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At least 829 records · Page 46

cldera-tools

SAND2025-03848O CLDERA-Tools is a small library for performing online calculation of quantity of interest derived from variables in the host application. The library stores pointers to the arrays of variables of the host model and uses them at every timestep to compute desired quantity of interests (prescribed via yaml input files). Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Watkins II, Jerry↗

Dori Tools v2.1.0

Dori Tools is a set of useful programs that support running a mid-range HPC cluster for BioInformatics workloads.

Rath, Georg [Lawrence Berkeley National Laboratory↗

BiCRS LCA Tool [SWR-26-005]

This is a biomass carbon removal and storage (BiCRS) life cycle analysis (LCA) tool. This version can be used to estimate the impacts of biochar burial BiCRS pathways.

Ware, Anne "Liz" [National Renewable Energy Labora↗

Open Source Software Prevalence Ingest Tool

The OSSP Ingest Tool accepts user-input organizational information, ingests IT/OT asset lists in Excel format, and ingests the associated CycloneDX SBOM's. It then performs analytics demonstrating the ability to answer the follow research questions: o RQ1. Ability to identify all OSS services running on, and all OSS components present within, an OT device o RQ1a: Ability to differentiate multiple versions of the same OSS component within each OT device. o RQ1b: Ability to differentiate running from not-running OSS components. o RQ1c: Ability to differentiate based on the originator of the component, because a supplier may have modified it after retrieval from the upstream software source. o RQ2. Ability to correlate the identity of a single OSS component across multiple OT devices, mitigating common name variations such as differences in capitalization, '-' vs '_', and so on. o RQ3. Ability to perform subset analysis of OSS components across multiple OT devices o RQ3a: Ability to perform subset analysis across OSS libraries, generating density & distribution graphs to identify commonly-used libraries and outliers. o RQ3b: Ability to perform subset analysis of a single OSS library, generating density & distribution by CI sector, by device type, by device make/model, and/or by firmware version. o RQ3c: Ability to perform subset analysis by grouping OSS libraries according to programming language, then overlay with RQ4b. o RQ3d: Ability to perform subset analysis by OSS upstream source, providing insight into degree of modifications performed by suppliers. o RQ4. Ability to identify dependencies (transitive and direct) of each differentiated OSS library within each OT device, and enable RQ1,2,3 iteratively for dependencies. o RQ1. Ability to identify all OSS services running on, and all OSS components present within, an OT device o RQ1a: Ability to differentiate multiple versions of the same OSS component within each OT device. o RQ1b: Ability Page

Kapadia, Shayna [Lawrence Livermore National Labor↗

Flash-X Recipe Tools

SF-24-102 A code generation tool for Flash-X to support their performance portability using a domain-specific runtime library.

Lee, Youngjun↗

CCE Tool Belt

The CCE Tool Belt is a desktop software application that supports analysts, investigators, and entity representatives in preparation for and throughout the process of a CCE engagement by providing a standardized approach to the CCE framework.

Dodge, JeffreyL.↗

Cyote Research Tool Library

The software is a library of individual proof-of-concept tools to be further developed in research efforts with partner utilities to detect indicators of Cyber Attacks within the Operational Technology Environments.

Wellman, LawrenceR.↗

Cyber-CHAMP Task Analysis Survey Tool

Cyber-CHAMP Task analysis survey tool is a web-hosted code platform for an individual to select their every day tasking, based on industry documentation and standards, and produce an education and training mapping to provide them the proper associated cyber competency level(s).

Stailey, ShaneD.↗

Manufactured Home Equipment Sizing and Selection Tool

This tool is for use for manufactured homes built to the HUD Code (thermal provisions of the Manufactured Housing Construction and Safety Standards, Subpart F, Section §3280), including manufactured homes certified as ENERGY STAR® and DOE Efficient New Homes. It provides a simple look-up procedure to assist equipment specifiers, HVAC contractors, home installers, retailers, manufacturers, and electric utility staff. For new manufactured homes, it guides in selection of single speed heat pumps and air conditioners. For existing homes, it determines design conditions and nominal equipment size. The guidelines provide a simple but accurate procedure that reduces oversizing and its associated problems.

