Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “ATLAS”

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 811 records · Page 45
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Visualization of texture components using MTEX

Knowledge of the appearance of texture components and fibres in pole figures, in inverse pole figures and in Euler space is fundamental for texture analysis. For cubic crystal systems, such as steels, an extensive literature exists and, for example, the book by Matthies, Vinel & Helming [Standard Distributions in Texture Analysis: Maps for the Case of Cubic Orthorhomic Symmetry, (1987), Akademie-Verlag Berlin] provides an atlas to identify texture components. For lower crystal symmetries, however, equivalent comprehensive overviews that can serve as guidance for the interpretation of experimental textures do not exist. Here, this paper closes this gap by providing a set of scripts for the MTEX package [Bachmann, Hielscher & Schaeben (2010). Solid State Phenom.160, 63–68] that allow the texture practitioner to compile such an atlas for a given material system, thus aiding orientation distribution function analysis also for non-cubic systems.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Measurement of the inclusive isolated-photon production cross section in pp collisions at $\mathbf {\sqrt{\textit{s}}=13}$ TeV

The production cross section of inclusive isolated photons has been measured by the ALICE experiment at the CERN LHC in pp collisions at centre-of-momentum energy of $\mathbf {\sqrt{\textit{s}}=13}$ TeV collected during the LHC Run 2 data-taking period. The measurement is performed by combining the measurements of the electromagnetic calorimeter EMCal and the central tracking detectors ITS and TPC, covering a pseudorapidity range of and a transverse momentum range of |η γ | < 0.67 and a transverse momentum range 7 < p$^{γ}_{T}$ < 200 GeV/c. The result extends to lower p$^{γ}_{T}$ and x$^{γ}_{T}$ = 2p$^{γ}_{T}$/$\sqrt{s}$ ranges, the lowest x$^{γ}_{T}$ of any isolated photon measurements to date, extending significantly those measured by the ATLAS and CMS experiments towards lower p$^{γ}_{T}$ at the same collision energy with a small overlap between the measurements. The measurement is compared with next-to-leading order perturbative QCD calculations and the results from the ATLAS and CMS experiments as well as with measurements at other collision energies. The measurement and theory prediction are in agreement with each other within the experimental and theoretical uncertainties.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

iDDS: intelligent distributed dispatch and scheduling for workflow orchestration

The intelligent distributed dispatch and scheduling (iDDS) service is a versatile workflow orchestration system designed for large-scale, distributed scientific computing. iDDS extends traditional workload and data management by integrating data-aware execution, conditional logic, and programmable workflows, enabling automation of complex and dynamic processing pipelines. Originally developed for the ATLAS experiment at the large hadron collider, iDDS has evolved into an experiment-agnostic platform that supports both template-driven workflows and a Function-as-a-Task model for Python-based orchestration. This paper presents the architecture and core components of iDDS, highlighting its scalability, modular message-driven design, and integration with systems such as PanDA and Rucio. We demonstrate its versatility through real-world use cases: fine-grained tape resource optimization for ATLAS, orchestration of large Directed Acyclic Graph (DAG) workflows for the Rubin Observatory, distributed hyperparameter optimization for machine learning applications, active learning for physics analyses, and AI-assisted detector design at the electron–ion collider. By unifying workload scheduling, data movement, and adaptive decision-making, iDDS reduces operational overhead and enables reproducible, high-throughput workflows across heterogeneous infrastructures. We conclude with current challenges and future directions, including interactive, cloud-native, and serverless workflow support.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Reduce, reuse, reinterpret: An end-to-end pipeline for recycling particle physics results

Searches for new physics at the Large Hadron Collider have constrained many models of physics beyond the Standard Model. Many searches also provide resources that allow them to be reinterpreted in the context of other models. We describe a reinterpretation pipeline that examines previously untested models of new physics using supplementary information from ATLAS Supersymmetry (SUSY) searches in a way that provides accurate constraints even for models that differ meaningfully from the benchmark models of the original analysis. The public analysis information, such as public analysis routines and serialized probability models, is combined with common event generation and simulation toolkits MADGRAPH, PYTHIA8, and DELPHES into workflows steered by TOML configuration files, and bundled into the mapyde Python package. The use of mapyde is demonstrated by constraining previously untested SUSY models with compressed sleptons and electroweakinos using ATLAS results.

