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DOE OSTI2024

Visualizing metagenomic and metatranscriptomic data: A comprehensive review

The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

DOECGF 23 Idaho National Laboratory Site Report

Visualization is key to the work we do at Idaho National Laboratory (INL). We support research computing, nuclear science, and educational outreach using both traditional and emerging visualization tools and technologies. In this presentation, we will introduce and summarize INL and its mission, describe some of the visualization resources INL provides, and present example applications from recent years.

99 - GENERAL AND MISCELLANEOUS↗

NASA NTRS2019

A Qualitative Review of Selected Infrared Flow Visualization Processing Techniques: Contrast Enhancement and Frequency Domain Analysis

The deployment and integration of high-sensitivity infrared cameras in a transonic wind tunnel test environment has resulted in a unique capability to image aerodynamic phenomena in real-time. Multi-camera infrared flow visualization data systems are now routinely utilized at the NASA Ames Unitary Plan Wind Tunnel. The small flow-induced temperature gradients on the surface of the wind tunnel test article coupled with the high bit-depth of the infrared camera sensor makes the processing of the image data critically important. An image processing routine must enhance features of interest with minimal artifacts. Additionally, the production wind tunnel test environment demands that these processed images are made available in a real-time, automatic fashion. Therefore, any image processing routine must be computationally economical and enhance the image data with minimal input from a human operator. The following seeks to qualitatively explore selected image processing techniques by assessing their effectiveness to resolve flow features on a wind tunnel test article. A multi-scale contrast enhancement technique is introduced as well as a new implementation of a multi-scale, non-interpolated adaptive histogram equalization. Finally, a novel method is introduced that demonstrates the ability to resolve flow features imaged on bare-steel test articles possessing low emissivity. This method merges frequency domain analysis with contrast enhancement and has the potential to extend the application of infrared flow-visualization within the wind tunnel test environment.

Infrared Imaging↗

NASA NTRSDate not supplied

Evaluation of Markerless Motion Capture for Monitoring Sensorimotor Performance

BACKGROUND Astronauts returning from long-duration exposure to microgravity frequently exhibit alterations in sensorimotor function leading to postural imbalance, impaired locomotion, and operational challenges to manual control. Mission duration and individual responses often influence both the severity of performance decrements and the variability in adaptation timelines. Postflight disruptions during functional tasks are often detected through body-worn inertial measurement unit (IMU) devices. While IMU sensors are relatively compact, the long-term wear may lead to discomfort, displacement of the sensors on the body, and restrictions in movement or crew behavior. Although IMU data offers valuable insights from a research standpoint, interpreting changes in pre- and post-flight measures can be difficult for crew support personnel beyond the research domain, which can hinder the application for medical assessments and rehabilitation. Finally, the availability of inertial sensors in-flight is limited. There is a need for unobtrusive monitoring tools to improve our ability to monitor adaptation following gravitational transitions in various postflight evaluations and rehabilitation settings. Markerless motion capture (MMC) is an evolving unobtrusive technology that builds upon decades of research with marker-based motion capture systems to provide 3D human pose estimation from multiple synchronized 2D camera views using deep learning algorithms. Markerless technology can revolutionize how data is captured pre- and post-flight and potentially in-flight during intravehicular activity by enabling pose estimation of multiple crew members from onboard camera hardware. METHODS The following presents the initial evaluation of a state-of-the-art commercial-off-the-shelf MMC system, Theia Markerless, compared to IMU devices during various ground-based functional tasks and environmental conditions. The featured functional tasks include assessments from Human Research Program (HRP) funded studies such as Sensorimotor Standard Measures and Sensorimotor Assessments. Synchronous data collected using both motion capture and IMUs are analyzed for six male and female subjects of varying anthropometry. The analysis includes limited assessments of clothing, capture volume configurations, and the tool's sensitivity to detecting performance changes after a spaceflight analog centrifuge exposure. The development of visualization tools to enhance the application of the pose estimation output is also presented. RESULTS Initial results demonstrate comparable root mean square error (RMSE) to existing literature evaluating markerless and marker-based motion capture systems. Considering the relative functional range of motion of the cervical spine, normalized error values for the markerless system’s accuracy of the head was 0.032 in pitch, 0.025 in roll, and 0.018 in yaw plane of motion across a subset of functional tasks. The raw RMSE values were 3.49, 2.25, and 2.81 degrees respectively. For the torso, results suggest normalized errors of 0.469 in pitch, 0.191 in roll, and 0.307 in yaw planes of motion and raw RMSE values of 3.52, 1.53, and 3.07 degrees respectively. The data suggests the functional demands of a particular task influences the estimation accuracy of the MMC system where more dynamic motion and cases where subjects are not upright may introduce diminished tracking accuracy. DISCUSSION The following work lays the foundation for future implementations leveraging markerless motion capture to assess the time course of recovery and provide insight for rehabilitation protocols to enhance crew readiness for the resumption of daily activities. These tools offer effective methods for anonymizing sensitive crew data, facilitating numerous applications across research, medical, and rehabilitation groups. Collaborations with the Anthropometry and Biomechanics Facility will provide further comparisons of the Markerless system to a marker-based system. ACKNOWLEDGEMENT</ This work is supported by NASA’s Exploration Systems Development Mission Directorate Mars Campaign Office Crew Health Countermeasures.

