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Deeplynx Dag Repository

The DeepLynx DAG repository will contain several Airflow DAGs (Directed Acyclic Graphs) which will be used in the context of DeepLynx's deployed Apache Airflow instance. These DAGs will be used for multiple data management tasks for DeepLynx data, including but not limited to: - bringing data from various sources and tools into DeepLynx - managing sequential data workflows, such as running Python scripts on data to perform analysis and returning the results to DeepLynx - performing any necessary transformation or pre-processing on data coming into DeepLynx from external sources or out of DeepLynx to go to external applications

Brownlee, JarenM.

HPC Campaign Management: Remote data access with user-defined error bound using ADIOS and ZFP

Remote access to large-scale scientific datasets, like those generated by combustion simulations or other high-performance computing (HPC) applications, presents a significant challenge. Downloading entire datasets is often impractical due to their size and the bandwidth limitations of typical networks. To address this challenge, we propose a novel approach that enables efficient remote access to large datasets distributed across multiple facilities. Our method enables technologies to download only the data values of a select variable, in a select region of interest, to a user-defined accuracy. For this purpose, we extended the ADIOS IO library to provide read functions with user-defined accuracy, a remote data server that understands multidimensional selections of specific variables, steps and accuracy from an ADIOS dataset, and which uses lossy compression on the remote site to reduce the data to be transferred back to the client. In addition, our extension of the ADIOS library collects metadata from multiple datasets in small files called Campaign Archives, which can be shared among project participants on any HPC, cloud or laptop, and which can easily facilitate the discovery of content and pointers to the data location as well as remote access to the data by local tools as if data was local. This feature called Campaign Management, enables a group of scientists to manage related datasets stored in multiple files, across multiple facilities as if it was in a single file/database. We demonstrate the effectiveness of our approach using a 1.5 TB dataset from the S3D combustion simulation on Frontier at the Oak Ridge Leadership Facility. Even a single variable from this dataset, at 64 GB, is too large to be processed on a standard laptop. We show two different reading patterns for 2D plots and 3D visualization, with careful settings that a scientist studying combustion data would do and show that running the same Python scripts on Frontier directly takes comparable time than running them on the local laptop with remote access to the data on Frontier.

Podhorszki, Norbert [ORNL] (ORCID:000000019647542X

The ECP SICM project: Managing complex memory hierarchies for exascale applications

The Exascale Computing Project (ECP)’s Simplified Interface to Complex Memories (SICM) effort focuses on developing universal interfaces for discovering, managing, and sharing data across complex memory hierarchies. These facilitate the exploitation of emerging memory technologies and support precise control over their various trade-offs such as high-bandwidth versus low-latency, persistent versus ephemeral, high-capacity versus low-capacity, and near-CPU versus near-GPU. SICM comprises three interrelated components: a low-level interface, a high-level interface, and a persistent-heap interface. The low-level SICM interface is intended for system and run-time developers as well as expert application developers who prefer full control of the memory objects used within their application. The high-level SICM interface builds upon the low-level interface, employing application-level profiling and analysis to optimize data management for complex memory hierarchies. The persistent-heap interface provides applications with a persistent memory allocator that can allocate custom C++ data structures in both block-storage and byte-addressable persistent memories.

97 MATHEMATICS AND COMPUTING

mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format

Advances in mass spectrometry (MS) instrumentation, such as higher resolution, faster scan speeds, and improved sensitivity, have significantly increased the volume and complexity of data. The growing adoption of imaging and ion mobility further amplifies these challenges across MS-based omics fields, including proteomics, metabolomics, and lipidomics. While these technologies unlock new possibilities, they also present significant challenges in data management, storage, and accessibility. Existing open formats, such as the XML-based community standards mzML and imzML, struggle to meet the demands of modern MS workflows due to their large file sizes, slow data access, and limited metadata support. Vendor-specific formats, while optimized for proprietary instruments, lack interoperability, comprehensive metadata support and long-term archival reliability. This white paper lays the groundwork for mzPeak, a next-generation community data format designed to address these challenges and support high-throughput, multi-dimensional MS workflows. By adopting a hybrid model that combines efficient binary storage for numerical data and both human and machine-readable metadata storage, mzPeak will reduce file sizes, accelerate data access, and offer a scalable, adaptable solution for evolving MS technologies. For researchers, mzPeak will enable enhanced interoperability across platforms, seamless support for complex workflows including ion mobility and MS imaging, and faster data access compared to existing community formats such as mzML. Its design will ensure data is managed in compliance with regulatory standards, essential for applications such as precision medicine and chemical safety, where long-term data integrity and accessibility are critical. For vendors, mzPeak provides a streamlined, open alternative to proprietary formats, reducing the burden of regulatory compliance while aligning with the industry's push for transparency and standardization. By offering a high-performance, interoperable solution, mzPeak positions vendors to meet customer demands for sustainable data management tools which will be able to handle emerging and future data types and workflows. mzPeak aspires to become the cornerstone of MS data management, empowering researchers, vendors, and developers to innovate and collaborate more effectively.

