Results for “data repositories” — Page 37

DOE OSTI2024

High-accuracy emulators for observables in ΛCDM, N eff, Σ m ν, and w cosmologies

ABSTRACT We use the emulation framework CosmoPower to construct and publicly release neural network emulators of cosmological observables, including the cosmic microwave background (CMB) temperature and polarization power spectra, matter power spectrum, distance-redshift relation, baryon acoustic oscillation (BAO) and redshift-space distortion (RSD) observables, and derived parameters. We train our emulators on Einstein–Boltzmann calculations obtained with high-precision numerical convergence settings, for a wide range of cosmological models including ΛCDM, wCDM, ΛCDM + Neff, and ΛCDM + Σmν. Our CMB emulators are accurate to better than 0.5 per cent out to ℓ = 104, which is sufficient for Stage-IV data analysis, and our P(k) emulators reach the same accuracy level out to $k=50 \, \, \mathrm{Mpc}^{-1}$, which is sufficient for Stage-III data analysis. We release the emulators via an online repository (CosmoPower Organisation), which will be continually updated with additional extended cosmological models. Our emulators accelerate cosmological data analysis by orders of magnitude, enabling cosmological parameter extraction analyses, using current survey data, to be performed on a laptop. We validate our emulators by comparing them to class and camb and by reproducing cosmological parameter constraints derived from Planck TT, TE, EE, and CMB lensing data, as well as from the Atacama Cosmology Telescope Data Release 4 CMB data, Dark Energy Survey Year-1 galaxy lensing and clustering data, and Baryon Oscillation Spectroscopic Survey Data Release 12 BAO and RSD data.

Astronomy & Astrophysics↗

DOE OSTI2022

WormBase in 2022—data, processes, and tools for analyzing Caenorhabditis elegans

WormBase (www.wormbase.org) is the central repository for the genetics and genomics of the nematode Caenorhabditis elegans. We provide the research community with data and tools to facilitate the use of C. elegans and related nematodes as model organisms for studying human health, development, and many aspects of fundamental biology. Throughout our 22-year history, we have continued to evolve to reflect progress and innovation in the science and technologies involved in the study of C. elegans. We strive to incorporate new data types and richer data sets, and to provide integrated displays and services that avail the knowledge generated by the published nematode genetics literature. Here, we provide a broad overview of the current state of WormBase in terms of data type, curation workflows, analysis, and tools, including exciting new advances for analysis of single-cell data, text mining and visualization, and the new community collaboration forum. Concurrently, we continue the integration and harmonization of infrastructure, processes, and tools with the Alliance of Genome Resources, of which WormBase is a founding member.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Observations of modal coupling due to bolted joints in an experimental benchmark structure

The goal of this paper is to present a set of measurements from a benchmark structure containing two bolted joints to support future efforts to predict the damping due to the joints and to model nonlinear coupling between the first two elastic modes. Bolted joints introduce nonlinearities in structures, typically causing a softening in the natural frequency and an increase in damping because of frictional slip between the contact interfaces within the joint. These nonlinearities pose significant challenges when characterizing the response of the structure under a large range of load amplitudes, especially when the modal responses become coupled, causing the effective damping and natural frequency to not only depend on the excitation amplitude of the targeted mode, but also the relative amplitudes of other modes. In this work, two nominally identical benchmark structures, known in some prior works as the S4 beam, are tested to characterize their nonlinear properties for the first two elastic modes. Detailed surface measurements are presented and validated through finite element analysis and reveal distinct contact interactions between the two sets of beams. The free-free test structures are excited with an impact hammer and the transient response is analyzed to extract the damping and frequency backbone curves. A range of impact amplitudes and drive points are used to isolate a single mode or to excite both modes simultaneously. Differences in the nonlinear response correlate with the relative strength of the modes that are excited, allowing one to characterize mode coupling. Each of the beams shows different nonlinear properties for each mode, which is attributed to the different contact pressure distributions between the parts, although the mode coupling relationship is found to be consistent between the two. Lastly, the test data key finding are presented in this paper and the supporting data is available on a public repository for interested researchers.

