Search NASA⌕ Search

SEARCH · Search NASA

Results for “Science Pipeline”

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.

At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

PoolDilutionR : An R package for easy optimization of isotope pool dilution calculations

Abstract Isotopic pool dilution is a powerful approach to quantify gross biogeochemical transformation rates, but remains seldom used despite its potential. To facilitate broader implementation of pool dilution methods, we present a user‐friendly R package that optimizes gross production and consumption rates (and optionally fractionation constants as well) based on standard pool dilution time series data. This package features extensive documentation and example analyses, and is easily integrated into analytical pipelines. With this open‐source tool, the biogeochemistry community will be able to readily apply isotope pool dilution to a wide range of processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Galba: genome annotation with miniprot and AUGUSTUS

The Earth Biogenome Project has rapidly increased the number of available eukaryotic genomes, but most released genomes continue to lack annotation of protein-coding genes. In addition, no transcriptome data is available for some genomes. Various gene annotation tools have been developed but each has its limitations. Here, we introduce GALBA, a fully automated pipeline that utilizes miniprot, a rapid protein-to-genome aligner, in combination with AUGUSTUS to predict genes with high accuracy. Accuracy results indicate that GALBA is particularly strong in the annotation of large vertebrate genomes. We also present use cases in insects, vertebrates, and a land plant. GALBA is fully open source and available as a docker image for easy execution with Singularity in high-performance computing environments. Our pipeline addresses the critical need for accurate gene annotation in newly sequenced genomes, and we believe that GALBA will greatly facilitate genome annotation for diverse organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A pipeline for targeted metagenomics of environmental bacteria

Background:Metagenomics and single cell genomics provide a window into the genetic repertoire of yet uncultivated microorganisms, but both methods are usually taxonomically untargeted. The combination of fluorescence in situ hybridization (FISH) and fluorescence activated cell sorting (FACS) has the potential to enrich taxonomically well-defined clades for genomic analyses. Methods:Cells hybridized with a taxon-specific FISH probe are enriched based on their fluorescence signal via flow cytometric cell sorting. A recently developed FISH procedure, the hybridization chain reaction (HCR)-FISH, provides the high signal intensities required for flow cytometric sorting while maintaining the integrity of the cellular DNA for subsequent genome sequencing. Sorted cells are subjected to shotgun sequencing, resulting in targeted metagenomes of low diversity. Results: Pure cultures of different taxonomic groups were used to (1) adapt and optimize the HCR-FISH protocol and (2) assess the effects of various cell fixation methods on both the signal intensity for cell sorting and the quality of subsequent genome amplification and sequencing. Best results were obtained for ethanol-fixed cells in terms of both HCR-FISH signal intensity and genome assembly quality. Our newly developed pipeline was successfully applied to a marine plankton sample from the North Sea yielding good quality metagenome assembled genomes from a yet uncultivated flavobacterial clade. Conclusions: With the developed pipeline, targeted metagenomes at various taxonomic levels can be efficiently retrieved from environmental samples. The resulting metagenome assembled genomes allow for the description of yet uncharacterized microbial clades.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Dataset Repository for Investigating Suicide Risk Using Social and Environmental Determinants of Health

