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Lab Homes

This dataset includes processed data from the Lab Homes (LH) Test Facility located on the PNNL campus in Richland, WA. This a set of 2 identical homes that allow for the side-by-side comparison/performance evaluation of different technologies under the same weather at any given time. The dataset spans December 6, 2021 to December 27, 2021 and represents a series of tests performed; calibration, set-point excitation, pre-heating, free-floating and warm up. The measurements correspond to whole building electrical power, HVAC energy use, water heating, appliances and lighting, as well as space temperatures, space humidity, window glass surface temperatures, through glass solar radiation, and meterological data from an onsite meteorological weather station. In addition to the measurements, a metadata .json file, a .ttl file to visualize the data as per BRICK schema, and a detailed .pdf description of the dataset are also provided.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

The Integration and Mapping of an Open-Source National Well Resource to Inform Geologic Carbon Storage Site Selection and Risk Prevention: The CO2-Locate Database

Geologic carbon storage (GCS) offers a way to capture and permanently store CO₂ from fossil fuel operations in underground geologic structures, aiding in the transition to a carbon-neutral energy economy. However, CO₂ injection sites can experience gas leakage through existing wells that penetrate storage reservoirs, making knowledge of well locations and characteristics crucial for permitting, infrastructure reusability, and risk assessment in GCS. Currently, public wellbore data from state, federal, and tribal entities are inconsistent and fragmented, with gaps and redundancies. To address this, the National Energy Technology Laboratory (NETL) developed CO2-Locate, an open-source, geospatial database and online application. CO2-Locate integrates over 50 data sources from federal, state, and tribal entities, creating a standardized national well database. Funded by the Bipartisan Infrastructure Law, the database is publicly available through the Energy Data eXchange (EDX) and viewable via the CO2-Locate web mapping application. This tool allows users to query, filter, and visualize well data to support GCS planning, permitting, and risk assessments. This presentation covers the methods used to create CO2-Locate, including data acquisition, processing, attribute mapping, and integration, much of which is automated for future updates. The web mapping application and its role in GCS site selection will also be discussed.

Tetteh, Daniel A.↗

Lake-Effect Snowstorm Events and Associated Snowfall Totals Integrated from NOAA Storm Reports, ERA5, and HRRR for the Laurentian Great Lakes (1997–2024)

Lake-effect snowstorms are localized, impactful winter weather phenomena that can generate substantial snowfall totals and pose significant challenges for forecasting, transportation, and regional infrastructure. To support the analysis and modeling of these events, this dataset compiles observational reports of lake-effect snowstorms alongside corresponding snowfall estimates derived from gridded atmospheric datasets. The observational component of the data originates from the National Weather Service (NWS) winter storm report, subset to lake-effect snow event type, covering 1997–2024. For each lake-effect snow event, this data provides the impacted county, event start and end datetimes at an hourly resolution, as well as relevant storm narratives. The complementary reanalysis-derived data is sourced from European Centre for Medium-Range Weather Forecasts (ECMWF) Reanalysis 5 (ERA5) and High-Resolution Rapid Refresh (HRRR) gridded data. For both gridded datasets, the maximum total snowfall (in units mm) was extracted, constrained by the county and datetimes specified by the observational report. ERA5 data covers the entire observational period (1997–2024), whereas HRRR data is only available from November 2016 – December 2024. Three CSV files are provided here: (1) the observational lake-effect snow event report, (2) ERA5 maximum snowfall detections for each event, and (3) HRRR maximum snowfall detections for each event. Relevant data from the observational files, such as impacted state and county, event datetimes, and event IDs, were included for convenience. Users can inspect and visualize the data using tools such as Microsoft Excel and Python pandas/matplotlib packages. This dataset may support a variety of applications, including climatological analyses of lake-effect snowfall, evaluation of snowfall representation in atmospheric datasets and numerical weather prediction models, and the development of machine learning approaches for detecting or predicting lake-effect snowfall events.

EARTH SCIENCE > ATMOSPHERE > PRECIPITATION > SOLID↗

BLDAP Intro to Python/Data Science Curriculum v1

The Github repository contains the Jupyter notebooks for the intro to Python / Data Science course for Berkeley Lab Director's Apprenticeship Program (BLDAP). This course is designed for students with little to no experience in coding to learn skills in Python necessary for data science. Students utilize Jupyter notebooks throughout the course. The overall goal is for students to learn how to use Python to clean, analyze, and visualize large data sets in order to communicate effectively their conclusions about the data set. Students apply the skills they learned on actual data sets provided by researchers in Berkeley Lab.

