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DOE OSTI2022

Guiding the choice of informatics software and tools for lipidomics research applications

Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Multicriteria Measures to Assess the Sustainability of Diets: A Systematic Review

Abstract Context Assessing the overall sustainability of a diet is a challenging undertaking requiring a holistic approach capable of addressing the multicriteria nature of this concept. Objective The aim was to identify and summarize the multicriteria measures used to assess the sustainability characteristics of diets reported at the individual level by healthy adults. Data Sources Articles were identified via PubMed, Scopus, and Web of Science. The search strategy consisted of key words and MeSH terms, and was concluded in September 2022, covering references in English, Spanish, and Portuguese. Data Extraction This systematic review followed the PRISMA guidelines. The search identified 5663 references, from which 1794 were duplicates. Two reviewers independently screened the titles and abstracts of each of the 3869 records and the full-text of the 144 references selected. Of these, 7 studies met the inclusion criteria. Data Analysis A total of 6 multicriteria measures were identified: 3 different Sustainable Diet Indices, the Quality Environmental Costs of Diet, the Quality Financial Costs of Diet, and the Environmental Impact of Diet. All of these incorporated a health/nutrition dimension, while the environmental and economic dimensions were the second and the third most integrated, respectively. A sociocultural sustainability dimension was included in only 1 of the measures. Conclusion Despite some methodological concerns in the development and validation process of the identified measures, their inclusion is considered indispensable in assessing the transition towards sustainable diets in future studies. Systematic Review Registration PROSPERO registration no. CRD42022358824.

Rei, Mariana (ORCID:0000000189453708)↗
DOE OSTI2021

The FEWSION for Community Resilience (F4R) Process: Building Local Technical and Social Capacity for Critical Supply Chain Resilience

Local business leaders, policy makers, elected officials, city planners, emergency managers, and private citizens are responsible for, and deeply affected by, the performance of critical supply chains and related infrastructures. At the center of critical supply chains is the food-energy-water nexus (FEW); a nexus that is key to a community’s wellbeing, resilience, and sustainability. In the 21st century, managing a local FEW nexus requires accurate data describing the function and structure of a community’s supply chains. However, data is not enough; we need data-informed conversation and technical and social capacity building among local stakeholders to utilize the data effectively. There are some resources available at the mesoscale and for food, energy, or water, but many communities lack the data and tools needed to understand connections and bridge the gaps between these scales and systems. As a result, we currently lack the capacity to manage these systems in small and medium sized communities where the vast majority of people, decisions, and problems reside. This study develops and validates a participatory citizen science process for FEW nexus capacity building and data-driven problem solving in small communities at the grassroots level. The FEWSION for Community Resilience (F4R) process applies a Public Participation in Scientific Research (PPSR) framework to map supply chain data for a community’s FEW nexus, to identify the social network that manages the nexus, and then to generate a data-informed conversation among stakeholders. F4R was piloted and co-developed with participants over a 2-year study, using a design-based research process to make evidence-based adjustments as needed. Results show that the F4R model was successful at improving volunteers’ awareness about nexus and supply chain issues, at creating a network of connections and communication with stakeholders across state, regional, and local organizations, and in facilitating data-informed discussion about improvements to the system. In this paper we describe the design and implementation of F4R and discuss four recommendations for the successful application of the F4R model in other communities: 1) embed opportunities for co-created PPSR, 2) build social capital, 3) integrate active learning strategies with user-friendly digital tools, and 4) adopt existing materials and structure.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Multi-scale Multi-physics Scientific Machine Learning for Water Cycle Extreme Events Identification, Labelling, Representation, and Characterization

Impacts of climate are usually felt through extreme events such as droughts, floods, thunderstorms, windstorms, wildfires, and so on, that are intimately tied to the water cycle. Predicting the frequency and severity of extreme events under climate change remains a significant challenge; meanwhile, the mechanisms and impacts of these extremes are far from well understood. There are several major science challenges: (1) Lack of labelled extreme events data and missing standards in defining extremes; (2) Computational demand of high-resolution ensemble climate modeling; (3) Modeling the multiscale multi-physics hierarchical structure of compound extremes; (4) Lack of understanding of mechanisms of extreme events; (5) Large uncertainty in extreme events impacts on infrastructure; (6) Subjective assessment of weather-related risk from seasonal to multi-decadal time scales and lack of metrics for risk assessment and mitigation control.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Landscape-scale Characterization of Arctic Tundra Vegetation Composition, Structure, and Function with a Multi-sensor Unoccupied Aerial System: Supporting Data.

