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At least 127 records · Page 7

NASA Access Mechanism - Graphical user interface information retrieval system

Access to online information sources of aerospace, scientific, and engineering data, a mission focus for NASA's Scientific and Technical Information Program, has always been limited by factors such as telecommunications, query language syntax, lack of standardization in the information, and the lack of adequate tools to assist in searching. Today, the NASA STI Program's NASA Access Mechanism (NAM) prototype offers a solution to these problems by providing the user with a set of tools that provide a graphical interface to remote, heterogeneous, and distributed information in a manner adaptable to both casual and expert users. Additionally, the NAM provides access to many Internet-based services such as Electronic Mail, the Wide Area Information Servers system, Peer Locating tools, and electronic bulletin boards.

Hunter, Judy F.↗

Using Machine Learning to Classify Earth Science Articles

Developing a machine learning pipeline to automatic the classification of research article topics, where topics are geophysical descriptors. The resulting classified documents will be added to the Usage-Based Discovery graph database, along with corresponding NASA Earth Science datasets, with the intent of linking the NASA data product with uses of it that can be searched by topic. The project will aid in the following goals (1) creating a wider representation of how and how much NASA Earth Science data products are used, (2) identifying when NASA data products have been used even when they are not clearly cited, and (3) providing the UBD search tool end-user with set of recommended datasets based on a given topic query.

Machine Learning↗

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

The PathoSystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center funded by the National Institute of Allergy and Infectious Diseases (https://www.patricbrc.org). PATRIC supports bioinformatic analyses of all bacteria with a special emphasis on pathogens, offering a rich comparative analysis environment that provides users with access to over 250 000 uniformly annotated and publicly available genomes with curated metadata. PATRIC offers web-based visualization and comparative analysis tools, a private workspace in which users can analyze their own data in the context of the public collections, services that streamline complex bioinformatic workflows and command-line tools for bulk data analysis. Over the past several years, as genomic and other omics-related experiments have become more cost-effective and widespread, we have observed considerable growth in the usage of and demand for easy-to-use, publicly available bioinformatic tools and services. Here we report the recent updates to the PATRIC resource, including new web-based comparative analysis tools, eight new services and the release of a command-line interface to access, query and analyze data.

59 BASIC BIOLOGICAL SCIENCES↗

Chemical-specific Parameters Dataset

The chemical-specific parameters dataset is searchable for physicochemical information for multiple chemicals simultaneously. After selecting chemicals of interest and the desired parameters, the RAIS will generate a table containing the values, chosen according to an established hierarchy. Results can be downloaded in Excel format. Over 40 parameters are available, including melting point, boiling point, density, density, vapor pressure, water solubility, and Henry’s Law constants. Thirteen primary sources are used to populate the dataset of chemical-specific parameters. These values should be used in cancer risk and noncancer hazard assessments for the calculation of preliminary remediation goals (PRGs), hazard characterization, and transport modeling. Users can select up to 1000 chemicals per query. The dataset supports environmental risk assessments, regulatory decision-making, and environmental planning with tools for benchmarking against risk-based standards. This structured approach ensures a robust evaluation of environmental risks tailored to regulatory needs.

Dolislager, Fred [Oak Ridge National Laboratory (O↗

Toxicity Values for Chemicals

The toxicity values for chemicals contained in this dataset comprise acute, subchronic, and chronic exposure durations. Cancer slope factors, inhalation unit risk, reference dose, and reference concentrations are available. These values should be used in cancer risk and noncancer hazard assessments for the calculation of preliminary remediation goals (PRGs) and hazard characterization. Users can select toxicity values from 10 combinations of exposure durations and cancer/noncancer toxicity values and select up to 1000 chemicals per query. The dataset supports environmental risk assessments, regulatory decision-making, and environmental planning with tools for benchmarking against risk-based standards. This structured approach ensures a robust evaluation of environmental risks tailored to regulatory needs.

