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At least 1,009 records · Page 56

Proteome-scale Deployment of Protein Structure Prediction Workflows on the Summit Supercomputer

Deep learning has contributed to major advances in the prediction of protein structure from sequence, a fundamental problem in structural bioinformatics. With predictions now approaching the accuracy of crystallographic experiments, and with accelerators like GPUs and TPUs making inference using large models rapid, genome-level structure prediction becomes an obvious aim. Leadership-class computing resources can be used to perform genome-scale protein structure prediction using state-of-the-art deep learning models, providing a wealth of new data for systems biology applications. Here we describe our efforts to efficiently deploy the AlphaFold v.2 program, for full-proteome structure prediction, at scale on the Oak Ridge Leadership Computing Facility's resources, including the Summit supercomputer. We performed inference to produce the predicted structures for 40,526 protein sequences, corresponding to four prokaryotic proteomes and one plant proteome, using under 4,400 total Summit node hours, equivalent to using the majority of the supercomputer for a little over one hour. We also designed an optimized structure refinement that reduced the time for the relaxation stage of the AlphaFold pipeline by over 10X for longer sequences. We demonstrate the types of analyses that can be performed on proteome-scale collections of sequences, including a search for novel quaternary structures and implications for functional annotation.

Gao, Mu↗

Transitioning from File-Based HPC Workflows to Streaming Data Pipelines with openPMD and ADIOS2

This paper aims to create a transition path from file-based IO to streaming-based workflows for scientific applications in an HPC environment. By using the openPMP-api, traditional workflows limited by filesystem bottlenecks can be overcome and flexibly extended for in situ analysis. The openPMD-api is a library for the description of scientific data according to the Open Standard for Particle-Mesh Data (openPMD). Its approach towards recent challenges posed by hardware heterogeneity lies in the decoupling of data description in domain sciences, such as plasma physics simulations, from concrete implementations in hardware and IO. The streaming backend is provided by the ADIOS2 framework, developed at Oak Ridge National Laboratory. This paper surveys two openPMD-based loosely-coupled setups to demonstrate flexible applicability and to evaluate performance. In loose coupling, as opposed to tight coupling, two (or more) applications are executed separately, e.g. in individual MPI contexts, yet cooperate by exchanging data. This way, a streaming-based workflow allows for standalone codes instead of tightly-coupled plugins, using a unified streaming-aware API and leveraging high-speed communication infrastructure available in modern compute clusters for massive data exchange. We determine new challenges in resource allocation and in the need of strategies for a flexible data distribution, demonstrating their influence on efficiency and scaling on the Summit compute system. The presented setups show the potential for a more flexible use of compute resources brought by streaming IO as well as the ability to increase throughput by avoiding filesystem bottlenecks.

Poeschel, Franz↗

leapR: An R Package for Multiomic Pathway Analysis

A generalized goal of many high-throughput data studies is to identify functional mecha-nisms that underlie observed biological phenomena, whether disease outcomes or metabolic out-put. Increasingly, studies that rely on multiple sources of high-throughput data (genomic, tran-scriptomic, proteomic, metabolomic) are faced with a challenge of utilizing the data in a way that maximizes utility. However, methods for integration of multiple forms of molecular data into a biolog-ically coherent frameworks are needed. Furthermore, we have developed a framework to assess biological pathway activity that relates to phenotypic outcome using multi-source data. Availability and implementation: The leapR package with user manual and example workflow is available for download from GitHub (https://github.com/biodataganache/leapR).

59 BASIC BIOLOGICAL SCIENCES↗

TR-XPS Realtime Analysis Tool (ArroyoXPS) v0.1

The ALS has developed a Time-Resolved X-ray Photoelectron Spectroscopy (TR-XPS) technique, which involves applying a specific pattern of voltage curves to a sample while measuring XPS peaks. This pattern is repeated over multiple cycles, and changes in the material's response provide valuable scientific insights. Traditionally, file-based analysis workflows have been used: scans are run for a predetermined time, and after one or more scans are complete, calculations are made. ArroyoXPS changes this by offering in-experiment scan and analysis, allowing researchers to gain insights before a scan is finished. This enables them to adjust experimental parameters quickly, potentially saving valuable beamtime. ArroyoXPS includes tools for integrating with beamline control systems, performing analysis, and visualizing scan data in a web browser.