Hannah M. Weiss↗

NASA NTRS2019

A Qualitative Investigation of Selected Infrared Flow Visualization Image Processing Techniques

The deployment and integration of high-sensitivity infrared cameras in a transonic wind tunnel testenvironment has resulted in a unique capability to image aerodynamic phenomena in real-time. Multi-camera infrared flow visualization data systems are now routinely utilized at the NASA Ames Unitary Plan Wind Tunnel. The small flow-induced temperature gradients on the surface of the wind tunnel test article coupled with the high bit-depth of the infrared camera sensor makes the processing of the image data critically important. An image processing routine must enhance features of interest with minimal artifacts. Additionally, the production wind tunnel test environment demands that these processed images are made available in a real-time, automatic fashion. Therefore, any image processing routine must be computationally economical and enhance the image data with minimal input from a human operator. The following seeks to qualitatively explore selected image processing techniques by assessing their effectiveness to resolve flow features on a wind tunnel test article. A multi-scale contrast enhancement technique is discussed as well as a new implementation of a multi-scale, non-interpolated adaptive histogram equalization. Finally, a novel method is introduced that demonstrates the ability to resolve flow features imaged on bare-steel test articles possessing low emissivity.This method makes use of dynamic mode decomposition and discrete-time filtering to separate the background reflections that dominate low emissivity surfaces from the aerodynamic driven surface temperature gradients.This process will be shown to resolve the onset of boundary layer transition on a bare metal wing as well as identify and resolve hidden features in the image data. While the implementation of this technique is very preliminary it demonstrates the potential to extend the application of infrared flow-visualization within the wind tunnel test environment.

Image Processeing↗

NASA NTRS1992

A fuzzy measure approach to motion frame analysis for scene detection

This paper addresses a solution to the problem of scene estimation of motion video data in the fuzzy set theoretic framework. Using fuzzy image feature extractors, a new algorithm is developed to compute the change of information in each of two successive frames to classify scenes. This classification process of raw input visual data can be used to establish structure for correlation. The algorithm attempts to fulfill the need for nonlinear, frame-accurate access to video data for applications such as video editing and visual document archival/retrieval systems in multimedia environments.

