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At least 289 records · Page 16

OpenSAMPL: An Open Source Library for Timing and Synchronization Measurements and Analytics

Today's power grid operators are implementing timing and synchronization solutions that provide resilience to Global Navigation Satellite System (GNSS) vulnerabilities. These vendor-specific solutions often come with additional software applications that are designed to monitor that vendor's synchronization performance data. However, resilient timing architectures often resulting in multi-vendor solutions, including approaches that blend terrestrial clocks with space-based subscription services. In such an environment, collecting, analyzing, and visualizing data from a variety of sources within a single platform was heretofore not possible. To address this need, the US Department of Energy's Center for Alternative Synchronization and Timing (CAST) developed OpenSAMPL, the Open Synchronized Analytics and Monitoring Platform, an open-source Python framework for processing, loading, and observing clock measurement data from distributed devices. OpenSAMPL enables the ingestion of diverse clock-probe sources into a scalable time-series database and applies robust analytics. OpenSAMPL currently supports two vendor data pipelines, and will be extended to more in the near future, enabling seamless monitoring of a variety of timing and synchronization devices in a common environment.

Grant, Josh [ORNL] (ORCID:0000000163475060)↗

The Neurodata Without Borders ecosystem for neurophysiological data science

The neurophysiology of cells and tissues are monitored electrophysiologically and optically in diverse experiments and species, ranging from flies to humans. Understanding the brain requires integration of data across this diversity, and thus these data must be findable, accessible, interoperable, and reusable (FAIR). This requires a standard language for data and metadata that can coevolve with neuroscience. We describe design and implementation principles for a language for neurophysiology data. Our open-source software (Neurodata Without Borders, NWB) defines and modularizes the interdependent, yet separable, components of a data language. We demonstrate NWB’s impact through unified description of neurophysiology data across diverse modalities and species. NWB exists in an ecosystem, which includes data management, analysis, visualization, and archive tools. Thus, the NWB data language enables reproduction, interchange, and reuse of diverse neurophysiology data. More broadly, the design principles of NWB are generally applicable to enhance discovery across biology through data FAIRness.

59 BASIC BIOLOGICAL SCIENCES↗

From Obsolete to Optimal (ATR Demineralized Water System)

My project was migrating a Human-Machine Interface (HMI) and Programmable Logic Controller (PLC) program from legacy software to a modern platform, enhancing operational efficiency and eliminating unsupported, obsolete equipment. Initially, I used a migration tool to transfer the programs to the new software, then manually updated variables to align with the new PLC. I optimized the PLC code by leveraging new scaling features in the I/O cards, removing over 45 obsolete rungs, and enhancing clarity with functional tag aliases. Next, I modernized the HMI's visuals with an updated color scheme and 3D buttons. I developed multiple interface versions iteratively refining them based on operator feedback. I also designed and created a dedicated "Rounds" screen incorporating insights from a previous intern’s project to streamline daily rounds. To improve clarity, consistency, and efficiency I redesigned the entire interface. Adding visual indicators to enhance operational awareness: red is used for values outside normal specifications, green for normal operating modes, yellow for manual mode, and grey for offline units. Additionally, I added a dynamic visual representation of tank levels, creating PLC logic to show the level in inches as well as inches and feet. I then incorporated a navigation sidebar to facilitate efficient screen transitions. Risk of human error was mitigated by defining narrow input ranges for tank level shutoff and password protecting setpoint changes. I also fixed issues with datatypes that caused inaccuracies in the original code. Overall, this comprehensive upgrade significantly enhanced the HMI's functionality, user experience, and operational reliability.

