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At least 397 records · Page 22

Exploration of Metagenome Assemblies with an Interactive Visualization Tool

Metagenomics, one of the fastest growing areas of modern genomic science, is the genetic profiling of the entire community of microbial organisms present in an environmental sample. Elviz is a web-based tool for the interactive exploration of metagenome assemblies. Elviz can be used with publicly available data sets from the Joint Genome Institute or with custom user-loaded assemblies. Elviz is available at genome.jgi.doe.gov/viz

Cantor, Michael↗

Hyperdimensional visualization tool

A method and apparatus for displaying data. Independent data in the data is displayed by a computer system in a two-dimensional graph in a graphical user interface on a display system. Dimensions of dependent data in the data that are dependent on the independent data are displayed by the computer system in the two-dimensional graph using graphical indicators.

97 MATHEMATICS AND COMPUTING↗

Tools for Visualization and Analysis of Small-Angle Neutron Scattering Data: Descriptions and Examples

A great deal of progress has been made in improving the data reduction experience for the SANS instruments at the SNS and HFIR at ORNL. The existing data reduction toolset, drtsans, makes it possible to integrate data analysis and visualization tools into the data reduction scripts, thereby providing new opportunities for more automated data processing for users of the SNS and HFIR. Here, the first set of tools developed is described with usage examples.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Visual Data Comm: A Tool for Visualizing Data Communication in the Multi Sector Planner Study

Data comm is a new technology proposed in future air transport system as a potential tool to provide comprehensive data connectivity. It is a key enabler to manage 4D trajectory digitally, potentially resulting in improved flight times and increased throughput. Future concepts with data comm integration have been tested in a number of human-in-the-loop studies but analyzing the results has proven to be particularly challenging because future traffic environment in which data comm is fully enabled has assumed high traffic density, resulting in data set with large amount of information. This paper describes the motivation, design, current and potential future application of Visual Data Comm (VDC), a tool for visualizing data developed in Java using Processing library which is a tool package designed for interactive visualization programming. This paper includes an example of an application of VDC on data pertaining to the most recent Multi Sector Planner study, conducted at NASA s Airspace Operations Laboratory in 2009, in which VDC was used to visualize and interpret data comm activities

Lee, Hwasoo Eric↗

Tractometry of the Human Connectome Project: resources and insights

The Human Connectome Project (HCP) has become a keystone dataset in human neuroscience, with a plethora of important applications in advancing brain imaging methods and an understanding of the human brain. We focused on tractometry of HCP diffusion-weighted MRI (dMRI) data. We used an open-source software library (pyAFQ; https://yeatmanlab.github.io/pyAFQ) to perform probabilistic tractography and delineate the major white matter pathways in the HCP subjects that have a complete dMRI acquisition (n = 1,041). We used diffusion kurtosis imaging (DKI) to model white matter microstructure in each voxel of the white matter, and extracted tract profiles of DKI-derived tissue properties along the length of the tracts. We explored the empirical properties of the data: first, we assessed the heritability of DKI tissue properties using the known genetic linkage of the large number of twin pairs sampled in HCP. Second, we tested the ability of tractometry to serve as the basis for predictive models of individual characteristics (e.g., age, crystallized/fluid intelligence, reading ability, etc.), compared to local connectome features. To facilitate the exploration of the dataset we created a new web-based visualization tool and use this tool to visualize the data in the HCP tractometry dataset. Finally, we used the HCP dataset as a test-bed for a new technological innovation: the TRX file-format for representation of dMRI-based streamlines. We released the processing outputs and tract profiles as a publicly available data resource through the AWS Open Data program's Open Neurodata repository. We found heritability as high as 0.9 for DKI-based metrics in some brain pathways. We also found that tractometry extracts as much useful information about individual differences as the local connectome method. We released a new web-based visualization tool for tractometry—“Tractoscope” (https://nrdg.github.io/tractoscope). We found that the TRX files require considerably less disk space-a crucial attribute for large datasets like HCP. In addition, TRX incorporates a specification for grouping streamlines, further simplifying tractometry analysis.