Stark, Giordon↗
DOE OSTI2024

Codebase release 0.5 for mapyde

Searches for new physics at the Large Hadron Collider have constrained many models of physics beyond the Standard Model. Many searches also provide resources that allow them to be reinterpreted in the context of other models. We describe a reinterpretation pipeline that examines previously untested models of new physics using supplementary information from ATLAS Supersymmetry (SUSY) searches in a way that provides accurate constraints even for models that differ meaningfully from the benchmark models of the original analysis. The public analysis information, such as public analysis routines and serialized probability models, is combined with common event generation and simulation toolkits MADGRAPH, PYTHIA8, and DELPHES into workflows steered by TOML configuration files, and bundled into the mapyde Python package. The use of mapyde is demonstrated by constraining previously untested SUSY models with compressed sleptons and electroweakinos using ATLAS results.

Stark, Giordon↗
DOE OSTI2022

BROOD: Bilevel and Robust Optimization and Outlier Detection for Efficient Tuning of High-Energy Physics Event Generators

The parameters in Monte Carlo (MC) event generators are tuned on experimental measurements by evaluating the goodness of fit between the data and the MC predictions. The relative importance of each measurement is adjusted manually in an often time-consuming, iterative process to meet different experimental needs. In this work, we introduce several optimization formulations and algorithms with new decision criteria for streamlining and automating this process. These algorithms are designed for two formulations: bilevel optimization and robust optimization. Both formulations are applied to the datasets used in the ATLAS A14 tune and to the dedicated hadronization datasets generated by the SHERPA generator, respectively. The corresponding tuned generator parameters are compared using three metrics. We compare the quality of our automatic tunes to the published ATLAS A14 tune. Moreover, we analyze the impact of a pre-processing step that excludes data that cannot be described by the physics models used in the MC event generators.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Investigations in Experimental High Energy Physics

This report summarizes the accomplishments the Iowa State group during the final year of its ATLAS effort (April 1, 2019 - March 31, 2020). The report briefly describes the five physics analyses and the ATLAS upgrade project on which the group was active during this period.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Improving High-Energy Particle Detectors with Machine Learning

Microseconds after the Big Bang, the universe existed in a state called the quark-gluon plasma (QGP). To experimentally study its properties, the QGP is recreated in high-energy nuclear collisions at the LHC, and the particles produced from the QGP are reconstructed from their energy deposition in the ATLAS calorimeter. This requires both classifying the particles and calibrating their deposited energy. The objective of this project is to improve the reconstruction by using machine learning techniques, where the energy depositions of clusters of cells, formed by ATLAS topo-clustering methods, are treated as three-dimensional images when inputted to neural networks. This approach significantly improves the calibration of deposited energies when cross-validating while training, and models trained on idealized data predict the calibrated energies of particles in more complex data sets well. Additionally, implementation of a data generator using uproot allows the program to load input data into memory as needed while training or predicting, significantly reducing the amount of memory used. The data generator also allows for use of multiprocessing to speed up training and evaluating. This work illustrates that using machine learning methods for both classification and calibration has the potential to significantly improve particle reconstruction.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Reduction of CO 2 Emissions Through Lightweight Body Panels (Project Final Report)