Airborne remote sensing data collected using the Brookhaven National Laboratory's (BNL) heavy-lift unoccupied aerial system (UAS) octocopter platform, the Osprey, operated by the Terrestrial Ecosystem Science and Technology (TEST) group (https://www.bnl.gov/testgroup). This package includes data from three flights flown over the NGEE-Arctic Council, Kougarok and Teller sites in July, 2018. The Osprey is a multi-sensor UAS platform that simultaneously measures very high spatial resolution optical red/green/blue (RGB) and thermal infrared (TIR) surface 'skin' temperature imagery, as well as surface reflectance at 1 nm intervals in the visible to near-infrared spectral range 350 - 1000 nm measured at regular intervals along each flight path. Derived image products include ortho-mosaiced RGB and TIR images, an RGB-based digital surface model (DSM) using the structure from motion (SfM) technique, digital terrain model (DTM), and a canopy height model (CHM). In addition, a VNIR surface reflectance file is provided for the trigger locations collected during each flight campaign. Ancillary aircraft data, flight mission parameters, and general flight conditions provided by the onboard flight and data collection computers are also included. Unprocessed and processed data products are included in this package (processing levels 0-3). Data and metadata are provided as text (*.txt, *.json, *.kml, *hdr, *.enp), tabular (*.dat, *.csv, *.waypoint, ENVI format (no extension)), point cloud (*.laz) and image (*.jpg, *.tif, *png) formats. This metadata document contains flight campaign, instrument and file metadata, along with a description of data processing levels, data products and file naming scheme.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy?s Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

UAS remote sensing (Osprey platform): Red-green-blue (RGB) imagery, thermal infrared (TIR) imagery, and canopy reflectance, Seward Peninsula, Alaska, 2019

Airborne remote sensing data collected using the Brookhaven National Laboratory's (BNL) heavy-lift unoccupied aerial system (UAS) octocopter platform - the Osprey - operated by the Terrestrial Ecosystem Science and Technology (TEST) group (https://www.bnl.gov/testgroup). This package includes data from 17 flights flown over the NGEE-Arctic Council Mile Maker 64 (MM64) and Teller MM27 sites in July, 2019. The Osprey is a multi-sensor UAS platform that simultaneously measures very high spatial resolution optical red/green/blue (RGB) and thermal infrared (TIR) surface "skin" temperature imagery, as well as surface reflectance at 1 nm intervals in the visible to near-infrared spectral range from ~350-1000 nm measured at regular intervals along each flight path. This package provide the Level 0 (raw, unprocessed) data collected by the Osprey platform. Ancillary aircraft data, flight mission parameters, and general flight conditions provided by the onboard flight and data collection computers are also included. Data and metadata are provided as text (*.txt, *.json), tabular (*.dat, *.csv, *.waypoint), and image (*.jpg) formats. This metadata document contains flight campaign, instrument and file metadata, along with a description of the L0 data, and file naming scheme. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Physiological Responses of Populus trichocarpa to Warming

This data set contains empirical physiological, morphological, and chemical data collected over time on Western Black Cottonwood (Populs trichocarpa Torr. & A.Gray ex Hook., Salicaceae) clones, between July and December 2019 at Oak Ridge National Lab. The project was designed to experimentally warm P. trichocarpa clones and assess their physiological acclimation of leaves versus roots. Branch cuttings of the Nisqually-1 genotype were obtained from the US Department of Energy Joint Genome Institute (JGI) in Stanford, California, and propagated in leach tubes. Ninety genetically identical clones were planted into specially constructed mesocosm growth boxes and grown for an initial six weeks in the greenhouse, and then grown at three temperature treatments for ten weeks. The daytime air temperatures of treatments were approximately 25°C, 29°C, and 33°C. Measurements on plant physiology and growth were conducted at various intervals throughout the experiment. This dataset contains nine data files in comma separate (*.csv) format.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