42 ENGINEERING↗

DOE OSTI2026

ENVnet provides a global molecular resource of dissolved organic matter

Dissolved organic matter (DOM) is an important component of Earth's carbon cycle and one of the planet's most chemically diverse pools, yet the molecular structures of its constituents remain largely unresolved. This limitation has hindered our ability to link DOM composition to microbial processes and ecosystem function. Here we present ENVnet, a global molecular repository built from tandem mass spectrometry data collected across 13 terrestrial and aquatic environment types, including 419 newly generated samples that expand publicly available DOM metabolomics data and cover previously underrepresented environments. By computationally deconvolving chimeric mass spectra, a longstanding challenge in environmental metabolomics, we recover high-quality fragmentation data for >22,000 distinct molecular features (defined by a specific precursor mass and fragmentation pattern). Using ENVnet, we uncover conserved and environment-specific molecular patterns in DOM composition and underlying biogeochemical processes. We also use molecular features encoded in ENVnet to train predictive models of DOM persistence, allowing molecular-level assessment of microbial turnover in independent systems.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Interactive Mobility Landscape App

This is the companion repository to NREL's Interactive Mobility Data Landscape (SEE: DOE Code ID 61284. NREL SWR-21-09). The landscapeapp is an upstream NPM module that supports building interactive landscape websites such as the CNCF Cloud Native Landscape (source) and the LF Artificial Intelligence Landscape (source). The application is managed by Dan Kohn of CNCF and is under active development by Andrey Kozlov (who did most of the development to date, 9/13/2021) and Jordi Noguera.

Shankari, Kalyanaraman↗

DOE OSTI2024

Interpolation Models and Error Bounds for Verifiable Scientific Machine Learning

This repository contains python scripts and numerical data accompanying the paper: "Leveraging Interpolation Models and Error Bounds for Verifiable Scientific Machine Learning," Tyler Chang, Andrew Gillette, Romit Maulik, 2024. The following subdirectories are included: - "interpolants" contains our interpolation scripts used for all studies - "experiments" contains scripts demonstrating our experiments with synthetic data - "airfoil" contains scripts demonstrating our experiments with the publicly available UIUC airfoil dataset. Further instructions are provided in READMEs within the sub-directories.

Gillette, Andrew↗

DOE OSTI2024

In-situ FTIR Spectral Deconvolution [SWR-24-60]

In-situ FTIR Spectral Deconvolution contains scripts for the fitting of gaussians to convoluted FTIR spectra. It was specifically developed to handle a time-series of in situ ATR-FTIR spectra, split the spectra into its individual gaussians, and track those peaks as they shift in intensity and energy. Along with the actual fitting script, this repository contains several support scripts for data analysis and recall of prior fit results.

Tremolet de Villers, Bertrand↗

DOE OSTI2023

Dataset for 'Ombadi et al. (2023). A warming-induced reduction in snow fraction amplifies rainfall extremes, Nature'

This package contains the main codes, sample input data and main result files to reproduce the analysis and results presented in the article: “Ombadi et al. (2023), A warming-induced reduction in snow fraction amplifies rainfall extremes, Nature”. The folder consists of the following: (1) “Raw data”: a folder that contains sample input data which is used in some of the codes for demonstration purposes. It also contains data that was not pre-processed such as Elevation data; (2) “Results”: this folder contains files of the main results presented in the paper including: “Annual-Max-Series”, “Change-rainfall-extremes”, “Change-snow-fraction”, “Warming levels_By scenario_model_year” and “Masks”. Description of these folders is detailed in the "Readme.rtf" file; (3) Python jupyter notebooks (Extract_Annual Max Series (AMS).ipynb, Elevation-dependent amplification of rainfall extremes.ipynb, Sensitivity_to_global_warming.ipynb) demonstrate the main steps of analysis. Further description of those notebooks is provided in the "Readme.rtf" file; (4) R code for extreme value analysis (Extreme_Value_Analysis.R). The sample and pre-processed dataset in "Raw data" is obtained from publicly available repositories of CMIP6 and ERA5 datasets; see Methods for more detail. This research was supported by Office of Science, Office of Biological and Environmental Research of the US Department of Energy under contract no. DE-AC02-05CH11231 for the CASCADE Scientific Focus (funded by the Regional and Global Model Analysis Program area within the Earth and Environmental Systems Modeling Program) and the iNAIADS Early Career Research Project (funded by the Environmental Systems Science program).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Charged Particle Transport Libraries (Final Report FY2020 Level-2 Milestone #7127)

