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At least 19 records

Dynamic CCS-EJ-SJ Database and Web Application - What's New

At the 2024 FECM/NETL Carbon Management Research Project Review Meeting, within the Carbon Transport and Storage Breakout Session 3, the presentation "Dynamic CCS-EJ-SJ Database and Web Application - What's New" highlights the critical tool designed to integrate environmental and social justice considerations into Carbon Capture and Storage (CCS) projects. Key features include an interactive dashboard for data access and visualization, which supports stakeholders in making informed decisions regarding CCS implementation, and updated data layers. The latest version enhances data integration and usability, providing a comprehensive resource for assessing the social and environmental impacts of CCS projects. There are 7 categories in the CCS EJSJ v2 database (released 03/31/2024): environmental justice, energy justice, economic justice, social justice, ecosystem assets, clean energy, and infrastructure. Most of the layers within each category have been updated in this version. As compared to the old database, there are 3 new categories in the v2 database: ecosystem assets, clean energy, and infrastructure.

Sharma, Maneesh↗

Leveraging Application Data Constraints to Optimize Database-Backed Web Applications

Exploiting the relationships among data is a classical query optimization technique. As persistent data is increasingly being created and maintained programmatically, prior work that infers data relationships from data statistics misses an important opportunity. We present Coco, the first tool that identifies data relationships by analyzing database-backed applications. Once identified, Coco leverages the constraints to optimize the application's physical design and query execution. Instead of developing a fixed set of predefined rewriting rules, Coco employs an enumerate-test-verify technique to automatically exploit the discovered data constraints to improve query execution. Each resulting rewrite is provably equivalent to the original query. Using 14 real-world web applications, our experiments show that Coco can discover numerous data constraints from code analysis and improve real-world application performance significantly.

Computer Science↗

The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters

Secondary metabolites are small molecules produced by all corners of life, often with specialized bioactive functions with clinical and environmental relevance. Secondary metabolite biosynthetic gene clusters (BGCs) can often be identified within DNA sequences by various sequence similarity tools, but determining the exact functions of genes in the pathway and predicting their chemical products can often only be done by careful, manual comparative analysis. To facilitate this, we report the first release of the secondary metabolism collaboratory (SMC), which aims to provide a comprehensive, tool-agnostic repository of BGC sequence data drawn from all publicly available and user-submitted bacterial and archaeal genome and contig sources. On the website, users are provided a searchable catalog of putative BGCs identified from each source, along with visualizations of gene and domain annotations derived from multiple sequence analysis tools. SMC’s data is also available through publicly-accessible application programming interface (API) endpoints to facilitate programmatic access. Users are encouraged to share their findings (and search for others’) through comment posts on BGC and source pages. At the time of writing, SMC is the largest repository of BGC information, holding 13.1M BGC regions from 1.3M source sequences and growing, and can be found at https://smc.jgi.doe.gov.

59 BASIC BIOLOGICAL SCIENCES↗

Augmented Reality Technologies for Radiation Safety Training: A Systematic Review of Sensor Integration and Visualization Approaches

This paper presents a comprehensive systematic review examining the application of augmented reality (AR) and sensor technologies for visualizing ionizing radiation in virtual training environments. The review methodology involved systematic identification and analysis of the relevant literature based on predetermined criteria including publication type, year of publication, application domain, and technological approach. The literature search encompassed publications from 2011 to 2021 across four major academic databases: Web of Science, Google Scholar, IEEE Xplore, and Scopus. Through rigorous screening following PRISMA 2020 guidelines, 23 research articles met the inclusion criteria for detailed analysis. From 404 initial database records, 360 were excluded during title/abstract screening (primarily for lacking AR components, radiation focus, or training applications) and 4 during full-text assessment (all for lacking sensor integration). The findings reveal that AR-based ionizing radiation visualization has been successfully implemented across diverse domains, including nuclear facility operations, medical procedures, CERN research activities, and educational and monitoring applications. The analysis identified multiple dimensions of impact, encompassing distinct benefits, emerging opportunities, and implementation challenges associated with AR deployment for ionizing radiation training. Each of these dimensions is comprehensively examined and documented within this review. Additionally, this study identifies critical research gaps that currently limit the full potential of AR technology in supporting ionizing radiation training programs. These gaps are systematically analyzed and discussed to establish clear directions for future research endeavors in this emerging field.

