structure that allows for personalization and customization of the learning material. This innovative tool provides a solid delivery and pedagogical backbone that can be applied to developing an interactive simulation-based training tool for the use and management of the Picture Archiving and Communication System (PACS) image information system. The disparity in the knowledge between health and IT professionals can be bridged by providing convenient modular teaching tools to fill the gaps in knowledge. An innovative teaching method in the whole PACS is deemed necessary for its successful implementation and operation since it has become widely distributed with many interfaces, components, and customizations. This paper will discuss the techniques for developing an interactive-based teaching tool, a case study of its implementation, and a perspective for applying this approach to an online PACS training tool. Copyright 2002 Elsevier Science Ltd.

Stereoscopic filming for investigating evasive side-stepping and anterior cruciate ligament injury risk

NASA Astrophysics Data System (ADS)

Lee, Marcus J. C.; Bourke, Paul; Alderson, Jacqueline A.; Lloyd, David G.; Lay, Brendan

2010-02-01

Non-contact anterior cruciate ligament (ACL) injuries are serious and debilitating, often resulting from the performance of evasive sides-stepping (Ssg) by team sport athletes. Previous laboratory based investigations of evasive Ssg have used generic visual stimuli to simulate realistic time and space constraints that athletes experience in the preparation and execution of the manoeuvre. However, the use of unrealistic visual stimuli to impose these constraints may not be accurately identifying the relationship between the perceptual demands and ACL loading during Ssg in actual game environments. We propose that stereoscopically filmed footage featuring sport specific opposing defender/s simulating a tackle on the viewer, when used as visual stimuli, could improve the ecological validity of laboratory based investigations of evasive Ssg. Due to the need for precision and not just the experience of viewing depth in these scenarios, a rigorous filming process built on key geometric considerations and equipment development to enable a separation of 6.5 cm between two commodity cameras had to be undertaken. Within safety limits, this could be an invaluable tool in enabling more accurate investigations of the associations between evasive Ssg and ACL injury risk.

Augmented Visual Experience of Simulated Solar Phenomena

NASA Astrophysics Data System (ADS)

Tucker, A. O., IV; Berardino, R. A.; Hahne, D.; Schreurs, B.; Fox, N. J.; Raouafi, N.

2017-12-01

The Parker Solar Probe (PSP) mission will explore the Sun's corona, studying solar wind, flares and coronal mass ejections. The effects of these phenomena can impact the technology that we use in ways that are not readily apparent, including affecting satellite communications and power grids. Determining the structure and dynamics of corona magnetic fields, tracing the flow of energy that heats the corona, and exploring dusty plasma near the Sun to understand its influence on solar wind and energetic particle formation requires a suite of sensors on board the PSP spacecraft that are engineered to observe specific phenomena. Using models of these sensors and simulated observational data, we can visualize what the PSP spacecraft will "see" during its multiple passes around the Sun. Augmented reality (AR) technologies enable convenient user access to massive data sets. We are developing an application that allows users to experience environmental data from the point of view of the PSP spacecraft in AR using the Microsoft HoloLens. Observational data, including imagery, magnetism, temperature, and density are visualized in 4D within the user's immediate environment. Our application provides an educational tool for comprehending the complex relationships of observational data, which aids in our understanding of the Sun.

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.

[Not Available].

PubMed

Pecevski, Dejan; Natschläger, Thomas; Schuch, Klaus

2009-01-01

The Parallel Circuit SIMulator (PCSIM) is a software package for simulation of neural circuits. It is primarily designed for distributed simulation of large scale networks of spiking point neurons. Although its computational core is written in C++, PCSIM's primary interface is implemented in the Python programming language, which is a powerful programming environment and allows the user to easily integrate the neural circuit simulator with data analysis and visualization tools to manage the full neural modeling life cycle. The main focus of this paper is to describe PCSIM's full integration into Python and the benefits thereof. In particular we will investigate how the automatically generated bidirectional interface and PCSIM's object-oriented modular framework enable the user to adopt a hybrid modeling approach: using and extending PCSIM's functionality either employing pure Python or C++ and thus combining the advantages of both worlds. Furthermore, we describe several supplementary PCSIM packages written in pure Python and tailored towards setting up and analyzing neural simulations.

Toward high-speed 3D nonlinear soft tissue deformation simulations using Abaqus software.

PubMed

Idkaidek, Ashraf; Jasiuk, Iwona

2015-12-01

We aim to achieve a fast and accurate three-dimensional (3D) simulation of a porcine liver deformation under a surgical tool pressure using the commercial finite element software Abaqus. The liver geometry is obtained using magnetic resonance imaging, and a nonlinear constitutive law is employed to capture large deformations of the tissue. Effects of implicit versus explicit analysis schemes, element type, and mesh density on computation time are studied. We find that Abaqus explicit and implicit solvers are capable of simulating nonlinear soft tissue deformations accurately using first-order tetrahedral elements in a relatively short time by optimizing the element size. This study provides new insights and guidance on accurate and relatively fast nonlinear soft tissue simulations. Such simulations can provide force feedback during robotic surgery and allow visualization of tissue deformations for surgery planning and training of surgical residents.

Long Range Plan for Embedded Computer Systems Support. Volume II

DTIC Science & Technology

1981-10-01

interface (pilot displays and controls plus visual system), and data collection (CMAC data, bus data and simulation data). Non-real time functions include...unless adequate upfront planning is implemented, the command will be controlled by the dynamics rather than controll - ing them. The upfront planning should...or should they be called manually? What amount and type of data should the various tools pass between each other? Under what conditions and controls

Current implementation and future plans on new code architecture, programming language and user interface

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

Brun, B.

1997-07-01

Computer technology has improved tremendously during the last years with larger media capacity, memory and more computational power. Visual computing with high-performance graphic interface and desktop computational power have changed the way engineers accomplish everyday tasks, development and safety studies analysis. The emergence of parallel computing will permit simulation over a larger domain. In addition, new development methods, languages and tools have appeared in the last several years.

NASA Center for Climate Simulation (NCCS) Presentation

NASA Technical Reports Server (NTRS)

Webster, William P.

