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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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DOE OSTI2019

Development and operational experience of the web based application to collect, manage, and release the alignment and calibration configurations for data processing at CMS

The alignment and calibration workflows at the Compact Muon Solenoid (CMS) experiment are fundamental to provide a high quality physics data and to maintain the design performance of the experiment. To facilitate the operational efforts required by the experiment, the alignment and calibration team has developed and deployed a set of web-based applications to search, navigate and prepare a consistent set of calibrations to be consumed in reconstruction of data for physics, accessible through the Condition DB Browser. The Condition DB Browser hosts also various data management tools, including a visualization tool that allows to easily inspect alignment an calibration contents, an user-defined notification agent for delivering updates on modification to the database, a logging service for the user and the automatic online-to-offline condition uploads. In this paper we report on the operational experience of this web application from 2017 data taking, with focus on new features and tools incorporated during this period.

Md, Hasbuddin↗

DOE OSTI2026

VirJenDB: a FAIR (meta)data and bioinformatics platform for all viruses

High-throughput sequencing has generated an unprecedented volume of data. However, researcher-submitted data in repositories requires extensive curation and quality control for reuse. These tasks are hindered by the multiplicity of repositories, the sheer volume of the data, and the complexity of virus (meta)data curation. To address these challenges, VirJenDB offers a user-friendly platform to facilitate versioned, community-driven curation, and ontology development. Virus sequences were ingested from 16 sources, including ~200 fields of metadata or standards, covering taxonomy, sample, and host information. Up to 85 metadata fields have undergone at least one round of curation, and are linked to 15.4 million virus sequences, with 88 % from those infecting eukaryotes and the remaining infecting prokaryotes. Subsets were created, including a novel collection of 0.91 million viral operational taxonomic unit (vOTU) sequences across all viruses, while keeping the original sequences from each vOTU to facilitate downstream analyses, e.g. sequence variation. The VirJenDB web portal (https://www.virjendb.org) provides HTTPS and Application Programming Interface (API) access to the sequence datasets and metadata, offering a search engine, filtering, download, visualizations, and documentation. VirJenDB aims to connect the phage and eukaryotic virus research communities by supporting webtool integration, meta-analyses, and metadata schema extensions.

Saghaei, Shahram↗

DOE OSTI2017

ProteoSign: an end-user online differential proteomics statistical analysis platform

Profiling of proteome dynamics is crucial for understanding cellular behavior in response to intrinsic and extrinsic stimuli and maintenance of homeostasis. Over the last 20 years, mass spectrometry (MS) has emerged as the most powerful tool for large-scale identification and characterization of proteins. Bottom-up proteomics, the most common MS-based proteomics approach, has always been challenging in terms of data management, processing, analysis and visualization, with modern instruments capable of producing several gigabytes of data out of a single experiment. Here, we present ProteoSign, a freely available web application, dedicated in allowing users to perform proteomics differential expression/abundance analysis in a userfriendly and self-explanatory way. Although several non-commercial standalone tools have been developed for post-quantification statistical analysis of proteomics data, most of them are not end-user appealing as they often require very stringent installation of programming environments, third-party software packages and sometimes further scripting or computer programming. To avoid this bottleneck, we have developed a user-friendly software platform accessible via a web interface in order to enable proteomics laboratories and core facilities to statistically analyse quantitative proteomics data sets in a resource-efficient manner. ProteoSign is available at http://bioinformatics.med.uoc.gr/ProteoSign and the source code at https://github.com/yorgodillo/ ProteoSign.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

GenomeDepot v1.0

GenomeDepot is a web-based platform for annotation, management, and comparative analysis of microbial genomic sequences and associated data including ortholog families, protein domains, operons, regulatory interactions, strain taxonomy, and sample metadata. GenomeDepot supports rapid creation of web-sites for user-defined genome collections that include bioinformatic tools for interactive genome browsing, BLAST search, annotation search, comparative genomic neighborhood visualization, and sequence download. Gene function annotations are generated by a customizable annotation pipeline. The pipeline runs annotation tools in Conda environments and can be easily extended with additional user-specified tools.