47 - OTHER INSTRUMENTATION↗

PySIDT: Subgraph Isomorphic Decision Trees for Molecular Property Prediction

Accurate molecular property prediction is important across all fields of chemistry. Deep neural networks (DNNs) have become increasingly popular due to their ability to train automatically, avoiding the incredibly tedious process of constructing and extending traditional property estimation schemes. However, DNNs require large amounts of training data, are challenging to interpret, require large amounts of memory to load even during inference, and have severe difficulties incorporating qualitative chemical knowledge, which are often desired for molecular property prediction tasks. Here, in this study, we present PySIDT (https://github.com/zadorlab/PySIDT), a software for training and running inference on Subgraph Isomorphic Decision Trees (SIDTs). SIDTs are graph-based decision trees made of nodes associated with molecular substructures. Inference is done by descending target molecular structures down the decision tree to nodes with matching subgraph isomorphic substructures and making predictions based on the final (most specific) nodes matched. SIDTs scale down well to dataset sizes much smaller than is feasible for DNNs. As trees of molecular substructures, SIDTs are inherently readable and easy to visualize, making them easy to analyze. They are also straightforward to extend and retrain, facilitate uncertainty estimation, and enable easy integration of expert knowledge. We demonstrate the SIDT approach discussing its application to a diverse range of molecular prediction tasks: rate coefficient estimation, diffusion coefficient estimation, thermochemistry estimation, transition state bond stretch prediction, p K a prediction, stability of molecular structures, stability of surface structures, and prediction of surface lateral interaction energetics. Additionally, we demonstrate the power of the SIDT algorithms in two direct learning curve vanilla comparisons with the popular DNN-based software Chemprop and the popular gradient boosted trees-based software XGBoost on enthalpy of formation and rate coefficient prediction tasks. In particular, in the enthalpy of formation case, vanilla PySIDT is able to outperform vanilla Chemprop and XGBoost across the full range of training/validation set sizes out to 11,560 data points.

Johnson, Matthew Sean [Sandia National Laboratorie↗

Nanopolysaccharide Builder: A User-Friendly Tool for Atomistic Models of Polysaccharide-Based Nanostructures

Here, we introduce Nanopolysaccharide Builder (NPB), a user-friendly software tool designed to construct polysaccharide nanostructures─mainly those based on cellulose, chitin, and chitosan─using experimental data or user-defined parameters. NPB enables the generation of cellulose and chitin allomorphs with customizable biochemical topologies and also facilitates the construction of large bundles that replicate nanostructures found in biological support systems, including plant cell walls and arthropod cuticles. The software outputs atomic Cartesian coordinates in Protein Data Bank (PDB) format and also provides atom connectivity files in PSF and PARM formats, ensuring seamless integration with major molecular dynamics (MD) engines such as NAMD, CHARMM, GROMACS, AMBER, OpenMM, and LAMMPS. Built on an interactive visualization framework, NPB features a graphical user interface (GUI) and supports both macOS and Linux operating systems. By enabling detailed atomic-scale studies of polysaccharide evolution in extracellular matrices and cell walls of algae, bacteria, fungi, and plants, NPB is poised to advance AI-guided research in sustainable chemical development and biomass utilization.

Wan, Zhangmin [Univ. of British Columbia, Vancouve↗

AutoEM

AutoEM is a software application intended to fully automate EM experiments. This automation includes incorporation of a Machine Learning component that will provide feedback analysis and experiment modification in a fully hands-free manner. AutoEM incorporates control of multiple devices, communication with external applications, and user visualization of images, device status, and ML feedback.

Hopkins, Derek [Pacific Northwest National Laborat↗

DFTT report for Signal Analysis (2023)

The Detection Framework Testbed and Toolkit (DFTT) is a database and associated java programs intended to facilitate the development and testing of algorithms for operating suites of correlation and subspace detectors. This framework is a generalization of the system described in Harris and Dodge (2011) and Dodge and Harris (2016). DFTT allows retrospective processing of sequences of data using various system configurations. Results are saved in a database, so it is easy to compare the results obtained using different configurations of the system. The principal software components of DFTT are the ConfigCreator, the framework_runner and the Builder program. ConfigCreator assembles the files necessary to define a particular configuration used for processing. The framework_runner operates suites of detectors and saves the results in an Oracle™ database. Builder allows visual examination of templates and detected signals and allows editing and creation of detectors. In addition, there are tools for importing continuous data into the database. DFTT is licensed under the MIT license and has LLNL release number LLNL-CODE-801881. In the current fiscal year DFTT has been used in two different projects. The first (NTL-funded) project investigates the feasibility of screening nuisance detections using correlation detectors. The second (GNEM-funded) project seeks to extend the results of Harris and Dodge (2021) to 3- D sources and multiple stations. Each of these efforts required that additional functionality be added to DFTT. In this report I will summarize the enhancements to DFTT in the context of the relevant research effort.