2012-01-01

The NASA Center for Climate Simulation (NCCS) offers integrated supercomputing, visualization, and data interaction technologies to enhance NASA's weather and climate prediction capabilities. It serves hundreds of users at NASA Goddard Space Flight Center, as well as other NASA centers, laboratories, and universities across the US. Over the past year, NCCS has continued expanding its data-centric computing environment to meet the increasingly data-intensive challenges of climate science. We doubled our Discover supercomputer's peak performance to more than 800 teraflops by adding 7,680 Intel Xeon Sandy Bridge processor-cores and most recently 240 Intel Xeon Phi Many Integrated Core (MIG) co-processors. A supercomputing-class analysis system named Dali gives users rapid access to their data on Discover and high-performance software including the Ultra-scale Visualization Climate Data Analysis Tools (UV-CDAT), with interfaces from user desktops and a 17- by 6-foot visualization wall. NCCS also is exploring highly efficient climate data services and management with a new MapReduce/Hadoop cluster while augmenting its data distribution to the science community. Using NCCS resources, NASA completed its modeling contributions to the Intergovernmental Panel on Climate Change (IPCG) Fifth Assessment Report this summer as part of the ongoing Coupled Modellntercomparison Project Phase 5 (CMIP5). Ensembles of simulations run on Discover reached back to the year 1000 to test model accuracy and projected climate change through the year 2300 based on four different scenarios of greenhouse gases, aerosols, and land use. The data resulting from several thousand IPCC/CMIP5 simulations, as well as a variety of other simulation, reanalysis, and observationdatasets, are available to scientists and decision makers through an enhanced NCCS Earth System Grid Federation Gateway. Worldwide downloads have totaled over 110 terabytes of data.

The virtual reality simulator dV-Trainer(®) is a valid assessment tool for robotic surgical skills.

PubMed

Perrenot, Cyril; Perez, Manuela; Tran, Nguyen; Jehl, Jean-Philippe; Felblinger, Jacques; Bresler, Laurent; Hubert, Jacques

2012-09-01

Exponential development of minimally invasive techniques, such as robotic-assisted devices, raises the question of how to assess robotic surgery skills. Early development of virtual simulators has provided efficient tools for laparoscopic skills certification based on objective scoring, high availability, and lower cost. However, similar evaluation is lacking for robotic training. The purpose of this study was to assess several criteria, such as reliability, face, content, construct, and concurrent validity of a new virtual robotic surgery simulator. This prospective study was conducted from December 2009 to April 2010 using three simulators dV-Trainers(®) (MIMIC Technologies(®)) and one Da Vinci S(®) (Intuitive Surgical(®)). Seventy-five subjects, divided into five groups according to their initial surgical training, were evaluated based on five representative exercises of robotic specific skills: 3D perception, clutching, visual force feedback, EndoWrist(®) manipulation, and camera control. Analysis was extracted from (1) questionnaires (realism and interest), (2) automatically generated data from simulators, and (3) subjective scoring by two experts of depersonalized videos of similar exercises with robot. Face and content validity were generally considered high (77 %). Five levels of ability were clearly identified by the simulator (ANOVA; p = 0.0024). There was a strong correlation between automatic data from dV-Trainer and subjective evaluation with robot (r = 0.822). Reliability of scoring was high (r = 0.851). The most relevant criteria were time and economy of motion. The most relevant exercises were Pick and Place and Ring and Rail. The dV-Trainer(®) simulator proves to be a valid tool to assess basic skills of robotic surgery.

Earthquakes in Action: Incorporating Multimedia, Internet Resources, Large-scale Seismic Data, and 3-D Visualizations into Innovative Activities and Research Projects for Today's High School Students

NASA Astrophysics Data System (ADS)

Smith-Konter, B.; Jacobs, A.; Lawrence, K.; Kilb, D.

2006-12-01

The most effective means of communicating science to today's "high-tech" students is through the use of visually attractive and animated lessons, hands-on activities, and interactive Internet-based exercises. To address these needs, we have developed Earthquakes in Action, a summer high school enrichment course offered through the California State Summer School for Mathematics and Science (COSMOS) Program at the University of California, San Diego. The summer course consists of classroom lectures, lab experiments, and a final research project designed to foster geophysical innovations, technological inquiries, and effective scientific communication (http://topex.ucsd.edu/cosmos/earthquakes). Course content includes lessons on plate tectonics, seismic wave behavior, seismometer construction, fault characteristics, California seismicity, global seismic hazards, earthquake stress triggering, tsunami generation, and geodetic measurements of the Earth's crust. Students are introduced to these topics through lectures-made-fun using a range of multimedia, including computer animations, videos, and interactive 3-D visualizations. These lessons are further enforced through both hands-on lab experiments and computer-based exercises. Lab experiments included building hand-held seismometers, simulating the frictional behavior of faults using bricks and sandpaper, simulating tsunami generation in a mini-wave pool, and using the Internet to collect global earthquake data on a daily basis and map earthquake locations using a large classroom map. Students also use Internet resources like Google Earth and UNAVCO/EarthScope's Jules Verne Voyager Jr. interactive mapping tool to study Earth Science on a global scale. All computer-based exercises and experiments developed for Earthquakes in Action have been distributed to teachers participating in the 2006 Earthquake Education Workshop, hosted by the Visualization Center at Scripps Institution of Oceanography (http://siovizcenter.ucsd.edu/workshop). In addition to daily lecture and lab exercises, COSMOS students also conduct a mini-research project of their choice that uses data ranging from the 2004 Parkfield Earthquake, to Southern California seismicity, to global seismicity. Students collect seismic data from the Internet and evaluate earthquake locations, magnitudes, temporal sequence of seismic activity, active fault planes, and plate tectonic boundaries using research quality techniques. Students are given the opportunity to build 3-D visualizations of their research data sets and archive these at the SIO Visualization Center's online library, which is globally accessible to students, teachers, researchers, and the general public (http://www.siovizcenter.ucsd.edu/library.php). These student- generated visualizations have become a practical resource for not only students and teachers, but also geophysical researchers that use the visual objects as research tools to better explore and understand their data. Through Earthquakes in Action, we offer both the tools for scientific exploration and the thrills of scientific discovery, providing students with valuable knowledge, novel research experience, and a unique sense of scientific contribution.

Unsteady flow simulations around complex geometries using stationary or rotating unstructured grids

NASA Astrophysics Data System (ADS)

Sezer-Uzol, Nilay

In this research, the computational analysis of three-dimensional, unsteady, separated, vortical flows around complex geometries is studied by using stationary or moving unstructured grids. Two main engineering problems are investigated. The first problem is the unsteady simulation of a ship airwake, where helicopter operations become even more challenging, by using stationary unstructured grids. The second problem is the unsteady simulation of wind turbine rotor flow fields by using moving unstructured grids which are rotating with the whole three-dimensional rigid rotor geometry. The three dimensional, unsteady, parallel, unstructured, finite volume flow solver, PUMA2, is used for the computational fluid dynamics (CFD) simulations considered in this research. The code is modified to have a moving grid capability to perform three-dimensional, time-dependent rotor simulations. An instantaneous log-law wall model for Large Eddy Simulations is also implemented in PUMA2 to investigate the very large Reynolds number flow fields of rotating blades. To verify the code modifications, several sample test cases are also considered. In addition, interdisciplinary studies, which are aiming to provide new tools and insights to the aerospace and wind energy scientific communities, are done during this research by focusing on the coupling of ship airwake CFD simulations with the helicopter flight dynamics and control analysis, the coupling of wind turbine rotor CFD simulations with the aeroacoustic analysis, and the analysis of these time-dependent and large-scale CFD simulations with the help of a computational monitoring, steering and visualization tool, POSSE.

