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At least 649 records · Page 36

Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases

Abstract Online, open access databases for biological knowledge serve as central repositories for research communities to store, find and analyze integrated, multi-disciplinary datasets. With increasing volumes, complexity and the need to integrate genomic, transcriptomic, metabolomic, proteomic, phenomic and environmental data, community databases face tremendous challenges in ongoing maintenance, expansion and upgrades. A common infrastructure framework using community standards shared by many databases can reduce development burden, provide interoperability, ensure use of common standards and support long-term sustainability. Tripal is a mature, open source platform built to meet this need. With ongoing improvement since its first release in 2009, Tripal provides full functionality for searching, browsing, loading and curating numerous types of data and is a primary technology powering at least 31 publicly available databases spanning plants, animals and human data, primarily storing genomics, genetics and breeding data. Tripal software development is managed by a shared, inclusive governance structure including both project management and advisory teams. Here, we report on the most important and innovative aspects of Tripal after 11 years development, including integration of diverse types of biological data, successful collaborative projects across member databases, and support for implementing FAIR principles.

59 BASIC BIOLOGICAL SCIENCES↗

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.↗

NGEE Arctic Integrated Modeling (IM2): Improved subgrid hillslope hydrologic connectivity

This data product represents the integration of new code capability for arctic tundra hillslope hydrologic processes into the Energy Exascale Earth System Model (E3SM), through the E3SM Land Model (ELM) component. This code integration is the result of collaborative effort between the NGEE Arctic project and the E3SM project. The current ELM represents water movement primarily through vertical processes, such as precipitation, canopy interception, evaporation, infiltration, and soil water movement. Lateral water movement—such as surface runoff, subsurface flow, and river transport—plays a significant role in the hydrological cycle, especially in regions with varied topography. While E3SM includes a runoff routing component representing water transport in the river network, the lateral transport of water at the subgrid scale within the land model has previously not been taken into account. With the recent development of topographic units within the ELM subgrid data structure, there is an opportunity to simulate hillslope hydrologic connectivity by introducing water transport along topographic gradients. We expect that more realistic representation of hillslope hydrologic processes will lead to improved predictions of both soil water content and river network flows. Lateral transport of water at and near the surface is represented as a sub-grid process in this new code development. Water is tracked as it moves from higher to lower elevations within a gridcell. This capability uses the nested hierarchical sub-grid scheme within ELM to connect water fluxes from sub-grid elements with higher elevation to those with lower elevation. This data record consists of a single document (pdf format) that describes the theoretical basis for the hillslope hydrology processes added to ELM, and describes the modifications made to the ELM code. The Methods section of this metadata record includes a link to the public E3SM code repository where the exact code modifications as integrated in E3SM can be accessed. 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).

Thornton, Peter E [ORNL] (ORCID:0000000247595158)↗

Temporal dynamics of the multi-omic response to endurance exercise training

Regular exercise promotes whole-body health and prevents disease, but the underlying molecular mechanisms are incompletely understood. Here, the Molecular Transducers of Physical Activity Consortium profiled the temporal transcriptome, proteome, metabolome, lipidome, phosphoproteome, acetylproteome, ubiquitylproteome, epigenome and immunome in whole blood, plasma and 18 solid tissues in male and female Rattus norvegicus over eight weeks of endurance exercise training. The resulting data compendium encompasses 9,466 assays across 19 tissues, 25 molecular platforms and 4 training time points. Thousands of shared and tissue-specific molecular alterations were identified, with sex differences found in multiple tissues. Temporal multi-omic and multi-tissue analyses revealed expansive biological insights into the adaptive responses to endurance training, including widespread regulation of immune, metabolic, stress response and mitochondrial pathways. Many changes were relevant to human health, including non-alcoholic fatty liver disease, inflammatory bowel disease, cardiovascular health and tissue injury and recovery. The data and analyses presented in this study will serve as valuable resources for understanding and exploring the multi-tissue molecular effects of endurance training and are provided in a public repository (https://motrpac-data.org/).