Stewart, Debra [Oak Ridge National Laboratory (ORN↗

Radionuclide-specific Parameters Dataset

The radionuclide-specific parameters dataset is searchable for radiological information for multiple isotopes simultaneously. After selecting radionuclides of interest and the desired parameters, the RAIS will generate a table containing the values, chosen according to an established hierarchy. Results can be downloaded in Excel format. 50 parameters are available, including atomic number, soil to animal transfer coefficients, plant uptake coefficients, half-life, specific activity, and water solubility. Seven primary sources are used to populate the dataset of radiological-specific parameters. These values should be used in cancer risk assessments for the calculation of preliminary remediation goals (PRGs), hazard characterization, and transport modeling. Users can select up to 1000 radionuclides per query. The dataset supports environmental risk assessments, regulatory decision-making, and environmental planning with tools for benchmarking against risk-based standards. This structured approach ensures a robust evaluation of environmental risks tailored to regulatory needs.

Manning, Karessa [Oak Ridge National Laboratory (O↗

Urban Environment Initiative

The Urban Environment Initiative (UEI), has been established as part of a Cooperative Agreement with the National Aeronautics and Space Administration (NASA). The UEI is part of NASA's overall High Performance Computing and Communications (HPCC) and the Information Infrastructure Technology Applications (IITA) programs. The goal of the UEI is to provide public access to Earth Science information and promote its use with a focus on the environment of urban areas. This goal will be accomplished through collaborative efforts of the UEI team with both community-based and local/regional governmental organizations. The UEI team is comprised of four organizations representing private industry, NASA, and universities: Prime Technologies Service Corporation, NASA's Minority University Space Interdisciplinary Network (MU-SPIN) California State University, at Los Angeles, and Central State University (Wilberforce, OH). "Urban Environment" refers to the web of environmental, economic, and social factors that combine to create the urban world in which we live. Examples of these factors are population distribution, neighborhood demographic profiles, economic resources, business activities, location and concentration of environmental hazards and various pollutants, proximity and level of urban services, which form the basis of the urban environment and ultimately affect our lives and experiences. The use of Geographic Information Systems (GIS) and remote sensing allows data to be visualized in the forms of maps and spatial images. The use of these tools allow analysis of information about urban environments. Also included are descriptions of the four query types which will assist in understanding the maps.

Source record↗

Tool for Viewing Faults Under Terrain

Multi Surface Light Table (MSLT) is an interactive software tool that was developed in support of the QuakeSim project, which has created an earthquake- fault database and a set of earthquake- simulation software tools. MSLT visualizes the three-dimensional geometries of faults embedded below the terrain and animates time-varying simulations of stress and slip. The fault segments, represented as rectangular surfaces at dip angles, are organized into collections, that is, faults. An interface built into MSLT queries and retrieves fault definitions from the QuakeSim fault database. MSLT also reads time-varying output from one of the QuakeSim simulation tools, called "Virtual California." Stress intensity is represented by variations in color. Slips are represented by directional indicators on the fault segments. The magnitudes of the slips are represented by the duration of the directional indicators in time. The interactive controls in MSLT provide a virtual track-ball, pan and zoom, translucency adjustment, simulation playback, and simulation movie capture. In addition, geographical information on the fault segments and faults is displayed on text windows. Because of the extensive viewing controls, faults can be seen in relation to one another, and to the terrain. These relations can be realized in simulations. Correlated slips in parallel faults are visible in the playback of Virtual California simulations.

Siegel, Herbert, L.↗

Axom

Axom is an open-source library of "building block" software components that provide core infrastructure capabilities for HPC applications. Such capabilities include: input file parsing and verification for various file formats, format specification for material shape input to multi-material simulations and tools for placing those shapes on meshes, parallel distributed coordination of diagnostic messages, geometric primitives, spatial queries and spatial search acceleration data structures, in memory key-value data store for managing simulation data and parallel file I/O. Axom components are used widely across LLNL Advanced Simulation and Computing program applications. It is also part of the LLNL institutionally-supported RADIUSS project, which promotes and funds its adoption by projects across LLNL.