Interactive 4D Visualization of Sediment Transport Models

NASA Astrophysics Data System (ADS)

Butkiewicz, T.; Englert, C. M.

2013-12-01

Coastal sediment transport models simulate the effects that waves, currents, and tides have on near-shore bathymetry and features such as beaches and barrier islands. Understanding these dynamic processes is integral to the study of coastline stability, beach erosion, and environmental contamination. Furthermore, analyzing the results of these simulations is a critical task in the design, placement, and engineering of coastal structures such as seawalls, jetties, support pilings for wind turbines, etc. Despite the importance of these models, there is a lack of available visualization software that allows users to explore and perform analysis on these datasets in an intuitive and effective manner. Existing visualization interfaces for these datasets often present only one variable at a time, using two dimensional plan or cross-sectional views. These visual restrictions limit the ability to observe the contents in the proper overall context, both in spatial and multi-dimensional terms. To improve upon these limitations, we use 3D rendering and particle system based illustration techniques to show water column/flow data across all depths simultaneously. We can also encode multiple variables across different perceptual channels (color, texture, motion, etc.) to enrich surfaces with multi-dimensional information. Interactive tools are provided, which can be used to explore the dataset and find regions-of-interest for further investigation. Our visualization package provides an intuitive 4D (3D, time-varying) visualization of sediment transport model output. In addition, we are also integrating real world observations with the simulated data to support analysis of the impact from major sediment transport events. In particular, we have been focusing on the effects of Superstorm Sandy on the Redbird Artificial Reef Site, offshore of Delaware Bay. Based on our pre- and post-storm high-resolution sonar surveys, there has significant scour and bedform migration around the sunken subway cars and other vessels present at the Redbird site. Due to the extensive surveying and historical data availability in the area, the site is highly attractive for comparing hindcasted sediment transport simulations to our observations of actual changes. This work has the potential to strengthen the accuracy of sediment transport modeling, as well as help predict and prepare for future changes due to similar extreme sediment transport events. Our visualization showing a simple sediment transport model with tidal flows causing significant erosion (red) and deposition (blue).

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.

Generating classes of 3D virtual mandibles for AR-based medical simulation.

PubMed

Hippalgaonkar, Neha R; Sider, Alexa D; Hamza-Lup, Felix G; Santhanam, Anand P; Jaganathan, Bala; Imielinska, Celina; Rolland, Jannick P

2008-01-01

Simulation and modeling represent promising tools for several application domains from engineering to forensic science and medicine. Advances in 3D imaging technology convey paradigms such as augmented reality (AR) and mixed reality inside promising simulation tools for the training industry. Motivated by the requirement for superimposing anatomically correct 3D models on a human patient simulator (HPS) and visualizing them in an AR environment, the purpose of this research effort was to develop and validate a method for scaling a source human mandible to a target human mandible within a 2 mm root mean square (RMS) error. Results show that, given a distance between 2 same landmarks on 2 different mandibles, a relative scaling factor may be computed. Using this scaling factor, results show that a 3D virtual mandible model can be made morphometrically equivalent to a real target-specific mandible within a 1.30 mm RMS error. The virtual mandible may be further used as a reference target for registering other anatomic models, such as the lungs, on the HPS. Such registration will be made possible by physical constraints among the mandible and the spinal column in the horizontal normal rest position.

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

LANL Summer 2016 Report

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

Mendoza, Paul Michael

The Monte Carlo N-Particle (MCNP) transport code developed at Los Alamos National Laboratory (LANL) utilizes nuclear cross-section data in a compact ENDF (ACE) format. The accuracy of MCNP calculations depends on the accuracy of nuclear ACE data tables, which depends on the accuracy of the original ENDF files. There are some noticeable differences in ENDF files from one generation to the next, even among the more common fissile materials. As the next generation of ENDF files is being prepared, several software tools were developed to simulate a large number of benchmarks in MCNP (over 1000), collect data from these simulations,more » and visually represent the results.« less

M.A.E.G.U.S.: Measuring alternate energy generation via unity simulation

NASA Astrophysics Data System (ADS)

Nataraja, Kavin Muhilan

This paper presents the MAEGUS serious game and a study to determine its efficacy as a pedagogical tool. The MAEGUS serious game teaches sustainable energy concepts through gameplay simulating wind turbines and solar arrays. Players take the role of an energy manager for a city and use realistic data and information visualizations to learn the physical factors of wind and solar energy generation. The MAEGUS serious game study compares game assisted learning to a more traditional teaching method such as reading material in a crossover study, the results of which can inform future serious game development for educational purposes.

Hierarchical Spatio-temporal Visual Analysis of Cluster Evolution in Electrocorticography Data

DOE PAGES

Murugesan, Sugeerth; Bouchard, Kristofer; Chang, Edward; ...

2016-10-02

Here, we present ECoG ClusterFlow, a novel interactive visual analysis tool for the exploration of high-resolution Electrocorticography (ECoG) data. Our system detects and visualizes dynamic high-level structures, such as communities, using the time-varying spatial connectivity network derived from the high-resolution ECoG data. ECoG ClusterFlow provides a multi-scale visualization of the spatio-temporal patterns underlying the time-varying communities using two views: 1) an overview summarizing the evolution of clusters over time and 2) a hierarchical glyph-based technique that uses data aggregation and small multiples techniques to visualize the propagation of clusters in their spatial domain. ECoG ClusterFlow makes it possible 1) tomore » compare the spatio-temporal evolution patterns across various time intervals, 2) to compare the temporal information at varying levels of granularity, and 3) to investigate the evolution of spatial patterns without occluding the spatial context information. Lastly, we present case studies done in collaboration with neuroscientists on our team for both simulated and real epileptic seizure data aimed at evaluating the effectiveness of our approach.« less

Lightweight computational steering of very large scale molecular dynamics simulations

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

Beazley, D.M.; Lomdahl, P.S.

1996-09-01

We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show howmore » this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages.« less

An Interactive Simulation Program for Exploring Computational Models of Auto-Associative Memory.

PubMed

Fink, Christian G

2017-01-01

While neuroscience students typically learn about activity-dependent plasticity early in their education, they often struggle to conceptually connect modification at the synaptic scale with network-level neuronal dynamics, not to mention with their own everyday experience of recalling a memory. We have developed an interactive simulation program (based on the Hopfield model of auto-associative memory) that enables the user to visualize the connections generated by any pattern of neural activity, as well as to simulate the network dynamics resulting from such connectivity. An accompanying set of student exercises introduces the concepts of pattern completion, pattern separation, and sparse versus distributed neural representations. Results from a conceptual assessment administered before and after students worked through these exercises indicate that the simulation program is a useful pedagogical tool for illustrating fundamental concepts of computational models of memory.

