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At least 415 records · Page 23

KG-Hub—building and exchanging biological knowledge graphs

Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing, exchanging, and facilitating the downstream use of KGs is lacking. Here we present KG-Hub, a platform that enables standardized construction, exchange, and reuse of KGs. Features include a simple, modular extract–transform–load pattern for producing graphs compliant with Biolink Model (a high-level data model for standardizing biological data), easy integration of any OBO (Open Biological and Biomedical Ontologies) ontology, cached downloads of upstream data sources, versioned and automatically updated builds with stable URLs, web-browsable storage of KG artifacts on cloud infrastructure, and easy reuse of transformed subgraphs across projects. Current KG-Hub projects span use cases including COVID-19 research, drug repurposing, microbial–environmental interactions, and rare disease research. KG-Hub is equipped with tooling to easily analyze and manipulate KGs. KG-Hub is also tightly integrated with graph machine learning (ML) tools which allow automated graph ML, including node embeddings and training of models for link prediction and node classification.

59 BASIC BIOLOGICAL SCIENCES↗

DEPRECATED Hasty [SWR-20-80]

DEPRECATED This repository was archived by the owner on Nov 18, 2022. It is now read-only. The software is a web app to create semantic metadata models, namely, Haystack and Brick. The purpose of Hasty is to assist in the auditing of building mechanical systems and controls. The software is designed to capture mechanical system topology and important information regarding real world controls implementations. The tool is intended to output Brick / Haystack / ASHRAE 223 compliant models.

Mosiman, Cory↗

WELLBASE - An Interactive Platform for Wellbore Material Assessment

This project seeks to build an open-source wellbore material data repository with adequate material performance and contextual data to support Geological Carbon Storage (GCS). By appropriately evaluating the data types as mentioned earlier made available by the WELLBASE tool, stakeholders can make more informed decisions regarding well selections, risk assessment, and economic analysis for geologic carbon storage projects. Advanced Natural Language Processing models and other custom python scripts will be deployed in an automated process to extract unstructured data from documents, reports, and web applications and subsequently parse to more usable formats. The processed data will then be integrated into a robust and comprehensive database architecture, optimizing data accessibility, and usability for analytical purposes. The final data products will be accessible through a user-friendly visualization platform that will allow users to query and visualize the data, as well as download data in usable formats.

Tetteh, Daniel A.↗

MyCrunchGPT: A LLM Assisted Framework for Scientific Machine Learning

Scientific machine learning (SciML) has advanced recently across many different areas in computational science and engineering. Here, the objective is to integrate data and physics seamlessly without the need of employing elaborate and computationally taxing data assimilation schemes. However, preprocessing, problem formulation, code generation, postprocessing, and analysis are still time- consuming and may prevent SciML from wide applicability in industrial applications and in digital twin frameworks. Here, we integrate the various stages of SciML under the umbrella of ChatGPT, to formulate MyCrunchGPT, which plays the role of a conductor orchestrating the entire workflow of SciML based on simple prompts by the user. Specifically, we present two examples that demonstrate the potential use of MyCrunchGPT in optimizing airfoils in aerodynamics, and in obtaining flow fields in various geometries in interactive mode, with emphasis on the validation stage. To demonstrate the flow of the MyCrunchGPT, and create an infrastructure that can facilitate a broader vision, we built a web app based guided user interface, that includes options for a comprehensive summary report. The overall objective is to extend MyCrunchGPT to handle diverse problems in computational mechanics, design, optimization and controls, and general scientific computing tasks involved in SciML, hence using it as a research assistant tool but also as an educational tool. While here the examples focus on fluid mechanics, future versions will target solid mechanics and materials science, geophysics, systems biology, and bioinformatics.