McReynolds, Dylan [Lawrence Berkeley National Labo↗

CHESS 2025: Waveform LiDAR data from NEON AOP surveys

This dataset provides Level 1 (L1) full-waveform light detection and ranging (LiDAR) data collected for the 2025 Colorado Headwaters Ecological Spectroscopy Study (CHESS). These data were acquired to enable characterization of vegetation structure and other three-dimensional features of the land surface, and to evaluate structural changes that may have occurred between a prior LiDAR acquisition in 2018 and the 2025 overflight. Waveform LiDAR data can provide more detailed information about objects on the ground than discrete point clouds typically do, and they are often used for granular target segmentation and characterization of subcanopy vegetation. The data were acquired over three study domains in the Upper Gunnison river basin: the upper East River watershed (CRBU); Almont Triangle and Taylor Canyon (ALMO); and Upper Taylor River watershed (UPTA) between 2025-06-13 and 2025-07-15. LiDAR data were acquired using the Optech Galaxy Prime Airborne LiDAR Terrain Mapper onboard the National Ecological Observatory Network (NEON) Airborne Observation Platform (AOP). These are the primary waveform LiDAR data delivered by NEON and are provided per flightline in compressed Pulsewaves format, an open-source binary file standard. A Pulsewaves object comprises a two files: a pulse (.pls) file, which stores the geographic origin, outgoing vector, and metadata for every laser pulse emitted by the scanner, and a wave file (.wvs), which stores the sequential amplitude samples of the outgoing pulse and the returning signals. The files are published here in their compressed forms (.plz, .wvz). All waveform data were processed following the theoretical workflow described in the NEON L0-to-L1 Waveform LiDAR Algorithm Theoretical Basis Document (Krause and Goulden 2022a); however, the Pulsewaves output format differs from a legacy format described in that document. Waveform amplitude samples are recorded at 1 nanosecond intervals. All coordinates are provided in meters. Horizontal coordinates are referenced in Universal Transverse Mercator (UTM) zone 13N and the World Geodetic System (WGS) 1984 ensemble datum. Elevations are referenced to Geoid12A. Waveform data for the UPTA survey area were collected without incident and the published records are complete. However, both the ALMO and CRBU collections experienced issues that resulted in incomplete data for those areas. On collection day 2018-06-16 a hardware failure caused the waveform digitizer to lose data from the eastern edge of the ALMO site (Figure 22). The waveform data for flightlines 2–20 could not be extracted from the digitizer, and the data proved unrecoverable. As a result, a portion of the site does not have coverage with waveform data. Although no hardware failure was observed during collection over the CRBU area, final waveform files generated by vendor software contained only ~25% of the expected number of return pulses. After discovery, NEON initiated troubleshooting with the vendor. The root cause of the data ablation had not been identified at the time of publication. Additional data will be published in an update to this package if further recovery proves successful. CHESS Project Description: The Colorado Headwaters Ecological Spectroscopy Study (CHESS) comprised a multi-week airborne remote sensing and field observation campaign in the Upper Gunnison Basin, Colorado, conducted in June and July of 2025. Airborne remote sensing was conducted by the National Ecological Observatory Network Airborne Observation Platform (NEON AOP), concurrent with a field campaign run by the Rocky Mountain Biological Laboratory (RMBL), the Lawrence Berkeley National Laboratory (LBNL) and SLAC National Accelerator Laboratory Watershed Function Science Focus Area (SFA), and NASA-JPL (Jet Propulsion Laboratory) Earth Surface Mineral Dust Source Investigation (EMIT) program. Between June 10 and July 18, 2025, the NEON AOP flight team collected high-resolution aerial imaging spectroscopy and Light Detection and Ranging (LiDAR) data over three domains: the Upper East River (CRBU), Almont Triangle (ALMO), and the Upper Taylor Basin (UPTA). In coordination with the flights, a field campaign acquired ground-truth observations, including observations of vegetation composition, foliar traits, forest demography, and subsurface properties in 18 core sampling areas within the domains. Additional surface water observations were taken at over 380 point locations. All CHESS campaign datasets can be found within the CHESS ESS-DIVE data portal: https://data.ess-dive.lbl.gov/portals/chess. Funding Acknowledgement: Field and remote-sensing data acquisition was performed under a grant from the National Aeronautics and Space Administration (80NSSC24K1005). This work was also supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