Suicide is frequently modeled as a function of genetics and environment, where the latter refers to factors other than direct biological consequences, such as air quality, financial level, social connectivity, transportation and food access, and homelessness status. According to the World Health Organization, clean air, a stable climate, adequate water, sanitation and hygiene, safe chemical use, radiation protection, healthy and safe workplaces, sound agricultural practices, health-supportive cities and built environments, and a preserved natural environment are all prerequisites for good health. Understanding the relationships between these determinants and mental health outcomes requires standardized data that can be included in healthcare programs and health outcome models. There is a wealth of publicly available data on social and environmental factors provided by various US organizations that can benefit the design of health care systems and public health interventions, as well as improve our comprehension of factors that impact health. Such information would not only help improve the understanding of individual and community risk but also identify new risk factors that have not previously been therapeutically targeted, especially in terms of their impact on mental health. However, curating and standardizing such datasets is challenging because they are often recorded at numerous geographical and temporal resolutions and with varying spatial and temporal granularities. To address this challenge, we launched an endeavor in conjunction with the Veterans Health Administration to collect publicly available socioeconomic and environmental determinants of health statistics in the US. In this manuscript, we describe a social and environmental determinants of health (SEDH) datasets repository, data curation documentation, and a pipeline framework for data generation; This effort started in 2020, when we began constructing a scalable pipeline to automate the download, extraction, preparation, analysis, and production of datasets. These datasets have been made available to the VHA and may be shared upon agreement with collaborating organizations.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Hydrogen Generation and Industrial Heat Opportunities for Nuclear Plants in the Gulf Coast

The United States (U.S.) nuclear-generation fleet stands as a critical national strategic asset, playing a pivotal role in achieving climate goals. Operating on light-water reactor (LWR) technologies, this fleet provides the largest share of U.S. carbon-free electrical generation, ensuring 24/7 clean-energy stability. With a proven track record of reliability while operating at high-capacity factors, consistently above 90%, the existing nuclear fleet serves as a cornerstone for sustainable energy. The Department of Energy’s (DOE’s) Light Water Reactor Sustainability (LWRS), Flexible Plant Operations and Generation pathway addresses U.S. nuclear power plant (NPP) grid integration challenges in the face of evolving energy landscapes. Research at Idaho National Laboratory (INL) highlights the potential synergy between high-temperature steam-electrolysis (HTSE) technology and nuclear steam and electricity during periods of high renewable grid penetration. Large-scale nuclear-integrated hydrogen production through HTSE presents significant potential for decarbonizing such energy-intensive sectors as oil refining, petrochemicals, ammonia, and fertilizers. The strategic advantage lies in the nuclear sector’s capability to deliver clean electrical and/or steam output during periods of low demand. Nuclear-produced hydrogen—with its ability to provide high-purity clean H 2 well below the national standard of 1 kg of CO 2 per kg of H 2 —represents a breakthrough methodology. This emphasizes the crucial role NPPs can fill in addressing the increasing need for clean hydrogen, establishing them as essential contributors to decarbonization. This report specifically delves into hydrogen-generation opportunities from the U.S. Gulf Coast region. This study aims to assess NPP capabilities for hydrogen production and to identify practical nearby industrial and pipeline-operator off-takers for nuclear-integrated hydrogen production as well as to present some specific case-study analysis showing the conditions under which nuclear hydrogen production and sale can be profitable. Also considered in this report is preliminary analysis of nuclear-heat opportunities accessible near Waterford NPP via transportation of hypothetical steam pipelines and heat-exchange equipment.

08 HYDROGEN↗
DOE OSTI2022

Drugsniffer: An Open Source Workflow for Virtually Screening Billions of Molecules for Binding Affinity to Protein Targets

The SARS-CoV2 pandemic has highlighted the importance of efficient and effective methods for identification of therapeutic drugs, and in particular has laid bare the need for methods that allow exploration of the full diversity of synthesizable small molecules. While classical high-throughput screening methods may consider up to millions of molecules, virtual screening methods hold the promise of enabling appraisal of billions of candidate molecules, thus expanding the search space while concurrently reducing costs and speeding discovery. Here, we describe a new screening pipeline, called drugsniffer, that is capable of rapidly exploring drug candidates from a library of billions of molecules, and is designed to support distributed computation on cluster and cloud resources. As an example of performance, our pipeline required ~40,000 total compute hours to screen for potential drugs targeting three SARS-CoV2 proteins among a library of ~3.7 billion candidate molecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

ADEPT: A Pedagogical Framework for Integrating Agentic AI with Deterministic Scientific Workflows