This document is the final report on the status and developments of the Charged-Particle Transport (CPT) Level-2 (“CP2020”) ASC/PEM Milestone work. This section gives an overview of the CP2020 work partitioned into two subsections: 1) a summary of the code tools used for generating CP (and other) data in Section 1.2; and 2) and library data and codes access information for end users in Section 1.3. Section 2 gives an overview of the status of previous work on charged-particle (CP) nuclear data, particularly focused on the work of the FY2011 CP Level-2 Milestone. New work for CP2020 is detailed in the following Section 3. Section 4 discusses testing and validation of the evaluated and processed data for the CP2020 library. Conclusions based on the experience of this Level-2 work and the outlook for future development of CPT-relevant data are given in the final Section 5. Appendices, detailed throughout the report, are provided for further information. This report, related documentation, codes, and the CPT nuclear data libraries are available via online repository.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Time-dependent THMC properties and microstructural evolution of damaged rocks in excavation damage zone

Modeling coupled thermo-hydro-mechanical-chemical (THMC) processes in host rocks near high-level nuclear waste (HLW) repositories at various time scales is an extremely challenging task. The current study integrates experimental, theoretical, and numerical methods in assessing the evolution of excavation damage zone (EDZ) over time and its implication on the long-term migration of hazardous species. Argillite and rock salt and are the focus of this study. The first part of the report presents a novel time-dependent directional microcrack damage theory for generic brittle rocks. It features detailed statistical description of the microcracks within a damaged solid, permitting a direct upscaling of microscale processes such as crack growth kinetics, crack closure/opening, sliding friction to explain the macroscopic creep, nonlinear elasticity, shear dilation, and loading-unloading hysteresis. This provides a basic platform for describing the anisotropic mechanical and transport properties of damaged rocks during excavation and subsequent THMC loadings. The model is validated and numerically implemented to Finite Element (FE) package ABAQUS through the user-defined material (UMAT) interface and have demonstrated great potential in resolving the time-dependent and anisotropic evolution of damage in the EDZ. The second part of the report presents a multi-scale experimental effort in characterizing the thermal, hydraulic, and mechanical properties of Mancos shale and Avery Island salt. For the Mancos shale, triaxial compression tests are performed at different confining pressures and temperatures to probe its thermomechanical properties relevant to HLW repositories. The obtained stress-strain data are interpreted using the proposed directional damage theory. Post-test specimens are subjected to gas permeability tests to reveal the correlation between permeability and the degree of microcracking. At microscale, temperature-controlled nanoindentation tests are performed and found a linear correlation between fracture toughness and elastic modulus from 25°C to 300°C. For Avery Island salt, we have designed and manufactured a novel relative-humidity controlled uniaxial creep device. Long-term creep tests at low stresses (< 5 MPa) are performed at different levels of relative humidity (RH). Besides confirming the much higher creep rates as one would expect through extrapolating the high-stress creep data, the results reveal that the steady-state creep rate of rock salt is strongly dependent on the ambient RH, an aspect that is often neglected in the literature. Both behaviors can be attributed to the pressure-solution creep mechanism which dominates at low stress and high RH levels. The third part of the report explores a set of numerical strategies in modeling the THMC behavior of porous geomaterials. A fully implicit, monolithic FE solution that can flexibly interface with different material models and coupling mechanisms for THMC problems is developed and verified through the ABAQUS user-defined element (UEL) interface. The scheme is used to study the THM response of a hypothetical HLW storage site with reference to an existing in-situ heater test. Strategies for integrating the UEL and the microcrack UMAT are suggested. Another numerical endeavor of this study is to implement a higher-order asymptotic homogenization method to account for the heterogeneous porous structures. The same method is then extended to perform microstructure-informed thermo-mechanical modeling of generalized continua. The above outcomes of this project provide a strong thrust towards enhancing the fundamental understanding and modeling capability of the long-term evolution of host rocks in EDZ, thus helping achieve the design goal of 1-million-year isolation of high-level nuclear wastes.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