59 BASIC BIOLOGICAL SCIENCES↗

Standard Analysis Report INV-SAR-81, Revision 0 Chemical and Cement Components 2023 Inventory Estimates for the Interim State Performance Assessment of the Waste Isolation Pilot Plant

This standard analysis report provides the estimates for the chemical (oxyanions and complexing agents) and cement components with a data collection cut-off date of December 31, 2023. These estimates will be included in a Performance Assessment Inventory Report developed for the U.S. Department of Energy (DOE) interim state repository configuration performance assessment (PA) for the 2026 Compliance Recertification Application (CRA).

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Dataset, Code, and Models for Training Deep Learning Potentials for Low Temperature Plasma-Surface Interactions

This repository contains datasets, training scripts, and finished models, and test simulations used in the development of DeepREBO— a machine-learned interatomic potential trained to emulate the REBO2 empirical potential. The data was generated to study deep potential development for simulations of plasma-surface interactions. It uses an active learning framework, starting from a minimal dataset and iteratively expanding it. Included are those generated datasets, the trained models, and simulations used to evaluate the performance of the training process. This resource supports reproducibility and provides a reference framework for training deep potentials in plasma-surface interaction studies.

active learning↗

Dark Energy Survey Supernova 5YR Data Release

This data set was generated by the Dark Energy Survey (DES) team, and was used for the cosmological analysis in the DES key supernova cosmology paper (arXiv:2401.02929). When using this data please cite both the data release paper (Sanchez et al. 2024, ApJ, arXiv:2406.05046) and the DES key paper (Dark Energy Survey Collaboration 2024, ApJL, arXiv:2401.02929). At DES-SN5YR Github Repo (https://github.com/des-science/DES-SN5YR), we provide a comprehensive list of references for the different data products (SALT3 light-curve model, calibration, DCR corrections, SN classification, SN distances and uncertainties covariance matrix). If you have questions, post an issue on the DES-SN5YR Github repository and/or get in touch with the contact people indicated on the Github repository.

Contractor, Fermilab [Fermilab]↗

EPIsembleVis: A geo-visual analysis and comparison of the prediction ensembles of multiple COVID-19 models

In this work, we present EPIsembleVis, a web-based comparative visual analysis tool for evaluating the consistency of multiple COVID-19 prediction models. Our approach analyzes a collection of COVID-19 predictions from different epidemiological models as an ensemble and utilizes two metrics to quantify model performance. These metrics include (a) prediction uncertainty (represented as the dispersion of predictions in each ensemble) and (b) prediction error (calculated by comparing individual model predictions with the recorded data). Through an interactive visual interface, our approach provides a data-driven workflow for (a) selecting and constructing the COVID-19 model prediction ensemble based on the spatiotemporal overlap of available predictions of multiple epidemiological models, (b) quantifying the model performance using both the uncertainty of each model prediction ensemble, and the error of each ensemble member that represents individual model predictions, and (c) visualizing the spatiotemporal variability in the projection performance of individual models using a suite of novel ensemble visualization techniques, such as the data availability map, a spatiotemporal textured-tile calendar, multivariate rose chart, and time-series leaflet glyph. We demonstrate the capability of our ensemble visual interface through a case study that investigates the performance of weekly COVID-19 predictions, which are provided through the COVID-19 Forecast Hub UMass-Amherst Influenza Forecasting Center of Excellence [47] for the United States and United States Territories. The EPIsembleVis tool is implemented using open-source web technologies and adaptive system design, rendering it interoperable with Elasticsearch and Kibana for automatically ingesting COVID-19 predictions from online repositories, and it is generalizable for analyzing worldwide projections from more epidemiological models.