2018 NEON and 2025 CHESS Campaigns↗

COVID-19 dynamics across the US: A deep learning study of human mobility and social behavior

This paper presents a deep learning framework for epidemiology system identification from noisy and sparse observations with quantified uncertainty. The proposed approach employs an ensemble of deep neural networks to infer the time-dependent reproduction number of an infectious disease by formulating a tensor-based multi-step loss function that allows us to efficiently calibrate the model on multiple observed trajectories. The method is applied to a mobility and social behavior-based SEIR model of COVID-19 spread. The model is trained on Google and Unacast mobility data spanning a period of 66 days, and is able to yield accurate future forecasts of COVID-19 spread in 203 US counties within a time-window of 15 days. Interestingly, a sensitivity analysis that assesses the importance of different mobility and social behavior parameters reveals that attendance of close places, including workplaces, residential, and retail and recreational locations, has the largest impact on the effective reproduction number. Furthermore, the model enables us to rapidly probe and quantify the effects of government interventions, such as lock-down and re-opening strategies. Taken together, the proposed framework provides a robust workflow for data-driven epidemiology model discovery under uncertainty and produces probabilistic forecasts for the evolution of a pandemic that can judiciously provide information for policy and decision making. All codes and data accompanying this manuscript are available at https://github.com/PredictiveIntelligenceLab/DeepCOVID19.

60 APPLIED LIFE SCIENCES↗

Coupling Microdroplet-Based Sample Preparation, Multiplexed Isobaric Labeling, and Nanoflow Peptide Fractionation for Deep Proteome Profiling of the Tissue Microenvironment

There is increasing interest in developing in-depth proteomic approaches for mapping tissue heterogeneity in a cell-type-specific manner to better understand and predict the function of complex biological systems such as human organs. Existing spatially resolved proteomics technologies cannot provide deep proteome coverage due to limited sensitivity and poor sample recovery. Herein, we seamlessly combined laser capture microdissection with a low-volume sample processing technology that includes a microfluidic device named microPOTS (microdroplet processing in one pot for trace samples), multiplexed isobaric labeling, and a nanoflow peptide fractionation approach. The integrated workflow allowed us to maximize proteome coverage of laser-isolated tissue samples containing nanogram levels of proteins. We demonstrated that the deep spatial proteomics platform can quantify more than 5000 unique proteins from a small-sized human pancreatic tissue pixel (∼60,000 μm2) and differentiate unique protein abundance patterns in pancreas. Furthermore, the use of the microPOTS chip eliminated the requirement for advanced microfabrication capabilities and specialized nanoliter liquid handling equipment, making it more accessible to proteomic laboratories.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Where Is the Provenance? Ethical Replicability and Reproducibility in GIScience and Its Critical Applications

As replicability and reproducibility (R&R) crises develop within emerging convergent inquiry, ethical use of provenance information is central to the establishment and preservation of trust in critical applications of GIScience and geospatial technologies. Today large volumes of geospatial data are generated at high velocity from satellite sensors and unmanned aircraft systems, citizen sensors, geolocation-based data services, global navigation satellite systems, and so on. The extensive use of these data for applications such as disaster and humanitarian response raises the issue of R&R from competing perspectives of location privacy and geospatial data quality. Although geospatial data can be integrated and linked with contextual information to identify individuals’ movements, steps taken to ensure privacy can complicate the multiuser development of high-quality geospatial workflows. Provenance information as digital records of historical (retrospective) and potential future (prospective) geospatial processes is often overlooked, misunderstood, or inadequately addressed. We explore the relationship between provenance information, location privacy, and geospatial data quality in the context of R&R with a focus on disaster analytics. Here, we argue that in the era of big data and deep learning, GIScientists and associated institutions bear greater responsibility both for geospatial workflow quality and for location privacy. Given vastly heterogenous computational landscapes, we provide practical recommendations for ethically driven provenance and R&R research and development within the GIScience community and beyond.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