97 MATHEMATICS AND COMPUTING↗

Clean Energy Solutions Center Services

The Clean Energy Solutions Center is a web-based resource that helps governments design and adopt policies and programs that support the deployment of clean energy technologies. The Solutions Center's three main offerings are Ask an Expert policy assistance, training and peer-to- peer learning forums and a rich library of technical tools and publications. These services are provided at no cost to users.

ask an expert↗

NFPA Distributed Energy Resources Safety Training (DERST) For Emergency Responders

The National Fire Protection Association, with support from the Department of Energy, executed a multi-year initiative to develop, enhance, and disseminate Distributed Energy Resources Safety Training (DERST) tools for U.S. emergency responders. As Distributed Energy Resources (DER)—such as solar photovoltaics, battery energy storage systems (ESS), electric vehicles (EVs), and associated infrastructure—become increasingly prevalent, the NFPA identified a critical need for up-to-date standardized, accessible, and effective safety training tailored for the fire service and related public safety professionals. The project delivered a comprehensive suite of educational resources to improve responders’ abilities to safely manage DER-related incidents. This included: • Revised Modular Training Courses: Updated classroom-based DER safety courses, now modular and accessible nationwide through fire academies and the North American Fire Training Directors (NAFTD) network. • Live Burn Testing & Research: A full-scale controlled burn of a DER-equipped residential structure provided real-world data and insights, forming the basis for updated best practices. • A Gamified Simulation Tool – Firefighters Incident Response Simulation Tool (FIRST): A first-of-its-kind, multiplayer, scenario-based simulation using the Unreal Engine 5.0 to train responders in a realistic virtual, multi-DER incident environment. • Field Familiarization Software Tools & Prop Guide: Digital DER field familiarization evolutions software guide and a prop development manual to support field-based DER training exercises, enhancing responders' hands-on familiarity with DER infrastructure and collaboration on virtual incident responses. • National Dissemination Strategy: Strategic partnerships with NAFTD, Vector Solutions, and others enabled wide-scale distribution, with over 5,000 departments accessing resources and 1,100+ departments adopting the simulator in the first seven months. Also provided a web portal for easy access to all training and simulation programs developed under this grant for the U.S. responder community. Key findings from the project—particularly from the burn test—led to paradigm shifts in fire response tactics. For example, traditional approaches to garage fires may be hazardous if DERs are present, due to explosive off gassing and thermal runaway risks. The new training emphasizes scene assessment, stand-off approaches, thermal imaging verification, and careful post-incident cooling of DER components to prevent reignition. This initiative has had a significant national impact, raising awareness, enhancing preparedness, and supporting safer DER incident response practices. Significant engagement from the media, public safety organizations, and PBS coverage has further amplified the reach and adoption of NFPA’s DER safety training, tools, and simulations.

14 SOLAR ENERGY↗

Solar Performance Insight (Final Report)

The PV Operations and Maintenance (O&M) service industry lacks an affordable, well-documented, intuitive PV modeling and analytics tool to calculate modeled performance from actual data from multiple data acquisition systems (DAS). We envision a performance modeling and analytics platform built on open-source, extensible, community-maintained code. The key innovation is the community-driven development of pvlib python delivered through a lightweight web service to provide configurable, consistent and reproducible PV modeling for O&M providers.

14 SOLAR ENERGY↗

CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems

Molecular modeling and simulation are invaluable tools for nanoscience that predict mechanical, physicochemical, and thermodynamic properties of nanomaterials and provide molecular-level insight into underlying mechanisms. However, building nanomaterial-containing systems remains challenging due to the lack of reliable and integrated cyberinfrastructures. Here we present Nanomaterial Modeler in CHARMM-GUI, a web-based cyberinfrastructure that provides an automated process to generate various nanomaterial models, associated topologies, and configuration files to perform state-of- the-art molecular dynamics simulations using most simulation packages. The nanomaterial models are based on the interface force field, one of the most reliable force fields (FFs). The transferability of nanomaterial models among the simulation programs was assessed by single-point energy calculations, which yielded 0.01% relative absolute energy differences for various surface models and equilibrium nanoparticle shapes. Three widely used Lennard-Jones (LJ) cutoff methods are employed to evaluate the compatibility of nanomaterial models with respect to conventional biomolecular FFs: simple truncation at r = 12 Å (12 cutoff), force-based switching over 10 to 12 Å (10-12 fsw), and LJ particle mesh Ewald with no cutoff (LJPME). The FF parameters with these LJ cutoff methods are extensively validated by reproducing structural, interfacial, and mechanical properties. As a result, we find that the computed density and surface energies are in good agreement with reported experimental results, although the simulation results increase in the following order: 10-12 fsw <12 cutoff < LJPME. Nanomaterials in which LJ interactions are a major component show relatively higher deviations (up to 4% in density and 8% in surface energy differences) compared with the experiment. Nanomaterial Modeler's capability is also demonstrated by generating complex systems of nanomaterial-biomolecule and nanomaterial-polymer interfaces with a combination of existing CHARMM-GUI modules. We hope that Nanomaterial Modeler can be used to carry out innovative nanomaterial modeling and simulations to acquire insight into the structure, dynamics, and underlying mechanisms of complex nanomaterial-containing systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