Methodology for functional MRI of simulated driving.

PubMed

Kan, Karen; Schweizer, Tom A; Tam, Fred; Graham, Simon J

2013-01-01

The developed world faces major socioeconomic and medical challenges associated with motor vehicle accidents caused by risky driving. Functional magnetic resonance imaging (fMRI) of individuals using virtual reality driving simulators may provide an important research tool to assess driving safety, based on brain activity and behavior. A fMRI-compatible driving simulator was developed and evaluated in the context of straight driving, turning, and stopping in 16 young healthy adults. Robust maps of brain activity were obtained, including activation of the primary motor cortex, cerebellum, visual cortex, and parietal lobe, with limited head motion (<1.5 mm deviation from mean head position in the superior∕inferior direction in all subjects) and only minor correlations between head motion, steering, or braking behavior. These results are consistent with previous literature and suggest that with care, fMRI of simulated driving is a feasible undertaking.

A dual-waveband dynamic IR scene projector based on DMD

NASA Astrophysics Data System (ADS)

Hu, Yu; Zheng, Ya-wei; Gao, Jiao-bo; Sun, Ke-feng; Li, Jun-na; Zhang, Lei; Zhang, Fang

2016-10-01

Infrared scene simulation system can simulate multifold objects and backgrounds to perform dynamic test and evaluate EO detecting system in the hardware in-the-loop test. The basic structure of a dual-waveband dynamic IR scene projector was introduced in the paper. The system's core device is an IR Digital Micro-mirror Device (DMD) and the radiant source is a mini-type high temperature IR plane black-body. An IR collimation optical system which transmission range includes 3-5μm and 8-12μm is designed as the projection optical system. Scene simulation software was developed with Visual C++ and Vega soft tools and a software flow chart was presented. The parameters and testing results of the system were given, and this system was applied with satisfying performance in an IR imaging simulation testing.

GTKDynamo: a PyMOL plug-in for QC/MM hybrid potential simulations

PubMed Central

Bachega, José Fernando R.; Timmers, Luís Fernando S.M.; Assirati, Lucas; Bachega, Leonardo R.; Field, Martin J.; Wymore, Troy

2014-01-01

Hybrid quantum chemical (QC)/molecular mechanical (MM) potentials are very powerful tools for molecular simulation. They are especially useful for studying processes in condensed phase systems, such as chemical reactions, that involve a relatively localized change in electronic structure and where the surrounding environment contributes to these changes but can be represented with more computationally efficient functional forms. Despite their utility, however, these potentials are not always straightforward to apply since the extent of significant electronic structure changes occurring in the condensed phase process may not be intuitively obvious. To facilitate their use we have developed an open-source graphical plug-in, GTKDynamo, that links the PyMOL visualization program and the pDynamo QC/MM simulation library. This article describes the implementation of GTKDynamo and its capabilities and illustrates its application to QC/MM simulations. PMID:24137667

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

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.

Robust multi-site MR data processing: iterative optimization of bias correction, tissue classification, and registration.

PubMed

Young Kim, Eun; Johnson, Hans J

2013-01-01

A robust multi-modal tool, for automated registration, bias correction, and tissue classification, has been implemented for large-scale heterogeneous multi-site longitudinal MR data analysis. This work focused on improving the an iterative optimization framework between bias-correction, registration, and tissue classification inspired from previous work. The primary contributions are robustness improvements from incorporation of following four elements: (1) utilize multi-modal and repeated scans, (2) incorporate high-deformable registration, (3) use extended set of tissue definitions, and (4) use of multi-modal aware intensity-context priors. The benefits of these enhancements were investigated by a series of experiments with both simulated brain data set (BrainWeb) and by applying to highly-heterogeneous data from a 32 site imaging study with quality assessments through the expert visual inspection. The implementation of this tool is tailored for, but not limited to, large-scale data processing with great data variation with a flexible interface. In this paper, we describe enhancements to a joint registration, bias correction, and the tissue classification, that improve the generalizability and robustness for processing multi-modal longitudinal MR scans collected at multi-sites. The tool was evaluated by using both simulated and simulated and human subject MRI images. With these enhancements, the results showed improved robustness for large-scale heterogeneous MRI processing.

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.

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

Color visual simulation applications at the Defense Mapping Agency

NASA Astrophysics Data System (ADS)

Simley, J. D.

1984-09-01

The Defense Mapping Agency (DMA) produces the Digital Landmass System data base to provide culture and terrain data in support of numerous aircraft simulators. In order to conduct data base and simulation quality control and requirements analysis, DMA has developed the Sensor Image Simulator which can rapidly generate visual and radar static scene digital simulations. The use of color in visual simulation allows the clear portrayal of both landcover and terrain data, whereas the initial black and white capabilities were restricted in this role and thus found limited use. Color visual simulation has many uses in analysis to help determine the applicability of current and prototype data structures to better meet user requirements. Color visual simulation is also significant in quality control since anomalies can be more easily detected in natural appearing forms of the data. The realism and efficiency possible with advanced processing and display technology, along with accurate data, make color visual simulation a highly effective medium in the presentation of geographic information. As a result, digital visual simulation is finding increased potential as a special purpose cartographic product. These applications are discussed and related simulation examples are presented.

A visual graphic/haptic rendering model for hysteroscopic procedures.

PubMed

Lim, Fabian; Brown, Ian; McColl, Ryan; Seligman, Cory; Alsaraira, Amer

2006-03-01

Hysteroscopy is an extensively popular option in evaluating and treating women with infertility. The procedure utilises an endoscope, inserted through the vagina and cervix to examine the intra-uterine cavity via a monitor. The difficulty of hysteroscopy from the surgeon's perspective is the visual spatial perception of interpreting 3D images on a 2D monitor, and the associated psychomotor skills in overcoming the fulcrum-effect. Despite the widespread use of this procedure, current qualified hysteroscopy surgeons have not been trained the fundamentals through an organised curriculum. The emergence of virtual reality as an educational tool for this procedure, and for other endoscopic procedures, has undoubtedly raised interests. The ultimate objective is for the inclusion of virtual reality training as a mandatory component for gynaecologic endoscopy training. Part of this process involves the design of a simulator, encompassing the technical difficulties and complications associated with the procedure. The proposed research examines fundamental hysteroscopy factors, current training and accreditation, and proposes a hysteroscopic simulator design that is suitable for educating and training.