Leigh, Albert B.↗

DOE OSTI2024

2024 INL Site Report

97 - MATHEMATICS AND COMPUTING↗

NASA NTRS2012

SERVIR Science Applications for Capacity Building

SERVIR is a regional visualization and monitoring system using Earth observations to support environmental management, climate adaptation, and disaster response in developing countries. SERVIR is jointly sponsored by NASA and the U.S. Agency for International Development (USAID). SERVIR has been instrumental in development of science applications to support the decision-making and capacity building in the developing countries with the help of SERVIR Hubs. In 2011, NASA Research Opportunities in Space and Earth Sciences (ROSES) included a call for proposals to form SERVIR Applied Sciences Team (SERVIR AST) under Applied Sciences Capacity Building Program. Eleven proposals were selected, the Principal Investigators of which comprise the core of the SERVIR AST. The expertise on the Team span several societal benefit areas including agriculture, disasters, public health and air quality, water, climate and terrestrial carbon assessments. This presentation will cover the existing SERVIR science applications, capacity building components, overview of SERVIR AST projects, and anticipated impacts.

Limaye, Ashutosh↗

NASA NTRS1966

Study made of application of stereoscopic display system to analog computer simulation

Stereoscopic visual display system provides both a qualitative and measurable presentation for functions of several variables. A primary application of such a display system is in analog computer simulation of sets of differential equations.

Kennel, H. F.↗

NASA NTRS1992

Automated digital motion-video abstraction - A fuzzy measure approach

This paper addresses a solution to the problem of scene estimation of motion video data in the fuzzy set theoretic framework. Using fuzzy image feature extractors, a new algorithm is developed to compute the change of information in each of two successive frames to classify scenes. This classification process of raw input visual data can be used to establish structure for correlation. The algorithm attempts to fulfill the need for non-linear, frame-accurate access to video data for applications such as video editing and visual document archival/retrieval systems in multimedia environments.

Leigh, Albert B.↗

DOE OSTI2019

Gibbs Energy Minimization Model for Solvent Extraction with Application to Rare-Earths Recovery

The emergence of technologies in which rare-earth elements provide critical functionality has increased the demand for these materials, with important implications for supply security. Recycling provides an option for mitigating supply risk and for creating economic value from the resale of recovered materials. While solvent extraction is a proven technology for rare-earth recovery and separation, its application often requires extensive trial-and-error experimentation to estimate parameter values and determine experimental design configurations. We describe a modeling strategy based on Gibbs energy minimization that incorporates parameter estimation for required thermodynamic properties as well as process design for solvent extraction and illustrate its applicability to rare earths separation. Visualization analysis during parameter estimation revealed a linear relationship between the standard enthalpies of the extractant and respective organo-metal complexes, analogous to the additivity principle for predicting molar volumes of organic compounds. Establishing this relationship reduced the size of the parameter estimation problem and yielded good agreement between model predictions and reported equilibrium extraction data, validating the property estimates for the organic phase species. Design exploration and optimization results map the space of feasible solvent extraction column configurations and identify the set of optimal design parameter values that meet recovery and purity targets.

Critical materials↗

DOE OSTI2025

MTUQ: a framework for estimating moment tensors, point forces, and their uncertainties

SUMMARY We introduce MTUQ, an open-source Python package for seismic source estimation and uncertainty quantification, emphasizing flexibility and operational scalability. MTUQ provides MPI-parallelized grid search and global optimization capabilities, compatibility with 1-D and 3-D Green’s function database formats, customizable data processing, C-accelerated waveform and first-motion polarity misfit functions, and utilities for plotting seismic waveforms and visualizing misfit and likelihood surfaces. Applicability to a range of full- and constrained-moment tensor, point force, and centroid inversion problems is possible via a documented application programming interface, accompanied by example scripts and integration tests. We demonstrate the software using three different types of seismic events: (1) a 2009 intraslab earthquake near Anchorage, Alaska; (2) an episode of the 2021 Barry Arm landslide in Alaska; and (3) the 2017 Democratic People’s Republic of Korea underground nuclear test. With these events, we illustrate the well-known complementary character of body waves, surface waves, and polarities for constraining source parameters. We also convey the distinct misfit patterns that arise from each individual data type, the importance of uncertainty quantification for detecting multimodal or otherwise poorly constrained solutions, and the software’s flexible, modular design.