58 GEOSCIENCES↗

Picometer-Precision Atomic Position Tracking through Electron Microscopy

The modern aberration-corrected scanning electron microscopes have successfully achieved direct visualization of atomic columns with sub-angstrom resolution. With this significant progress, advanced image quantification and analysis is still at its early stages. In this work, we present the complete pathway for the metrology of atomic resolution STEM images. This includes: 1) tips for acquiring high-quality STEM images; 2) denoising and drift-correction for enhancing measurement accuracy; 3) obtaining initial atom positions; 4) indexing the atoms based on unit cell vectors; 4) quantifying the atom column positions with either 2D-gaussian single peak fitting or 5) multi-peak fitting routines for slightly overlapping atomic columns; 6) quantification of lattice distortion/strain within the crystal structures or at the defects/interfaces where the lattice periodicity is disrupted, and 7) some common methods to visualize and present the analysis. Furthermore, a simple self-developed free MATLAB app (EASY-STEM) with a graphical user interface (GUI) will be introduced that can help with the analysis of STEM images without the need for writing dedicated analysis code or software. The advanced data analysis methods presented here can be applied for the local quantification of defect relaxations, local structural distortions, local phase transformations, and non-centrosymmetry in a wide range of materials.

47 OTHER INSTRUMENTATION↗

Efficient Clustering of Software Vulnerabilities using Self Organizing Map (SOM)

The common vulnerabilities and exposures (CVE) database was created with a mission to ``identify, define, and catalog publicly disclosed cybersecurity vulnerabilities''. This rich body of information can be used to enable rapid and efficient response to secure and defend cyber operations and protect critical cyber infrastructure. The main goal of this paper is to develop a visual analytics tool to enable deep analysis of CVEs using unsupervised clustering techniques. We enhance our analysis by first mapping CVEs to hierarchical-classes in Common Weakness Enumeration (CWE) using information in the National Vulnerability Database (NVD). Both the mapping and the numerical representation of CVEs are enabled by V2W-BERT, which uses natural language processing of the extensive information in NVD to generate a large tabular database of 137,226 CVE entries from 1999 to 2020, where each CVE is represented by a vector of 768 numerical features. The vectorized data is processed by Self-Organizing Maps (SOM), which is an unsupervised machine learning technique for dimensionality reduction, visual representation and clustering. Using a Torus map of 6417 units, we achieve ~10-fold data compression of ~140k CVEs using SOM. The trained map is further clustered using standard K-means clustering into 138 clusters of CVEs. We conducted a brief investigation of the rich mapping of CVEs to best-matching-units to K-means clusters, as well as CVEs to CWEs. For example, this novel mapping provided insight into the role of CWE-59 and CWE-264 in several CVEs that is otherwise hard to explore in the original data. We conclude that our this novel approach will not only enable deep analysis of the complex relationships between CVEs and CWEs, but also a mechanism to quickly respond to and design mitigation actions for rapidly evolving vulnerabilities that have not been mapped to existing CWEs.

Panchal, Khyati↗

MILK : a Python scripting interface to MAUD for automation of Rietveld analysis

Modern diffraction experiments ( e.g. in situ parametric studies) present scientists with many diffraction patterns to analyze. Interactive analyses via graphical user interfaces tend to slow down obtaining quantitative results such as lattice parameters and phase fractions. Furthermore, Rietveld refinement strategies ( i.e. the parameter turn-on-off sequences) tend to be instrument specific or even specific to a given dataset, such that selection of strategies can become a bottleneck for efficient data analysis. Managing multi-histogram datasets such as from multi-bank neutron diffractometers or caked 2D synchrotron data presents additional challenges due to the large number of histogram-specific parameters. To overcome these challenges in the Rietveld software Material Analysis Using Diffraction ( MAUD ), the MAUD Interface Language Kit ( MILK ) is developed along with an updated text batch interface for MAUD . The open-source software MILK is computer-platform independent and is packaged as a Python library that interfaces with MAUD . Using MILK , model selection ( e.g. various texture or peak-broadening models), Rietveld parameter manipulation and distributed parallel batch computing can be performed through a high-level Python interface. A high-level interface enables analysis workflows to be easily programmed, shared and applied to large datasets, and external tools to be integrated with MAUD . Through modification to the MAUD batch interface, plot and data exports have been improved. The resulting hierarchical folders from Rietveld refinements with MILK are compatible with Cinema: Debye–Scherrer , a tool for visualizing and inspecting the results of multi-parameter analyses of large quantities of diffraction data. In this manuscript, the combined Python scripting and visualization capability of MILK is demonstrated with a quantitative texture and phase analysis of data collected at the HIPPO neutron diffractometer.