ChemEnv : a fast and robust coordination environment identification tool

Coordination or local environments have been used to describe, analyze and understand crystal structures for more than a century. Here, a new tool called ChemEnv, which can identify coordination environments in a fast and robust manner, is presented. In contrast to previous tools, the assessment of the coordination environments is not biased by small distortions of the crystal structure. Its robust and fast implementation enables the analysis of large databases of structures. The code is available open source within the pymatgen package and the software can also be used through a web app available on http://crystaltoolkit.org through the Materials Project.

42 ENGINEERING↗

Integrated, Interoperable Software Environment for Fusion Simulation and Data Analysis Tools SBIR Phase II

This SBIR effort was focused on developing a production ready system to address the integration and interoperability challenges with analysis and visualization in fusion simulations. Our overarching technical objective was to minimize the code development simulation scientists incur when coupling their simulation codes with different analysis frameworks. To this end, we developed an open-source software library to make data exchange between application easier and a Web application to manage and display analysis extracts from simulations. We have also augmented existing libraries funded by DOE such as ADIOS and VTK-m. When used together, these make it significantly easier to integrate simulation and analysis capability. We demonstrated the flexibility of our approach using two common simulation codes in the fusion community, XGC1 and GTC.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Application of Manufacturing Quality Management Principles to PV System Installations

To help SETO/DOE achieve its goals, the IBTS team proposed a project addressing system reliability by improving installation standards and quality management. The proposed approach was designed to help achieve measurable reductions in installation defect density and improvements in the performance of PV systems by optimizing design and installation of residential and commercial PV systems. This approach addressed the soft costs associated with installations and quality management. The project demonstrated improved system reliability and reduced PV system installation costs. The software developed improved operations, decreased risk, and increased the overall value of PV systems across their lifecycle. The project used several data collection methods, including extensive industry surveys, face-to-face high-level interviews at industry conferences, stakeholder teleconferences, and in-depth interviews conducted by IBTS staff. Results from the research found the industry needs a uniform assessment method for national providers to be more efficient; the software should support both code officials and installers; most industry stakeholders would find value in a centralized software system that allows them to collect, report, and review information on in-process and completed solar installations; and mobile solutions that bridge existing knowledge gaps with inspectors and integrate with existing methodologies (such as permitting software) are of great value. The software solution developed is web-based, allowing for national access, and is built on a Google Firebase platform that can handle significant users and data. It can be used onsite or remotely, allowing for code compliance to continue despite ongoing pandemic related delays or shutdowns for local economies. The information provided by the software tool allows users to uniformly assess a system for compliance and use that aggregated data to identify training topics or create internal process designed to improving issues and reducing occurrence. This solution has multiple benefits in managing quality at time of use and promoting an increase in future safety and quality through education. Perhaps most importantly, this software increases public safety by ensuring compliance of installed systems and allows for local AHJs to remotely engage specialized and qualified solar specific expertise for oversite of the installation in their jurisdictions. Data analysis provides the quality feedback loop identifying the root cause of failure and drives installation practices to improve through training and education, resulting in systems with higher performance, greater reliability, and reduced operations and maintenance costs. With the successful completion of this project, the industry can expect reduced soft costs and increased performance and safety and will ultimately benefit from longer performing systems that cost less to operate.