58 GEOSCIENCES↗

DOE OSTI2024

GRid Analysis and Visualization Interface (GRAVI) [SWR-24-16]

GRAVI (GRid Analysis and Visualization Interface) is a web application for viewing and analyzing nodal Production Cost Model (PCM) and Capacity Expansion Model (CEM) simulations. The web application provides the ability to animate geospatially coupled timeseries data in an agnostic way regardless of the underlying simulation tool used to generate the data. GRAVI also provides capabilities to animate non-geospatial data relevant to a PCM or CEM model. Furthermore, this web application can be tailored as an real-time operational tool to better understand a live grid.

Webb, Micah↗

DOE OSTI2025

rmon (Resource monitor) [SWR-24-128]

The resource monitor application provides monitoring, collection, and visualization of resource utilization in compute nodes. This package contains utilities to monitor system resource utilization (CPU, memory, disk, network). Here are the ways you can use it: -Monitor resource utilization for a compute node for a given set of resource types and process IDs. -Start a process and monitor its resource utilization. -Monitor resource utilization for a compute node asynchronously with the ability to dynamically change the resource types and process IDs being monitored. -Produce JSON reports of aggregated metrics. -Produce interactive HTML plots of the statistics.

Thom, Daniel [National Renewable Energy Laboratory↗

DOE OSTI2023

Model data for numerical evaluation of photosensitive tracers as a strategy for separating surface and subsurface transient storage in streams

This model-data archive pertains to a study aimed at the numerical evaluation of the photosensitive tracers as a potential strategy for separating the effects of surface and hyporheic storage zones (SSZs and HSZs, respectively). Separating effects of SSZ and HSZ are important for accurately representing stream function as HSZs and SSZs expose solutes to significantly different biogeochemical conditions. We perform numerical experiments using a multiscale reactive transport model for stream corridors implemented in ATS code, which allows for representing multiple storage zones with their respective travel time distributions and biogeochemistry. For each of the numerical experiment, we provide in this model-data archive python wrapper to drive ATS (forward_model.py), synthetic observation (synthetic_btc.py, BTC_observed.csv), forward model files including ATS input (multiscale_transport.tpl), PFLOTRAN inputs (reactions_channel.tpl, reactions_hz.tpl, reactions_sz.tpl), MCMC (mcmc_run.py), predictive uncertainty (pred_uncert.py, BTCs_simulated_day.csv, BTCs_simulated_night.csv), MCMC outputs (tracer_test_GR.npy, tracer_test_logps.npy, tracer_test_parameters.npy) and Jupyter notebook for post-processing and visualization (post-processing.ipynb). For the denitrification application, ATS input file (denitrification_multisubgrid.tpl), PFLOTRAN input files (denitrification_channel.in, denitrification_hz.in), predictive uncertainty (pred_uncert_denitrification.py, BTCs_simulated_DO.csv, BTCs_simulated_DOC.csv, BTCs_simulated_Nitrate.csv).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

WELLS Database

The Wellbore Exploration and Location Logistic System (WELLS) is a living national wellbore database - created and maintained by the National Energy Technology Laboratory (NETL). This resource contains more than seven million public wellbore records from state, federal, and tribal resources. Sourced from over 65 authoritative, yet disparate resources, the WELLS Database combines and synthesizes well data from oil, gas, underground injection, research, geothermal, geotechnical, groundwater and other types of wells in a single, unified system. This resource can be explored and visualized through the WELLS Interactive Application, also on EDX: https://edx.netl.doe.gov/dataset/wells-interactive-application The WELLS Database (formerly titled CO2-Locate) is an integrated national well dataset, representing open-source wellbore data from disparate state, tribal, and federal entities. The database provides publicly available well header data with key attributes such as well age, depth, and status. The database contains a fully integrated CSV file with all values in numerical columns, such as depth, converted into numbers. This version has a NETL derived API (American Petroleum Institute) number column and has been handled for redundancies, resulting in one record for every unique API number. The database also contains a fully integrated CSV file, where all original data are kept as text values. Additionally, the database includes a shapefile containing key attributes and coordinates from the integrated dataset, reformatted public wells CSV files, and a proprietary well density grid shapefile. Notes for consideration: The WELLS Database will be updated periodically with new datasets and information. A field dictionary with field (i.e., attribute) coverage across acquired public well resources, and the resulting integrated public well datasets are available in the spreadsheet, WELLS_Field_Dictionary.xlsx. Summary layers provided in this database are derived from proprietary layers and do not always contain key features (status, type, true vertical depth, or spud year) and therefore might not be shown when data are queried for those features.