Zagaris, George↗

dsgrid (Demand-Side Grid Toolkit) [SWR-21-52]

The demand-side grid model harnesses decades of sector-specific energy modeling expertise to understand current and future U.S. electricity load for power systems analyses. The API provides tools for submitting datasets to dsgrid projects, validating individual datasets and project data as a whole, querying, analysis, and visualization.

Hale, Elaine↗

The ESIS query environment pilot project

The European Space Information System (ESIS) was originally conceived to provide the European space science community with simple and efficient access to space data archives, facilities with which to examine and analyze the retrieved data, and general information services. To achieve that ESIS will provide the scientists with a discipline specific environment for querying in a uniform and transparent manner data stored in geographically dispersed archives. Furthermore it will provide discipline specific tools for displaying and analyzing the retrieved data. The central concept of ESIS is to achieve a more efficient and wider usage of space scientific data, while maintaining the physical archives at the institutions which created them, and has the best background for ensuring and maintaining the scientific validity and interest of the data. In addition to coping with the physical distribution of data, ESIS is to manage also the heterogenity of the individual archives' data models, formats and data base management systems. Thus the ESIS system shall appear to the user as a single database, while it does in fact consist of a collection of dispersed and locally managed databases and data archives. The work reported in this paper is one of the results of the ESIS Pilot Project which is to be completed in 1993. More specifically it presents the pilot ESIS Query Environment (ESIS QE) system which forms the data retrieval and data dissemination axis of the ESIS system. The others are formed by the ESIS Correlation Environment (ESIS CE) and the ESIS Information Services. The ESIS QE Pilot Project is carried out for the European Space Agency's Research and Information center, ESRIN, by a Consortium consisting of Computer Resources International, Denmark, CISET S.p.a, Italy, the University of Strasbourg, France and the Rutherford Appleton Laboratories in the U.K. Furthermore numerous scientists both within ESA and space science community in Europe have been involved in defining the core concepts of the ESIS system.

Fuchs, Jens J.↗

Design and performance of AI agents interfacing with an atomic layer deposition tool

In this work, we introduce the design of an atomic layer deposition (ALD) reactor augmented with an AI interface for autonomous materials synthesis. Our modular design encapsulates the particularities of the hardware behind a Python interface that communicates with the ALD control software via transmission control protocol. This interface is compatible with model context protocol interfaces used in agentic frameworks. We have integrated our tool with a simple AI agent that leverages a large language model to transform user-supplied queries into ALD processes that are then run in our reactor. Our approach uses a JavaScript object notation schema to encode ALD processes. Our experimental results show that the AI interface does not impose a significant overhead to our control software, at least within our fastest 10 ms scale. We also carried out a detailed evaluation of the agent performance using leading models in two classes of tasks: basic instruction and process discovery tasks, where the agent is presented with a target material and needs to identify the correct ALD process compatible with the reactor configuration. Despite the simplicity of our agent design, we observed that most of the advanced models excelled at the instruction tasks. However, only recent models, such as o1, o3, GPT-5, and Claude Opus 4, performed well in process discovery tasks. We also observed significant variability in the response for the hardest challenges. While the results obtained are promising, we identify areas where AI research could improve the performance of agents for ALD.

47 OTHER INSTRUMENTATION↗

A dataset of cyber-induced mechanical faults on buildings with network and buildings data

We have collected data of cyber-induced mechanical faults on buildings using a simulation platform. A DOE reference building model was used for running the simulation under a Rogue device attack and collected the network data as well as the physical buildings data to better understand the impacts of cyber attacks on the building and help identify the source of the mechanical fault with the network data. Alfalfa is the tool used for simulating the DOE reference buildings and acts as an interface to the model for querying the status and providing input externally. The Building Automation System (BAS) is the centralized controller providing control commands to other BACnet devices on the network based on the building status received from Alfalfa. The BACnet devices like damper will listen for the control commands from BAS on the BACnet network and implement it. The attacker is the malicious actor on the network creating disruptions by placing cyber-attacks.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Description of data base management activities