Source record↗

A Reverse Logistics Tool For Ev Battery Recycling And Repurposing,

The demand for electric vehicles (EVs) in the United States is projected to rise significantly, with sales expected to reach approximately 4.1 million units by 2030. However, the U.S. remains heavily reliant on imports for the batteries and critical raw materials—such as lithium, cobalt, and nickel—that power these vehicles. As of 2024, around 70% of these imports originate from China. This dependency has become even more precarious following China’s imposition of export restrictions in April 2025, a retaliatory move against U.S. tariffs. These developments highlight the strategic vulnerabilities posed by China’s dominant position in the critical materials market. Compounding the issue, decades of intensive extraction have severely depleted global reserves of critical materials, widening the gap between supply and growing demand. This situation underscores the urgent need for the U.S. and other nations to diversify their sources of critical materials and enhance domestic capabilities to secure these resources—an essential step toward ensuring long-term energy security. At the end of their lifecycle—whether due to the battery’s degradation or the retirement of the vehicle—EV batteries are often improperly disposed of or sent to landfills. However, many of these batteries still retain usable capacity and can follow one of three alternative pathways: (a) Re-used: deployed in another vehicle with a shorter driving range, (b) Re-purposed: utilized act as a backup storage/power for data centers, solar panels, and e-scotters or (c) Recycled: broken down to recover the critical materials. To that end, the proposed tool (REBORN) is designed to optimize the reverse logistics network for battery repurposing and recycling. Its goal is to minimize associated costs while identifying optimal locations for battery collection and processing. Ultimately, REBORN ensures that each battery is used to its fullest potential.

Srinivas, SrikarV. [Idaho National Laboratory (INL↗

An Interactive Spectral Analysis Tool for Chemical Identification and Quantification of Gas-Phase Species in Complex Spectra

A spectral analysis tool has been developed to interactively identify and quantify individual gas-phase species from complex infrared absorbance spectra obtained from laboratory or field data. The SpecQuant program has an intuitive graphical interface that accommodates both reference and experimental data with varying resolution and instrumental lineshape, as well as algorithms to readily align the wavenumber axis of a sample spectrum with the raster of a reference spectrum. Using a classical least squares model in conjunction with reference spectra such as those from the Pacific Northwest National Laboratory (PNNL) gas-phase infrared database or simulated spectra derived from the HITRAN line-by-line database, the mixing ratio of each identified species is determined along with its associated estimation error. After correcting the wavelength and intensity of the field data, SpecQuant displays the calculated mixing ratio versus the experimental data for each analyte along with the residual spectrum with any or all analyte fits subtracted for visual inspection of the fit and residuals. The software performance for multianalyte quantification was demonstrated using moderate resolution (0.5 cm –1 ) infrared spectra that were collected during the time-resolved infrared photolysis of methyl iodide.

Thompson, Christopher J.↗

TULIP: An RNA-seq-based Primary Tumor Type Prediction Tool Using Convolutional Neural Networks

Background: With cancer as one of the leading causes of death worldwide, accurate primary tumor type prediction is critical in identifying genetic factors that can inhibit or slow tumor progression. There have been efforts to categorize primary tumor types with gene expression data using machine learning, and more recently with deep learning, in the last several years. Methods In this paper, we developed four 1-dimensional (1D) Convolutional Neural Network (CNN) models to classify RNA-seq count data as one of 17 highly represented primary tumor types or 32 primary tumor types regardless of imbalanced representation. Additionally, we adapted the models to take as input either all Ensembl genes (60,483) or protein coding genes only (19,758). Unlike previous work, we avoided selection bias by not filtering genes based on expression values. RNA-seq count data expressed as FPKM-UQ of 9,025 and 10,940 samples from The Cancer Genome Atlas (TCGA) were downloaded from the Genomic Data Commons (GDC) corresponding to 17 and 32 primary tumor types respectively for training and validating the models. Results: All 4 1D-CNN models had an overall accuracy of 94.7% to 97.6% on the test dataset. Further evaluation indicates that the models with protein coding genes only as features performed with better accuracy compared to the models with all Ensembl genes for both 17 and 32 primary tumor types. For all models, the accuracy by primary tumor type was above 80% for most primary tumor types. Conclusions: We packaged all 4 models as a Python-based deep learning classification tool called TULIP (TUmor CLassIfication Predictor) for performing quality control on primary tumor samples and characterizing cancer samples of unknown tumor type. Further optimization of the models is needed to improve the accuracy of certain primary tumor types.

Jones, Sara↗

CYPminer: an automated cytochrome P450 identification, classification, and data analysis tool for genome data sets across kingdoms

Background: Cytochrome P450 monooxygenases (termed CYPs or P450s) are hemoproteins ubiquitously found across all kingdoms, playing a central role in intracellular metabolism, especially in metabolism of drugs and xenobiotics. The explosive growth of genome sequencing brings a new set of challenges and issues for researchers, such as a systematic investigation of CYPs across all kingdoms in terms of identification, classification, and pan-CYPome analyses. Such investigation requires an automated tool that can handle an enormous amount of sequencing data in a timely manner. Results: CYPminer was developed in the Python language to facilitate rapid, comprehensive analysis of CYPs from genomes of all kingdoms. CYPminer consists of two procedures i) to generate the Genome-CYP Matrix (GCM) that lists all occurrences of CYPs across the genomes, and ii) to perform analyses and visualization of the GCM, including pan-CYPomes (pan- and core-CYPome), CYP co-occurrence networks, CYP clouds, and genome clustering data. The performance of CYPminer was evaluated with three datasets from fungal and bacterial genome sequences. Conclusions: CYPminer completes CYP analyses for large-scale genomes from all kingdoms, which allows systematic genome annotation and comparative insights for CYPs. CYPminer also can be extended and adapted easily for broader usage.