Lightweight construction is an integral part of Volkswagen’s overall strategy of reducing CO 2 emissions. Due to its low cost, steel is the most commonly used material for automotive exterior body panels today. Unfortunately, steel has a high density, resulting in a relatively low specific strength. Glass fiber based sheet molding compounds (SMC) provide high properties in combination with lower density. The high specific strength of SMC offers an enormous lightweight potential. To unlock the full potential of SMC materials in combination with cutting edge manufacturing processes, Volkswagen Group of America worked together with IACMI (Institute for Advanced Composites Manufacturing Innovation) and the academic partners: University of Tennessee Knoxville, Purdue University and Michigan State University; as well as the industry partners: Ashland, IDI, Owens Corning and Continental Structural Plastics. Leveraging the expertise of all project partners, reaching over the entire supply chain the project demonstrated the potential of these materials. This report will highlight the major steps in the development process on the way to technology readiness for SMC using the example of the Volkswagen Atlas Liftgate. Over the 36-month period of the project, the work focused on three R&D areas: material development, design and simulation, and development of the manufacturing process. Material selection included alternative fibers and resin systems, and accounted for material availability, properties, and cost-efficiency. The work undertaken in the field of design and simulation has pushed the envelope of short fiber reinforced thermoset molding compound process simulation. Design iterations were virtually tested, while the final design was used to validate the simulation software against physical parts. Manufacturing development used cutting-edge technology, while experts along the supply chain were working together to ensure the best possible results. In the final stage of the project, liftgates were molded, trimmed, bonded, painted and assembled before exhaustive testing. The result is an e-coat (electrophoretic dip coating) capable Class-A SMC liftgate, which is ready for high-volume production, and can be used as a technology demonstrator. The prototypes manufactured in the scope of this work have exhibited a mass reduction for the Volkswagen Atlas liftgate of up to 35% compared to the series production steel version, without a degradation of the functionalities.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Regional Assessment for the CO 2 Storage Potential in the Northern Niagaran Pinnacle Reef Trend

The Midwest Regional Carbon Sequestration Partnership (MRCSP) was founded in 2003 as part of the U.S. Department of Energy’s (DOE’s) Regional Carbon Sequestration Partnership initiative. Since its founding, MRCSP has made significant strides toward making CCUS a viable option for states in the region. The public/private consortium, funded through the DOE Regional Carbon Sequestration Initiative, brings together nearly 40 industry partners and 10 states. Battelle, as the project lead, oversees research, development and operations and coordinates activities among the partners. The incremental, phased approach has built a valuable knowledge base for the industry and paved the way for commercial-scale adoption of CCUS technologies. From 2008 to 2020, MRCSP Phase III focused on the development of large-scale injection projects. This report is part of a series of reports prepared under the Midwestern Regional Carbon Sequestration Partnership (MRCSP) Phase III (Development Phase). These reports summarize and detail the findings of the work conducted under the Phase III project. The report describes the regional analysis of the Northern Niagaran Pinnacle Reef Trend (NNPRT) in Northern Michigan as part of the MRCSP programs Regional Assessment goals. The goal of this task was to perform an initial assessment of the geologic storage capacity and injectivity of the Northern Fairway of Michigan’s Niagaran Reef Trend. This was achieved through three main objectives: 1) development of a reef atlas, 2) understanding the regional trends in geology, and 3) estimating CO 2 and CO 2 -EOR resources. Data collected across multiple subtasks were integrated into a mappable database that could be accessed from many of the leading software. The reef atlas was used to map the reefs and associated characteristics across the entire NNPRT. Several methodologies were explored to estimate the CO 2 and CO 2 -EOR resources across the trend which included three scenarios: 1) storage only using fluid substitution and volumetric estimations, 2) CO 2 -EOR which applied proximity analysis concepts and measured performance metrics from the Core Energy reefs to predict performance at all oil reefs, and 3) enhanced storage scenario which combined CO 2 -EOR with fluid substitution to represent maximized storage after completion of CO 2 -EOR.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2023

Quantum Information Science in High Energy Physics at the Large Hadron Collider (Final Report-QuantISED)