60 APPLIED LIFE SCIENCES↗

NGEE Arctic Integrated Modeling (IM3): Improved snow-vegetation interaction

This data product represents the integration of new code capability for arctic tundra snow-vegetation-terrain interactions into the Energy Exascale Earth System Model (E3SM), through the E3SM Land Model (ELM) component. This code integration is the result of collaborative effort between the NGEE Arctic project and the E3SM project. The NGEE Arctic project developed a total of six Integrated Modeling (IM) modules informed by observations and experiments. New ELM capability represented by this data product (IM3) falls into three categories: 1) Downscaling from gridcell to topographic unit level when working through the existing coupler bypass code. 2) Four new parameters (taper, stocking, bendresist, and vegshape) have been added to ELM to allow for flexible definition of snow-vegetation interactions. 3) Vegshape and bendresist parameters are used to calculate the fraction of leaf area and/or stem area buried by snow for a given snow depth. This data record consists of a single document (pdf format) that describes the theoretical basis for the snow-vegetation-terrain interactions added to ELM, and describes the modifications made to the ELM code. The Methods section of this metadata record includes a link to the public E3SM code repository where the exact code modifications as integrated in E3SM can be accessed. 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).

Thornton, Peter E [ORNL] (ORCID:0000000247595158)↗

HamLib: A Library of Hamiltonians for Benchmarking Quantum Algorithms and Hardware

For a considerable time, large datasets containing problem instances have proven valuable for analyzing computer hardware, software, and algorithms. One notable example of the value of large datasets is ImageNet [1], a vast repository of images that has been instrumental in testing numerous deep learning packages. Similarly, in the domain of computational chemistry and materials science, the availability of extensive datasets such as the Protein Data Bank [2], the Materials Project [3], and QM9 [4] has greatly facilitated the evaluation of new algorithms and software approaches, while also promoting standardization within the field. These well-defined datasets and problem instances, in turn, serve as the foundation for creating benchmarking suites like MLPerf [5] and LINPACK [6], [7]. These suites enable fair and rigorous comparisons of different methodologies and solutions, fostering continuous advancements in various areas of computer science and beyond.

Sawaya, Nicolas PD↗

HYBRID Modeling Validation and Verification Status Matrix

The HYBRID modeling repository is a premier resource for integrated energy systems modeling. HYBRID models have been developed since 2015 to describe the physical operation of tightly coupled thermal systems including power generators, thermal transport systems, thermal storage, thermal-to-electric conversion systems, and other thermal applications. Due to the increased size of the repository, a concise summary matrix of available models is desired. This matrix will consolidate not only the list of available models but also indicate original information sources, publications that have model examples, and level of validation and verification that exists for the models. Validation and verification (V&V) levels begin from simplified algebraic relationship and advance to dynamic data validation. Moving forward, as new models are contributed to HYBRID, their V&V level will be included, updating this matrix.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Python codes for the paper - "Trade-offs in the latent representation of microstructure evolution"

SAND2024-00946O Python codes used in "Trade-offs in the latent representation of microstructure evolution," a manuscript accepted for publication in Acta Materialia, are part of a repository. The code was developed to perform analysis of microstructure evolution. The repository consists of two main directories: models, which train and test models such as autoencoders and diffusion maps, and analysis, which analyzes microstructures. Source code is used to perform dimensionality reduction of microstructure data for analysis of its evolution in time. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Dingreville, Remi↗

Evaluation of Nuclear Spent Fuel Disposal in Clay-Bearing Rock - Process Model Development and Experimental Studies