59 BASIC BIOLOGICAL SCIENCES↗

FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research

ABSTRACT The FaceBase Consortium was established by the National Institute of Dental and Craniofacial Research in 2009 as a ‘big data’ resource for the craniofacial research community. Over the past decade, researchers have deposited hundreds of annotated and curated datasets on both normal and disordered craniofacial development in FaceBase, all freely available to the research community on the FaceBase Hub website. The Hub has developed numerous visualization and analysis tools designed to promote integration of multidisciplinary data while remaining dedicated to the FAIR principles of data management (findability, accessibility, interoperability and reusability) and providing a faceted search infrastructure for locating desired data efficiently. Summaries of the datasets generated by the FaceBase projects from 2014 to 2019 are provided here. FaceBase 3 now welcomes contributions of data on craniofacial and dental development in humans, model organisms and cell lines. Collectively, the FaceBase Consortium, along with other NIH-supported data resources, provide a continuously growing, dynamic and current resource for the scientific community while improving data reproducibility and fulfilling data sharing requirements.

60 APPLIED LIFE SCIENCES↗

A Verification of Flux Sensitivity Estimates Using the MCNP Tally Perturbation Tool

Nuclear data is commonly used in applications such as nuclear nonproliferation, safeguards, and criticality safety. More specifically, nuclear data is used in predictive simulation codes like the Monte-Carlo N-Particle (MCNP ® ) transport code, Serpent, and similar radiation transport codes. The improvement of nuclear data enables more precise and accurate simulations, which result in higher fidelity designs and reduced operational/procedural costs. Therefore, the improvement of nuclear data is of paramount importance across the nuclear community. Nuclear data is improved and validated through integral benchmark experiments. The design of benchmark experiments is an extensive process; therefore, these experiments are often optimized on multiple characteristics, including sensitivity to the nuclear data, during the design process. Sensitivity is a measure of how much a quantity changes due to changes in independent variables such as experimental configuration. An experimental design that has a larger sensitivity to the nuclear data of interest will have a larger impact on the accuracy and precision of the validated data. Past integral benchmark experiments have primarily used the effective multiplication factor ($k_{eff}$) as the predominant measured quantity; however, experiments designed with other quantities in mind would be able to optimize on validating different areas of the nuclear data. A primary goal of the EUCLID project is to design, constrain, and reduce compensating errors in experiments focused on quantities other than $k_{eff}$ to better validate nuclear data across the board. Currently, there is a capability in MCNP to easily calculate the sensitivity of $k_{eff}$ to specific nuclear data of numerous reactions types and isotopes (KSEN card); however, the sensitivity of other quantities must be estimated in more strenuous manners. For example, the perturbation feature (PERT card) of MCNP can be used to estimate first-order sensitivities of some response in fixed source simulations. A recent announcement revealed that the first- and second-order perturbation features in previous releases of MCNP contained a bug. It was identified that particles were being scored into the wrong energy bin. The bug is in the most recent public release (MCNP6.2); however, a patch has been added to the most up to date version (MCNP6.2.2) that has not been released publicly. A direct comparison of the PERT card results for an F4 (neutron flux averaged over a cell) tally before and after the patch are shown in figure 1. All simulations used in the sensitivity estimates in this report were performed with MCNP6.2.2. This work verifies the patched MCNP perturbation tool by comparing first order sensitivities made using the PERT card to estimates made using manual perturbation of the compact ENDF (ACE) files.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Understanding the tool influence function during sub-aperture belt-on-wheel glass polishing

The tool influence function (TIF) during sub-aperture belt-on-wheel polishing has been evaluated as a function of various process conditions (belt use/wear, dwell time, displacement, belt velocity, and wheel modulus and diameter) on fused silica glass workpieces using C e O 2 polishing media. TIF spots are circular or elliptical in shape with a largely flat bottom character. Furthermore, the volumetric removal rate varies significantly with belt use (or wear), stabilizing after ~<!-- ~ --> 15 m i n of use. A modified Preston model, where the pressure dependence is adjusted using a different scaling of the wheel modulus ( E w 0.5 ), largely predicts the volumetric removal rate over the range of process conditions evaluated. The relatively high volumetric removal rate of 30 -<!-- - --> 60 m m 3 / h using a fixed C e O 2 -in-resin-host belt offers a rapid, and hence, more economical, initial polish of aspheric and freeform optics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