The integration of Large Language Models (LLMs) into scientific research promises to accelerate discovery, yet a significant gap remains between the dynamic reasoning of Artificial Intelligence (AI) agents and the static, deterministic nature of canonical scientific workflows. This paper introduces ADEPT (Agentic Discovery and Exploration Platform for Tools), a reference architecture and pedagogical framework explicitly designed to bridge this gap. ADEPT's primary mission is to provide a transparent, "glass-box" environment where researchers and engineers can learn to effectively wrap established scientific software (e.g., BLAST, Nextflow pipelines) and compose it into reliable, agent-driven workflows. We describe its modular, multi-server architecture, which leverages the Model Context Protocol (MCP) for tool serving, LangGraph for robust agentic orchestration, and a secure nsjail-based sandbox for safe code execution. By prioritizing architectural clarity, safety, and modularity, ADEPT serves as an extensible blueprint for building trustworthy AI-augmented systems and fosters the collaborative development necessary to responsibly employ agentic AI for science. We provide practical examples of how to adapt and extend this framework, highlighting its utility in workforce development and AI-readiness capabilities across research and development projects.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Deep-Learning-Derived Evaluation Metrics Enable Effective Benchmarking of Computational Tools for Phosphopeptide Identification

Tandem mass spectrometry (MS/MS)-based phosphoproteomics is a powerful technology for global phosphorylation analysis. However, applying four computational pipelines to a typical mass spectrometry (MS)-based phosphoproteomic dataset from a human cancer study, we observed a large discrepancy among the reported phosphopeptide identification and phosphosite localization results, underscoring a critical need for benchmarking. While efforts have been made to compare performance of computational pipelines using data from synthetic phosphopeptides, evaluations involving real application data have been largely limited to comparing the numbers of phosphopeptide identifications due to the lack of appropriate evaluation metrics. We investigated three deep learning-derived features as potential evaluation metrics: phosphosite probability, Delta RT and spectral similarity. Predicted phosphosite probability is computed by MusiteDeep, which provides high accuracy as previously reported; Delta RT is defined as the absolute retention time (RT) difference between RTs observed and predicted by AutoRT; and spectral similarity is defined as the Pearson’s correlation coefficient between spectra observed and predicted by pDeep2. Using a synthetic peptide dataset, we found that both Delta RT and spectral similarity provided excellent discrimination between correct and incorrect peptide-spectrum matches (PSMs) both when incorrect PSMs involved wrong peptide sequences and even when incorrect PSMs were caused by only incorrect phosphosite localization. Based on these results, we used all the three deep learning-derived features as evaluation metrics to compare different computational pipelines on diverse set of phosphoproteomic datasets and showed their utility in benchmarking performance of the pipelines. The benchmark metrics demonstrated in this study will enable users to select computational pipelines and parameters for routine analysis of phosphoproteomics data and will offer guidance for developers to improve computational methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Prediction of the Cu oxidation state from EELS and XAS spectra using supervised machine learning

Abstract Electron energy loss spectroscopy (EELS) and X-ray absorption spectroscopy (XAS) provide detailed information about bonding, distributions and locations of atoms, and their coordination numbers and oxidation states. However, analysis of XAS/EELS data often relies on matching an unknown experimental sample to a series of simulated or experimental standard samples. This limits analysis throughput and the ability to extract quantitative information from a sample. In this work, we have trained a random forest model capable of predicting the oxidation state of copper based on its L-edge spectrum. Our model attains an R 2 score of 0.85 and a root mean square error of 0.24 on simulated data. It has also successfully predicted experimental L-edge EELS spectra taken in this work and XAS spectra extracted from the literature. We further demonstrate the utility of this model by predicting simulated and experimental spectra of mixed valence samples generated by this work. This model can be integrated into a real-time EELS/XAS analysis pipeline on mixtures of copper-containing materials of unknown composition and oxidation state. By expanding the training data, this methodology can be extended to data-driven spectral analysis of a broad range of materials.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Synchrotron‐source micro‐x‐ray computed tomography for examining butterfly eyes