Hales, Laurel [Lawrence Berkeley National Laborato↗

Ionospheric Disturbances in GNSS TEC Data: SpaceX Falcon 9 Deorbit Maneuvers Over CONUS in April–May 2024

Traveling ionospheric disturbances (TIDs) driven by a large number of internal and external sources are detectable with dense networks of ground‐based Global Navigation Satellite System (GNSS) receivers' measurements of total electron content (TEC). We present the newly developed System for Rapid Analysis of Ionospheric Dynamics (S‐RAID), providing data and visual GNSS TEC products of TIDs of periods ~2–120 min and horizontal resolution up to tens of kilometers for years 2017–2024. The S‐RAID data reveal myriad natural and anthropogenic TIDs from meteorology and space weather, and from human spaceflight activities. In this report, we focus on new prominent disturbances found during SpaceX second stage deorbit maneuvers in April–May 2024. Signatures include waves emanating from the Falcon's trajectory above California and depletions following its deorbit and passage over Arizona. These findings suggest further opportunities to detect and quantify small‐scale events in the ionosphere as well as to understand the responses of the atmosphere‐ionosphere system to known inputs.

58 GEOSCIENCES↗

Towards Autonomous Experiments by Connecting High Performance Microscopy with High Performance Computing

The digitization of controls, data, and analysis in microscopy is bringing the idea of autonomous microscopes closer to reality than ever before. Automated transmission electron microscopy (TEM) is already fairly routine for some experiments the only require simple repetitive tasks such as imaging biological macromolecules for single particle cryoEM [1], tilt series for electron tomography [2], and movies for crystallography [3]. The vast majority of TEM experiments are conducted completely by human operators who choose the regions of interest, optimize experimental parameters, and make decisions about data quality visually during an experiment. The field is still a long way from having completely autonomous TEMs that can adapt to sample difficulties and tune experimental parameters based on data quality and desired experimental outcomes. Part of the issue is the lack of capability for feeding information learned from on-line, live data analysis back into the on-going experiment [4]. Furthermore, this presentation will discuss current capabilities for large scale data reduction and analysis using high performance computing (i.e. supercomputing) and progress towards developing a true feed-back loop that places data analysis and theory in the experimental loop.

97 MATHEMATICS AND COMPUTING↗

Web-Based Tools for Data-Informed Remedy Optimization: Software Theory and User Guide

This report documents the development and application of two web-based decision-support tools for pump-and-treat (P&T) groundwater remediation systems: PTOLEMY (Pump-and-Treat Optimized Location Evaluation to Maximize Yields) and OPTIMA (Optimization for Pump-and-Treat Implementation, Management, & Assessment). These tools enhance remedy design and management by leveraging advanced computational methods – specifically deep learning and multi-objective optimization – within a user-friendly platform. By integrating data-driven models with established hydrogeological knowledge, PTOLEMY and OPTIMA enable more efficient evaluation of well placement and operational strategies, helping site managers balance multiple remediation objectives under complex conditions. Both tools are implemented as modules within the SOCRATES (Suite Of Comprehensive Rapid Analysis Tools for Environmental Sites) web platform, which provides data access, visualization, and analytics to support remedy optimization across sites in the U.S. Department of Energy Office of Environmental Management complex. PTOLEMY is a rapid screening module designed to identify promising locations for new extraction wells. It employs a multi-channel three-dimensional convolutional neural network (MC3D-CNN) trained on high-fidelity simulation data to predict the relative performance (in terms of contaminant mass recovery) of potential well sites. Through an interactive web interface, PTOLEMY visualizes the probability of high performance across a site, highlighting areas where an extraction well is likely to yield above-threshold contaminant removal over a multi-year period. PTOLEMY’s map-based displays and exportable results support transparent communication of screening analyses. By focusing attention on the most favorable candidate locations, the tool augments traditional engineering judgment and physics-based modeling, providing a data informed basis for subsequent detailed evaluations. OPTIMA is a multi objective optimization module designed to find wellfield layouts and operating schedules that meet various cleanup goals. It quickly evaluates thousands of candidate setups – combinations of well locations, timing, and rates – and returns a small set of best trade-off options for comparison. At its core, OPTIMA uses a U-Net-based surrogate model – a deep-learning emulator of a groundwater flow and transport simulator – to dramatically accelerate scenario evaluations. Coupling this fast surrogate with the NSGA-II (Non-dominated Sorting Genetic Algorithm II) evolutionary algorithm, OPTIMA explores a wide decision space of well locations and schedules to identify Pareto-optimal solutions that trade off key objectives (e.g., minimizing cleanup time, maximizing contaminant mass removal, and minimizing plume extent). The tool outputs a family of optimal configurations and visualizes their trade-offs (Pareto frontiers of cleanup metrics and maps of optimized well placements). Site managers can use these results to understand the range of viable strategies and to select candidate designs for more detailed verification. OPTIMA is currently under active development and not yet fully released; this guide provides early documentation to support planning and gather user feedback.