RIPPLELAB: A Comprehensive Application for the Detection, Analysis and Classification of High Frequency Oscillations in Electroencephalographic Signals

PubMed Central

Alvarado-Rojas, Catalina; Le Van Quyen, Michel; Valderrama, Mario

2016-01-01

High Frequency Oscillations (HFOs) in the brain have been associated with different physiological and pathological processes. In epilepsy, HFOs might reflect a mechanism of epileptic phenomena, serving as a biomarker of epileptogenesis and epileptogenicity. Despite the valuable information provided by HFOs, their correct identification is a challenging task. A comprehensive application, RIPPLELAB, was developed to facilitate the analysis of HFOs. RIPPLELAB provides a wide range of tools for HFOs manual and automatic detection and visual validation; all of them are accessible from an intuitive graphical user interface. Four methods for automated detection—as well as several options for visualization and validation of detected events—were implemented and integrated in the application. Analysis of multiple files and channels is possible, and new options can be added by users. All features and capabilities implemented in RIPPLELAB for automatic detection were tested through the analysis of simulated signals and intracranial EEG recordings from epileptic patients (n = 16; 3,471 analyzed hours). Visual validation was also tested, and detected events were classified into different categories. Unlike other available software packages for EEG analysis, RIPPLELAB uniquely provides the appropriate graphical and algorithmic environment for HFOs detection (visual and automatic) and validation, in such a way that the power of elaborated detection methods are available to a wide range of users (experts and non-experts) through the use of this application. We believe that this open-source tool will facilitate and promote the collaboration between clinical and research centers working on the HFOs field. The tool is available under public license and is accessible through a dedicated web site. PMID:27341033

Development of interactive graphic user interfaces for modeling reaction-based biogeochemical processes in batch systems with BIOGEOCHEM

NASA Astrophysics Data System (ADS)

Chang, C.; Li, M.; Yeh, G.

2010-12-01

The BIOGEOCHEM numerical model (Yeh and Fang, 2002; Fang et al., 2003) was developed with FORTRAN for simulating reaction-based geochemical and biochemical processes with mixed equilibrium and kinetic reactions in batch systems. A complete suite of reactions including aqueous complexation, adsorption/desorption, ion-exchange, redox, precipitation/dissolution, acid-base reactions, and microbial mediated reactions were embodied in this unique modeling tool. Any reaction can be treated as fast/equilibrium or slow/kinetic reaction. An equilibrium reaction is modeled with an implicit finite rate governed by a mass action equilibrium equation or by a user-specified algebraic equation. A kinetic reaction is modeled with an explicit finite rate with an elementary rate, microbial mediated enzymatic kinetics, or a user-specified rate equation. None of the existing models has encompassed this wide array of scopes. To ease the input/output learning curve using the unique feature of BIOGEOCHEM, an interactive graphic user interface was developed with the Microsoft Visual Studio and .Net tools. Several user-friendly features, such as pop-up help windows, typo warning messages, and on-screen input hints, were implemented, which are robust. All input data can be real-time viewed and automated to conform with the input file format of BIOGEOCHEM. A post-processor for graphic visualizations of simulated results was also embedded for immediate demonstrations. By following data input windows step by step, errorless BIOGEOCHEM input files can be created even if users have little prior experiences in FORTRAN. With this user-friendly interface, the time effort to conduct simulations with BIOGEOCHEM can be greatly reduced.

Design of an immersive simulator for assisted power wheelchair driving.

PubMed

Devigne, Louise; Babel, Marie; Nouviale, Florian; Narayanan, Vishnu K; Pasteau, Francois; Gallien, Philippe

2017-07-01

Driving a power wheelchair is a difficult and complex visual-cognitive task. As a result, some people with visual and/or cognitive disabilities cannot access the benefits of a power wheelchair because their impairments prevent them from driving safely. In order to improve their access to mobility, we have previously designed a semi-autonomous assistive wheelchair system which progressively corrects the trajectory as the user manually drives the wheelchair and smoothly avoids obstacles. Developing and testing such systems for wheelchair driving assistance requires a significant amount of material resources and clinician time. With Virtual Reality technology, prototypes can be developed and tested in a risk-free and highly flexible Virtual Environment before equipping and testing a physical prototype. Additionally, users can "virtually" test and train more easily during the development process. In this paper, we introduce a power wheelchair driving simulator allowing the user to navigate with a standard wheelchair in an immersive 3D Virtual Environment. The simulation framework is designed to be flexible so that we can use different control inputs. In order to validate the framework, we first performed tests on the simulator with able-bodied participants during which the user's Quality of Experience (QoE) was assessed through a set of questionnaires. Results show that the simulator is a promising tool for future works as it generates a good sense of presence and requires rather low cognitive effort from users.

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.

Nested Tracking Graphs

DOE PAGES

Lukasczyk, Jonas; Weber, Gunther; Maciejewski, Ross; ...

2017-06-01

Tracking graphs are a well established tool in topological analysis to visualize the evolution of components and their properties over time, i.e., when components appear, disappear, merge, and split. However, tracking graphs are limited to a single level threshold and the graphs may vary substantially even under small changes to the threshold. To examine the evolution of features for varying levels, users have to compare multiple tracking graphs without a direct visual link between them. We propose a novel, interactive, nested graph visualization based on the fact that the tracked superlevel set components for different levels are related to eachmore » other through their nesting hierarchy. This approach allows us to set multiple tracking graphs in context to each other and enables users to effectively follow the evolution of components for different levels simultaneously. We show the effectiveness of our approach on datasets from finite pointset methods, computational fluid dynamics, and cosmology simulations.« less

Rapid processing of data based on high-performance algorithms for solving inverse problems and 3D-simulation of the tsunami and earthquakes

NASA Astrophysics Data System (ADS)

Marinin, I. V.; Kabanikhin, S. I.; Krivorotko, O. I.; Karas, A.; Khidasheli, D. G.

2012-04-01

We consider new techniques and methods for earthquake and tsunami related problems, particularly - inverse problems for the determination of tsunami source parameters, numerical simulation of long wave propagation in soil and water and tsunami risk estimations. In addition, we will touch upon the issue of database management and destruction scenario visualization. New approaches and strategies, as well as mathematical tools and software are to be shown. The long joint investigations by researchers of the Institute of Mathematical Geophysics and Computational Mathematics SB RAS and specialists from WAPMERR and Informap have produced special theoretical approaches, numerical methods, and software tsunami and earthquake modeling (modeling of propagation and run-up of tsunami waves on coastal areas), visualization, risk estimation of tsunami, and earthquakes. Algorithms are developed for the operational definition of the origin and forms of the tsunami source. The system TSS numerically simulates the source of tsunami and/or earthquakes and includes the possibility to solve the direct and the inverse problem. It becomes possible to involve advanced mathematical results to improve models and to increase the resolution of inverse problems. Via TSS one can construct maps of risks, the online scenario of disasters, estimation of potential damage to buildings and roads. One of the main tools for the numerical modeling is the finite volume method (FVM), which allows us to achieve stability with respect to possible input errors, as well as to achieve optimum computing speed. Our approach to the inverse problem of tsunami and earthquake determination is based on recent theoretical results concerning the Dirichlet problem for the wave equation. This problem is intrinsically ill-posed. We use the optimization approach to solve this problem and SVD-analysis to estimate the degree of ill-posedness and to find the quasi-solution. The software system we developed is intended to create technology «no frost», realizing a steady stream of direct and inverse problems: solving the direct problem, the visualization and comparison with observed data, to solve the inverse problem (correction of the model parameters). The main objective of further work is the creation of a workstation operating emergency tool that could be used by an emergency duty person in real time.