An Open-Source Frequency-Domain Model for Floating Wind Turbine Design Optimization

A new frequency-domain dynamics model has been developed that uses open-source components to efficiently represent a complete floating wind turbine system. The model, called RAFT (Response Amplitudes of Floating Turbines), incorporates quasi-static mooring reactions, strip-theory and potential-flow hydrodynamics, blade-element-momentum aerodynamics, and linear turbine control. The formulation is compatible with a wide variety of support structure configurations and no manual or time-domain preprocessing steps are required, making RAFT very practical in design and optimization workflows. The model is applied to three reference floating wind turbine designs and its predictions are compared with results from time-domain OpenFAST simulations. There is good agreement in mean offsets as well the statistics and spectra of the dynamic response, verifying RAFT’s general suitability for floating wind analysis. Follow-on work will include verification of potential-flow and turbine-control features and application to optimization problems.

17 WIND ENERGY↗

BESTEST-GSR (Building Energy Simulation Test - Generation Simulation and Reporting) 2023 [SWR 18-23]

Building Energy Simulation Test (BESTEST) is an NREL-developed method to validate the qualitative performance of different whole building simulations engines relative to each other. https://www.nrel.gov/docs/legosti/old/6231.pdf The purpose of this repository is to generate BESTEST test case models, run simulations, and populate data for ASHRAE Standard 140 reporting spreadsheets for EnergyPlus® based whole building simulation tools. It was originally setup for 2014 version of Standard 140. In May of 2022 it was updated to the 2020 version of Standard 140. This update included updates and additions to existing test suites, the bulk of which was in Section 5.2 (Building Thermal Envelope and Fabric Load Tests). We did not add Section 5.5 Airside HVAC Equipment Performance, but we hope to add that later in 2022. At some point we also hope to add Section 5.2.4 ground modeling, which is currently excluded. Supported Tools The default IDF generation is based on the OpenStudio® CLI, but the workflow supports a 'Bring your own IDF' use case. Additionally, for non-EnergyPlus® based tools the post processing scripts can be used if simulation results are provided as a CSV file.The scripts on this repository should work on Mac, Windows, and Linux. Dependencies Install OpenStudio® 3.4.0 make sure command line can recognize the 'openstudio' command This includes EnergyPlus® 22.1 Install Ruby on your system if it isn't already setup. 2.7 is used for development but other versions may work Since OpenStudio has its own embedded Ruby, which is used for running measures, you don't necessarily have to use a version of Ruby supported by OpenStudio. Install RubyXL Ruby gem This is used to modify Microsoft Excel spreadsheets Install Parallel Ruby gem This allows the CLI to run simulations in parallel

Goldwasser, David↗

The Future of NASA Earth Science in the Commercial Cloud: Challenges and Opportunities

NASA produces a large volume and variety of data products that are used every day to support research, decision making, and education. The widespread use of NASA’s Earth Science data is enabled by NASA’s Earth Science Data System (ESDS) program, which oversees the archiving and distribution of these data and invests in the development of new data systems and tools. However, NASA’s current approach to Earth Science data distribution — based on distributed institutional archives with individual on-premises high-performance computing capabilities — faces some significant challenges, including massive increases in data volume from upcoming missions, a greater need for transdisciplinary science that synthesizes many different kinds of observations, and a push to make science more open, inclusive, and accessible. To address these challenges, NASA is aggressively migrating its Earth Science data and related tools and services into the commercial cloud. Migration of data into the commercial cloud can significantly improve NASA’s existing data system capabilities by (1) providing more flexible options for storage and compute (including rapid, as-needed access to state-of-the-art capabilities); (2) by centralizing and standardizing data access, which gives all of NASA’s institutional data centers access to all of each other’s datasets; and (3) by facilitating “analysis-in-place”, whereby users can bring their own computational workflows and tools to the data rather than having to maintain their own copies of NASA datasets. However, migration to the commercial cloud also poses some significant challenges, including (1) managing costs under a “pay-as-you-go” model; (2) incompatibility with existing tools and data formats with object-based storage and network access; (3) vendor lock-in; (4) challenges with data access for workflows that mix on-premise and cloud computing; and (5) standardization for highly diverse data as is present in NASA’s data archive. I conclude with two examples of recent NASA activities showcasing capabilities enabled by the commercial cloud: An interactive analysis and development platform for analyzing airborne imaging spectroscopy data, and a new collection of tools and services for data discovery, analysis, publication, and data-driven storytelling (Visualization, Exploration, and Data Analysis, VEDA).