NASA NTRS2000

Network Configuration of Oracle and Database Programming Using SQL

A database can be defined as a collection of information organized in such a way that it can be retrieved and used. A database management system (DBMS) can further be defined as the tool that enables us to manage and interact with the database. The Oracle 8 Server is a state-of-the-art information management environment. It is a repository for very large amounts of data, and gives users rapid access to that data. The Oracle 8 Server allows for sharing of data between applications; the information is stored in one place and used by many systems. My research will focus primarily on SQL (Structured Query Language) programming. SQL is the way you define and manipulate data in Oracle's relational database. SQL is the industry standard adopted by all database vendors. When programming with SQL, you work on sets of data (i.e., information is not processed one record at a time).

Davis, Melton↗

NASA NTRS2017

The NASA Ames Life Sciences Data Archive: Biobanking for the Final Frontier

The NASA Ames Institutional Scientific Collection involves the Ames Life Sciences Data Archive (ALSDA) and a biospecimen repository, which are responsible for archiving information and non-human biospecimens collected from spaceflight and matching ground control experiments. The ALSDA also manages a biospecimen sharing program, performs curation and long-term storage operations, and facilitates distribution of biospecimens for research purposes via a public website (https:lsda.jsc.nasa.gov). As part of our best practices, a tissue viability testing plan has been developed for the repository, which will assess the quality of samples subjected to long-term storage. We expect that the test results will confirm usability of the samples, enable broader science community interest, and verify operational efficiency of the archives. This work will also support NASA open science initiatives and guides development of NASA directives and policy for curation of biological collections.

Biobank↗

NASA NTRS2019

Science Driven By Space Biology Omics Data Utilizing NASA's GeneLab Platform

Determining the biological impact of spaceflight through novel approaches is essential to reduce the health risks to astronauts for long-term space missions. The current established health risks due to spaceflight are only reflecting known symptomatic and physiologic responses and do not reflect early onset of other potential diseases. There are many unknown variables which still need to be identified to fully understand the health impacts due to the environmental factors in space. One method to uncover potential novel biological mechanisms responsible for health risks in astronauts is by utilizing NASA's GeneLab Data Systems (genelab.nasa.gov). GeneLab is public repository that hosts multiple omics datasets generated from space biology experiments that include experiments flown in space, simulated cosmic radiation.

Beheshti, Afshin↗

NASA NTRSDate not supplied

Laying The Foundations for FAIR-ER Science: ISA And LSDA Data Submission Process in NASA’s Evolving Data Management Environment

The Life Sciences Data Archive (LSDA) archives data resulting from research on the effects of spaceflight on humans and the development of countermeasures to mitigate spaceflight hazards. Archivists work with researchers to ensure that unique and high value data products and their metadata are preserved and managed to support current and future research. Currently, LSDA is updating its procedures and data submission requirements in response to the evolving data preservation environment at NASA. LSDA is implementing best practices for research data management through the establishment of clear data submission guidelines, integration of the FAIR (Findability, Accessibility, Interoperability, Reusability) principles, and use of the ISA (Investigation, Study, Assay) research metadata framework for data discoverability and transparency into the data management processes. These changes directly impact LSDA’s requirements for research data submissions. The newly revised Research Data Submission Agreement (RDSA), formerly the Data Submission Agreement (DSA), introduces ISA-compatible metadata collection standards to LSDA’s process. Adherence to LSDA’s data submission guidelines enhances the FAIR-ness of the repository’s collections for future users. This presentation will discuss (1) how submission of research data and associated metadata are impacted by current data management policies, (2) benefits of the adoption of FAIR principles and the ISA metadata framework for retrospective studies utilizing existing LSDA datasets and historic data collections, and (3) the support LSDA will provide to researchers during this transition.

