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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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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

PERCEPTIVE: an R shiny $\underline{p}$ipelin$\underline{e}$ for the p$\underline{r}$edi$\underline{c}$tion of $\underline{ep}$igenetic modula$\underline{t}$ors $\underline{i}$n no$\underline{v}$el sp$\underline{e}$cies

Epigenetic processes are central to regulating gene expression, genome stability, and metabolic function across the tree of life; yet, their roles remain underexplored in microalgae, especially as new species continue to be identified and characterized. This is likely due to the cumbersome nature and species-dependent attributes of epigenetic wet-lab methodologies, which preclude the rapid identification of epigenetic modifications and modulators. However, there is high conservation of epigenetic processes from budding yeast to humans; in many cases, one may infer how behavior and function are epigenetically regulated in novel species by identifying epigenetic modulators, or the proteins responsible for conferring epigenetic modifications. Here, to this end, we have developed a graphical software package, titled PERCEPTIVE (pipeline for the prediction of epigenetic modulators in novel species). This platform solely uses the genomic sequence of an algal species, and preexisting information from other model organisms, to predict the epigenetic modulators and associated modifications in algae. Predictions are presented to the user in a graphical interface, which provides literature-based interpretation of results, enabling users to quickly understand potential epigenetic processes in their algal species of interest and plan follow-up experiments. To test PERCEPTIVE, we predicted epigenetic modulators in several feedstock candidate algae species. To validate these predictions, wet-lab studies were performed, including mass spectrometry; these results underscore the high accuracy of PERCEPTIVE predictions. Overall, PERCEPTIVE represents a powerful in silico tool for the research and manipulation of algal species, which does not require a priori knowledge of epigenetics and is accessible to a broad set of investigators.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Python STXM Control (pystxmcontrol) v0.1

The software is a complete solution for controlling scanning microscopes. It provides a low level interface to device hardware via drivers, communication and coordination layers for managing scan execution and data acquisition, a graphical interface and scripting interface for user interaction. With optimized hardware drivers and low software overhead this software is 10 times faster than the legacy software it is replacing.

Shapiro, David [Lawrence Berkeley National Laborat↗
DOE OSTI2022

merlin , an improved framework for the reconstruction of high-quality genome-scale metabolic models

Abstract Genome-scale metabolic models have been recognised as useful tools for better understanding living organisms’ metabolism. merlin (https://www.merlin-sysbio.org/) is an open-source and user-friendly resource that hastens the models’ reconstruction process, conjugating manual and automatic procedures, while leveraging the user's expertise with a curation-oriented graphical interface. An updated and redesigned version of merlin is herein presented. Since 2015, several features have been implemented in merlin, along with deep changes in the software architecture, operational flow, and graphical interface. The current version (4.0) includes the implementation of novel algorithms and third-party tools for genome functional annotation, draft assembly, model refinement, and curation. Such updates increased the user base, resulting in multiple published works, including genome metabolic (re-)annotations and model reconstructions of multiple (lower and higher) eukaryotes and prokaryotes. merlin version 4.0 is the only tool able to perform template based and de novo draft reconstructions, while achieving competitive performance compared to state-of-the art tools both for well and less-studied organisms.

Capela, João (ORCID:0000000212352922)↗
DOE OSTI2022

Demonstrating solarpilot ’s Python Application Programmable Interface Through Heliostat Optimal Aimpoint Strategy Use Case

solarpilot is a software package that generates solar field layouts and characterizes the optical performance of concentrating solar power (CSP) tower systems. solarpilot was developed by the National Renewable Energy Laboratory (NREL) as a stand-alone desktop application but has also been incorporated into NREL’s System Advisor Model (SAM) in a simplified format. Prior means for user interaction with solarpilot have included the application’s graphical interface, the SAM routines with limited configurability, and through a built-in scripting language called “LK.” This article presents a new, full-featured, python-based application programmable interface (API) for solarpilot, which we hereafter refer to as CoPylot. CoPylot enables python users to perform detailed CSP tower analysis utilizing either the Hermite expansion technique (analytical) or the SolTrace ray-tracing engine. CoPylot’s enables CSP researchers to perform analysis that was previously not possible through solarpilot’s existing interfaces. This article discusses the capabilities of CoPylot and presents a use case wherein we populate a model that obtains optimal solar field aiming strategies.