54 ENVIRONMENTAL SCIENCES↗

LevSeq: Rapid Generation of Sequence-Function Data for Directed Evolution and Machine Learning

Sequence-function data provides valuable information about the protein functional landscape but is rarely obtained during directed evolution campaigns. Here, we present Long-read every variant Sequencing (LevSeq), a pipeline that combines a dual barcoding strategy with nanopore sequencing to rapidly generate sequence-function data for entire protein-coding genes. LevSeq integrates into existing protein engineering workflows and comes with open-source software for data analysis and visualization. The pipeline facilitates data-driven protein engineering by consolidating sequence-function data to inform directed evolution and provide the requisite data for machine learning-guided protein engineering (MLPE). LevSeq enables quality control of mutagenesis libraries prior to screening, which reduces time and resource costs. Simulation studies demonstrate LevSeq’s ability to accurately detect variants under various experimental conditions. Lastly, we show LevSeq’s utility in engineering protoglobins for new-to-nature chemistry. Widespread adoption of LevSeq and sharing of the data will enhance our understanding of protein sequence-function landscapes and empower data-driven directed evolution.

59 BASIC BIOLOGICAL SCIENCES↗

Streaming Data in HPC Workflows Using ADIOS

The “IO Wall” problem, in which the gap between computation rate and data access rate grows continuously, poses significant problems to scientific workflows which have traditionally relied upon using the filesystem for intermediate storage between workflow stages. One way to avoid this problem in scientific workflows is to stream data directly from producers to consumers and avoiding storage entirely. However, the manner in which this is accomplished is key to both performance and usability. This paper presents the Sustainable Staging Transport, an approach which allows direct streaming between traditional file writers and readers with few application changes. SST is an ADIOS “engine”, accessible via standard ADIOS APIs, and because ADIOS allows engines to be chosen at run-time, many existing file-oriented ADIOS workflows can utilize SST for direct application-to-application communication without any source code changes. This paper describes the design of SST and presents performance results from various applications that use SST, for feeding model training with simulation data with substantially higher bandwidth than the theoretical limits of Frontier’s file system, for strong coupling of separately developed applications for multiphysics multiscale simulation, or for in situ analysis and visualization of data to complete all data processing shortly after the simulation finishes.

Podhorszki, Norbert [ORNL] (ORCID:000000019647542X↗

Refining HPCToolkit for application performance analysis at exascale

As part of the US Department of Energy’s Exascale Computing Project (ECP), Rice University has been refining its HPCToolkit performance tools to better support measurement and analysis of applications executing on exascale supercomputers. To efficiently collect performance measurements of GPU-accelerated applications, HPCToolkit employs novel non-blocking data structures to communicate performance measurements between tool threads and application threads. To attribute performance information in detail to source lines, loop nests, and inlined call chains, HPCToolkit performs parallel analysis of large CPU and GPU binaries involved in the execution of an exascale application to rapidly recover mappings between machine instructions and source code. To analyze terabytes of performance measurements gathered during executions at exascale, HPCToolkit employs distributed-memory parallelism, multithreading, sparse data structures, and out-of-core streaming analysis algorithms. To support interactive exploration of profiles up to terabytes in size, HPCToolkit’s hpcviewer graphical user interface uses out-of-core methods to visualize performance data. The result of these efforts is that HPCToolkit now supports collection, analysis, and presentation of profiles and traces of GPU-accelerated applications at exascale. These improvements have enabled HPCToolkit to efficiently measure, analyze and explore terabytes of performance data for executions using as many as 64K MPI ranks and 64K GPU tiles on ORNL’s Frontier supercomputer. HPCToolkit’s support for measurement and analysis of GPU-accelerated applications has been employed to study a collection of open-science applications developed as part of ECP. This paper reports on these experiences, which provided insight into opportunities for tuning applications, strengths and weaknesses of HPCToolkit itself, as well as unexpected behaviors in executions at exascale.