WHONDRS Summer 2019 Sampling Campaign: Global River Corridor Sediment FTICR-MS, Dissolved Organic Carbon, Aerobic Respiration, Elemental Composition, Grain Size, Total Nitrogen and Organic Carbon Content, Bacterial Abundance, and Stable Isotopes (v10)

The WHONDRS Summer 2019 Sampling (S19S) Campaign collected samples in 97 globally distributed river corridor systems between July and September 2019. Surficial streambed sediments were collected at three locations within each site (upstream, midstream, and downstream). Surface water was collected at the downstream site. This dataset includes a portion of the data types produced from the sediment samples and does not include any results from the surface water. Surface water data can be found at https://data.ess-dive.lbl.gov/view/doi:10.15485/1603775. The S19S campaign was designed with the science community to ask questions associated with links among core/transient metabolomes, microbial metabolism, biogeochemical function, and physical properties of watershed and river corridor systems. This data package was originally published in December 2020. It was updated in April 2021 (v2; modified files), May 2022 (v3; new and modified files), November 2022 (v4; new and modified files), January 2023 (v5 and v6; new and modified files), February 2023 (v7; new and modified files), August 2023 (v8; new and modified files), July 2025 (v9; new and modified files), and June 2026 (v10; new and modified files). Version 10 includes major restructuring of the files and their formats. See the change history in the readme for details. In addition to a readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset contains (1) readme, (2) data dictionary, (3) file level metadata, (4) sampling protocol, (5) a data checks report, (6) field metadata, (7) international generic sample number (IGSN) mapping file, (8) joint genome institute (JGI) mapping file, (9) a folder of site photos, and (10) a folder of sample data. The sample data folder contains (1) dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC) and FTICR methods; (2) respiration rates and normalized respiration rates calculated from laboratory sediment incubations, (3) X-ray fluorescence (XRF) elemental composition, (4) grain size distribution from the < 2 millimeter fraction of sediment, (5) total organic carbon and total nitrogen content, (6) bacterial abundance flow cytometry data, (7) sediment stable isotopes (C and N), (8) laboratory methods, (9) water and sediment mass and volume used in incubations, (10) a folder with code, inputs, and plots for the respiration rates, (11) a folder containing XRF data, (12) a folder containing unaligned, peak-picked high resolution characterization of dissolved organic matter from sediment via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory), (12) and a folder containing processed FTICR-MS data. All files are .msa, .txt, .spx, .xml, .csv, .pdf, .txt, .jpg, or .jpeg.

13C↗
DOE OSTI2023

Thermal acclimation of plant photosynthesis and autotrophic respiration in a northern peatland

Peatlands contain one-third of global soil carbon (C), but the responses of peatland ecosystems to long-term warming are not well understood. Here, we pursue an emergent understanding of warming effects on ecosystem C fluxes at peatlands by constraining a process-oriented model, the terrestrial ECOsystem model, with observational data from a long-term warming experiment at the Spruce and Peatland Responses Under Changing Environments site. Model-based assessments show that ecosystem-level photosynthesis and autotrophic respiration exhibited significant thermal acclimation, with temperature sensitivities being linearly decreased with warming. Using the thermal-acclimated parameter values, simulated gross primary production, net primary production, and plant autotrophic respiration (R a ), were all lower than those simulated with non-thermal acclimated parameter values. In contrast, ecosystem respiration simulated with thermal acclimated parameter values was higher than that simulated with non-thermal acclimated parameter values. Net ecosystem CO 2 exchange was much higher after constraining model parameters with observational data from the warming treatments, releasing C at a rate of 28.3 g C m -2 yr -1 °C -1 . Our data-model integration study suggests that peatlands are likely to release more C than previously estimated. Earth system models may overestimate C uptake by peatlands under warming if physiological thermal acclimation of plants is not incorporated. Thus, it is critical to consider the long-term physiological thermal acclimation of plants in the models to better predict global C dynamics under future climate and their feedback to climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Detecting Process Equipment Failures Using Acoustic Data and Machine Learning