SCALING AN URBAN EMERGENCY EVACUATION FRAMEWORK: CHALLENGES AND PRACTICES

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

Karthik, Rajasekar; Lu, Wei

2014-01-01

Critical infrastructure disruption, caused by severe weather events, natural disasters, terrorist attacks, etc., has significant impacts on urban transportation systems. We built a computational framework to simulate urban transportation systems under critical infrastructure disruption in order to aid real-time emergency evacuation. This framework will use large scale datasets to provide a scalable tool for emergency planning and management. Our framework, World-Wide Emergency Evacuation (WWEE), integrates population distribution and urban infrastructure networks to model travel demand in emergency situations at global level. Also, a computational model of agent-based traffic simulation is used to provide an optimal evacuation plan for traffic operationmore » purpose [1]. In addition, our framework provides a web-based high resolution visualization tool for emergency evacuation modelers and practitioners. We have successfully tested our framework with scenarios in both United States (Alexandria, VA) and Europe (Berlin, Germany) [2]. However, there are still some major drawbacks for scaling this framework to handle big data workloads in real time. On our back-end, lack of proper infrastructure limits us in ability to process large amounts of data, run the simulation efficiently and quickly, and provide fast retrieval and serving of data. On the front-end, the visualization performance of microscopic evacuation results is still not efficient enough due to high volume data communication between server and client. We are addressing these drawbacks by using cloud computing and next-generation web technologies, namely Node.js, NoSQL, WebGL, Open Layers 3 and HTML5 technologies. We will describe briefly about each one and how we are using and leveraging these technologies to provide an efficient tool for emergency management organizations. Our early experimentation demonstrates that using above technologies is a promising approach to build a scalable and high performance urban emergency evacuation framework that can improve traffic mobility and safety under critical infrastructure disruption in today s socially connected world.« less

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.

Automated detection and analysis of particle beams in laser-plasma accelerator simulations

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

Ushizima, Daniela Mayumi; Geddes, C.G.; Cormier-Michel, E.

Numerical simulations of laser-plasma wakefield (particle) accelerators model the acceleration of electrons trapped in plasma oscillations (wakes) left behind when an intense laser pulse propagates through the plasma. The goal of these simulations is to better understand the process involved in plasma wake generation and how electrons are trapped and accelerated by the wake. Understanding of such accelerators, and their development, offer high accelerating gradients, potentially reducing size and cost of new accelerators. One operating regime of interest is where a trapped subset of electrons loads the wake and forms an isolated group of accelerated particles with low spread inmore » momentum and position, desirable characteristics for many applications. The electrons trapped in the wake may be accelerated to high energies, the plasma gradient in the wake reaching up to a gigaelectronvolt per centimeter. High-energy electron accelerators power intense X-ray radiation to terahertz sources, and are used in many applications including medical radiotherapy and imaging. To extract information from the simulation about the quality of the beam, a typical approach is to examine plots of the entire dataset, visually determining the adequate parameters necessary to select a subset of particles, which is then further analyzed. This procedure requires laborious examination of massive data sets over many time steps using several plots, a routine that is unfeasible for large data collections. Demand for automated analysis is growing along with the volume and size of simulations. Current 2D LWFA simulation datasets are typically between 1GB and 100GB in size, but simulations in 3D are of the order of TBs. The increase in the number of datasets and dataset sizes leads to a need for automatic routines to recognize particle patterns as particle bunches (beam of electrons) for subsequent analysis. Because of the growth in dataset size, the application of machine learning techniques for scientific data mining is increasingly considered. In plasma simulations, Bagherjeiran et al. presented a comprehensive report on applying graph-based techniques for orbit classification. They used the KAM classifier to label points and components in single and multiple orbits. Love et al. conducted an image space analysis of coherent structures in plasma simulations. They used a number of segmentation and region-growing techniques to isolate regions of interest in orbit plots. Both approaches analyzed particle accelerator data, targeting the system dynamics in terms of particle orbits. However, they did not address particle dynamics as a function of time or inspected the behavior of bunches of particles. Ruebel et al. addressed the visual analysis of massive laser wakefield acceleration (LWFA) simulation data using interactive procedures to query the data. Sophisticated visualization tools were provided to inspect the data manually. Ruebel et al. have integrated these tools to the visualization and analysis system VisIt, in addition to utilizing efficient data management based on HDF5, H5Part, and the index/query tool FastBit. In Ruebel et al. proposed automatic beam path analysis using a suite of methods to classify particles in simulation data and to analyze their temporal evolution. To enable researchers to accurately define particle beams, the method computes a set of measures based on the path of particles relative to the distance of the particles to a beam. To achieve good performance, this framework uses an analysis pipeline designed to quickly reduce the amount of data that needs to be considered in the actual path distance computation. As part of this process, region-growing methods are utilized to detect particle bunches at single time steps. Efficient data reduction is essential to enable automated analysis of large data sets as described in the next section, where data reduction methods are steered to the particular requirements of our clustering analysis. Previously, we have described the application of a set of algorithms to automate the data analysis and classification of particle beams in the LWFA simulation data, identifying locations with high density of high energy particles. These algorithms detected high density locations (nodes) in each time step, i.e. maximum points on the particle distribution for only one spatial variable. Each node was correlated to a node in previous or later time steps by linking these nodes according to a pruned minimum spanning tree (PMST). We call the PMST representation 'a lifetime diagram', which is a graphical tool to show temporal information of high dense groups of particles in the longitudinal direction for the time series. Electron bunch compactness was described by another step of the processing, designed to partition each time step, using fuzzy clustering, into a fixed number of clusters.« less

STRING 3: An Advanced Groundwater Flow Visualization Tool

NASA Astrophysics Data System (ADS)

Schröder, Simon; Michel, Isabel; Biedert, Tim; Gräfe, Marius; Seidel, Torsten; König, Christoph