Comparative anatomy is an important tool for investigating evolutionary relationships among species, but the lack of scalable imaging tools and stains for rapidly mapping the microscale anatomies of related species poses a major impediment to using comparative anatomy approaches for identifying evolutionary adaptations. We describe a method using synchrotron source micro-x-ray computed tomography (syn-μXCT) combined with machine learning algorithms for high-throughput imaging of Lepidoptera (i.e., butterfly and moth) eyes. Our pipeline allows for imaging at rates of ~15 min/mm 3 at 600 nm 3 resolution. Image contrast is generated using standard electron microscopy labeling approaches (e.g., osmium tetroxide) that unbiasedly labels all cellular membranes in a species-independent manner thus removing any barrier to imaging any species of interest. To demonstrate the power of the method, we analyzed the 3D morphologies of butterfly crystalline cones, a part of the visual system associated with acuity and sensitivity and found significant variation within six butterfly individuals. Despite this variation, a classic measure of optimization, the ratio of interommatidial angle to resolving power of ommatidia, largely agrees with early work on eye geometry across species. We show that this method can successfully be used to determine compound eye organization and crystalline cone morphology. Our novel pipeline provides for fast, scalable visualization and analysis of eye anatomies that can be applied to any arthropod species, enabling new questions about evolutionary adaptations of compound eyes and beyond.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

The Impact of Time-Aware Design Choices in ICS Anomaly Detection

Industrial control systems (ICS) remain vulnerable to increasingly sophisticated cyberattacks, yet evaluating anomaly detection models in these environments is challenging due to temporal dependencies, missing-not-at-random patterns, and extremely imbalanced datasets. These factors make common practices—especially random data splits and na¨ıve imputation— prone to severe temporal leakage, which can inflate reported performance and obscure real-world limitations. In this work, we systematically examine classical machine learning models, temporal deep learning architecture, and tensordecomposition– based methods on a gas-pipeline dataset using a fully temporally separated evaluation pipeline designed to mimic realistic deployment conditions. Our findings show that proper temporal handling and MNAR-aware preprocessing significantly alter the relative performance of popular anomaly-detection methods, providing practical guidance for designing reliable, leakage-resistant ICS intrusion-detection systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Red-Ox Robust SOFC Stacks for Affordable, Reliable Distributed Generation Power Systems

While SOFC systems are expected to operate reliably and with limited degradation in steady state or transient performance, SOFC stacks may ultimately fail due to the loss of structural integrity of one or several of the cells as a result of the weakening of the materials and interfaces due to physico-chemical changes that occur during continuous operation as a result of plastic and creep deformations, modification of the temperature profile, and/or degradation of the electrochemical performance of the cells. Degradation mechanisms originating from the cell components include coarsening of the microstructure over time; decomposition of materials; chemical reaction of electrode materials with electrolyte at the interface; delamination from each other; and for the anode, coking and sulfur poisoning. Of all the reliability issues that may occur for SOFCs, the main limitation for Ni-based cermet anodes (e.g., NiO-YSZ) is the poor stability during reduction-oxidation (red-ox) cycling. This project was aimed at the development of ceramic anode SOFCs based on SFCM (SrFe0.2Co0.4Mo0.4O3), which is a conductive perovskite that is red-ox stable. Additionally, the project involved the development of a red-ox robust stack. Scale up of SFCM-based cells to a large format (10 cm by 10 cm) cell size was achieved as well as a maximum power density of 0.9 W/cm 2 at 600 °C (>0.6 W/cm 2 at 0.6 V). Up to a 10-cell stack was successfully assembled and demonstrated, and cells showed similar performance in reformed, pipeline natural gas as in hydrogen. Finally, a 3-cell stack was red-ox cycled without degradation for 40 cycles at ~600 °C.