This report represents the milestone deliverable M2SF-23SN010301072 “Evaluation of Nuclear Spent Fuel Disposal in Clay-Bearing Rock - Process Model Development and Experimental Studies” The report provides a status update of FY23 activities for the work package Argillite Disposal work packages for the DOE-NE Spent Fuel Waste Form Science and Technology (SFWST) Program. Clay-rich geological media (often referred as shale or argillite) are among the most abundant type of sedimentary rock near the Earth’s surface. Argillaceous rock formations have the following advantageous attributes for deep geological nuclear waste disposal: widespread geologic occurrence, found in stable geologic settings, low permeability, self-sealing properties, low effective diffusion coefficient, high sorption capacity, and have the appropriate depth and thickness to host nuclear waste repository concepts. The DOE R&D program under the Spent Fuel Waste Science Technology (SFWST) campaign has made key progress (through experiment, modeling, and testing) in the study of chemical and physical phenomena that could impact the long-term safety assessment of heat-generating nuclear waste disposition in clay/shale/argillaceous rock. International collaboration activities comprising field-scale heater tests, field data monitoring, and laboratory-scale experiments provide key information on changes to the engineered barrier system (EBS) material exposed high thermal loads. Moreover, consideration of direct disposal of large capacity dual-purpose canisters (DPCs) as part of the back-end SNF waste disposition strategy has generated interest in improving our understanding of the effects of elevated temperatures on the engineered barrier system (EBS) design concepts. Chemical and structural analyses of sampled bentonite material from laboratory tests at elevated temperatures are key to the characterization of thermal effects affecting bentonite clay barrier performance. The knowledge provided by these experiments is crucial to constrain the extent of sacrificial zones in the EBS design during the thermal period. Thermal, hydrologic, mechanical, and chemical (THMC) data collected from heater tests and laboratory experiments have been used in the development, validation, and calibration of THMC simulators to model near-field coupled processes. This information leads to the development of simulation approaches to assess issues on coupled processes involving porous media flow, transport, geomechanical phenomena, chemical interactions with barrier/geologic materials, and the development of EBS concepts. These lines of knowledge are central to the design of deep geological backfilled repository concepts where temperature plays a key role in the EBS behavior, potential interactions with host rock, and long-term performance in the safety assessment.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Metadata Schemas and Ontologies for Building Energy Applications: A Critical Review and Use Case Analysis

With the increasing digitalization of processes throughout the lifecycle of buildings, data exchanged between stakeholders and between building systems has grown significantly. However, a lack of semantic interoperability between data in different systems is still prevalent, hindering the development of applications that can be reused across buildings and limiting the scalability of innovative solutions. Semantics refers to the description of the meaning of the data in a way that can be consistently understood by applications. Recently, several competing initiatives have been developing metadata schemas and ontologies to express this semantic information for different applications in the building domain. This paper systematically reviews these schemas and conducts an analysis of five of them to evaluate their applicability to three high-value use cases for building operations: energy audits, automated fault detection and diagnostics and optimal control. The survey finds 40 schemas published in the last 10 years but but their actual use in industry is difficult to estimate. Among the five selected ontologies, several gaps are highlighted in relation to the three use cases. Recommendations for the future include better harmonization of these initiatives, more centralized repositories and search engines for these schemas as well as better industry engagement to facilitate their adoption.

Smart Building, Sematic, Metadata, Ontology, Data ↗

CRCNS22 Learning Rules in the Hippocampus and their Mapping to Neuromorphic Systems (Final Technical Report)