14 SOLAR ENERGY↗
DOE OSTI2022

VERAView User's Manual

VERAView has been developed as an interactive graphical interface for the visualization and engineering analyses of output data from VERA. The Python-based software is easy to install, intuitive to use, and provides instantaneous 2D and 3D images, 1D plots, and alpha-numeric data from VERA multi-physics simulations. This document provides a brief overview of the software and some description of the major features of the application, including examples of each of the encapsulated “widgets” that have been implemented thus far. VERAView is still under major development and large changes in the software and this document are still anticipated.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Demonstrating SolarPILOT's Python API Through Heliostat Optimal Aimpoint Strategy Use Case: Preprint

SolarPILOT is a software package that generates heliostat field layouts and characterizes the optical performance of concentrating solar power (CSP) tower systems. SolarPILOT was developed by the National Renewable Energy Laboratory (NREL) as a stand-alone desktop application but has also been incorporated into NREL's System Advisor Model (SAM) in a simplified format. Prior means for user interaction with SolarPILOT have included the application's graphical interface, the SAM routines with limited configurability, and through a built-in scripting language called "LK." This paper presents a new, full-featured Python-based application programmable interface (API) for SolarPILOT, which we hereafter refer to as CoPylot. CoPylot provides access to all SolarPILOT's capabilities to generate and characterize power tower CSP systems seamlessly through Python. Supported capabilities include (i) creating and destroying a model instances with message reporting tools; (ii) accessing and setting any SolarPILOT variable including custom land boundaries for field layout; (iii) programmatically managing receiver and heliostat objects with varied attributes for systems with multiple receiver or heliostat types; (iv) generating, assigning, and modifying heliostat field layouts including the ability to set individual heliostat locations, aimpoints, soiling rates, and reflectivity levels; (v) simulating heliostat field performance; (vi) returning detailed results describing performance of individual heliostats, the aggregate field, and receiver flux; and, (vii) exporting Python-based model instances to multiple file formats. CoPylot enables Python users to perform detailed tower CSP analysis utilizing either the Hermite expansion technique (analytical) or the SolTrace ray-tracing engine. In addition to CoPylot's functionality, Python users have access to the over 100,000 open-source libraries to develop, analyze, optimize, and visualize CSP tower research.

41 EE - Solar Energy Technologies Office (EE-4S)↗
DOE OSTI2021

Demonstrating SolarPILOT’s Python API Through Heliostat Optimal Aimpoint Strategy Use Case

SolarPILOT is a software package that generates solar field layouts and characterizes the optical performance of concentrating solar power (CSP) tower systems. SolarPILOT was developed by the National Renewable Energy Laboratory (NREL) as a stand-alone desktop application but has also been incorporated into NREL’s1 System Advisor Model (SAM) in a simplified format. Prior means for user interaction with SolarPILOT have included the application’s graphical interface, the SAM routines with limited configurability, and through a built-in scripting language called “LK.” This paper presents a new, full-featured, Python-based application programmable interface (API) for SolarPILOT, which we hereafter refer to as CoPylot. CoPylot provides access to all SolarPILOT’s capabilities to generate and characterize power tower CSP systems seamlessly through Python. Supported capabilities include (i) creating and destroying a model instance with message reporting tools; (ii) accessing and setting any SolarPILOT variable including custom land boundaries for field layouts; (iii) programmatically managing receiver and heliostat objects with varied attributes for systems with multiple receiver or heliostat types; (iv) generating, assigning, and modifying solar field layouts including the ability to set individual heliostat locations, aimpoints, soiling rates, and reflectivity levels; (v) simulating solar field performance; (vi) returning detailed results describing performance of individual heliostats, the aggregate field, and receiver flux distribution; and, (vii) exporting Python-based model instances to multiple file formats. CoPylot enables Python users to perform detailed CSP tower analysis utilizing either the Hermite expansion technique (analytical) or the SolTrace ray-tracing engine. In addition to CoPylot’s functionality, Python users have access to the over 100,000 open-source libraries to develop, analyze, optimize, and visualize power tower CSP research. This enables CSP researchers to perform analysis that was previously not possible through SolarPILOT’s existing interfaces. This paper discusses the capabilities of CoPylot and presents a use case wherein we demonstrate optimal solar field aiming strategies.