03 NATURAL GAS↗
DOE OSTI2021

Feature Extraction: Improving Remote Sensor Classification of Non-Proliferation

This research focuses on developing algorithms for nuclear non-proliferation detection using remote sensor modeling. To improve the performance of classification models, we implemented a data pipeline with feature extraction. This pipeline takes raw data and transforms it into smaller data points called features that still describe the model. Improving this classification works towards the departments of energy’s missions of ensuring American’s security and prosperity by creating technology that addresses nuclear challenges. To conduct this analysis, we used the Python programming language and some key packages, including tsfresh and TSFEL. Originally tsfresh was selected because it has the most statistical features out of all the packages. Later TSFEL was incorporated due to the additional features it can extract from data, such as temporal and spectral. However, feature extraction becomes challenging in the presence of missing values. In this case, two additional Python packages were added to our workflow, NumPy and pandas, allowing for the feature extraction process to handle unknown values. Our data pipeline was tested on data collected from a simulation that describes the process state of a physical example. The results show the pipeline’s capability to consume and extract a total 17 features from tabular data. Future work includes producing classifications using decision tree-based models such as XGBoost and improving data collection by analyzing feature importance.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

DESI Spectroscopy of HETDEX Emission-line Candidates. I. Line Discrimination Validation

The Hobby–Eberly Dark Energy Experiment (HETDEX) is an untargeted spectroscopic galaxy survey that uses Lyα-emitting galaxies (LAEs) as tracers of 1.9 < z < 3.5 large-scale structure. Most detections consist of a single emission line, whose identity is inferred via a Bayesian analysis of ancillary data. To determine the accuracy of these line identifications, HETDEX detections were observed with the Dark Energy Spectroscopic Instrument (DESI). In two DESI pointings, high-confidence spectroscopic redshifts are obtained for 1157 sources, including 982 LAEs. The DESI spectra are used to evaluate the accuracy of the HETDEX object classifications and tune the methodology to achieve the HETDEX science requirement of ≲2% contamination of the LAE sample by low-redshift emission-line galaxies, while still assigning 96% of the true Lyα emission sample with the correct spectroscopic redshift. We compare emission-line measurements between the two experiments assuming a simple Gaussian line fitting model. Fitted values for the central wavelength of the emission line, the measured line flux, and line widths are consistent between the surveys within uncertainties. Derived spectroscopic redshifts, from the two classification pipelines, when both agree as an LAE classification, are consistent to within $\langle$Δz/(1 + z)$\rangle$ = 6.9 × 10 −5 with an rms scatter of 3.3 × 10 −4 . Data are available at https://data.desi.lbl.gov/desi/public/dr1/vac/dr1/hetdex.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

High–throughput measurement of plant fitness traits with an object detection method using Faster R–CNN

Revealing the contributions of genes to plant phenotype is frequently challenging because loss-of-function effects may be subtle or masked by varying degrees of genetic redundancy. Such effects can potentially be detected by measuring plant fitness, which reflects the cumulative effects of genetic changes over the lifetime of a plant. However, fitness is challenging to measure accurately, particularly in species with high fecundity and relatively small propagule sizes such as Arabidopsis thaliana. An image segmentation-based method using the software ImageJ and an object detection-based method using the Faster Region-based Convolutional Neural Network (R-CNN) algorithm were used for measuring two Arabidopsis fitness traits: seed and fruit counts. The segmentation-based method was error-prone (correlation between true and predicted seed counts, r 2 = 0.849) because seeds touching each other were undercounted. By contrast, the object detection-based algorithm yielded near perfect seed counts (r 2 = 0.9996) and highly accurate fruit counts (r 2 = 0.980). Comparing seed counts for wild-type and 12 mutant lines revealed fitness effects for three genes; fruit counts revealed the same effects for two genes. Our study provides analysis pipelines and models to facilitate the investigation of Arabidopsis fitness traits and demonstrates the importance of examining fitness traits when studying gene functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A Carbon Dioxide Refinery: The Core of a Sustainable Carbon-based Circular Economy