data formats

DOE BSSD Performance Management Metrics Report Q3

Microbiome data is complex, spanning information from microbial genomes within diverse communities, protein and metabolite readouts, and contextual information (metadata) captured from the environments from which these samples were collected. While the variety and scale of microbiome data generation has dramatically expanded over the past twenty years, infrastructure to support data management, sharing, and access has lagged. New ways to improve interoperability across existing resources and advancing community standards are necessary to support how researchers create, use, and reuse data. The National Microbiome Data Collaborative (NMDC) aims to advance a microbiome data sharing network through infrastructure, data standards, and community building.

54 ENVIRONMENTAL SCIENCES

Data for Propagation Method and Planting Density Influence Canopy Developmental Transition and Biomass Productivity in Miscanthus × giganteus

Understanding how establishment practices influence the mechanisms underlying Miscanthus × giganteus (miscanthus) productivity and canopy development is critical for optimizing management. Data was collected during the juvenile (2011–2013) and mature (2024) phases of a long-term field experiment established in Urbana, Illinois, to evaluate the effects of propagation method (plug propagation [PP] and rhizome propagation [RP]), planting density (1.0, 0.75, and 0.25 plants m⁻²), and nitrogen application (0 and 67 kg N ha⁻¹) on end-of-season biomass yield, tiller mass, tiller density, and tiller height. Linear regression models identified the dominant predictors of yield across stand ages and management regimes. Planting density, nitrogen (N) application, and propagation method significantly influenced early yield and canopy development. During the juvenile phase, biomass yield was driven by tiller density due to canopy expansion; in the mature phase, yield became driven by tiller mass. The PP plots produced higher tiller density than the RP plots, resulting in faster canopy closure and higher juvenile-phase yields. Rhizome-propagated (RP) plots produced lower tiller density, but individual tillers were 3.3–6.4 g tiller−1 heavier than PP tillers. After the canopy reached equilibrium, the PP and RP yields were similar because greater RP tiller mass compensated for its lower tiller density. Higher planting density resulted in greater yield and tiller density during the second year (2012), but this effect was absent from the third year (2013) onward. In the juvenile phase, N fertilization enhanced yield by 1.6–3.4 Mg ha−1. Initiating fertilization in 2013 on unfertilized plots produced biomass similar to that in fertilized plots, suggesting yield recovery in the mature phase. These findings revealed that establishment strategies, including propagation method and planting density, influence juvenile miscanthus canopy development and productivity, transitioning from tiller-density- to mass-dominated yields, but not mature phase productivity.

Miscanthus

DeepLynx Ecosystem 2025

Poor data integration and governance continue to plague complex engineering projects, resulting in missed cost, schedule, and performance targets. Departments operate in isolated systems with manual data exchange, creating fragmented information that compounds errors and leads to significant delays and cost overruns. The DeepLynx ecosystem addresses these challenges through an open-source, modular data management platform that transforms fragmented project data into an integrated digital thread. Built on a federated microservice architecture, the ecosystem comprises seven specialized tools centered around DeepLynx Nexus, a unified data catalog with hierarchical organization and graph-based navigation capabilities. The ecosystem includes: DeepLynx Stream for real-time timeseries data ingestion from industrial sources; DeepLynx Ingest for governed data uploads with formal review workflows; DeepLynx Lattice for ontology-based entity and relationship extraction; DeepLynx Run for workflow orchestration and secure AI/ML compute; DeepLynx Visualize for 3D digital twin visualization; and DeepLynx Insight for AI-assisted document analysis with traceable, grounded responses. Deployable in cloud, on-premise, or hybrid environments using containerized Docker applications and Helm charts, the DeepLynx ecosystem provides flexible infrastructure that adapts to organizational requirements. By consolidating project data into a unified data lake with role-based access controls and OAuth2 authentication, DeepLynx enables digital thread and digital twin capabilities that improve decision-making, reduce risk, and support complex engineering workflows throughout the project lifecycle.

42 - ENGINEERING

A Grassroots Network and Community Roadmap for Interconnected Autonomous Science Laboratories for Accelerated Discovery

Scientific discovery is being revolutionized by AI and autonomous systems, yet current autonomous laboratories remain isolated islands unable to collaborate across institutions. We present the Autonomous Interconnected Science Lab Ecosystem (AISLE), a grassroots network transforming fragmented capabilities into a unified system that shorten the path from ideation to innovation to impact and accelerates discovery from decades to months. AISLE addresses five critical dimensions: (1) cross-institutional equipment orchestration, (2) intelligent data management with FAIR compliance, (3) AI-agent driven orchestration grounded in scientific principles, (4) interoperable agent communication interfaces, and (5) AI/ML-integrated scientific education. By connecting autonomous agents across institutional boundaries, autonomous science can unlock research spaces inaccessible to traditional approaches while democratizing cutting-edge technologies. This paradigm shift toward collaborative autonomous science promises breakthroughs in sustainable energy, materials development, and public health.