41 EE - Solar Energy Technologies Office (EE-4S)↗
DOE OSTI2023

JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom

Abstract Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Interactive Quantum Chemistry Enabled by Machine Learning, Graphical Processing Units, and Cloud Computing

Modern quantum chemistry algorithms are increasingly able to accurately predict molecular properties that are useful for chemists in research and education. Despite this progress, performing such calculations is currently unattainable to the wider chemistry community, as they often require domain expertise, computer programming skills, and powerful computer hardware. In this review, we outline methods to eliminate these barriers using cutting-edge technologies. We discuss the ingredients needed to create accessible platforms that can compute quantum chemistry properties in real time, including graphical processing units–accelerated quantum chemistry in the cloud, artificial intelligence–driven natural molecule input methods, and extended reality visualization. We end by highlighting a series of exciting applications that assemble these components to create uniquely interactive platforms for computing and visualizing spectra, 3D structures, molecular orbitals, and many other chemical properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

hpMCA: A Python-based Graphical Program for Energy Dispersive X-Ray Diffraction Data Collection and Analysis

Energy-dispersive X-ray diffraction (EDXD) at synchrotron beamlines is commonly used for the study of material properties under high pressure and/or high temperature. Experimenters typically rely on the availability of robust data collection and analysis at a beamline, but this has become increasingly difficult, especially with the introduction of multi-element detectors that generate complex, multi-dimensional data sets. These data sets have energy resolution, and they can also be resolved in relation to sample position, diffraction angle, or different external stimuli. We report a new Python-based graphical program, hpMCA, for EDXD data collection and analysis that streamlines the experimental process for the beamline users. The program features a user-friendly interface, capability for online viewing and analyzing data from multi-element energy-dispersive detectors, and includes features useful for working with samples under high pressure and/or high temperature, such as crystal phase identification, real-time unit cell lattice refinement, and pressure determination based on an equation of state.

data analysis software↗
DOE OSTI2020

GNET2: an R package for constructing gene regulatory networks from transcriptomic data

Abstract Motivation The Gene Network Estimation Tool (GNET) is designed to build gene regulatory networks (GRNs) from transcriptomic gene expression data with a probabilistic graphical model. The data preprocessing, model construction and visualization modules of the original GNET software were developed on different programming platforms, which were inconvenient for users to deploy and use. Results Here, we present GNET2, an improved implementation of GNET as an integrated R package. GNET2 provides more flexibility for parameter initialization and regulatory module construction based on the core iterative modeling process of the original algorithm. The data exchange interface of GNET2 is handled within an R session automatically. Given the growing demand for regulatory network reconstruction from transcriptomic data, GNET2 offers a convenient option for GRN inference on large datasets. Availability and implementation The source code of GNET2 is available at https://github.com/jianlin-cheng/GNET2. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

jaxhps: An elliptic PDE solver built with machine learning in mind

Elliptic partial differential equations (PDEs) can model many physical phenomena, such as electrostatics, acoustics, wave propagation, and diffusion. In scientific machine learning settings, a high-throughput PDE solver may be required to generate a training dataset, run in the inner loop of an iterative algorithm, or interface directly with a deep neural network. To provide value to machine learning users, such a PDE solver must be compatible with standard automatic differentiation frameworks, scale efficiently when run on graphics processing units (GPUs), and maintain high accuracy for a large range of input parameters. We have designed the jaxhps package with these use-cases in mind by implementing a highly efficient and accurate solver for elliptic problems with native hardware acceleration and automatic differentiation support.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

User's Manual for RESRAD-BUILD Code Version 4: Vol. 2 - User's Guide for RESRAD-BUILD Code Version 4

The RESRAD-BUILD computer code is designed to assess radiological doses to individuals who live or work in a building contaminated with radioactive material. The code is equipped with a user-friendly interface that has many features to facilitate using the computer code and understanding the results. The design of the interface provides various options, from entering data and performing calculations to displaying calculation results. General and context-specific help are available, providing information on editing and viewing the radionuclide database, the definitions of input parameters and their use in the calculations, and the selection of the calculation results for placement into other applications. Two types of sensitivity analysis are supported by the code, i.e., deterministic and probabilistic, that can be used to study the influence of input parameters on the calculation results. This user’s guide provides instructions to help users on how to install the RESRAD-BUILD code, navigate the interface, and use the various features to set up a dose/risk analysis and to view/print the results in text and graphical outputs.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2024

GDSA framework, a computational framework for complex modeling problems in radioactive waste management

This paper details a computational framework to produce automated, graphical workflows, and how this framework can be deployed to support complex modeling problems like those in nuclear engineering. Key benefits of the framework include: automating previously manual workflows; intuitive construction and communication of workflows through a graphical interface; and automated file transfer and handling for workflows deployed across heterogeneous computing resources. This paper demonstrates the framework's application to probabilistic post-closure performance assessment of systems for deep geologic disposal of nuclear waste. However, the framework is a general capability that can help users running a variety of computational studies.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Deep residual networks for crystallography trained on synthetic data