We pursue scientific research at the interface of High Energy Physics and Quantum Information Science. This includes studies of thermal radiation and quantum entanglement in high-energy collisions at the Large Hadron Collider (LHC), with special emphasis on entanglement entropy and the Higgs boson. This project has also been extended to include quantum entanglement and charged current weak interactions using Fermilab results. And most recently, we have begun tests of the temporal entanglement using LHC data. Collider experiments such as proton-proton collisions at the LHC yield hadrons that exhibit an exponential behavior at low transverse momenta. This surprising behavior is seen in data from both the ATLAS and CMS collaborations. We attribute this phenomenon to quantum entanglement between the regions in the nucleon wave function. The exponential component to the transverse momentum distribution is a result of thermal radiation that is akin to Hawking or Unruh radiation that should exist at the event horizon of astrophysical black holes and neutron stars. The Principal Investigator, in collaboration with a theoretical physicist at Stony Brook University and Brookhaven National Laboratory, and with Yale University students, has shown evidence for this thermal radiation in several production and decay processes in the ATLAS and CMS data, and its connection to entanglement entropy (O.K. Baker and D.E Kharzeev, Phys. Rev. D 98, 054007 (2018)), including even the Higgs boson sector. Interestingly, this thermal behavior is also seen in momentum distributions of charged current weak interactions according to our studies. These findings suggest a deep connection between quantum entanglement (entanglement entropy) and thermalization in both hadron collisions at the energy frontier and neutrino scattering at the intensity frontier. We have confirmed the proposed relation between the effective temperature and the hard-scattering scale at lower energies using the most recent LHC data for the following systems: Higgs bosons, top quarks, and charged hadrons. Additionally, we have results for hadron production in neutrino scattering from nuclei using Fermilab weak interaction data. This study is carried out using data from the MINERvA collaboration. In those cases where entanglement is expected, there is an exponential component to the momentum distribution, while this component is absent in those processes where no entanglement is expected. This research thus tests the hypothesis about a link between quantum entanglement and thermalization in strong and weak interactions. See Phys Lett B 811, 135948 (2020). We also initiated research applying a quantum search algorithm (Grover's Algorithm) to LHC data. This quantum algorithm was used to show how rare events in LHC data can be searched for in large, unsorted databases, with quadratic speedup compared to classical search algorithms on classical computers. See "Application of a Quantum Search Algorithm to High- Energy Physics Data at the Large Hadron Collider", arXiv:2010.00649 [quant-ph].