Nuclear power plant (NPP) process equipment such as fans, motors, valves, and pumps generate frequent or continuous noise, and deviations from the normal operational sounds made by this equipment can indicate potential issues. These deviations can be identified via automated acoustic anomaly detection, which involves using acoustic sensors (i.e., microphones) alongside detection algorithms to continuously monitor for changes in acoustic signatures. This task is made challenging by the substantial background noise that exists, such as operators opening and closing doors, manipulating valves, and conversing—in addition to typical plant noises. In collaboration with a nuclear power utility partner, this effort assessed the efficacy of acoustic anomaly detection when using a specific acoustic sensor that compresses data into a fixed set of features that are transferable over a standard Internet of Things communication protocol, thereby improving usability but potentially degrading detection performance. Two methods of performing automated acoustic anomaly detection were evaluated: one-class support vector machine (OC-SVM) and isolation forest (iForest). To enable the use of high-quality acoustic data encompassing both normal and anomalous conditions, the study utilized the publicly available Malfunctioning Industrial Machine Investigation and Inspection dataset, which includes real measured acoustic sensor data for a range of equipment types, model numbers, and signal-to-noise ratios (SNRs), along with a benchmark set of detection results. Using this dataset, the methods were tested and then compared against the benchmark results. The results indicated that although the specific acoustic sensor did not enable as rich a feature set extraction, the proposed methods with the limited feature set performed just as well. This provides solid justification for both the methods and the use of the proposed acoustic sensor.

46 - INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AN↗
DOE OSTI2023

Capturing high‐resolution digital images for use in forensic document examination

Abstract In the past, pattern disciplines within forensic science have periodically faced criticism due to their subjective and qualitative nature and the perceived absence of research evaluating and supporting the foundations of their practices. Recently, however, forensic scientists and researchers in the field of pattern evidence analysis have developed and published approaches that are more quantitative, objective, and data driven. This effort includes automation, algorithms, and measurement sciences, with the end goal of enabling conclusions to be informed by quantitative models. Before employing these tools, forensic evidence must be digitized in a way that adequately balances high‐quality detail and content capture with minimal background noise imparted by the selected technique. While the current work describes the process of optimizing a method to digitize physical documentary evidence for use in semi‐automated trash mark examinations, it could be applied to assist other disciplines where the digitization of physical items of evidence is prevalent. For trash mark examinations specifically, it was found that high‐resolution photography provided optimal digital versions of evidentiary items when compared to high‐resolution scanning.

Riley, Paige↗
DOE OSTI2023

RadVolViz: An Information Display-Inspired Transfer Function Editor for Multivariate Volume Visualization

In volume visualization transfer functions are widely used for mapping voxel properties to color and opacity. Typically, volume density data are scalars which require simple 1D transfer functions to achieve this mapping. If the volume densities are vectors of three channels, one can straightforwardly map each channel to either red, green or blue, which requires a trivial extension of the 1D transfer function editor. Here, we devise a new method that applies to volume data with more than three channels. These types of data often arise in scientific scanning applications, where the data are separated into spectral bands or chemical elements. Our method expands on prior work in which a multivariate information display, RadViz, was fused with a radial color map, in order to visualize multi-band 2D images. In this work, we extend this joint interface to blended volume rendering. The information display allows users to recognize the presence and value distribution of the multivariate voxels and the joint volume rendering display visualizes their spatial distribution. We design a set of operators and lenses that allow users to interactively control the mapping of the multivariate voxels to opacity and color. This enables users to isolate or emphasize volumetric structures with desired multivariate properties. Furthermore, it turns out that our method also enables more insightful displays even for RGB data. We demonstrate our method with three datasets obtained from spectral electron microscopy, high energy X-ray scanning, and atmospheric science.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Uncertainty-Guided Prediction Horizon of Phase-Resolved Ocean Wave Forecasting Under Data Sparsity: Experimental and Numerical Evaluation