2016-04-01

The visualization of 3D groundwater flow is a challenging task. Previous versions of our software STRING [1] solely focused on intuitive visualization of complex flow scenarios for non-professional audiences. STRING, developed by Fraunhofer ITWM (Kaiserslautern, Germany) and delta h Ingenieurgesellschaft mbH (Witten, Germany), provides the necessary means for visualization of both 2D and 3D data on planar and curved surfaces. In this contribution we discuss how to extend this approach to a full 3D tool and its challenges in continuation of Michel et al. [2]. This elevates STRING from a post-production to an exploration tool for experts. In STRING moving pathlets provide an intuition of velocity and direction of both steady-state and transient flows. The visualization concept is based on the Lagrangian view of the flow. To capture every detail of the flow an advanced method for intelligent, time-dependent seeding is used building on the Finite Pointset Method (FPM) developed by Fraunhofer ITWM. Lifting our visualization approach from 2D into 3D provides many new challenges. With the implementation of a seeding strategy for 3D one of the major problems has already been solved (see Schröder et al. [3]). As pathlets only provide an overview of the velocity field other means are required for the visualization of additional flow properties. We suggest the use of Direct Volume Rendering and isosurfaces for scalar features. In this regard we were able to develop an efficient approach for combining the rendering through raytracing of the volume and regular OpenGL geometries. This is achieved through the use of Depth Peeling or A-Buffers for the rendering of transparent geometries. Animation of pathlets requires a strict boundary of the simulation domain. Hence, STRING needs to extract the boundary, even from unstructured data, if it is not provided. In 3D we additionally need a good visualization of the boundary itself. For this the silhouette based on the angle of neighboring faces is extracted. Similar algorithms help to find the 2D boundary of cuts through the 3D model. As interactivity plays a big role for an exploration tool the speed of the drawing routines is also important. To achieve this, different pathlet rendering solutions have been developed and benchmarked. These provide a trade-off between the usage of geometry and fragment shaders. We show that point sprite shaders have superior performance and visual quality over geometry-based approaches. Admittedly, the point sprite-based approach has many non-trivial problems of joining the different parts of the pathlet geometry. This research is funded by the Federal Ministry for Economic Affairs and Energy (Germany). [1] T. Seidel, C. König, M. Schäfer, I. Ostermann, T. Biedert, D. Hietel (2014). Intuitive visualization of transient groundwater flow. Computers & Geosciences, Vol. 67, pp. 173-179 [2] I. Michel, S. Schröder, T. Seidel, C. König (2015). Intuitive Visualization of Transient Flow: Towards a Full 3D Tool. Geophysical Research Abstracts, Vol. 17, EGU2015-1670 [3] S. Schröder, I. Michel, T. Seidel, C.M. König (2015). STRING 3: Full 3D visualization of groundwater Flow. In Proceedings of IAMG 2015 Freiberg, pp. 813-822

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.

Integrating neuroinformatics tools in TheVirtualBrain.

PubMed

Woodman, M Marmaduke; Pezard, Laurent; Domide, Lia; Knock, Stuart A; Sanz-Leon, Paula; Mersmann, Jochen; McIntosh, Anthony R; Jirsa, Viktor

2014-01-01

TheVirtualBrain (TVB) is a neuroinformatics Python package representing the convergence of clinical, systems, and theoretical neuroscience in the analysis, visualization and modeling of neural and neuroimaging dynamics. TVB is composed of a flexible simulator for neural dynamics measured across scales from local populations to large-scale dynamics measured by electroencephalography (EEG), magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI), and core analytic and visualization functions, all accessible through a web browser user interface. A datatype system modeling neuroscientific data ties together these pieces with persistent data storage, based on a combination of SQL and HDF5. These datatypes combine with adapters allowing TVB to integrate other algorithms or computational systems. TVB provides infrastructure for multiple projects and multiple users, possibly participating under multiple roles. For example, a clinician might import patient data to identify several potential lesion points in the patient's connectome. A modeler, working on the same project, tests these points for viability through whole brain simulation, based on the patient's connectome, and subsequent analysis of dynamical features. TVB also drives research forward: the simulator itself represents the culmination of several simulation frameworks in the modeling literature. The availability of the numerical methods, set of neural mass models and forward solutions allows for the construction of a wide range of brain-scale simulation scenarios. This paper briefly outlines the history and motivation for TVB, describing the framework and simulator, giving usage examples in the web UI and Python scripting.

Integrating neuroinformatics tools in TheVirtualBrain

PubMed Central

Woodman, M. Marmaduke; Pezard, Laurent; Domide, Lia; Knock, Stuart A.; Sanz-Leon, Paula; Mersmann, Jochen; McIntosh, Anthony R.; Jirsa, Viktor

2014-01-01

TheVirtualBrain (TVB) is a neuroinformatics Python package representing the convergence of clinical, systems, and theoretical neuroscience in the analysis, visualization and modeling of neural and neuroimaging dynamics. TVB is composed of a flexible simulator for neural dynamics measured across scales from local populations to large-scale dynamics measured by electroencephalography (EEG), magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI), and core analytic and visualization functions, all accessible through a web browser user interface. A datatype system modeling neuroscientific data ties together these pieces with persistent data storage, based on a combination of SQL and HDF5. These datatypes combine with adapters allowing TVB to integrate other algorithms or computational systems. TVB provides infrastructure for multiple projects and multiple users, possibly participating under multiple roles. For example, a clinician might import patient data to identify several potential lesion points in the patient's connectome. A modeler, working on the same project, tests these points for viability through whole brain simulation, based on the patient's connectome, and subsequent analysis of dynamical features. TVB also drives research forward: the simulator itself represents the culmination of several simulation frameworks in the modeling literature. The availability of the numerical methods, set of neural mass models and forward solutions allows for the construction of a wide range of brain-scale simulation scenarios. This paper briefly outlines the history and motivation for TVB, describing the framework and simulator, giving usage examples in the web UI and Python scripting. PMID:24795617

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

Using virtual reality technology for aircraft visual inspection training: presence and comparison studies.

PubMed

Vora, Jeenal; Nair, Santosh; Gramopadhye, Anand K; Duchowski, Andrew T; Melloy, Brian J; Kanki, Barbara

2002-11-01

The aircraft maintenance industry is a complex system consisting of several interrelated human and machine components. Recognizing this, the Federal Aviation Administration (FAA) has pursued human factors related research. In the maintenance arena the research has focused on the aircraft inspection process and the aircraft inspector. Training has been identified as the primary intervention strategy to improve the quality and reliability of aircraft inspection. If training is to be successful, it is critical that we provide aircraft inspectors with appropriate training tools and environment. In response to this need, the paper outlines the development of a virtual reality (VR) system for aircraft inspection training. VR has generated much excitement but little formal proof that it is useful. However, since VR interfaces are difficult and expensive to build, the computer graphics community needs to be able to predict which applications will benefit from VR. To address this important issue, this research measured the degree of immersion and presence felt by subjects in a virtual environment simulator. Specifically, it conducted two controlled studies using the VR system developed for visual inspection task of an aft-cargo bay at the VR Lab of Clemson University. Beyond assembling the visual inspection virtual environment, a significant goal of this project was to explore subjective presence as it affects task performance. The results of this study indicated that the system scored high on the issues related to the degree of presence felt by the subjects. As a next logical step, this study, then, compared VR to an existing PC-based aircraft inspection simulator. The results showed that the VR system was better and preferred over the PC-based training tool.