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

6.26 Low Cost Basalt Fiber for Automotive Applications

Vehicle lightweighting is an essential component to the automotive industry to improve fuel economy of internal combustion engine (ICE) vehicles to meet ever improving emission standards and to improve the range of electric vehicles (EV). Composite materials offer high specific modulus and specific strength, which makes them appealing for these light weighting efforts. Sheet molding compounds (SMC) are particularly interesting from an automotive perspective because of the relatively low cost and high volume of producing SMC parts. Traditionally, composite materials for automotive application are glass fiber reinforced because of the attractive price - performance ratio, but basalt fibers are a cost and recycling competitive reinforcement alternative in this market. The aim of this project was to examine the feasibility of utilizing basalt fiber for automotive applications. More specifically, an effort was made to examine different fiber sizings on basalt fiber combined with vinyl-ester (VE) resin, and their performance as part of an SMC process. In addition to offering vehicle lightweighting with fiber reinforced polymer composites, basalt fiber is a fully recyclable material and thus supports the IACMI technical goal of: Demonstrate that the technology is capable at a sufficient scale for >80% recyclability or reuse of fiber reinforced polymer composites in five years into useful components with projected cost and quality at commercial scale competitive with virgin materials on a pathway to 95% recyclability or reuse starting in ten years. Three different fiber sizings were applied to a continuous roving of basalt fiber and compared to a traditional Electrical/Chemical Resistance (E-CR) glass fiber that is typically used in these types of applications. Fiber tows were examined for Loss on Ignition percentage (LOI%), Tex, and tow strength. Some sizings clearly outperformed others, and the ability to process these fibers on a pilot scale SMC line was demonstrated. A test plan for the manufacturing and mechanical testing of SMC panels was developed. This work continues outside the time frame allocated for this project. When this work is completed, it will be added to this report and posted as Appendix C. Glass fiber reinforced SMC materials have already proven feasible as a light weighting method for traditionally steel parts like the Volkswagen (VW) Atlas lift-gate (Figure 1); this project team is seeking the feasibility of basalt fiber as a drop-in replacement for glass fiber reinforced SMC. Sizing development for basalt fibers has proven that the mechanical properties are better than E-glass and closer to S-glass, which makes it an interesting material for SMC applications. Better mechanical properties translate to less material needed to achieve load case requirement for target applications. The business case has already been demonstrated for 100,000 parts per year of glass fiber reinforced SMC Atlas lift-gates compared to traditional steel manufacturing processes. Reduced overhead and assembly costs are offset by glass fiber SMC higher cost per kg beyond 100,000 parts per year, which is still a relatively low volume for the automotive industry. For basalt fiber reinforced SMC to become feasible for automotive applications, the price-performance ratio has to be precisely determined. Based on the mechanical performance it is possible to establish a range of applications and technical solutions in which the potential of basalt SMC can be utilized, while the price of the material can be used to compile the business case for such applications. Based on these business cases and the sustainability indicators, glass fiber reinforcement (or other) materials can be directly substituted. Volkswagen’s commitment to reducing carbon emissions cannot be understated. Basalt fiber shows promise of reducing the carbon footprint in SMC materials, especially if sizing optimizations can be made with thermoplastic based SMC. To fully realize the value of basalt fiber reinforced materials, a lifecycle cost analysis should be performed on basalt’s production and recycling, and then compared against E-glass. From this assessment, a true judgement can be made on the commercialization potential of this material. Figure 1. Example of Fiber Reinforced Polymer Composite Liftgate As a conclusion, we can state that Mafic basalt fiber is not a direct replacement for E-glass or E-CR glass based on price, but should be considered a technical solution when E-glass does not provide adequate performance in a composite design and S-glass, aramid and carbon fibers are too costly. Mafic basalt fiber can be placed on the high-performance fiber spectrum next to S-glass for performance but at one third the price. It should be considered for more technically challenging structural designs wherein the performance can demonstrate 20-25% performance enhancement over E-glass to elicit more strength or a weight reduction. Both Michelman and Mafic produce thermoplastic sizings which, in combination with Nylon and polypropylene resin and fibers, can further advance high speed composite implementations while maintaining an eco-friendly manufacturing process.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Manufacturability Advancement of Low-Temperature Titanium Electroplating Methods

Three tasks were proposed for this work. All three were completed. The tasks were as follows: Task 1: A larger plating system will be purchased for process scale-up. TiF 3 will be tested as the metal precursor in an effort to reduce water sensitivity of the process. Task 2: Ti on steel samples will be created at PNNL and shipped to Atlas Technologies. Atlas Technologies will diffusion bond the samples to aluminum and test the bond strength. The results will be reported to PNNL. Task 3: Investigation into DOE mission relevant Ti and Zr alloys and demonstration on larger scale work pieces.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Transforming our understanding of chloroplast-associated genes through comprehensive characterization of protein localizations and protein-protein interactions