Ferreira da Silva, Rafael [Oak Ridge National Labo

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

Schema Elements for Granta Annual Report: FY2024

Granta: Materials Intelligence (Granta: MI) is a commercial database software distributed by Ansys, Inc. that is utilized by the Nuclear Security Enterprise (NSE) to organize and store relevant materials data. Lack of standard and well-documented database schema is the primary obstacle to an NSE materials data management solution, so the objective of this project is to create and document such a schema. In FY21, an approach for designing, documenting, and managing a standard database schema was described based on the creation of schema elements (collections of attributes used to describe particular aspects of the data) to be used as building blocks for creating various database tables without duplication. In FY22, these methods were applied through a multi-site collaboration to create and document the schema elements necessary to build a thermogravimetric analysis (TGA) testing table. In FY23 the schema was expanded to include elements for a differential scanning calorimetry (DSC) table, along with schema for supporting metadata tables including Instruments, Projects, Documents, and Testing Series. In FY24 the following progress was made, again through multi-site collaboration: • The existing schema elements were modified to accommodate thermomechanical analysis (TMA) data, and a table, Test Data: TMA, was created for managing TMA data. • The elements necessary for the following additive manufacturing (AM) data tables (directed at data specific to selective laser sintering AM technology) were created: • AM Builds • AM Processes • AM Part Designs • Built AM Parts • AM Feedstock Materials • AM Feedstock Material Batches • The elements necessary for creating a Calibrated Material Models table were created, and the Calibrated Material Models table was created. In FY25 the existing schema will be deployed on the production enterprise Granta instance on the enterprise secure network. Schema elements will be appended, and new elements created as necessary, to allow the creation of tables specifically to support materials testing, AM process development, and design and analysis for modernization programs.

36 MATERIALS SCIENCE

Untargeted, tandem mass spectrometry (LC/MS-MS) metaproteomes from soil samples in control and warming plots in Blodgett Forest, CA (2014-2021)

The pathways of carbon transport and loss through and from soils—soil organic matter (SOM) depolymerization to dissolved organic carbon and mineralization to carbon dioxide (CO2)—are fundamentally driven by microbial activity, which is strongly regulated by environmental conditions. As part of Lawrence Berkeley National Laboratory (LBNL) Terrestrial Ecosystem Science (TES) Belowground Biogeochemistry Science Focus Area (SFA), we have established a novel whole-soil long-term warming experiment at the University of California (UC) Blodgett Forest Research Station (Sierra Nevada) in 2014, where we study the role of biogeochemical, microbial and geochemical process interactions in SOM decomposition and stabilization. This package contains soil metaproteomics data in the context of site specific metagenomes from soil depth profiles in three paired control and warming plots from a temperate mixed forest in Northern California. Each paired plot had been subjected to experimental warming since June 2014 to simulate a predicted climate change scenario for northern California. These metaproteomes were collected in 2018 after 4.5 years of warming from five depth intervals (0-10 cm, 10-30 cm, 30-45 cm, 45-60 cm, 60-80 cm). For protein identification, the collected spectra were searched following a target-decoy search strategy against a database of metagenome predicted proteins (covering 96 samples from 2014 to 2021) representing the complete sequence diversity at the site. Data was searched with mass spectrometry database search tool (MS-GF+) using Pacific Northwest National Laboratory (PNNL)'s Data Management System (DMS) Processing pipeline. The metagenomes are published as part of another data package. Raw metaproteomic data and the data products from MS-GF+ are deposited in the Mass Spectrometry Interactive Virtual Environment (MassIVE) database under accession no. MSV000097826. Here we present a dataset that includes spectral counts for the detected proteins across samples (EMSL50964_BrodieAllMAGs_Globals_SC.txt), the sequences of the detected proteins, and sample metadata file that contains site information for the soil metaproteome samples.

Belowground Biogeochemistry Science Focus Area

Best Practices for Nuclear Experiment Data Preservation at Idaho National Laboratory: A Guide for Researchers and Reactor Operators

Preserving experimental data is essential for supporting advancements in nuclear science and ensuring the longevity of Idaho National Laboratory's contributions to reactor technology and safety. This report provides a comprehensive guide to best practices for experimental data management and preservation, focusing on standardized data formats, redundancy in storage, metadata documentation, and alignment with international standards. By following these recommendations, experimentalists and reactor operators can enhance the accessibility, reproducibility, and utility of critical datasets for regulatory review, validation computational methods, and future research.