97 MATHEMATICS AND COMPUTING↗

Data Analysis Approach for Large Data Volumes in a Connected Community

Recent advancements within smart neighborhoods where utilities are enabling automatic control of appliances such as heating, ventilation, and air conditioning (HVAC) and water heater (WH) systems are providing new opportunities to minimize energy costs through reduced peak load. This requires systematic collection, storage, management, and in-memory processing of large volumes of streaming data for fast performance. In this paper, we propose a multi-tier layered IoT software framework that enables effective descriptive and predictive data analysis for understanding live operation of the neighborhood, fault identification, and future opportunities for further optimization of load curves. We then demonstrate how we achieve live situational awareness of the connected neighborhood through a suite of visualization components. Finally, we discuss a few analytic dashboards that address questions such as peak load reductions obtained due to optimization, customer preference for automatic control of appliances (do they override the automatic control of HVAC?, etc.). 1 1 This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a nonexclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan).

Chinthavali, Supriya↗

TITUS: Visualization of Neutrino Events in Liquid Argon Time Projection Chambers

The amount and complexity of data recorded by high energy physics experiments are rapidly growing, and with these grow the difficulties in visualizing such data. To study the physics of neutrinos, a type of elementary particle, scientists use liquid argon time projection chamber (LArTPC) detectors, among other technologies. LArTPCs have a very high spatial resolution and resolve many of the elementary particles that come out of a neutrino interacting within the argon in the detector. Visualizing these neutrino interactions is of fundamental importance to understanding the properties of neutrinos, but also monitoring and checking on the detector conditions and operations. From these ideas, we have developed TITUS, an event display that shows images recorded by these neutrino detectors. TITUS is a piece of software that reads data coming from LArTPC detectors (as well as the corresponding simulation) and allows users to explore such data in multiple ways. TITUS is flexible to enable fast prototyping and customization.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

AFUE Analysis Software Tool

The Annual Fuel Utilization Efficiency (AFUE) analysis of residential and light commercial furnaces follows ANSI/ASHRAE Standard 103-2017 (i.e., Method of Testing for Annual Fuel Utilization Efficiency of Residential Central Furnaces and Boilers) . The analysis is a complex, comprehensive method based on furnace configuration and specific components equipped, requiring detailed furnace testing and measurement data. For this reason, an AFUE Analysis Tool using Microsoft Excel enabled with Visual Basic for Applications (VBA) was developed with a user-friendly interface and comprehensive coverage. The tool consists of three worksheets: unit and configuration selection, geometry and measurement data input, and AFUE plus key results. This tool can be used to estimate the AFUE of both condensing and noncondensing furnaces with single-stage, two-stage, and step-modulating functions. The tool was validated with experimental data from Oak Ridge National Laboratory’s natural gas furnace projects that are commercially available. The results indicate the tool is reasonably accurate in the evaluation of a new R&D modified furnace unit.

Gao, Zhiming [Oak Ridge National Laboratory (ORNL)↗

DeepDiagnostics: A Software Package for Streamlined Posterior Evaluation

Automated prediction techniques like simulation-based inference (SBI) are important tasks for science experiments that produce large amounts of complex, raw data. However, their development remains in its early stages because the uncertainties of these techniques lack sufficient trustworthiness and interpretability. Packages for SBI provide a growing set of diagnostics; however, the software requirements are substantial, as they are tied to the inference technology itself, and the APIs lack adaptability. We introduce the DeepDiagnostics package for diagnosing posteriors from analytic likelihood-based methods and SBI methods, such as neural posterior estimation. DeepDiagnostics produces a comprehensive set of high-quality visualizations and metrics in a highly accessible, easy-to-use, and flexible package. We address all of these goals by providing a command-line inference tool and a Python API that is controlled through a configuration file. The package includes common diagnostics, such as parity plots, corner (covariance) plots, simulation-based calibration (SBC) diagnostics (including posterior coverage and rank histograms), Lemos et al. s PQMass and TARP, Masserano et al. s WALDO, Linhart et al. s LC2ST, as well as credible region diagnostics developed by our group.