Bioenergy crops are a renewable source of fuels and are a critical base for building a carbon-neutral economy. Rational engineering of bioenergy crops has the potential to enhance the yields. However, our ability to engineer plants is limited because the functions of most genes remain unknown. Systematic characterization of gene function in plants thus has the potential to greatly accelerate bioenergy research. Here, we focus on the chloroplast, an underexplored energy-producing organelle that is a hallmark of plants. The chloroplast is one of the promising targets of biofuel crop engineering efforts because of its central role in photosynthesis, metabolism, and intracellular signaling. However, the protein composition of the chloroplast and the functions of most of its proteins remain poorly characterized. At the core of this project, we sought to comprehensively determine the localization of chloroplast-associated proteins and generate a spatially defined protein-protein interaction network for chloroplast. For this purpose, we used the leading model alga Chlamydomonas reinhardtii, which greatly increased experimental speed and throughput. We illustrated the value of our findings to land plants by determining the localization of Arabidopsis thaliana land plant homologs of the Chlamydomonas proteins. Altogether, we were successful in determining the localization of 1,034 chloroplast-associated proteins in Chlamydomonas. The localizations provide numerous insights into the spatial organization of chloroplasts and how they function to support photosynthesis. The localization patterns of distinct proteins revealed new chloroplast structures and revealed new spatial organization inside the chloroplast. We also identified new components of known chloroplast structures, such as the chloroplast envelope, nucleoid, plastoglobuli, and pyrenoid. We identified these new components by investigating the interacting partners of known proteins. Many proteins localized in both the chloroplast and other cellular structures, thereby hinting at new functions and communication between cellular structures. We also applied machine learning on the atlas to generate predictions for the location of all of the proteins in Chlamydomonas. This enabled us to assign putative functions to many uncharacterized proteins based on their cellular location. Altogether, this research establishes a rich resource that opens new avenues of investigation and guides future work in deciphering and manipulating chloroplast function. Next, we developed an extensive protein-protein interaction network for the chloroplast by performing affinity purification-mass spectrometry on ~1,150 tagged chloroplast-associated proteins, the first such large-scale study in any photosynthetic organism. This dataset reveals 4,694 high-confidence protein-protein interactions, offering insights into the functions of thousands of conserved poorly-characterized chloroplast proteins. This systematic identification of protein-protein interactions in the chloroplast also provides multiple exciting new research directions and a detailed blueprint of the chloroplast's operation. This research lays the groundwork to decipher the inner workings of the chloroplast, the cell structure at the heart of photosynthesis. The spatial atlas and protein-protein interactions reveal chloroplast organizational features that would not have been accessible with traditional approaches. The localization mapping, insights into the function, and research materials generated further provide a rich resource for the research community to advance the understanding of how the chloroplast is organized to enable engineering of enhanced photosynthetic organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Celeritas R&D Report: Accelerating Geant4

Celeritas is a new Monte Carlo (MC) detector simulation code designed for computationally intensive applications on high-performance heterogeneous architectures. In the past two years Celeritas has advanced from prototyping a Graphics Processing Unit (GPU)-based single physics model in infinite medium to implementing a full set of electromagnetic (EM) physics processes in complex geometries. The current release of Celeritas, version 0.4, has incorporated full device-based navigation, an event loop in the presence of magnetic fields, and detector hit scoring. New functionality incorporates a scheduler to offload electromagnetic physics to the GPU within a Geant4-driven simulation, enabling straightforward integration of Celeritas into the high energy physics (HEP) experimental frameworks CMSSW and ATLAS FullSimLight. On the Perlmutter supercomputer, Celeritas performs EM physics between 3× and 18× faster using the machine’s Nvidia GPUs compared to using only CPUs, corresponding to an electrical power efficiency up to a factor of 5. When running a multithreaded Geant4 ATLAS test beam application with full hadronic physics, using Celeritas to accelerate the EM physics results in an overall simulation speedup of 1.7–2.2× on GPU and 1.2× on CPU. In a CMS test application using tt¯ events and the prototype Run 4 configuration, compared to Geant4 CPU, Celeritas with a Nvidia A100 improves overall throughput up to a factor of 2.7× but cannot be efficiently shared with more than 8 cores.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Stress Testing the Standard Model of Particle Physics at the Large Hadron Collider

Final technical report for the DOE grant "Stress Testing the Standard Model of Particle Physics at the Large Hadron Collider", awarded to Prof. Aram Apyan at Brandeis University. The work focused on the ATLAS experiment at LHC. During the award period the group worked on ATLAS physics analyses, all-silicon Inner Tracker (ITk) detector upgrade, and reconstruction and calibration.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research