Alexey N Shiklomanov↗

GridOPTICS/GridPACK

GridPACK is a software framework consisting of a set of modules designed to simplify the development of programs that model the power grid and run on parallel, high performance computing platforms. It also contains several fully developed applications, including powerflow, dynamic simulation, state estimation, Kalman filter analysis (dynamic state estimation), contingency analysis and real time path rating. These applications can be used either standalone or as components in more complicated workflows that combine several different types of application together. The framework modules are available as a combination of libraries and software templates and consist of components for setting up and distributing power grid networks, support for modeling the behavior of individual buses and branches in the network, converting the network models to the corresponding algebraic equations, and parallel routines for manipulating and solving large algebraic systems. The framework also contains a module for distributing tasks evenly amongst computing resources, even if individual tasks vary widely in their execution times. Additional modules support input and output, basic statistical analysis of contingency based calculations, distributed data structures, as well as basic profiling and error management.

Palmer, Bruce↗

Device and Method for Parallel Measurement of Phosphoproteome and Proteome from Single Cells

We present the development of an immobilized metal affinity chromatography (IMAC) chip designed to enable nanoscale phosphopeptide enrichment within microfabricated nanowells. This novel platform leverages surface chemistry to immobilize high-density Nickel-Nitrilotriacetic Acid (Ni-NTA) molecules on nanowells, followed by applying Fe 3+ . The nanowell surface serves as a capture media to enrich phosphopeptides based on IMAC. The system's efficiency was validated using ß-casein as a model protein, demonstrating the chip’s capability to significantly enrich phosphopeptides. Future applications of this technology are anticipated to enable the detection of over 100 phosphopeptides from individual cells and more than 500 phosphopeptides from pools of 100 cells, offering exciting potential for single-cell phosphoproteomics. We will next apply an integrated proteomics workflow to perform multi-omics measurements, including single-cell isolation, protein digestion, and phosphopeptide enrichment, followed by LC-MS analysis of both the global proteome and phosphoproteome. Future research will explore the use of this technology to study phosphorylation dynamics in cancer cells, enhancing our understanding of cellular signaling and disease mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗

A multi-scale time-series dataset of anthropogenic heat from buildings in Los Angeles County

The dataset contains hourly Anthropogenic heat (AH) from buildings in Los Angeles County, based on weather data from 2018. The hourly AH is aggregated at three spatial resolutions: 450m x 450m grid, 12km x 12km grid, and census tract. The AH is broken down into three components: building envelope surface convection, heating, ventilation, and air conditioning (HVAC) system heat release, and zone exfiltration and exhaust air heat loss. The dataset is created with the physics-based EnergyPlus building energy models to calculate individual buildings' AH considering WRF-UCM simulated microclimate conditions. Please refer to the paper "A multi-scale time-series dataset of anthropogenic heat from buildings in Los Angeles County" for more information about the data generation workflow and the data validation procedure. The data set contains two folders: the "output_data" folder holds the simulation results (EP_output and EP_output_csv), building metadata (building_metadata.geojson and building_metadata.csv), aggregated heat emission and energy consumption time-series data (hourly_heat_energy), and geographical data (geo_data) associated with the GEOID referenced in heat and energy consumption data. The "input_data" folder contains the raw data used to generate files in the "output_data" folder as well as data sets used in the validation. The code repository (https://github.com/IMMM-SFA/xu_etal_2022_sdata) holds the processing scripts for data curation, validation, and visualization.