Voetberg, Maggie [Fermilab]↗

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

Background Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling. Results We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric “MW-score” (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~ 3 h with 40 CPU threads to process ~ 100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~ 45 min, while it takes ~ 5 h to complete hmmsearch for ~ 3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut. Conclusion METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3 at https://github.com/AnantharamanLab/METABOLIC.

59 BASIC BIOLOGICAL SCIENCES↗

Grid Modernization of Cooperatives and Municipal Utilities via Breakthrough System Monitoring, Control and Optimization (CRADA Final Report)

This project aims at developing and demonstrating successful implementation of breakthrough approaches in real-time data visualization as well as real-time distributed DER control and optimization to provide ample benefits to both utilities and end users. The National Renewable Energy Laboratory (NREL), Holy Cross Energy (HCE), National Rural Electric Cooperative Association (NRECA) and Survalent are collaborating to enable Cooperative and Municipal utilities to fully leverage DERs as part of their strategies for providing safe, reliable, and affordable electric services to their customers and help meet DOE Grid modernization goal of achieving at least 10% active devices to provide grid flexibility by 2035. This project will use novel real-time control algorithms and approaches for distributed control recently developed under DOE-funded projects, using the date from the Survalent’s basic SCADA engine, GIS and AMI engines deployed at HCE combined with NRECA’s globally-used MultiSpeak(R) software interoperability specification for seamless and real-time communications between electric utility enterprise software to embrace DER as part of their strategies for providing safe, reliable and affordable electric service to their customers.

24 POWER TRANSMISSION AND DISTRIBUTION↗

MEASUR - Manufacturing Energy Assessment Software for Utility Reduction

MEASUR your energy savings with the free DOE MEASUR software The Department of Energy (DOE), with Oak Ridge National Laboratory (ORNL), released version 1.0 of their energy efficiency software tool MEASUR (Manufacturing Energy Assessment Software for Utility Reduction). MEASUR has been available for several years as a beta version, being tested by industry experts and real users, and will continue to be updated and improved in the coming years. It is an integrated suite of tools to aid manufacturers in improving the efficiency of energy systems and equipment within a plant, including motors, pumps, fans, process heating, steam, and compressed air. Additionally, there are modules for wastewater energy analysis and to help perform energy treasure hunts. Several calculators are also included, allowing users to independently perform smaller calculations and analyses (such as estimating pump head, performing a fan traverse analysis, estimating waste heat recovery potential, and cataloging compressed air leaks). The MEASUR modules are based on previous DOE software tools that have been used by industry since the early 2000s (such as MotorMaster, AirMaster+, PSAT, PHAST, and FSAT). The original tools only ran on Windows operating systems, and by Windows 10, most of them were inoperable. DOE started their energy efficiency software tool revitalization effort in 2016, first with PSAT (for pumps), then began to integrate the other tools and expand their functionality and utility. The new MEASUR suite provides an extensively more user-friendly, modern, and versatile set of tools. All the assessment modules and most of the calculators have several visual components and graphs and detailed help text for every user input. To help reach international users, the tool utilizes Google translate and users can easily change unit systems, even converting existing user inputs if desired. The assessment files can be organized within the internal file system and easily shared to other users, regardless of their operating system. The entire suite is free, open-source, and can be downloaded on Windows, Mac, or Linux operating systems.

Accawi, Gina [Oak Ridge National Lab. (ORNL), Oak ↗

PARETO UI 1.1.0 Release

PARETO is an open-source Python-based software package for oilfield produced water management and beneficiary reuse optimization. PARETO supports produced water industry by providing cost-effective water management solutions. This version introduced an updated User Interface (UI) which makes it easier to navigate and understand the solution for industry users. New Features: - Map files are added for visualization - Added output export function button - Water residual view added - Workflow was streamlined - File extension was expanded - Minor bugfix

AS↗