ARC's current and future data processing needs have been identified and defined. Requirements for improved data processing capabilities are listed: (1) Centralized control of system data files. Establish a DBA/data base administrator position with responsibility for management of the Centers numerous data bases; (2) Programmer tools to improve efficiency of performance; (3) Direct and timely access to information. Presently, the user submits query requests to the data processing department where they are prioritized with other queries and then batch processed using a report generator; (4) On line data entry. With the merger of the Dryden facility with ARC on line data entry, edit and updates have become mandatory for timely operation and reporting. A DBMS software package was purchased to meet the above requirements.

Source record↗

Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.org research-focused web portal. We report substantial additions to the tools and visualization features available at RCSB.org, which now delivers more than 227000 experimentally determined atomic-level three-dimensional (3D) biostructures stored in the global PDB archive alongside more than 1 million Computed Structure Models (CSMs) of proteins (including models for human, model organisms, select human pathogens, crop plants and organisms important for addressing climate change). In addition to providing support for 3D structure motif searches with user-provided coordinates, new features highlighted herein include query results organized by redundancy-reduced Groups and summary pages that facilitate exploration of groups of similar proteins. Newly released programmatic tools are also described, as are enhanced training opportunities.

Burley, Stephen K.↗

PNNL-CIM-Tools/EASY-CIM

Extracting Attributes in a Simple DictionarY of CIM (EASY-CIM) is a python library to reduce the time and burden of model queries using simplified data representations of CIM power system models.

Anderson, Alex↗

Using advanced data structures to enable responsive security monitoring

Write-optimized data structures (WODS), offer the potential to keep up with cyberstream event rates and give sub-second query response for key items like IP addresses. These data structures organize logs as the events are observed. To work in a real-world environment and not fill up the disk, WODS must efficiently expire older events. As the basis for our research into organizing security monitoring data, we implemented a tool, called Diventi, to index IP addresses in connection logs using RocksDB (a write-optimized LSM tree). In this work, we extended Diventi to automatically expire data as part of the data structures’ normal operations. We guarantee that Diventi always tracks the N most recent events and tracks no more than N + k events for a parameter k < N, while ensuring the index is opportunistically pruned. To test Diventi at scale in a controlled environment, we used anonymized traces of IP communications collected at SuperComputing 2019. We synthetically extended the 2.4 billion connection events to 100 billion events. We tested Diventi vs. Elasticsearch, a common log indexing tool. In our test environment, Elasticsearch saw an ingestion rate of at best 37,000 events/s while Diventi sustained ingestion rates greater than 171,000 events/s. Our query response times were as much as 100 times faster, typically answering queries in under 80 ms. Furthermore, we saw no noticeable degradation in Diventi from expiration. We have deployed Diventi for many months where it has performed well and supported new security analysis capabilities.

97 MATHEMATICS AND COMPUTING↗

Plant Metabolic Network 16: expansion of underrepresented plant groups and experimentally supported enzyme data

Abstract The Plant Metabolic Network (PMN) is a free online database of plant metabolism available at https://plantcyc.org. The latest release, PMN 16, provides metabolic databases representing >1200 metabolic pathways, 1.3 million enzymes, >8000 metabolites, >10 000 reactions and >15 000 citations for 155 plant and green algal genomes, as well as a pan-plant reference database called PlantCyc. This release contains 29 additional genomes compared with PMN 15, including species listed by the African Orphan Crop Consortium and nonflowering plant species. Furthermore, 52 new enzymes with experimentally supported function information have been included in this release. The single-species databases contain a combination of experimental information from the literature and computationally predicted information obtained through PMN’s database generation pipeline for a single species, while PlantCyc contains only experimental information but for any species within Viridiplantae. PMN is a comprehensive resource for querying, visualizing, analyzing and interpreting omics data with metabolic knowledge. It also serves as a useful and interactive tool for teaching plant metabolism.

Hawkins, Charles (ORCID:0000000312849047)↗