Large scale biologically-realistic computational models are key to investigating the interplay between structure and function in nervous systems, thus paving the way to new clinical methods and neuro-inspired computing solutions. This project focuses on the hippocampus, in particular the CA3-CA1 regions, due to their role in associative learning and memory, pattern separation and completion, and spatial navigation. Investigations into the neuronal organization and learning rule(s) of this circuit can shed light into how declarative memories are formed, stored, recalled and forgotten and inform computational, experimental and clinical neuroscience work. Our project aims at developing a novel data-driven methodology supported by a broad heterogeneous base of neuroscience experimental knowledge and inspired from advances in computer science and engineering. Specifically, this work will benchmark existing and new learning rules within a full-scale spiking neural network simulation of the CA3-CA1 region. The model will be based on an open-source repository, called the Hippocampome, which contains neuronal morphologies, firing patterns, synapse probabilities, and most other required parameters for all known neuron types in the rodent hippocampal formation. The model will be first trained in a supervised fashion for associative memory tasks using backpropagation through time traditionally used in computer science, enhanced with a new technique called the surrogate gradient method. This optimization method will be used to obtain a global loss minimization, but it is not biologically inspired as it assumes the use of data not locally available to the synapses. However, we propose its use as a benchmarking tool, to compare the training performance of local biologically plausible and hardware-mappable learning rules at scale. New rules or combinations will be proposed and tested as needed, based on the obtained results. Progress in this area will also drive the development of novel hardware-mappable algorithms for continual lifelong learning and categorization of new events from few presented examples. This project goes beyond the existing state-of-the-art by looking at large scale realistic neuronal circuits as networks trainable via global optimization methods such as surrogate gradient descent. The objective function of the brain that supports learning is largely unknown, but it is likely that it operates through local learning rules. Studying network trajectories around local minima as proposed in this work represents a useful strategy for understanding whether a network is training by using a specific (set of) learning rule(s). Starting from a completely untrained network is a challenging test since it is difficult to determine how the learning rule affects the trajectory of the network. This interdisciplinary project will help understand what rule governs learning in these regions or if multiple learning rules are involved. The work will develop a robust methodology to measure if the network is converging to the target solution, oscillating around it, or diverging away.

59 BASIC BIOLOGICAL SCIENCES↗

Classified library celebrates two-year anniversary print your own commemorative history posters

Today is the National Security Research Center’s second anniversary. These two years, though, have been eight decades in the making, said NSRC Director Riz Ali. “We opened our doors in 2019, but the Center’s beginnings date back to World War II when J. Robert Oppenheimer created the Lab in Los Alamos to develop the first-ever nuclear weapons,” Ali said. “An important part of opening the Lab included standing up a technical reports library. Since then, we have amassed millions of holdings and today we are one of the top research institutions in the country.” What had long-been a repository of classified archival materials is today a dynamic, vibrant library that outsizes the collections of other similar research libraries around the country. Today, the NSRC houses the Laboratory’s classified nuclear weapons research, data and reports, as well as unclassified historical artifacts – the stories, photos, films and more from the people who have been a part of the Lab from the start.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Benched: Upgrading and Updating the Los Alamos Benchmark Suite for the 21st Century [Slides]

The presentation begins by stating that most organizations make choices to handle specific things when preparing input files for validation, such as which elemental abundance data to use, how to decompose specific elements, and setting calculation precision. It also discusses the consequences, which include differing calculation results between different organizations for the same case, even when using the same code. This is illustrated by the intercomparison exercise and input files that are prepared by one organization and are not necessarily correct for another. The presentation explains that the Los Alamos Benchmark Suite is a centralized repository of high-quality benchmark models currently under development at LANL. The objectives of the new repository are to remain up to date with the latest ICSBEP revision, to have a formal review and revision process, to (eventually) be an open-source repository, and to provide new tools for improved input and output file generation and review.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species

Abstract Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research. The Monarch App is an integrated platform combining data about genes, phenotypes, and diseases across species. Monarch's APIs enable access to carefully curated datasets and advanced analysis tools that support the understanding and diagnosis of disease for diverse applications such as variant prioritization, deep phenotyping, and patient profile-matching. We have migrated our system into a scalable, cloud-based infrastructure; simplified Monarch's data ingestion and knowledge graph integration systems; enhanced data mapping and integration standards; and developed a new user interface with novel search and graph navigation features. Furthermore, we advanced Monarch's analytic tools by developing a customized plugin for OpenAI’s ChatGPT to increase the reliability of its responses about phenotypic data, allowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be found at monarchinitiative.org and its corresponding code repository at github.com/monarch-initiative/monarch-app.

60 APPLIED LIFE SCIENCES↗