Energy↗

Collaborative Resource Allocation

Collaborative Resource Allocation Networking Environment (CRANE) Version 0.5 is a prototype created to prove the newest concept of using a distributed environment to schedule Deep Space Network (DSN) antenna times in a collaborative fashion. This program is for all space-flight and terrestrial science project users and DSN schedulers to perform scheduling activities and conflict resolution, both synchronously and asynchronously. Project schedulers can, for the first time, participate directly in scheduling their tracking times into the official DSN schedule, and negotiate directly with other projects in an integrated scheduling system. A master schedule covers long-range, mid-range, near-real-time, and real-time scheduling time frames all in one, rather than the current method of separate functions that are supported by different processes and tools. CRANE also provides private workspaces (both dynamic and static), data sharing, scenario management, user control, rapid messaging (based on Java Message Service), data/time synchronization, workflow management, notification (including emails), conflict checking, and a linkage to a schedule generation engine. The data structure with corresponding database design combines object trees with multiple associated mortal instances and relational database to provide unprecedented traceability and simplify the existing DSN XML schedule representation. These technologies are used to provide traceability, schedule negotiation, conflict resolution, and load forecasting from real-time operations to long-range loading analysis up to 20 years in the future. CRANE includes a database, a stored procedure layer, an agent-based middle tier, a Web service wrapper, a Windows Integrated Analysis Environment (IAE), a Java application, and a Web page interface.

Wang, Yeou-Fang↗

A multiomics mass spectrometry workflow for fast and comprehensive strain optimization (Abstract CRADA 726 )

The Agile Biofoundry (ABF) is a multi-national lab consortium funded by the DOE Bioenergy Technologies Office that has developed a biofoundry that enables the rapid deployment of bioproducts into the market. The ABF is a flexible platform that can adjust to the needs of numerous government, academic and industrial partners, thus enabling them to rapidly develop and optimize the production of a wide range of bioproducts. To enhance this capability, PNNL and Agilent Technologies are collaborating to expand and demonstrate a prototype system that processes hundreds of samples per day by liquid chromatography-mass spectrometry-based untargeted and targeted methods, and artificial intelligence software for multiomics applications, including metabolomics, lipidomics and proteomics.

Bilbao, Aivett (ORCID:0000000329858249)↗

HP-MDR: High-performance and Portable Data Refactoring and Progressive Retrieval with Advanced GPUs

Scientific applications produce vast amounts of data, posing grand challenges in the underlying data management and analytic tasks. Progressive compression is a promising way to address this problem, as it allows for on-demand data retrieval with significantly reduced data movement cost. However, most existing progressive methods are designed for CPUs, leaving a gap for them to unleash the power of today’s heterogeneous computing systems with GPUs.In this work, we propose HP-MDR, a high-performance and portable data refactoring and progressive retrieval framework for GPUs. Our contributions are four-fold: (1) We carefully optimize the bitplane encoding and lossless encoding, two key stages in progressive methods, to achieve high performance on GPUs; (2) We propose pipeline optimization and incorporate it with data refactoring and progressive retrieval workflows to further enhance the performance for large data process; (3) We leverage our framework to enable high-performance data retrieval with guaranteed error control for common Quantities of Interest; (4) We evaluate HP-MDR and compare it with state of the arts using five real-world datasets. Experimental results demonstrate that HP-MDR delivers an average 13.68 × and 6.31 × throughput in data refactoring and progressive retrieval tasks, respectively. It also leads to 11.22 × throughput for recomposing required data representations under Quantity-of-Interest error control and 6.04 × performance for the corresponding end-to-end data retrieval, when compared with state-of-the-art solutions.

Li, Yanliang [University of Oregon]↗

Smart Handoffs: Preserving User Context Between Tools and Services Related to NASA's EOSDIS Data Archive

NASA's Earth Observing System Data and Information System (EOSDIS) is tasked with archiving and distributing Earth Observation data across a range of disciplines, including atmospheric science, oceanography, land processes, natural hazards, solar radiance and even socioeconomic aspects relating to the environment. Given the breadth of disciplines and depth of data that EOSDIS provides, the efficient and intuitive discovery and usage of data by a scientist is of paramount importance. An effective data gathering workflow may involve switching from general use discovery tools to a more bespoke services designed specifically for the scientist's discipline. Providing concrete interoperability between such tools could vastly improve the efficiency of a scientist's workflow.

Analytics↗