61 - RADIATION PROTECTION AND DOSIMETRY↗

NRC Reactor Operating Experience Analysis and Trend Summary: 2020 Update

This report presents a summary of the reliability and frequency trends identified in the 2020 update reports for component performance study, loss of offsite power analysis, initiating events analysis, and system study provided on the Nuclear Regulatory Commission (NRC) Reactor Operating Experience Results and Databases web site (https://nrcoe.inl.gov/).

99 GENERAL AND MISCELLANEOUS↗

Web-accessible sorption database (Interim Progress Report)

This progress report (Level 4 Milestone Number M4SF-26LL010204053) summarizes research conducted at Lawrence Livermore National Laboratory (LLNL) within the Crystalline Host Rock Properties & Processes - LLNL Number SF-26LL01020405. This research is focused on the development of a web-accessible database of sorption data for minerals and rocks (bentonite backfill and crystalline host rock) that are likely to be present in a US hosted repository, including elevated temperature data that are expected in a DPC DGR scenario.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A new database website for nuclear level densities

We introduce a new open-access, web-based database (http://nld.ascsn.net), Current Archive of Nuclear Density of Levels (CANDL), that hosts experimental nuclear level density (NLD) datasets from a variety of techniques and energy ranges. Built using the Dash framework in Python, the database is designed to be interactive and user-friendly, allowing researchers to search, visualize, fit, and export NLD data with minimal effort. This resource includes data extracted from evaporation spectra, Oslo method variants, and other experimental techniques that cover excitation energies beyond the neutron resonance region. The database supports on-the-fly fitting with two widely-used phenomenological models—the Constant Temperature (CT) model and the Back-Shifted Fermi Gas (BSFG) model—selected for their simplicity and computational efficiency. Future versions aim to include additional datasets and model types, as well as easy-to-use interfaces to data science techniques. Here, this platform offers a vital tool for the nuclear physics, astrophysics, medicine, and reactor design communities.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

GBCGE Subsurface Database Explorer and APIs

This submission defines a DOI for the Great Basin Center for Geothermal Energy's (GBCGE) Subsurface Database Explorer web application and underlying data services, and acknowledges the INGENIOUS project as a major source of funding for data compilation and quality assurance. The GBCGE Subsurface Database Explorer is an interactive web mapping application that provides public access to the GBCGE Subsurface Database, and its collection of datasets pertinent to geothermal exploration, oil and gas exploration, critical mineral exploration, and other subsurface characterization for the Great Basin Region, western US. This is a living database, and will be continuously updated with new data and datasets as funding and motivations allow. The underlying database views that populate the web application are on an automated refresh schedule. Data sources and acknowledgements: We thank our partners with the Nevada Division of Minerals (NDOM), the Southern Methodist University (SMU), and Great Basin State Geological Surveys for their active efforts in data curation, schema design, and quality assurance. We also thank contributors among the USGS, Oregon Institute of Technology, State Divisions of Water Resources, State Divisions of Oil, Gas, and Minerals, and State Geological Surveys for open data availability and direct contributions made under the National Geothermal Data System (NGDS).

15 GEOTHERMAL ENERGY↗

IDB Loader

SAND2024-08428O The IDB Loader is a database designed to hold gamma spectra. IDB is a web-accessible database of reference gamma spectra for measuring uranium (U) and plutonium (Pu) isotopic composition. The database, developed by the International Atomic Energy Agency (IAEA), provides access to well-characterized groups of gamma spectra curated by international experts in gamma spectroscopy. It was created to promote sustainability and maintenance of software used to determine the isotopic abundances of U and Pu. The IDB Loader works by uploading one set of spectral data into an existing IDB. The Data Loader package includes documentation describing the IDB's table, the format of the spectral data, and a description of the loader program. The IDB is currently hosted by the IAEA at: https://nds.iaea.org/idb 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.

