Search NASA⌕ Search

SEARCH · Search NASA

Results for “background software”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

44 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

HostSub_GP: Precise Galaxy Background Subtraction in Transient Long-slit Spectroscopy with Gaussian Processes

We present a novel host galaxy subtraction technique in long-slit spectroscopy for extragalactic transients. Unlike classic methods which generally estimate the background using simple interpolation of local galaxy flux in the 2D spectrum, our approach leverages multi-band archival images of the host galaxies to model the background emission from the galaxy in the 2D spectrum. Such imaging encodes the wavelength-dependent galaxy profile along the slit, and is readily accessible through wide-field imaging surveys. We construct a smooth prior for the 2D galaxy profile with a Gaussian process (GP) based on these reference images, and use another GP to model the correlated deviations from the prior in the observed spectrum. This enables accurate inference of the galaxy flux blended with the transient. On synthetic long-slit data of a spiral galaxy extracted from a Multi Unit Spectroscopic Explorer hyper-spectral cube, the GP method remains robust as long as the host galaxy is spatially resolved and consistently outperforms classic methods. We apply the method to archival Keck spectra of two real transients, SN 2019eix and AT 2019qiz, to further demonstrate how the method uniquely recovers weak spectral features amid strong galaxy contamination, enabling refined constraints on the properties of both transients. We have released the software implementation, HostSub_GP, a scalable toolkit that leverages JAX, with an MIT license.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Surface science insight note: Optimizing XPS instrument performance for quantification of spectra

X-ray photoelectron spectroscopy (XPS) provides quantitative information from photoemission peaks and shapes observed within the background due to the inelastic scattering of photoelectrons. To quantify the signal, both photoemission peaks and background in spectra must be adjusted for instrumental transmission variations that are a consequence of changes in efficiency when recording electrons with different kinetic energy. While it is generally assumed that correcting spectroscopic data for transmission is a necessary part of quantification by XPS, there are consequences for the quantification of spectra measured using an instrument for which transmission has significant curvature. In this Insight, the implications of curvature in transmission characteristics are discussed and a method based on XPS microscopy is proposed that ensures the transmission response of an instrument is free from significant curvature. An example of an instrument for which a flat transmission response is presented is achieved through collecting spectra using lens modes designed to measure stigmatic images.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

LinkML: an open data modeling framework

Background Scientific research relies on well-structured, standardized data; however, much of it is stored in formats such as free-text lab notebooks, nonstandardized spreadsheets, or data repositories. This lack of structure challenges interoperability, making data integration, validation, and reuse difficult. Findings LinkML (Linked Data Modeling Language) is an open framework that simplifies the process of authoring, validating, and sharing data. LinkML can describe a range of data structures, from flat, list-based models to complex, interrelated, and normalized models that utilize polymorphism and compound inheritance. It offers an approachable syntax that is not tied to any one technical architecture and can be integrated seamlessly with many existing frameworks. The LinkML syntax provides a standard way to describe schemas, classes, and relationships, allowing modelers to build well-defined, stable, and optionally ontology-aligned data structures. Once defined, LinkML schemas may be imported into other LinkML schemas. These key features make LinkML an accessible platform for interdisciplinary collaboration and a reliable way to define and share data semantics. Conclusions LinkML helps reduce heterogeneity, complexity, and the proliferation of single-use data models while simultaneously enabling compliance with FAIR (Findable, Accessible, Interoperable, and Reusable) data standards. LinkML has seen increasing adoption in various fields, including biology, chemistry, biomedicine, microbiome research, finance, electrical engineering, transportation, and commercial software development. In short, LinkML makes implicit models explicitly computable and allows data to be standardized at their origin. LinkML documentation and code are available at https://linkml.io/.

AI-ready data↗
DOE OSTI2024

XRF-XFS-XAS-Auto v1.0 - Beta release

This software allows to analyze XRF maps, XFS spectra and XAS spectra collected at the Advanced Light Source's Beamline 10.3.2. Features include: 1) XRF maps: - process XRF maps, all elemental maps are saved as bmp automatically and labeled with the incident energy used, the scale bar is also labeled and can be controlled. - XRF elemental correlation plots, save the correlation plots automatically - Extract single or multiple transects in XRF maps on one or several regions of interest, each transect profile is numbered and saved in a corresponding folder, along with the corresponding maps showing transect location. 2) XFS spectra - save in log10 scale the XFS spectra, either a single or multiple files all at once. The files are saved as .bmp. - XFS spectra are labeled according to tabulated fluorescence emission lines. 3) XAS spectra - allows to plot individual scalers in the raw data. - allows calibration of the spectra using an Io internal glitch present in all spectra and performing 1st derivative. - Least-square linear combination fitting of XANES or extended XANES spectra using a database of standards using 1, 2 or 3 components maximum. It also provides the 5 top combinations and provide the user for the possibility of saving the 2nd, 3rd, 4th and 5th best combinations in addition to the best one. The processed spectra (pre-edge background substracted, post-edge normalized), the fits and residuals are automatically saved. A table of the component, with fit% and SSN is provided and saved automatically as well.