The use of artificial intelligence to process diffraction images is challenged by the need to assemble large and precisely designed training data sets. To address this, a codebase called Resonet was developed for synthesizing diffraction data and training residual neural networks on these data. Here, two per-pattern capabilities of Resonet are demonstrated: (i) interpretation of crystal resolution and (ii) identification of overlapping lattices. Resonet was tested across a compilation of diffraction images from synchrotron experiments and X-ray free-electron laser experiments. Crucially, these models readily execute on graphics processing units and can thus significantly outperform conventional algorithms. While Resonet is currently utilized to provide real-time feedback for macromolecular crystallography users at the Stanford Synchrotron Radiation Lightsource, its simple Python-based interface makes it easy to embed in other processing frameworks. This work highlights the utility of physics-based simulation for training deep neural networks and lays the groundwork for the development of additional models to enhance diffraction collection and analysis.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Novel Results Visualization for Dynamic PSA and New Modeling Features in EMRALD

The Event Modeling Risk Assessment Linked Diagram (EMRALD) tool, developed at the Idaho National Laboratory (INL), was designed to simplify the creation of dynamic models and support various research projects. One of the primary goals of EMRALD was to provide visual methods for modeling. EMRALD consists of two main components: a web-based user interface for model development and a solve engine for running model simulations. Over time, it has evolved to meet the diverse needs of its users. Initially, EMRALD's results were simple text outputs with final key state percentages and uncertainty bounds. However, because EMRALD utilizes a three-phase discrete event simulation and tracks the paths of each simulation run leading to a key state, there is significant potential to analyze large sets of path results data, including state paths, events, and timing. Visualizing this data meaningfully posed a challenge. To address this, a novel time-based Sankey diagram was developed. EMRALD exports results data in a format that can be opened in this Sankey viewer, allowing users to visualize paths, occurrences, events, and probability data for the entire simulation run in a single diagram. Moreover, when EMRALD was first created, there were limited tools capable of meeting its graphical requirements, many of which are no longer supported. In 2024, a new web-based interface was developed using modern graphing tools, enabling additional modeling features. This paper discusses the new dynamic PSA results visualization capability and the enhanced modeling tools available in EMRALD.

97 - MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Verification of RESRAD-OFFSITE Code (V.4)

This report documents the verification of RESRAD-OFFSITE Version 4.0 and describes, where necessary, the verification of the following: • The data comprising the standard dose and risk coefficient libraries in the RESRAD database files Master_dcf_ICRP07.mdb and Master_dcf_2k.mdb. • The extraction and transfer of the data from the selected database file to the computational code by the RESRAD-OFFSITE 4.0 interface, ResOWin.exe. • The different processes that are modeled by the main computational code in RESRAD OFFSITE 4.0, ResOMain.exe. • The data displayed in the graphical and text reports. Many verifications were performed as part of the quality assurance quality control program associated with the development and release of RESRAD-OFFSITE 4.0, namely: • developer testing, • internal independent testing, and • release testing. Some were also performed in response to questions from users regarding the performance of the code. The main text of the report focuses on summarizing a subset of those tests, both independent and developer tests that verified the computations performed by the code. The verifications included in this report served as the basis for the development of the release tests of the computational executables and provided the quantitative results to be compared with the code output. The input and output interfaces and the data transfers between the various executables of the code were tested while performing the verification testing. They were tested intentionally during release testing. This report also provides some basic information to help in understanding the activities that were verified. The report: • outlines the components of RESRAD-OFFSITE 4.0 and the interconnections between these components, • outlines the processes modeled by the computational code, • provides summary figures and tables to offer confirmation of the verification of the computational components of the code, • reproduces the verifiers’ reports, if available, in individual appendices, • refers to the previous verification report (Yu et al. 2011) for more details about some of the verifications, and • reproduces the test cases and the testers’ reports from the release testing in individual appendices, when possible.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

SonicPy: a suite of programs for ultrasound pulse-echo data acquisition and analysis

Sound speed and elastic constants measurements in solids and liquids are commonly performed using the ultrasound pulse-echo technique. Recent advances have expanded the use of this technique at numerous high pressure synchrotron beamlines and offline laboratories. However, the increased experimental throughput has revealed many limitations in existing software for handling the rapid measurement and the subsequent data-reduction. Here, we report the development of a collection of computer programs for sound speed measurements using the ultrasound pulse-echo technique, compatible with stepped multi-frequency, as well as broadband-pulse, couplant-corrected methods. The programs provide a highly interactive graphical interface, enable efficient measurement, exploration and near real-time analysis of the ultrasound data, and contain features useful for working with samples under high pressure and/or high temperature. The included analysis programs can alleviate the time required for data reduction from hours to less than a minute, allowing users to make timely and informed decisions regarding the appropriate experimental parameters.

97 MATHEMATICS AND COMPUTING↗