Schwartz, Steven↗

The AQUA-MER databases and aqueous speciation server: A web resource for multiscale modeling of mercury speciation

To assess the chemical reactivity, toxicity, and mobility of pollutants in the environment, knowledge of their species distributions is critical. Because their direct measurement is often infeasible, speciation modeling is widely adopted. Mercury (Hg) is a representative pollutant for which study of its speciation benefits from modeling. However, Hg speciation modeling is often hindered by a lack of reliable thermodynamic constants. Although computational chemistry (e.g., density functional theory [DFT]) can generate these constants, methods for directly coupling DFT and speciation modeling are not available. Here, we combine computational chemistry and continuum-scale modeling with curated online databases to ameliorate the problem of unreliable inputs to Hg speciation modeling. Our AQUA-MER databases and web server (https://aquamer.ornl.gov) provides direct speciation results by combining web-based interfaces to a speciation calculator, databases of thermodynamic constants, and a computational chemistry toolkit to estimate missing constants. Lastly, although Hg is presented as a concrete use case, AQUA-MER can also be readily applied to other elements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Status and Availability of OPTD, the Out-of-Pile Transient Database

The DOE Advanced Reactor Technology program has supported knowledge preservation efforts to recover and preserve fuel data from the US sodium cooled fast reactor (SFR) program. Databases have been established containing experimental data generated during the Integral Fast Reactor program (from in-pile experiments at EBR-II, FFTF, and TREAT) and during related outof-pile examinations of EBR-II-irradiated fuels. The information in these databases is essential to support further development and licensing activities for advanced fast reactor designs. OPTD, the Out-of-Pile Transient Database, is an organized, searchable archive of records describing out-ofpile furnace transient tests conducted on metallic fuels. It includes records of over 150 tests on irradiated fuel pins conducted in furnace apparatuses constructed in the Alpha-Gamma Hot Cell Facility at ANL. This report presents the content, functions, and accessibility of the Out-of-Pile Transient Database (OPTD). It describes the information presently available in the database, the web interface created to provide access to this information, the activities undertaken to build OPTD, and the enabling of online access to the database for DOE users. Plans for FY2021 and beyond are also included.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants

Abstract FatPlants, an open-access, web-based database, consolidates data, annotations, analysis results, and visualizations of lipid-related genes, proteins, and metabolic pathways in plants. Serving as a minable resource, FatPlants offers a user-friendly interface for facilitating studies into the regulation of plant lipid metabolism and supporting breeding efforts aimed at increasing crop oil content. This web resource, developed using data derived from our own research, curated from public resources, and gleaned from academic literature, comprises information on known fatty-acid-related proteins, genes, and pathways in multiple plants, with an emphasis on Glycine max, Arabidopsis thaliana, and Camelina sativa. Furthermore, the platform includes machine-learning based methods and navigation tools designed to aid in characterizing metabolic pathways and protein interactions. Comprehensive gene and protein information cards, a Basic Local Alignment Search Tool search function, similar structure search capacities from AphaFold, and ChatGPT-based query for protein information are additional features. Database URL: https://www.fatplants.net/

59 BASIC BIOLOGICAL SCIENCES↗

BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data

Abstract BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, training of artificial intelligence models and computational chemistry methods development. This update reports significant growth and enhancements since our last review in 2016. Of note, the database now contains 2.9 million binding measurements spanning 1.3 million compounds and thousands of protein targets. This growth is largely attributable to our unique focus on curating data from US patents, which has yielded a substantial influx of novel binding data. Recent improvements include a remake of the website following responsive web design principles, enhanced search and filtering capabilities, new data download options and webservices and establishment of a long-term data archive replicated across dispersed sites. We also discuss BindingDB’s positioning relative to related resources, its open data sharing policies, insights gleaned from the dataset and plans for future growth and development.

Liu, Tiqing↗

Building Toward the Future in Chemical and Materials Simulation with Accessible and Intelligently Designed Web Applications

Over the last few decades, significant progress has been made in the development and use of electronic structure and other molecular simulation methods. As these methods become more mature and are able to simulate larger and more complex chemical simulations, the need for improvement in scientific visualization, molecular builders, simplified input to simulation methods, and the development of new approaches and languages to describe simulations, along with workflows to carry them out, becomes more apparent. In this chapter, we describe our recent efforts in developing a prototype open-source computational tool called Arrows that combines NWChem, SQL and NoSQL databases, email, web APIs, and web applications in a way that make molecular and materials modeling accessible to all scientists and engineers. At the same time, because of its simplified input, it provides a framework for expert users to carry out large numbers of calculations and run complex workflows.