Sensor Based Framework for Secure Multimedia Communication in VANET

PubMed Central

Rahim, Aneel; Khan, Zeeshan Shafi; Bin Muhaya, Fahad T.; Sher, Muhammad; Kim, Tai-Hoon

2010-01-01

Secure multimedia communication enhances the safety of passengers by providing visual pictures of accidents and danger situations. In this paper we proposed a framework for secure multimedia communication in Vehicular Ad-Hoc Networks (VANETs). Our proposed framework is mainly divided into four components: redundant information, priority assignment, malicious data verification and malicious node verification. The proposed scheme jhas been validated with the help of the NS-2 network simulator and the Evalvid tool. PMID:22163462

Emerging CAE technologies and their role in Future Ambient Intelligence Environments

NASA Astrophysics Data System (ADS)

Noor, Ahmed K.

2011-03-01

Dramatic improvements are on the horizon in Computer Aided Engineering (CAE) and various simulation technologies. The improvements are due, in part, to the developments in a number of leading-edge technologies and their synergistic combinations/convergence. The technologies include ubiquitous, cloud, and petascale computing; ultra high-bandwidth networks, pervasive wireless communication; knowledge based engineering; networked immersive virtual environments and virtual worlds; novel human-computer interfaces; and powerful game engines and facilities. This paper describes the frontiers and emerging simulation technologies, and their role in the future virtual product creation and learning/training environments. The environments will be ambient intelligence environments, incorporating a synergistic combination of novel agent-supported visual simulations (with cognitive learning and understanding abilities); immersive 3D virtual world facilities; development chain management systems and facilities (incorporating a synergistic combination of intelligent engineering and management tools); nontraditional methods; intelligent, multimodal and human-like interfaces; and mobile wireless devices. The Virtual product creation environment will significantly enhance the productivity and will stimulate creativity and innovation in future global virtual collaborative enterprises. The facilities in the learning/training environment will provide timely, engaging, personalized/collaborative and tailored visual learning.

Relating Standardized Visual Perception Measures to Simulator Visual System Performance

NASA Technical Reports Server (NTRS)

Kaiser, Mary K.; Sweet, Barbara T.

2013-01-01

Human vision is quantified through the use of standardized clinical vision measurements. These measurements typically include visual acuity (near and far), contrast sensitivity, color vision, stereopsis (a.k.a. stereo acuity), and visual field periphery. Simulator visual system performance is specified in terms such as brightness, contrast, color depth, color gamut, gamma, resolution, and field-of-view. How do these simulator performance characteristics relate to the perceptual experience of the pilot in the simulator? In this paper, visual acuity and contrast sensitivity will be related to simulator visual system resolution, contrast, and dynamic range; similarly, color vision will be related to color depth/color gamut. Finally, we will consider how some characteristics of human vision not typically included in current clinical assessments could be used to better inform simulator requirements (e.g., relating dynamic characteristics of human vision to update rate and other temporal display characteristics).

Bringing "Scientific Expeditions" Into the Schools

NASA Technical Reports Server (NTRS)

Watson, Val; Lasinski, T. A. (Technical Monitor)

1995-01-01

Two new technologies, the FASTexpedition and Remote FAST, have been developed that provide remote, 3D, high resolution, dynamic, interactive viewing of scientific data (such as simulations or measurements of fluid dynamics). The FASTexpedition permits one to access scientific data from the World Wide Web, take guided expeditions through the data, and continue with self controlled expeditions through the data. Remote FAST permits collaborators at remote sites to simultaneously view an analysis of scientific data being controlled by one of the collaborators. Control can be transferred between sites. These technologies are now being used for remote collaboration in joint university, industry, and NASA projects in computational fluid dynamics (CFD) and wind tunnel testing. Also, NASA Ames Research Center has initiated a project to make scientific data and guided expeditions through the data available as FASTexpeditions on the World Wide Web for educational purposes. Previously, remote visualiZation of dynamic data was done using video format (transmitting pixel information) such as video conferencing or MPEG movies on the Internet. The concept for this new technology is to send the raw data (e.g., grids, vectors, and scalars) along with viewing scripts over the Internet and have the pixels generated by a visualization tool running on the viewer's local workstation. The visualization tool that is currently used is FAST (Flow Analysis Software Toolkit). The advantages of this new technology over using video format are: 1. The visual is much higher in resolution (1280xl024 pixels with 24 bits of color) than typical video format transmitted over the network. 2. The form of the visualization can be controlled interactively (because the viewer is interactively controlling the visualization tool running on his workstation). 3. A rich variety of guided expeditions through the data can be included easily. 4. A capability is provided for other sites to see a visual analysis of one site as the analysis is interactively performed. Control of the analysis can be passed from site to site. 5. The scenes can be viewed in 3D using stereo vision. 6. The network bandwidth used for the visualization using this new technology is much smaller than when using video format. (The measured peak bandwidth used was 1 Kbit/sec whereas the measured bandwidth for a small video picture was 500 Kbits/sec.)

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

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

Rosetta CONSERT operations and data analysis preparation: simulation software tools.

NASA Astrophysics Data System (ADS)

Rogez, Yves; Hérique, Alain; Cardiet, Maël; Zine, Sonia; Westphal, Mathieu; Micallef, Mickael; Berquin, Yann; Kofman, Wlodek

2014-05-01

The CONSERT experiment onboard Rosetta and Philae will perform the tomography of the 67P/CG comet nucleus by measuring radio waves transmission from the Rosetta S/C to the Philae Lander. The accurate analysis of travel time measurements will deliver unique knowledge of the nucleus interior dielectric properties. The challenging complexity of CONSERT operations requirements, combining both Rosetta and Philae, allows only a few set of opportunities to acquire data. Thus, we need a fine analysis of the impact of Rosetta trajectory, Philae position and comet shape on CONSERT measurements, in order to take optimal decisions in a short time. The integration of simulation results and mission parameters provides synthetic information to evaluate performances and risks for each opportunity. The preparation of CONSERT measurements before space operations is a key to achieve the best science return of the experiment. In addition, during Rosetta space operations, these software tools will allow a "real-time" first analysis of the latest measurements to improve the next acquisition sequences. The software tools themselves are built around a 3D electromagnetic radio wave simulation, taking into account the signal polarization. It is based on ray-tracing algorithms specifically designed for quick orbit analysis and radar signal generation. This allows computation on big domains relatively to the wavelength. The extensive use of 3D visualization tools provides comprehensive and synthetic views of the results. The software suite is designed to be extended, after Rosetta operations, to the full 3D measurement data analysis using inversion methods.