Kazakov, Alexey [Lawrence Berkeley National Labora↗

DOE OSTI2018

Global Oil & Gas Infrastructure Features Database EDX Spatial Web Map

This submission offers a link to a web mapping application hosted instance of the Global Oil & Gas Features Database (GOGI), via EDX Spatial. This offers users with the ability to visualize, interact, and create maps with data of their choice, as well as download specific attributes or fields of view from the database. This data can also be downloaded as a File Geodatabse from EDX at https://edx.netl.doe.gov/dataset/global-oil-gas-features-database. Access the technical report describing how this database was produced using the following link: https://edx.netl.doe.gov/dataset/development-of-an-open-global-oil-and-gas-infrastructure-inventory-and-geodatabase” This data was developed using a combination of big data computing, custom search and data integration algorithms, and expert driven search to collect open oil and gas data resources worldwide. This approach identified over 380 data sets and integrated more than 4.8 million features into the GOGI database. Acknowledgements: This work was funded under the Climate and Clean Air Coalition (CCAC) Oil and Gas Methane Science Studies. The studies are managed by United Nations Environment in collaboration with the Office of the Chief Scientist, Steven Hamburg of the Environmental Defense Fund. Funding was provided by the Environmental Defense Fund, OGCI Companies (Shell, BP, ENI, Petrobras, Repsol, Total, Equinor, CNPC, Saudi Aramco, Exxon, Oxy, Chevron, Pemex) and CCAC.

gas↗

DOE OSTI2015

Evolving the Land Information System into a Cloud Computing Service

The Land Information System (LIS) was developed to use advanced flexible land surface modeling and data assimilation frameworks to integrate extremely large satellite- and ground-based observations with advanced land surface models to produce continuous high-resolution fields of land surface states and fluxes. The resulting fields are extremely useful for drought and flood assessment, agricultural planning, disaster management, weather and climate forecasting, water resources assessment, and the like. We envisioned transforming the LIS modeling system into a scientific cloud computing-aware web and data service that would allow clients to easily setup and configure for use in addressing large water management issues. The focus of this Phase 1 project was to determine the scientific, technical, commercial merit and feasibility of the proposed LIS-cloud innovations that are currently barriers to broad LIS applicability. We (a) quantified the barriers to broad LIS utility and commercialization (high performance computing, big data, user interface, and licensing issues); (b) designed the proposed LIS-cloud web service, model-data interface, database services, and user interfaces; (c) constructed a prototype LIS user interface including abstractions for simulation control, visualization, and data interaction, (d) used the prototype to conduct a market analysis and survey to determine potential market size and competition, (e) identified LIS software licensing and copyright limitations and developed solutions, and (f) developed a business plan for development and marketing of the LIS-cloud innovation. While some significant feasibility issues were found in the LIS licensing, overall a high degree of LIS-cloud technical feasibility was found.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2014

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↗

DOE OSTI2022

The ParFlow Sandtank: An interactive educational tool making invisible groundwater visible

Physical aquifer models are a highly effective teaching tool for hydrology education, however they come with inherent limitations that include the high cost to purchase, the static configuration of the model materials, the time required to visualize hydrogeological phenomena, and the effort to reset and clean them over time. To address these and other limitations, we have developed an interactive computer simulation of a physical aquifer model called the ParFlow Sandtank. In this gamified interface, users run the simulation using a familiar web-app like interface with sliders and buttons while learning real hydrologic concepts. Our user interface allows participants to dive into the world of hydrology, understanding assumptions about model parameters such as hydraulic conductivity, making decisions about inputs to groundwater aquifer systems such as pumping rates, visualizing outputs such as stream flow, transport, and saturation, and exploring various factors that impact real environmental systems such as climate change. The ParFlow Sandtank has already been used in a variety of educational settings with more than 9,000 users per year, and we feel this emerging educational tool can be used broadly in educational environments and can be scaled-up to provide greater accessibility for students and educators. Here we present the capabilities and workflow of the ParFlow Sandtank, two use cases, and additional tools and custom templates that have been developed to support and enhance the reach of the ParFlow Sandtank.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2019

Visualization of Simulation and TAP Interaction

The Temporal Analysis of Products (TAP) Reactor applies transient kinetics to analyze sophisticated chemical reaction mechanisms, rapidly changing temperature, flow rate, pressure or concentration and then monitoring the system’s time dependent response. A simulation tool exists for the TAP reactor, but it requires a visualization platform to interface effectively with researchers. This graphical user interface remedies this problem, fixing many of the difficulties caused by users interacting directly with the simulation code by providing an intuitive web application that satisfies the simulation input parameters for fast generation of data. This tool will ensure robust and repeatable simulation results, expedite the data generating process and enhance the overall ability of TAP to produce significant findings.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Closed Loop Geothermal Working Group: GeoCLUSTER App, Subsurface Simulation Results, and Publications