AS↗

DOE OSTI2024

gcamfaostat: An R package to prepare, process, and synthesize FAOSTAT data for global agroeconomic and multisector dynamic modeling

The gcamfaostat R package is designed for the preparation, processing, and synthesis of the Food and Agriculture Organization (FAO) Statistics (FAOSTAT) agroeconomic data. The primary purpose is to facilitate FAOSTAT data use in global economic and multisector dynamic models while ensuring transparency, traceability, and reproducibility. Here, we provide an overview of the development of gcamfaostat (v1.0) and demonstrate its capabilities in generating and maintaining agroeconomic data required for the Global Change Analysis Model (GCAM). Our initiative seeks to enhance the quality and accessibility of data for the global agroeconomic modeling community, with the aim of fostering more robust and harmonized outcomes in a collaborative, efficient, and open-source framework. One of the important features of the package is the possibility to construct the FAO Food Balance Sheets at the disaggregated commodity level (with over 500 commodities), which provides a comprehensive and detailed data input for a variety of analytical and modeling applications. The processed data and visualizations offered by gcamfaostat can also be valuable to a broader audience interested in gaining insights into the intricacies of global agriculture.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

CO 2 Storage Site Screening Platform Development and CO 2 Storage Resource Analysis in SECARB Offshore Reservoirs Using SAS Viya

A major goal of the SECARB Offshore Partnership (DE-FE0031557) is to screen deep saline aquifers and hydrocarbon reservoirs in the central Gulf of Mexico for CO 2 sequestration and CO 2 -enhanced oil and gas recovery (EOR/EGR) and estimate the corresponding CO 2 storage resources for select reservoirs. CO 2 storage potential associated with offshore CO 2 -EOR is considerable and likely represents “low hanging fruit” for near-term CO 2 storage given the in-place infrastructure in the region. It is for these reasons that this assessment focuses on oil and gas fields. To this end, three major objectives have been completed and include (1) managing geological data derived from different sources, (2) building a reservoir screening platform for CO 2 storage, and (3) ranking the reservoirs based on the estimated CO 2 storage resources. The SAS ® Viya platform was used for data management and analytics. The Viya platform is a cloud service platform that provides data integration, data management, quick analytics, data visualization, machine learning functions, and application programming interfaces (APIs) for multi-programming languages. Different sources of data containing geologic information, reservoir properties, and EOR/EGR information were collected, cleaned, formatted, and loaded into the SAS ® Viya platform for evaluation. The major geological characteristics of both shelf and deep-water areas of the central Gulf were examined and compared to define the appropriate reservoir screening criteria. Next, a CO 2 storage site screening system was built in the SAS ® Viya platform with the pre-defined criteria. Finally, the CO 2 storage resources of the screened reservoirs were calculated and reported at the BOEM field level to identify fields with the highest estimated CO 2 storage resource. The fields with the largest total estimated CO 2 storage resource are located in the Mississippi Canyon protraction area. Due to proximity to the Mississippi Delta (indicative of less infrastructure) and large estimated CO 2 storage resources, future development activities may wish to focus efforts in the Mississippi Canyon protraction area.

02 PETROLEUM↗