The atmospheric carbon dioxide (CO 2 ) accumulation (2–2.5 ppmv/year) is the result of the enormous gap between its emissions (37 Gton/year) and its capture, storage, and utilization (<500 Mton/year). Climate has been dramatically affected due to the failure of natural sinks, in working effectively. To address this Gton-scale gap, numerous uses and applications are needed particularly, those consuming vast volumes of this compound and/or rendering longevous products or long lifecycle services. Thus, carbon utilization (CU) can be seen as the step to close the carbon cycle. Among CU, R&D on CO 2 chemical conversion has proposed a variety of processes, with different degrees of developmental maturity. These chemical process technologies could be efficiently and effectively integrated into refineries to upgrade emitted CO 2 . A technology pipeline consisting of a database of these processes and the technology market status should be defined based on published scientific results and patents. Then, an innovative top-down methodology is proposed to eco-design configurations of that refinery, to warrant a sustainable carbon cycle (in terms of energy, environment, and economy) and to change the ways of producing fuels, chemicals, and materials. Additionally, the proposed methodology could be used to identify research and development gaps and needs, for orienting science and technology investments and measures. Hopefully, sustainable CO 2 refineries will be implemented to close the carbon cycle of a circular C-based economy and underpin a decarbonized chemical industry.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

pathSQE : an automated workflow for single-crystal inelastic neutron scattering data processing and analysis

Inelastic neutron scattering (INS) experiments utilizing modern time-of-flight spectrometers enable the comprehensive mapping of the energy (E)- and momentum (Q)-resolved dynamical structure factor of single crystals, probing both the lattice and magnetic excitations. Yet, the large size and complexity of four-dimensional INS data are challenging current analysis workflows, often resulting in an underutilization of the measured information. To help address this issue, this paper introduces new software interfaced with the Mantid framework, pathSQE, designed to streamline the processing, analysis and interpretation of 4D single-crystal INS data. By automating key tasks such as 1D/2D slicing, symmetrization, Brillouin zone folding, data visualization, prioritization and filtering, and comparisons with simulations, pathSQE facilitates and accelerates INS data analysis workflows. Here, this paper outlines the features and implementation and provides several illustrations of the use of pathSQE on data collected on single crystals using direct-geometry time-of-flight spectrometers at the Spallation Neutron Source, including Ge, FeSi, MnO and SnS single-crystal measurements on the ARCS, HYSPEC and CNCS neutron spectrometers. Beyond streamlining post-experiment data processing, pathSQE establishes an automated and modular processing pipeline that could support future real-time experiment steering.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Optical Biosensor Platforms Display Varying Sensitivity for the Direct Detection of Influenza RNA

Detection methods that do not require nucleic acid amplification are advantageous for viral diagnostics due to their rapid results. These platforms could provide information for both accurate diagnoses and pandemic surveillance. Influenza virus is prone to pandemic-inducing genetic mutations, so there is a need to apply these detection platforms to influenza diagnostics. Here, we analyzed the Fast Evaluation of Viral Emerging Risks (FEVER) pipeline on ultrasensitive detection platforms, including a waveguide-based optical biosensor and a flow cytometry bead-based assay. The pipeline was also evaluated in silico for sequence coverage in comparison to the U.S. Centers for Disease Control and Prevention’s (CDC) influenza A and B diagnostic assays. The influenza FEVER probe design had a higher tolerance for mismatched bases than the CDC’s probes, and the FEVER probes altogether had a higher detection rate for influenza isolate sequences from GenBank. When formatted for use as molecular beacons, the FEVER probes detected influenza RNA as low as 50 nM on the waveguide-based optical biosensor and 1 nM on the flow cytometer. In addition to molecular beacons, which have an inherently high background signal we also developed an exonuclease selection method that could detect 500 pM of RNA. The combination of high-coverage probes developed using the FEVER pipeline coupled with ultrasensitive optical biosensors is a promising approach for future influenza diagnostic and biosurveillance applications.

59 BASIC BIOLOGICAL SCIENCES↗