59 BASIC BIOLOGICAL SCIENCES↗

Communicating the Threat of a Tropical Cyclone to the Eastern Range

The 45th Weather Squadron (45 WS) has developed a tool to help visualize the Wind Speed Probability product from the National Hurricane Center (NHC) and to help communicate that information to space launch customers and decision makers at the 45th Space Wing (45 SW) and Kennedy Space Center (KSC) located in east central Florida. This paper reviews previous work and presents the new visualization tool, including initial feedback as well as the pros and cons. The NHC began issuing their Wind Speed Probability product for tropical cyclones publicly in 2006. The 45 WS uses this product to provide a threat assessment to 45 SW and KSC leadership for risk evaluations with an approaching tropical cyclone. Although the wind speed probabilities convey the uncertainty of a tropical cyclone well, communicating this information to customers is a challenge. The 45 WS continually strives to provide the wind speed probability information to customers in a context which clearly communicates the threat of a tropical cyclone. First, an intern from the Florida Institute of Technology (FIT) Atmospheric Sciences department, sponsored by Scitor Corporation, independently evaluated the NHC wind speed probability product. This work was later extended into a M.S. thesis at FIT, partially funded by Scitor Corporation and KSC. A second thesis at FIT further extended the evaluation partially funded by KSC. Using this analysis, the 45 WS categorized the probabilities into five probability interpretation categories: Very Low, Low, Moderate, High, and Very High. These probability interpretation categories convert the forecast probability and forecast interval into easily understood categories that are consistent across all ranges of probabilities and forecast intervals. As a follow-on project, KSC funded a summer intern to evaluate the human factors of the probability interpretation categories, which ultimately refined some of the thresholds. The 45 WS created a visualization tool to express the timing and risk for multiple locations in a single graphic. Preliminary results on an on-going project by FIT will be included in this paper. This project is developing a new method of assigning the probability interpretation categories and updating the evaluation of the performance of the NHC wind speed probability analysis.

Winters, Katherine A.↗

Another Set of Python Tools for Visualizing and Manipulating Small-Angle Neutron Scattering Data: Descriptions and Examples

The GP-SANS, Bio-SANS and EQ-SANS instruments at ORNL utilize drtsans for data reduction. drtsans is built on Python, and it can be run using python scripts and Jupyter notebooks. The flexibility afforded by Python makes it possible to incorporate additional actions into the scripts used for data reduction, such as analysis and visualization. Here, a new set of tools for visualizing and manipulating SANS data that can be incorporated into the data reduction scripts for the ORNL SANS instruments, or employed during post–processing, is presented that expands the capabilities of the two previously-released tool sets.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A New Collaborative Tool for Visually Understanding National Health Indicators

The authors propose a new online collaborative tool for visually understanding national health indicators, which facilitates the full spectrum of investigation of indicators, from an overview of all the correlation coefficients between variables, to investigation of subsets of selected variables, and to individual data element analysis. this tool is publicly accessible at http://cda.ornl.gov/heat/heatmap.html. In this paper, they discuss the key issues regarding the interface design and implementation. They also illustrate how to use their interface for analyzing the health indicator dataset by showing some key system views. In the end, they introduce and discuss some ongoing research efforts extending this work.

59 BASIC BIOLOGICAL SCIENCES↗

How does the connectivity of open-framework conglomerates within multi-scale hierarchical fluvial architecture affect oil-sweep efficiency in waterflooding?

Understanding multi-phase fluid flow and transport processes within aquifers, candidate reservoirs for CO 2 sequestration, and petroleum reservoirs requires understanding a diverse set of geologic properties of the aquifer or reservoir, over a wide range of spatial and temporal scales. We focus on multiphase flow dynamics with wetting (e.g., water) and non-wetting (e.g., gas or oil) fluids, with one invading another. This problem is of general interest in a number of fields and is illustrated here by considering the sweep efficiency of oil during a waterflood. Using a relatively fine-resolution grid throughout a relatively large domain in these simulations and probing the results with advanced scientific visualization tools (Reservoir Visualization Analysis [RVA]/ ParaView software) promote a better understanding of how smaller-scale features affect the aggregate behavior at larger scales. We studied the effects on oil-sweep efficiency of the proportion, hierarchical organization, and connectivity of high-permeability open-framework conglomerate (OFC) cross-sets within the multi-scale stratal architecture found in fluvial deposits. We further analyzed oil production rate, water breakthrough time, and spatial and temporal distribution of residual oil saturation. As expected, the effective permeability of the reservoir exhibits large-scale anisotropy created by the organization of OFC cross-sets within unit bars, and the organization of unit bars within compound- bars. As a result, oil-sweep efficiency critically depends on the direction of the pressure gradient. However, contrary to expectations, the total amount of trapped oil due to the effect of capillary trapping does not depend on the magnitude of the pressure gradient within the examined range. Hence the pressure difference between production and injection wells does not affect sweep efficiency; although the spatial distribution of oil remaining in the reservoir depends on this value. Whether or not clusters of connected OFC span the domain affects only the absolute rate of oil production—not sweep efficiency.

58 GEOSCIENCES↗

Boxfish

Boxfish is a tool for visualizing performance data. It allows users to quickly project performance data gathered from parallel applications onto intuitive domains. It also includes a projection mechanism that automatically finds relations in performance data so the the data can easily be mapped onto non-obviously related domains. For this release, Boxfish allows performance data to be projected onto the nodes and links of a computer network, as well as onto grids or patch-structured applications. This allows a user of the visualization tool to quickly see correlations between performance data and network structure, application data, or communication patterns.

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