To better understand the heat production, electricity generation performance, and economic viability of closed-loop geothermal systems in hot-dry rock, the Closed-Loop Geothermal Working Group -- a consortium of several national labs and academic institutions has tabulated time-dependent numerical solutions and levelized cost results of two popular closed-loop heat exchanger designs (u-tube and co-axial). The heat exchanger designs were evaluated for two working fluids (water and supercritical CO2) while varying seven continuous independent parameters of interest (mass flow rate, vertical depth, horizontal extent, borehole diameter, formation gradient, formation conductivity, and injection temperature). The corresponding numerical solutions (approximately 1.2 million per heat exchanger design) are stored as multi-dimensional HDF5 datasets and can be queried at off-grid points using multi-dimensional linear interpolation. A Python script was developed to query this database and estimate time-dependent electricity generation using an organic Rankine cycle (for water) or direct turbine expansion cycle (for CO2) and perform a cost assessment. This document aims to give an overview of the HDF5 database file and highlights how to read, visualize, and query quantities of interest (e.g., levelized cost of electricity, levelized cost of heat) using the accompanying Python scripts. Details regarding the capital, operation, and maintenance and levelized cost calculation using the techno-economic analysis script are provided. This data submission will contain results from the Closed Loop Geothermal Working Group study that are within the public domain, including publications, simulation results, databases, and computer codes. GeoCLUSTER is a Python-based web application created using Dash, an open-source framework built on top of Flask that streamlines the building of data dashboards. GeoCLUSTER provides users with a collection of interactive methods for streamlining the exploration and visualization of an HDF5 dataset. The GeoCluster app and database are contained in the compressed file geocluster_vx.zip, where the "x" refers to the version number. For example, geocluster_v1.zip is Version 1 of the app. This zip file also contains installation instructions. **To use the GeoCLUSTER app in the cloud, click the link to "GeoCLUSTER on AWS" in the Resources section below. To use the GeoCLUSTER app locally, download the geocluster_vx.zip to your computer and uncompress this file. When uncompressed this file comprises two directories and the geocluster_installation.pdf file. The geo-data app contains the HDF5 database in condensed format, and the GeoCLUSTER directory contains the GeoCLUSTER app in the subdirectory dash_app, as app.py. The geocluster_installation.pdf file provides instructions on installing Python, the needed Python modules, and then executing the app.

15 GEOTHERMAL ENERGY↗

DOE OSTI2018

Remote visual analysis of large turbulence databases at multiple scales

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 methods 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.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

Gamification and Visualization of Sensor Data Analysis in Research Buildings

The use of video game elements in non-gaming systems, or gamification , has potential value in transforming data analysis. Our study focused on creating a web-based videogame that models two physical test buildings, each of which contains hundreds of sensors. After the application renders the models, the player can walk through the environments and interact with the virtual representations of the sensors inside. Rather than trudging through a database with textual commands and screens full of data, the user can (virtually) walk up to a sensor and view its data graphically. But these features only scratch the surface of what is possible using our new gamification approach. We anticipate being able to show that recent progress in game design techniques and capacities can contribute to the field of analysis through gamification. The net result could be more stimulating, intuitive, user-friendly interfaces, as well as potentially more informative and insightful applications.

Stone, Jackson A↗

DOE OSTI2017

P-MartCancer–Interactive Online Software to Enable Analysis of Shotgun Cancer Proteomic Datasets

P-MartCancer is a new interactive web-based software environment that enables biomedical and biological scientists to perform in-depth analyses of global proteomics data without requiring direct interaction with the data or with statistical software. P-MartCancer offers a series of statistical modules associated with quality assessment, peptide and protein statistics, protein quantification and exploratory data analyses driven by the user via customized workflows and interactive visualization. Currently, P-MartCancer offers access to multiple cancer proteomic datasets generated through the Clinical Proteomics Tumor Analysis Consortium (CPTAC) at the peptide, gene and protein levels. P-MartCancer is deployed using Azure technologies (http://pmart.labworks.org/cptac.html), the web-service is alternatively available via Docker Hub (https://hub.docker.com/r/pnnl/pmart-web/) and many statistical functions can be utilized directly from an R package available on GitHub (https://github.com/pmartR).

Webb-Robertson, Bobbie-Jo M.↗

DOE OSTI2023

Toward a Smart Metaverse City: Immersive Realism and 3D Visualization of Digital Twin Cities

Metaverse and its related extended reality technologies can enable immersive, realistic, and participatory visualization of 3D data, and their use and the potential within a smart city can be effective for supporting urban research and urban operations management. This book chapter describes a vision for prototyping a “Smart Metaverse City” to combine the unique advantage of the Metaverse technology with the two-way connectivity of a digital twin city application. This synergy aims to create a virtual environment for immersive geovisualization to help researchers and the public understand the complex urban system through science-based and data-driven approaches. This book chapter selectively reviews past technological and paradigm advancements for collecting, analyzing, and visualizing 3D urban big data. Then we present a prototyping Geographic Information System (GIS) framework, together with some relevant data sources and open-source web technologies, to help researchers create a smart Metaverse city. We demonstrate our vision and discuss its application opportunities through a real-world example, a digital twin city developed at the Oak Ridge National Laboratory, to facilitate participatory, smart, and sustainable campus management.