Data submission↗

NASA NTRSDate not supplied

Laying the Foundations for FAIR-er Science: ISA and the LSDA Data Submission Process in NASA's Evolving Data Management Environment

The Life Sciences Data Archive (LSDA) archives data resulting from research on the effects of spaceflight on humans and the development of countermeasures to mitigate spaceflight hazards. Archivists work with researchers to ensure that unique and high value data products and their metadata are preserved and managed to support current and future research. Currently, LSDA is updating its procedures and data submission requirements in response to the evolving data preservation environment at NASA. LSDA is implementing best practices for research data management through the establishment of clear data submission guidelines, integration of the FAIR (Findability, Accessibility, Interoperability, Reusability) principles, and use of the ISA (Investigation, Study, Assay) research metadata framework for data discoverability and transparency into the data management processes. These changes directly impact LSDA’s requirements for research data submissions. The newly revised Research Data Submission Agreement (RDSA), formerly the Data Submission Agreement (DSA), introduces ISA-compatible metadata collection standards to LSDA’s process. Adherence to LSDA’s data submission guidelines enhances the FAIR-ness of the repository’s collections for future users. This presentation will discuss (1) how submission of research data and associated metadata are impacted by current data management policies, (2) benefits of the adoption of FAIR principles and the ISA metadata framework for retrospective studies utilizing existing LSDA datasets and historic data collections, and (3) the support LSDA will provide to researchers during this transition.

LSDA↗

NASA NTRSDate not supplied

Metadata Entry Optimization for NASA's Biological Institutional Scientific Collection (NBISC)

The NASA Biological Institutional Sample Collection (NBISC) at NASA’s Ames Research Center is a critical resource housing non-human samples collected from spaceflight missions and ground analog studies, primarily consisting of specimens from rats, mice, and select microbes. The primary objective of NBISC is to systematically receive, document, preserve, and facilitate access to these samples for the global scientific community. NBISC promotes international collaboration and maximizes the return on investment for precious tissues from spaceflight and analog experiments. Researchers can request physical samples through an online request form and subsequent written proposal review process. This study addresses two core research objectives: streamlining the NBISC sample lifecycle processes and strategizing for managing an influx of 50,000 tissue samples from a series of cosmic radiation analog experiments carried out at the NASA Space Radiation Laboratory (NSRL) by Drs. Eleanor Chang (Lawrence Berkeley Laboratory) and Polly Blakely (SRI). The Chang/Blakely studies investigated Harderian gland (HG) tumorigenesis in mice exposed to low dose and LET radiation comprising 8 different exposure protocols in over 4000 mice. NBISC sample metadata is stored in a Laboratory Information Management System (SLIMS). To streamline sample data entry, we customize python scripts using information extracted from the individual experimental protocols. The scripts automate entry into multiple SLIMS data fields including protocol name, unique sample barcode, tissue and sub-tissue information, freezer location, sample preservation method, etc. The semi-automated procedure significantly decreases the time spent on data entry by several orders of magnitude. Automation and data organization are essential, as they free up time for curation and promotion of the collection which, in turn, increase the accessibility of samples to the broader research community. NBISC benefits from streamlined data ingestion, and the methodologies developed here are applicable to other projects which use SLIMS including the NASA Biospecimen Sharing Program and GeneLab. As of Fall 2023, plans include transferring sample data from SLIMS to public facing repositories (OSDR and NLSP), expanding the reach of the Chang/Blakely sample collection. The Human Research Program Space Radiation Element plans to transfer non-human tissues from many more investigations to NBISC in the coming year.