Introduction The agriculture genomics community has numerous data submission standards available, but the standards for describing and storing single-cell (SC, e.g., scRNA- seq) data are comparatively underdeveloped. Methods To bridge this gap, we leveraged recent advancements in human genomics infrastructure, such as the integration of the Human Cell Atlas Data Portal with Terra, a secure, scalable, open-source platform for biomedical researchers to access data, run analysis tools, and collaborate. In parallel, the Single Cell Expression Atlas at EMBL-EBI offers a comprehensive data ingestion portal for high-throughput sequencing datasets, including plants, protists, and animals (including humans). Developing data tools connecting these resources would offer significant advantages to the agricultural genomics community. The FAANG data portal at EMBL-EBI emphasizes delivering rich metadata and highly accurate and reliable annotation of farmed animals but is not computationally linked to either of these resources. Results Herein, we describe a pilot-scale project that determines whether the current FAANG metadata standards for livestock can be used to ingest scRNA-seq datasets into Terra in a manner consistent with HCA Data Portal standards. Importantly, rich scRNA-seq metadata can now be brokered through the FAANG data portal using a semi-automated process, thereby avoiding the need for substantial expert curation. We have further extended the functionality of this tool so that validated and ingested SC files within the HCA Data Portal are transferred to Terra for further analysis. In addition, we verified data ingestion into Terra, hosted on Azure, and demonstrated the use of a workflow to analyze the first ingested porcine scRNA-seq dataset. Additionally, we have also developed prototype tools to visualize the output of scRNA-seq analyses on genome browsers to compare gene expression patterns across tissues and cell populations. This JBrowse tool now features distinct tracks, showcasing PBMC scRNA-seq alongside two bulk RNA-seq experiments. Discussion We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem based on Findable, Accessible, Interoperable, and Reusable (FAIR) SC principles to facilitate SC-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural species.

Genetics & Heredity↗
DOE OSTI2025

Single-nuclei transcriptome analysis of IgM+ cells isolated from channel catfish (Ictalurus punctatus) spleen

Catfish production is the primary aquaculture sector in the United States, and the key cultured species is channel catfish (Ictalurus punctatus). The major causes of production losses are pathogenic diseases, and the spleen, an important site of adaptive immunity, is implicated in these diseases. To examine the channel catfish immune system, single-nuclei transcriptomes of sorted and captured IgM + cells were produced from adult channel catfish. Three channel catfish (~1 kg) were euthanized, the spleen dissected, and the tissue dissociated. The lymphocytes were isolated using a Ficoll gradient and IgM + cells were then sorted with flow cytometry. The IgM + cells were lysed and single-nuclei libraries generated using a Chromium Next GEM Single Cell 3’ GEM Kit and the Chromium X Instrument (10x Genomics) and sequenced with the Illumina NovaSeq X Plus sequencer. The reads were aligned to theI. punctatusreference assembly (Coco_2.0) using Cell Ranger, and normalization, cluster analysis, and differential gene expression analysis were carried out with Seurat. Across the three samples, approximately 753.5 million reads were generated for 18,686 cells. After filtering, 10,637 cells remained for the cluster analysis. The cluster analysis identified 16 clusters which were classified as B cells (10,276), natural killer-like (NK-like) cells (178), T cells or natural killer cells (45), hematopoietic stem and progenitor cells (HSPC)/megakaryocytes (MK) (66), myeloid/epithelial cells (40), and plasma cells (32). The B cell clusters were further defined as different populations of mature B cells, cycling B cells, and plasma cells. The plasma cells highly expressedighmand we demonstrated that the secreted form of the transcript was largely being expressed by these cells. This atlas provides insight into the gene expression of IgM + immune cells in channel catfish. The atlas is publicly available and could be used garner more important information regarding the gene expression of splenic immune cells.

Immunology↗