22 GENERAL STUDIES OF NUCLEAR REACTORS

Trust Not Verify? The Critical Need for Data Curation Standards in Materials Informatics

The importance of data curation has been recognized in multiple areas of research; however, the discussion of this important issue is only beginning to emerge in materials science. In this Perspective, we highlight the benefits of using the standardized data curation protocols in materials science and discuss current gaps in accurate and reproducible data reporting using case studies drawn from high-impact materials science papers and well-known databases such as the Crystallography Open Database (COD) and the Cambridge Structural Database (CSD). We argue that both experimental and computational materials scientists need to embrace a culture of rigorous data curation as part of modern research data management. We propose a sample data curation pipeline for materials chemistry and illustrate its use by creating two new materials chemistry databases. Here, we hope that this perspective will serve to catalyze further discussion and promote the continuous development of rigorous data curation practices within the materials science research community. We posit that adherence to best practices of data curation will promote and enhance the reliability, reproducibility, and integrity of materials research and enable the development of reliable AI and machine learning models that critically depend on the use of quality data.

Chemical structure

NDMAS Overview

Overview of the Nuclear Data Management and Analysis System detailed as: Overview of NDMAS System, NDMAS NQA-1 process, Data in NDMAS, and Future work and new additions.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS

An open-access simulated earthquake ground-motion database for an M7 Hayward Fault earthquake in the San Francisco Bay Region

Comprehensive understanding of earthquake ground motions, particularly in the near-fault region of large-magnitude events, is limited by gaps in strong-motion data. This challenge is prominent in areas with high seismic hazard but infrequent large earthquakes where data is sparse and difficult to interpret. These data limitations lead to uncertainties in the development of site-specific ground motions, which are crucial for engineering risk assessments. To address these challenges, physics-based regional-scale ground-motion simulations have been developed. With the emergence of exaflop-scale computing ecosystems, it is now possible to simulate regional earthquake processes at unprecedented fidelity and generate the large number of fault rupture realizations necessary to characterize both intra- and inter-event ground-motion variability. This article introduces a new database of simulated earthquake ground motions, created for applications in earthquake engineering, earthquake planning, and emergency response. The inaugural version of the database features simulated ground motions for a magnitude 7 Hayward Fault earthquake in the San Francisco Bay Region (SFBR), using the EarthQuake SIMulation (EQSIM) simulation framework and the Graves–Pitarka kinematic rupture model. The aim is to provide high-fidelity, spatially dense, three-component motions generated on the Department of Energy’s (DOE) newest generation of graphics processing unit (GPU)-accelerated supercomputers. These motions are being made openly available to the engineering, scientific, and disaster planning communities. In addition, this work develops protocols for the efficient dissemination of these large data sets and emphasizes community engagement to build confidence in their application. This article discusses the methodology behind the data, underlying software verification and validation, scalable data management, and a user interface for data access. The goal is to facilitate widespread use and elicit expert feedback to maximize the utility and exploitation of simulated motions. While the initial focus is on the San Francisco Region, simulations for additional regions will be added as the DOE program progresses.

Simulated ground-motion database

AI-Ready Control System for the Fermilab Accelerator Complex

Reliable, high-intensity operation of the Fermilab Accelerator Complex is critical to the success of the Long-Baseline Neutrino Facility and Deep Underground Neutrino Experiment. We describe the requirements and infrastructure necessary to support routine use of artificial intelligence and machine learning (AI/ML) in the accelerator control system. Three capabilities are identified: a machine learning operations (MLOps) framework standardizing the lifecycle of AI/ML automation from data management through deployment and monitoring; a data quality framework defining and enforcing standards required to build trustworthy AI/ML applications; and workflow integration with large language models to assist physicists, engineers, and operators with information retrieval, code development, and routine analysis. Use cases spanning beam diagnostics, beam control, and support system automation illustrate the technical requirements across the complex.

43 PARTICLE ACCELERATORS

Pipeline for Integrated Projects in Energy Systems (PIPES): A Tool for Integrated System Planning [Slides]

The Pipeline for Integrated Projects in Energy Systems (PIPES) is a comprehensive project, data, and workflow management tool designed for integrated modeling teams. PIPES facilitates the management of data requirements, tasks, and progress tracking, serving as a higher-level integration layer that works across various data and modeling software. This tool integrates models, data, and tools to perform large-scale, integrated analysis work at scale. PIPES is designed to streamline integrated modeling projects, enhance collaboration, and ensure the quality and efficiency of data management and workflow processes. This presentation introduces PIPES a multi-model tool for integrated system planning; it describes the underlying architecture, deep dives into common user workflows, and outlines the upcoming development roadmap beyond its current alpha state.

29 ENERGY PLANNING, POLICY, AND ECONOMY