Accurate short-term wave forecasting is critical for the safe and efficient operation of marine structures that rely on real-time, phase-resolved ocean wave information for control and monitoring purposes (e.g., digital twins). These systems often depend on environmental sensors (e.g., waverider buoys, wave-sensing LIDAR). Challenges arise when upstream sensor data are missing, sparse, or phase-shifted due to drift. This study investigates the performance of two machine learning models, time-series dense encoder (TiDE) and long short-term memory (LSTM), for forecasting phase-resolved ocean surface elevations under varying degrees of data degradation. We introduce the τ-trimming algorithm, which adapts the prediction horizon based on uncertainty thresholds derived from historical forecasts. Numerical wave tank (NWT) and wave basin experiments are used to benchmark model performance under short- and long-term data masking, spatially coarse sensor grids, and upstream phase shifts. Results show under a 50% probability of upstream data loss, the τ-trimmed TiDE model achieves a 46% reduction in error at the most upstream target, compared to 22% for LSTM. Furthermore, phase misalignment in upstream data introduces a near-linear increase in forecast error. Under moderate model settings, a ±3 s misalignment increases the mean absolute error by approximately 0.5 m, while the same error is accumulated at ±4 s using the more conservative approach. These findings inform the design of resilient, uncertainty-aware wave forecasting systems suited for realistic offshore sensing environments.

42 ENGINEERING↗
DOE OSTI2021

Prototype Data Acquisition and Slow Control Systems for the Mu2e Experiment

The Mu2e experiment at the Fermilab Muon Campus will search for the coherent neutrinoless conversion of a muon into an electron in the field of an aluminum nucleus with a sensitivity improvement by a factor of 10 000 over existing limits. Such a charged lepton flavor-violating reaction probes new physics at a scale unavailable with direct searches at either present or planned high-energy colliders. The Mu2e Trigger and Data Acquisition (TDAQ) system exploits otsdaq as its online Data Acquisition System (DAQ) solution. Furthermore, developed at Fermilab, otsdaq integrates both the artdaq DAQ and the art analysis frameworks for event transfer, filtering, and processing. otsdaq is an online DAQ software suite with a focus on flexibility and scalability and provides a multi-user, web-based, interface accessible through a web browser. The read out controllers (ROCs) stream out zero-suppressed data continuously from the detector subsystems to the data transfer controllers (DTCs). The data stream is then read over the peripheral component interconnect express (PCIe) bus to a software filter algorithm that selects events which are combined with the data flux coming from a cosmic-ray veto (CRV) system. The detector control system (DCS) has been developed using the experimental physics and industrial control system (EPICS) open source platform for monitoring, controlling, alarming, and archiving. The DCS has been integrated into otsdaq. A prototype of the TDAQ system and the DCS has been built at Fermilab's Feynman Computing Center. In this article, we report on the progress of the integration of this prototype in the online otsdaq software.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Processes in DNA damage response from a whole-cell multi-omics perspective

Technological advances have made it feasible to collect multi-condition multi-omic time courses of cellular response to perturbation, but the complexity of these datasets impedes discovery due to challenges in data management, analysis, visualization, and interpretation. Here, we report a whole-cell mechanistic analysis of HL-60 cellular response to bendamustine. We integrate both enrichment and network analysis to show the progression of DNA damage and programmed cell death over time in molecular, pathway, and process-level detail using an interactive analysis framework for multi-omics data. Our framework, Mechanism of Action Generator Involving Network analysis (MAGINE), automates network construction and enrichment analysis across multiple samples and platforms, which can be integrated into our annotated gene-set network to combine the strengths of networks and ontology-driven analysis. Taken together, our work demonstrates how multi-omics integration can be used to explore signaling processes at various resolutions and demonstrates multi-pathway involvement beyond the canonical bendamustine mechanism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

WHONDRS Summer 2019 Sampling Campaign: Global River Corridor Surface Water FTICR-MS, NPOC, TN, Anions, Stable Isotopes, Bacterial Abundance, and Dissolved Inorganic Carbon (v8)