Sample Repository↗

NASA NTRSDate not supplied

Metadata Entry Optimization For NASA's Biological Institutional Scientific Collection (NBISC)

The NASA Biological Institutional Sample Collection (NBISC) at NASA’s Ames Research Center is a critical resource housing non-human samples collected from spaceflight missions and ground analog studies, primarily consisting of specimens from rats, mice, and select microbes. The primary objective of NBISC is to systematically receive, document, preserve, and facilitate access to these samples for the global scientific community. NBISC promotes international collaboration and maximizes the return on investment for precious tissues from spaceflight and analog experiments. Researchers can request physical samples through an online request form and subsequent written proposal review process. This study addresses two core research objectives: streamlining the NBISC sample lifecycle processes and strategizing for managing an influx of 50,000 tissue samples from a series of cosmic radiation analog experiments carried out at the NASA Space Radiation Laboratory (NSRL) by Drs. Eleanor Chang (Lawrence Berkeley Laboratory) and Polly Blakely (SRI). The Chang/Blakely studies investigated Harderian gland (HG) tumorigenesis in mice exposed to low dose and LET radiation comprising 8 different exposure protocols in over 4000 mice. NBISC sample metadata is stored in a Laboratory Information Management System (SLIMS). To streamline sample data entry, we customize python scripts using information extracted from the individual experimental protocols. The scripts automate entry into multiple SLIMS data fields including protocol name, unique sample barcode, tissue and sub-tissue information, freezer location, sample preservation method, etc. The semi-automated procedure significantly decreases the time spent on data entry by several orders of magnitude. Automation and data organization are essential, as they free up time for curation and promotion of the collection which, in turn, increase the accessibility of samples to the broader research community. NBISC benefits from streamlined data ingestion, and the methodologies developed here are applicable to other projects which use SLIMS including the NASA Biospecimen Sharing Program and GeneLab. As of Fall 2023, plans include transferring sample data from SLIMS to public facing repositories (OSDR and NLSP), expanding the reach of the Chang/Blakely sample collection. The Human Research Program Space Radiation Element plans to transfer non-human tissues from many more investigations to NBISC in the coming year.

Biospecimen↗

DOE OSTI2021

Added Value for Integrated Marine Energy Data Systems (February 2021)

Launched in 2019, the Portal and Repository for Information on Marine Renewable Energy (PRIMRE) provides centralized access, standardization, community building, and integration of United States (U.S.) databases, tools and codes, and other resources that cover a range of marine energy information. The PRIMRE universe contains a series of Knowledge Hubs that represent data and information on testing of marine energy devices (MHKDR); environmental effects (Tethys); engineering and technical papers (Tethys Engineering); descriptions of marine energy companies and technologies (Marine Energy Projects Database); codes and models (Marine Energy Software); and guidance on testing and measurements (Telesto). Content is added to PRIMRE by applying a set of Guidelines and Best Practices (PRIMRE Guidelines). An aggregate search across the PRIMRE site enables users to find data and information from all the PRIMRE Knowledge Hubs simultaneously, using a single entry-point (PRIMRE Search). In addition to providing access to a range of data and information on marine energy development, testing, and effects, PRIMRE allows for the development of valueadded products and processes that will help move the marine energy industry forward. The PRIMRE team has recently launched two key initiatives in the U.S.-Signature Projects and Lessons Learned. Outputs and outcomes from these two initiatives will be highlighted in this paper. The Signature Projects initiative is intended to bring focus to a selection of ongoing and completed marine energy projects funded by the U.S. Department of Energy's Water Power Technologies Office (WPTO), and to inform the marine energy community of what investigations have been undertaken, what tools are available, and where gaps in information persist. Each Signature Project tags papers, reports, and data from large marine energy research projects, providing easy access and attention to all the output and associated products from each project. The Lessons Learned initiative is intended to ensure that hard-won achievements are recognized and available for those who come later, that missteps and unfortunate outcomes can be prevented in future, and that efficiencies and effective shortcuts can be publicized and used as the marine energy industry moves forward. This initiative builds off the Knowledge Hubs and reaches out to members of the marine energy community, particularly technology developers and researchers, to integrate experience in the development, deployment, assessment, success, challenges while creating this new industry and field of study.

data sharing↗