Xu, Haowen↗

DOE OSTI2025

bmdrc: Python package for quantifying phenotypes from chemical exposures with benchmark dose modeling

Though chemical exposures are known to potentially have negative impacts on health, including contributing to chronic diseases such as cancer, the quantitative contribution of risk is not fully understood for every chemical. A commonly used approach to quantify levels of risk is to measure the proportion of organisms (such as a total number of zebrafish on a plate or mice in a cage) with abnormal behavioral responses or morphology at increasing concentrations of chemical exposure. A particular challenge with processing the proportional data from these assays is the appropriate estimation of chemical concentration levels that result in malformations or acute toxicity, as these values typically vary between experimental measurements. The recommended approach by the Environmental Protection Agency (EPA) is to fit benchmark dose curves with specific filters and model fitting steps, which are crucial to properly processing the proportional data. Several tools exist for the fitting of benchmark dose response curves, but none are standalone Python libraries built to process both morphological and behavioral data as proportions with all the EPA recommended filters, filter parameters, models, and model parameters. Thus, here we present the benchmark dose response curve (bmdrc) Python library, which was built to closely follow these EPA guidelines with helpful visualizations of filters and fitted model curves, and reports for reproducibility purposes. bmdrc is open-source and has demonstrated utility as a support package to an existing web portal for information on chemicals (https://srp.pnnl.gov). Our package will support any toxicology analysis where the response is a proportional value at increasing levels of a concentration of a chemical or chemical mixture.

Superfund↗

DOE OSTI2024

USAID Haiti Training Session #1: Engage Orientation [Slides]

Welcome to Engage! Engage is a capacity expansion modeling tool supported by the National Renewable Energy Laboratory and based on the Calliope open-source capacity expansion model developed by the ETH Zurich University, maintained at the TU Delft University. Engage is an accessible (free, open-access, web-hosted) and flexible web-based energy system planning application for rapid multiple-energy-form energy system scenario exploration. Its cloud-based, collaborator-sharable data model, intuitive interface and visualization capabilities facilitate collaboration and communication among teams, with experts, and among diverse stakeholder groups exploring energy system implications at from district to national-scale models. This training series was developed under USAID to empower Haitian stakeholders to explore modeling scenarios in Engage to develop a Haiti Energy Master Plan. This training series includes a general overview of how Engage works along with tailored exercises that target Haiti's specific energy needs, such as modeling the capacity expansion of the bulk power system, fuel scarcity challenges, the development of microgrids, and the economic viability of transmission strategies. See NREL/PR-7A40-89366 for the French translation of this document.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2024

USAID Haiti Training Session #2: Introduction to Engage [Slides]

Welcome to Engage! Engage is a capacity expansion modeling tool supported by the National Renewable Energy Laboratory and based on the Calliope open-source capacity expansion model developed by the ETH Zurich University, maintained at the TU Delft University. Engage is an accessible (free, open-access, web-hosted) and flexible web-based energy system planning application for rapid multiple-energy-form energy system scenario exploration. Its cloud-based, collaborator-sharable data model, intuitive interface and visualization capabilities facilitate collaboration and communication among teams, with experts, and among diverse stakeholder groups exploring energy system implications from district to national-scale models. This training series was developed under USAID to empower Haitian stakeholders to explore modeling scenarios in Engage to develop a Haiti Energy Master Plan. This training series includes a general overview of how Engage works along with tailored exercises that target Haiti's specific energy needs, such as modeling the capacity expansion of the bulk power system, fuel scarcity challenges, the development of microgrids, and the economic viability of transmission strategies. See NREL/PR-7A40-89369 for the French translation of this document.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2024

USAID Haiti Training Session #3: Capacity Expansion [Slides]

Welcome to Engage! Engage is a capacity expansion modeling tool supported by the National Renewable Energy Laboratory and based on the Calliope open-source capacity expansion model developed by the ETH Zurich University, maintained at the TU Delft University. Engage is an accessible (free, open-access, web-hosted) and flexible web-based energy system planning application for rapid multiple-energy-form energy system scenario exploration. Its cloud-based, collaborator-sharable data model, intuitive interface and visualization capabilities facilitate collaboration and communication among teams, with experts, and among diverse stakeholder groups exploring energy system implications from district to national-scale models. This training series was developed under USAID to empower Haitian stakeholders to explore modeling scenarios in Engage to develop a Haiti Energy Master Plan. This training series includes a general overview of how Engage works along with tailored exercises that target Haiti's specific energy needs, such as modeling the capacity expansion of the bulk power system, fuel scarcity challenges, the development of microgrids, and the economic viability of transmission strategies. See NREL/PR-7A40-89365 for the French translation of this document.

24 POWER TRANSMISSION AND DISTRIBUTION↗