The WHONDRS Summer 2019 Sampling (S19S) Campaign collected samples in 97 globally distributed river corridor systems between July and September 2019. Surficial streambed sediments were collected at three locations within each site (upstream, midstream, and downstream). Surface water was collected at the downstream site. This dataset includes a portion of the data types produced from the surface water samples and does not include any results from the sediment. Sediment data can be found at https://data.ess-dive.lbl.gov/view/doi:10.15485/1729719. The S19S campaign was designed with the science community to ask questions associated with links among core/transient metabolomes, microbial metabolism, biogeochemical function, and physical properties of watershed and river corridor systems. This data package was originally published in March 2020. It was updated in October 2020 (v2, new and modified files), July 2021 (v3, new and modified files), January 2023 (v4, new and modified files), February 2023 (v5, new and modified files), August 2023 (v6, new and modified files), July 2025 (v7,new and modified files), and August 2026 (v8, new and modified files). Version 8 includes major restructuring of the files and their formats. See the change history section in readme for more details. In addition to a readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset contains (1) readme, (2) data dictionary, (3) file level metadata, (4) sampling protocol, (5) a data checks report, (6) field metadata, (7) international generic sample number (IGSN) mapping file, (8) joint genome institute (JGI) mapping file, and (9) a folder of sample data. The sample data folder contains (1) dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC) and FTICR methods, (2) dissolved inorganic carbon (DIC), (3) stable water isotopes (O and H), (4) specific conductivity, (5) total dissolved nitrogen (TN), (6) anions, (7) flow cytometry bacterial abundance data, (8) laboratory methods, and (9) a folder containing unaligned, peak-picked high resolution characterization of dissolved organic matter from sediment via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) through the Environmental Molecular Sciences Laboratory (EMSL, https://www.pnnl.gov/environmental-molecular-sciences-laboratory), and (12) a folder containing processed FTICR-MS data. All files are .msa, .txt, .spx, .xml, .csv, .pdf, .txt, .html, .jpg, or .jpeg.

18-O↗
DOE OSTI2024

Introducing Molecular Hypernetworks for Discovery in Multidimensional Metabolomics Data

Orthogonal separations of data from high-resolution mass spectrometry can provide insight into sample composition and address challenges of complete annotation of molecules in untargeted metabolomics. “Molecular networks” (MNs), as used in the Global Natural Products Social Molecular Networking platform, are a prominent strategy for exploring and visualizing molecular relationships and improving annotation. MNs are mathematical graphs showing the relationships between measured multidimensional data features. MNs also show promise for using network science algorithms to automatically identify targets for annotation candidates and to dereplicate features associated with a single molecular identity. Here, this paper introduces “molecular hypernetworks” (MHNs) as more complex MN models able to natively represent multiway relationships among observations. Compared to MNs, MHNs can more parsimoniously represent the inherent complexity present among groups of observations, initially supporting improved exploratory data analysis and visualization. MHNs also promise to increase confidence in annotation propagation, for both human and analytical processing. We first illustrate MHNs with simple examples, and build them from liquid chromatography- and ion mobility spectrometry-separated MS data. We then describe a method to construct MHNs directly from existing MNs as their “clique reconstructions”, demonstrating their utility by comparing examples of previously published graph-based MNs to their respective MHNs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

US Department of Energy, Office of Science, High-Performance Computing Facility: 2023 Operational Assessment Oak Ridge Leadership Computing Facility

The Oak Ridge Leadership Computing Facility (OLCF) was established to accelerate scientific discovery by providing world-leading computational performance and advanced data infrastructure. As a US Department of Energy (DOE) Office of Science user facility, the OLCF has managed the successful deployment and operation of a succession of leadership-class resources dedicated to open science. In addition to these resources, the OLCF staff continually strive to develop innovative processes and technologies, improve security, and empower users through effective allocation management and comprehensive user support and training. These efforts support the advancement of science by the OLCF users and benefit high-performance computing (HPC) facilities around the world. In calendar year (CY) 2023, the OLCF supported 1,676 users and 598 projects and exceeded all targets for user satisfaction. The facility received an average satisfaction score of 4.52 out of 5 on the annual user survey, and 94% of respondents reported a high satisfaction rate with the OLCF overall. Of the 3,619 user tickets submitted in CY 2023, OLCF staff resolved 97% within 3 business days. The facility opened Frontier to full scientific operations this year. Two projects conducted on Frontier received the Association for Computing Machinery (ACM) Gordon Bell Prize and the Gordon Bell Special Prize for Climate Modeling, and a third earned a nomination as a Gordon Bell Prize finalist. The facility’s previous flagship machine, Summit, gained new life and was extended through 2024 in part to help provide resources to the Integrated Research Infrastructure (IRI) projects and the National Artificial Intelligence Research Resource (NAIRR) pilot program. The facility instantiated an Advanced Computing Ecosystem testbed in part to support IRI workflows. OLCF made interactivity easier and more accessible to users than ever through tools like Jupyter notebooks and workflows.

97 MATHEMATICS AND COMPUTING↗