DNA Sequence-Based Identification of Fusarium : A Work in Progress

Accurate species-level identification of an etiological agent is crucial for disease diagnosis and management because knowing the agent’s identity connects it with what is known about its host range, geographic distribution, and toxin production potential. This is particularly true in publishing peer-reviewed disease reports, where imprecise and/or incorrect identifications weaken the public knowledge base. This can be a daunting task for phytopathologists and other applied biologists that need to identify Fusarium in particular, because published and ongoing multilocus molecular systematic studies have highlighted several confounding issues. Paramount among these are: (i) this agriculturally and clinically important genus is currently estimated to comprise more than 400 phylogenetically distinct species (i.e., phylospecies), with more than 80% of these discovered within the past 25 years; (ii) approximately one-third of the phylospecies have not been formally described; (iii) morphology alone is inadequate to distinguish most of these species from one another; and (iv) the current rapid discovery of novel fusaria from pathogen surveys and accompanying impact on the taxonomic landscape is expected to continue well into the foreseeable future. To address the critical need for accurate pathogen identification, our research groups are focused on populating two web-accessible databases (FUSARIUM-ID v.3.0 and the nonredundant National Center for Biotechnology Information nucleotide collection that includes GenBank) with portions of three phylogenetically informative genes (i.e., TEF1, RPB1, and RPB2) that resolve at or near the species level in every Fusarium species. The objectives of this Special Report, and its companion in this issue ( Torres-Cruz et al. 2022 ), are to provide a progress report on our efforts to populate these databases and to outline a set of best practices for DNA sequence-based identification of fusaria.

Plant Sciences↗

IPPOG: a global network for particle physics outreach and education

We present the International Particle Physics Outreach Group (IPPOG), a global network dedicated to connecting students, educators, and the general public with the world of particle physics. In this paper, we outline the need to bridge the existing gap between the particle physics community and the wider audience, and we present the solutions that IPPOG has implemented to overcome it through three pillar Activities: the International Masterclasses and the Global Cosmics hands-on activities network, which have engaged together over 200,000 high-school students to date, and the curation of an Outreach Resource Database and web portal.

Abreu, Pedro [University of Lisboa (Portugal); IPP↗

The development of yield-based sooting tendency measurements and modeling to enable advanced combustion fuels

This project produced clear evidence that biofuels can reduce particulate emissions from road vehicles compared with petroleum-derived fuels. It also produced fundamental knowledge that can be used to select fuel compositions and engine designs that will maximize this benefit. This information has been disseminated through more than 20 peer-reviewed publications, more than 30 conference presentations, and 5 freely available internet databases and web tools. This project also provided educational opportunities to 17 students at the high school, undergraduate, and graduate levels.

09 BIOMASS FUELS↗

LSE-163: Data Products Definition Document

This document describes the data products and processing services to be delivered by the NSF-DOE Vera C. Rubin Observatory whilst performing the Legacy Survey of Space and Time (LSST). LSST will deliver three levels of data products and services. Prompt data products are computed and released within 24 hours of observation, and include images, difference images, catalogs of sources and objects detected in difference images, and catalogs of Solar System objects. Their primary purpose is to enable rapid follow-up of time-domain events. Data Release data products are computed during annual processing campaigns, and include well-calibrated single-epoch images, deep coadds, and catalogs of objects, sources, and forced sources, enabling static sky and precision time-domain science. The Science Platform will allow for the creation of User Generated data products and will enable science cases that greatly benefit from co-location of user processing and/or data within the Rubin Observatory Data Access Center. LSST will also devote 10% of observing time to programs with special cadence. Their data products will be created using the same software and hardware as Prompt and Data Release products. All data products will be made available using user-friendly databases and web services.

79 ASTRONOMY AND ASTROPHYSICS↗