Adhianto, Laksono↗

Advancing $otsdaq$ for Optimized Data Acquisition

High-energy physics (HEP) experiments demand data acquisition (DAQ) systems capable of orchestrating complex detector operations, high data throughput, and responsive, real-time feedback. Traditional systems often have steep learning curves, making onboarding difficult for new users. The Off-The-Shelf Data Acquisition $otsdaq$ framework was developed to address these issues by providing a modular and flexible interface that is easier to operate while remaining customizable enough for experimental setups. As the upcoming Mu2e experiment prepares for deployment, improving stability, usability, and performance has become increasingly critical. Our work enhances $otsdaq$ with features that streamline visualization, correct data metrics, improve debugging workflows, and stabilize the user interface.

Mohammed, Ali (ORCID:0009000860386626)↗

STM/S Grid LDOS Data and Analysis Code for Deciphering Majorana Zero Modes in Topological Superconductor

This dataset provides raw millikelvin scanning tunneling microscopy/spectroscopy (STM/S) grid spectroscopy data and Python analysis scripts supporting the manuscript “Deciphering Majorana Zero Modes in Topological Superconductor FeTe0.55Se0.45 with Machine-Learning-Assisted Spectral Deconvolution.” The dataset includes a raw grid spectroscopy file acquired on FeTe0.55Se0.45 at 40 mK under magnetic field, together with Python/Jupytext analysis scripts used for STM/S data processing, visualization, spectral deconvolution, Lorentzian peak fitting, feature extraction, machine-learning-assisted clustering, and figure generation. These files support the analysis of vortex-core local density of states and the identification of zero-bias-peak-related spectral components from complex in-gap states. The dataset is intended to provide a citable archival record of the data and analysis code associated with the published manuscript and to support transparency and reproducibility of the reported STM/S and machine-learning workflow.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

I/O in Machine Learning Applications on HPC Systems: A 360-degree Survey

Growing interest in Artificial Intelligence (AI) has resulted in a surge in demand for faster methods of Machine Learning (ML) model training and inference. This demand for speed has prompted the use of high performance computing (HPC) systems that excel in managing distributed workloads. Because data is the main fuel for AI applications, the performance of the storage and I/O subsystem of HPC systems is critical. In the past, HPC applications accessed large portions of data written by simulations or experiments or ingested data for visualizations or analysis tasks. ML workloads perform small reads spread across a large number of random files. This shift of I/O access patterns poses several challenges to modern parallel storage systems. In this paper, we survey I/O in ML applications on HPC systems, and target literature within a 6-year time window from 2019 to 2024. We define the scope of the survey, provide an overview of the common phases of ML, review available profilers and benchmarks, examine the I/O patterns encountered during offline data preparation, training, and inference, and explore I/O optimizations utilized in modern ML frameworks and proposed in recent literature. Lastly, we seek to expose research gaps that could spawn further R&D.

97 MATHEMATICS AND COMPUTING↗

Quantum Computing and Visualization Research Challenges and Opportunities

Here, quantum computing (QC) has experienced rapid growth in recent years with the advent of robust programming environments, readily accessible software simulators and cloud-based QC hardware platforms, and growing interest in learning how to design useful methods that leverage this emerging technology for practical applications. From the perspective of the field of visualization, this article examines research challenges and opportunities along the path from initial feasibility to practical use of QC platforms applied to meaningful problems.

Data visualization↗

Reimagining Disassembly Interfaces With Visualization: Combining Instruction Tracing and Control Flow With DisViz

In applications where efficiency is critical, developers may examine their compiled binaries, seeking to understand how the compiler transformed their source code and what performance implications that transformation may have. This analysis is challenging due to the vast number of disassembled binary instructions and the many-to-many mappings between them and the source code. These problems are exacerbated as source code size increases, giving the compiler more freedom to map and disperse binary instructions across the disassembly space. Interfaces for disassembly typically display instructions as an unstructured listing or sacrifice the order of execution. Here, we design a new visual interface for disassembly code that combines execution order with control flow structure, enabling analysts to both trace through code and identify familiar aspects of the computation. Central to our approach is a novel layout of instructions grouped into basic blocks that displays a looping structure in an intuitive way. We add to this disassembly representation a unique block-based mini-map that leverages our layout and shows context across thousands of disassembly instructions. Finally, we embed our disassembly visualization in a web-based tool, DisViz, which adds dynamic linking with source code across the entire application. DizViz was developed in collaboration with program analysis experts following design study methodology and was validated through evaluation sessions with ten participants from four institutions. Participants successfully completed the evaluation tasks, hypothesized about compiler optimizations, and noted the utility of our new disassembly view. Our evaluation suggests that our new integrated view helps application developers in understanding and navigating disassembly code.