Fakra, Sirine↗
DOE OSTI2026

From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture

Background Characterizing the physical organization of the genome is essential for understanding long-range gene regulation, chromatin compartmentalization, and epigenetic accessibility. Hi-C experiments generate two-dimensional (2D) genome-wide contact maps of chromatin interactions by capturing the spatial proximity between genomic loci, which reveal interaction frequencies but lack the spatial resolution needed to interpret the three-dimensional (3D) genome structure(s). Emerging evidence suggests that epigenetic regulation is closely linked to 3D genome architecture, and that structural changes over time (4D) drive key biological processes in development, disease, and environmental response. Thus, integrating 3D structure with functional data is critical for a more complete understanding of genome regulation. Previous work, most notably the 4DHiC chromosome modeling framework, has shown that physical multi-dimensional modeling approaches rooted in polymer physics and molecular dynamics can resolve these structures at biologically meaningful resolutions by integrating temporal Hi-C data with physical constraints to uncover dynamic chromosome reorganization. Thus, molecular dynamics simulations, constrained by Hi-C contact matrices, can resolve fine-scale structural changes and reveal functionally significant transitions in chromatin conformation. Results Herein, we present the 4D Genome Browser Workflow (4DGBWorkflow) and the 4D Genome Browser (4DGB). The algorithm is based on the 4DHiC method, and the containerized tool is an end-to-end workflow that can transform, filter, and view 4D epigenomics and chromatin datasets, allowing non-specialists to apply three-dimensional modeling principles to diverse datasets and experimental conditions. The software executes on a laptop running macOS, Linux or Windows. From input Hi-C files (.hic), the 4DGBWorkflow produces 3D reconstructions of chromosomes, integrates the reconstruction with track data (e.g., epigenetic marks, transcriptome profiles), and provides comparative visualization of the results in a single workflow. Conclusions The 4DGBWorkflow and 4D Genome Browser are open-source tools for comparative analysis and visualization of 4D chromosome datasets, including chromatin architecture and epigenomic signals. Automatic integration of Hi-C data with molecular dynamics democratizes the construction of time resolved 3D genome structures, simplifying complex simulations and data integration schemes.

3D Genome Browser↗
DOE OSTI2026

Methods for safely sharing dual-use genetic data

Background: Some genetic data has dual-use potential. Sharing pathogen data has shown tremendous value. For example therapeutic development and lineage tracking during the COVID pandemic. This data sharing is complicated by the fact that these data have the potential to be used for harm. The genome sequence of a pathogen can be used to enable malicious genetic engineering approaches or to recreate the pathogen from synthetic DNA. Standard data security methods can be applied to genetic data, but when data is shared between institutions, ensuring appropriate security can be difficult. Sensitive data that is shared internationally among a wide array of institutions can be especially difficult to control. Methods for securely storing and sharing genetic data with potential for dual-use are needed to mitigate this potential harm.Results: Here we propose new methods that allow genetic data to be shared in a data format that prevents a nefarious actor from accessing sensitive aspects of the data. Our methods obfuscate raw sequence data by pooling reads from different samples. This approach can ensure that data is secure while stored and during electronic transfer. We demonstrate that by pooling raw sequence data from multiple samples of the same organism, the ability to fully reconstruct any individual sample is prevented. In the pooled data, most genomic information remains, but reads or mutations cannot be directly attributed to any individual sample. To further restrict access to information, regions of a genome can be removed from the reads.Conclusion: Our methods obscure genomic information within raw sequence reads. This method can allow genetic data to be stored and shared while preventing a nefarious actor from being able to perfectly reconstruct an organism. Broad-scale sequence information remains, while fine scale details about specific samples are difficult or impossible to reconstruct. Our software is available at https://github.com/Geneinfosec-Inc/ReadMixer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

The Cosmic Evolution of C IV Absorbers at 1.4 < z < 4.5: Insights from 100,000 Systems in DESI Quasars

We present the largest catalog to date of triply ionized carbon (C IV ) absorbers detected in quasar spectra from the Dark Energy Spectroscopic Instrument. Using an automated matched-kernel convolution method with adaptive signal-to-noise thresholds, we identify 101,487 C IV systems in the redshift range 1.4 < z < 4.5 from 300,637 quasar spectra. Completeness is estimated via Monte Carlo simulations, and the catalog is 50% complete at EW C IV ≥ 0.4 Å. The differential equivalent width frequency distribution declines exponentially and shows weak redshift evolution. The absorber incidence per unit comoving path increases by a factor of 2–5 from z ≈ 4.5 to z ≈ 1.4, with stronger redshift evolution for strong systems. Using column densities derived from the apparent optical depth method, we constrain the cosmic mass density of C IV , Ω C IV , which increases by a factor of ∼3.8 from (0.82 ± 0.05) × 10 −8 at z ≈ 4.5 to (3.16 ± 0.2) × 10 −8 at z ≈ 1.4. From Ω C IV , we estimate a lower limit on intergalactic medium metallicity ${\mathrm{log}}({Z}_{{\rm{IGM}}}/{Z}_{\odot })\gtrsim -3.25$ at z ∼ 2.3, with a smooth decline at higher redshifts. These trends trace the cosmic star formation history and He II photoheating rate, suggesting a link between C IV enrichment, star formation, and UV background over ∼3 Gyr. The catalog also provides a critical resource for future studies connecting circumgalactic metals to galaxy evolution, especially near cosmic noon.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

The Early Data Release of the Dark Energy Spectroscopic Instrument

The Dark Energy Spectroscopic Instrument (DESI) completed its 5 month Survey Validation in 2021 May. Spectra of stellar and extragalactic targets from Survey Validation constitute the first major data sample from the DESI survey. This paper describes the public release of those spectra, the catalogs of derived properties, and the intermediate data products. In total, the public release includes good-quality spectral information from 466,447 objects targeted as part of the Milky Way Survey, 428,758 as part of the Bright Galaxy Survey, 227,318 as part of the Luminous Red Galaxy sample, 437,664 as part of the Emission Line Galaxy sample, and 76,079 as part of the Quasar sample. In addition, the release includes spectral information from 137,148 objects that expand the scope beyond the primary samples as part of a series of secondary programs. Here, we describe the spectral data, data quality, data products, Large-Scale Structure science catalogs, access to the data, and references that provide relevant background to using these spectra.

79 ASTRONOMY AND ASTROPHYSICS↗