Computer science↗

Microreactor Optimization Using Simulation And Economics (mouse)

Microreactor Optimization Using Simulation and Economics (MOUSE) is a tool that integrates both nuclear microreactor design and reactor economics to provide comprehensive evaluations and optimizations. This tool enables stakeholders to explore the interplay between technical and economic variables, guiding them towards effective and competitive microreactor solutions. For the reactor core simulations, MOUSE leverages the OpenMC Monte Carlo Particle Transport Code to perform detailed core simulations for various microreactor designs. The included OpenMC models are 2D core designs of a Liquid Metal Thermal Microreactor (LMTR), a Gas-Cooled TRISO-Fueled Microreactor (GCMR), and a Heat Pipe Microreactor. Beyond core design, MOUSE includes simplified calculations for: - Calculating the masses of heat exchangers within the system. - Mechanical power of pumps. - Estimating the area occupied by various buildings within the nuclear plant. For the economic analysis, MOUSE provides detailed bottom-up cost estimates, encompassing a wide range of costs including preconstruction costs, direct costs, indirect costs, training costs, financial costs, operation & maintenance (O&M) costs, and fuel costs. These cost estimations are developed using data from the MARVEL project and additional literature sources, enabling the calculation of total capital costs and levelized cost of energy for both first-of-a-kind and nth-of-a-kind microreactors. MOUSE also enables analysis of the cost drivers and competitiveness in the electricity market. MOUSE allows users to modify a wide array of technical and economic parameters to evaluate different scenarios and their impacts. Examples of these parameters include: Fuels, coolants, or reflector materials Enrichment levels Control drum materials and geometry Fuel pin geometry and materials Moderator pin geometry and materials Reactor core and reflector dimensions Packing factor for the TRISO particles Nuclear reactor power and reactor burnup Number of sensors Shielding thickness Reactor vessel and guard vessel dimensions Operational staff requirements Number of emergency shutdowns Levelization period Interest rate Construction duration Since MOUSE is powered by the WATTS toolkit, it supports optimization studies, parametric analyses, and uncertainty calculations/propagation. The optimization techniques enable users to identify optimal design and economic configurations. The parametric analysis tools allow users to explore the sensitivity of various parameters, while uncertainty propagation helps quantify the impact of uncertainties on overall performance and cost. User Interface and Workflow: Currently, MOUSE is a command-line-based tool. Users can input various reactor design or economic parameters, modify the designs, run simulations, and visualize results through comprehensive data visualization and reporting capabilities. The typical workflow involves setting up the reactor model, defining economic parameters, running simulations, and analyzing the results to make informed decisions. By combining advanced design calculations with detailed economic modeling, MOUSE provides a robust framework for optimizing nuclear microreactor technologies, enhancing their competitiveness, and guiding stakeholders towards innovative and cost-effective solutions.

Hanna, Botros [Idaho National Laboratory (INL), Id↗

MODE: A Web Application for Interactive Visualization and Exploration of Omics Data

Studies generating transcriptomics, proteomics, lipidomics, and metabolomics (colloquially referred to as “omics”) data allow researchers to find biomarkers or molecular targets, or understand complex biological structures and functions by identifying changes in biomolecule abundance and expression between experimental conditions. Omics data is multi-dimensional and oftentimes summarization techniques such as principal component analysis (PCA) are used to identify high-level patterns in data. Though useful, these summaries don’t allow exploration of detailed patterns in omics data that may have biological relevance. The use of interactive HTML displays with plots allows researchers to interact with omics data at a detailed level, but building these displays requires significant coding expertise. To overcome this barrier, the software MODE was built to empower users to build their own interactive HTML displays to support scientific discovery. These displays are easily shareable, do not depend on a specific operating system, and allow users to effortlessly sort and filter plots by categorical or numerical variables. MODE allows users to build and share these displays with several options for plot design and meta selection. In conclusion, the MODE web application and its capabilities are presented and then demonstrated on lipidomics data from a leaf wounding study.

lipidomics↗