14 SOLAR ENERGY↗

Applying the Risk Management Framework: The Distributed Energy Resource Risk Manager

As part of a multiyear effort, the National Renewable Energy Laboratory (NREL) has dedicated resources to understand and identify cybersecurity weaknesses in distributed energy resources (DERs) by performing assessments. Due to a lack of standardization and rapidly increasing adoption of DERs, there is a critical need to address cybersecurity needs for DER systems in an interactive way. Furthermore, federal agencies, which are required to obtain an authority to operate, are challenged by the complexities of including their DERs. To help meet this need, in early 2020, NREL released the Distributed Energy Resources Cybersecurity Framework (DERCF) and accompanying Web application. This process is supported by the Risk Management Framework (RMF) developed by the National Institute of Standards and Technology. This project, referred to as the DERCF RMF application, expands on the existing DERCF work to include methods that support walking a user through the seven RMF steps. The tool will be available for download at no cost from [link ]. The purpose of this paper is to describe the steps the DERCF team at NREL took to understand Steps 1-5 of the RMF process. Additionally, this document will identify future work on the first five steps as well as a plan for Steps 6 and 7.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Pathways to a Sustainable Aviation Ecosystem: Flight DNA: An Anonymized Aviation Data Tool and Repository

The National Renewable Energy Laboratory (NREL) has deep experience developing secure, national data repositories, which it augments with analysis, technology and market expertise, high-performance computing, and innovative data visualization. By adapting the architecture of existing mobility databases (i.e., Fleet DNA, the Transportation Secure Data Center, the National Fuel Cell Technology Evaluation Center), NREL can build a powerful aviation data clearinghouse - Flight DNA - that helps stakeholders navigate the web of pitfalls and possibilities generated by new aviation technologies.

aviation↗

Chapter 18: Learning and Tracking Ad Hoc Fiducial Markers in Spatial Augmented Reality

We describe a spatial augmented reality system with a tangible user interface used to control computer simulations of complex systems. In spatial augmented reality, the user’s physical space is augmented with projected imagery, blending real objects with projected information, and a tangible user interface enables users to manipulate physical objects as controllers for interactive visualizations. Our system learns ad hoc objects in the user’s environment as fiducial markers (i.e., objects that are visually recognized and tracked). When combined with simulation and visualization tools, these interfaces allow the user to control simulations or ensembles of simulations via physical objects using apt metaphors. While other research has leveraged the use of depth cameras, our system enables the use of standard cameras in readily available smartphones and webcams and has an implementation that runs completely in JavaScript in the web browser. We discuss the prerequisite object-recognition requirements for such tangible user interfaces and describe computer-vision and machine-learning algorithms meeting those requirements. We conclude by presenting example applications, which are also available online.

energy distribution↗

ScholarGuard

The ScholarGuard framework aims to address the gap in archiving and preservation efforts for scholarly artifacts beyond traditional research papers, such as software source code, datasets, presentation slides, workflows, protocols, videos, and more. It introduces a prototype system designed to automatically track researchers' outputs across various scholarly productivity portals on the open web, including platforms like GitHub, Slideshare, Figshare, and Wikipedia. The system detects the availability of new scholarly artifacts and applies modern web archiving technology to create a durable archival record, including high-level metadata for each artifact. This metadata is displayed within the system, linking both to the live version and the archived version of the resource, ensuring long-term accessibility and preservation of diverse research outputs. The software serves as a critical tool for preserving the broader spectrum of scholarly contributions, facilitating visibility, searchability, and long-term access to research artifacts beyond the traditional scope of journal publications.

Balakireva, Lyudmila↗

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↗

Distributed Energy Resource Cybersecurity Framework Best Practices

Current cybersecurity challenges for distributed energy resources (DERs) stem from the integration of various systems and the cyber-physical security concerns they bring. Although frameworks exist for industrial control systems and other energy systems, a simple guided tool that can prioritize recommended actions for controls specific to DERs is lacking. Additionally, the novelty of the field has made it difficult to create a standardized procedure for DERs with cybersecurity in mind. In response to this critical need to address cybersecurity risk management, the National Renewable Energy Laboratory (NREL) has developed a framework and accompanying web application known as the Distributed Energy Resources Cybersecurity Framework (DERCF) (Powell, 2019). A brief overview of the DERCF can be found in Section 1.2. This document provides a guide to cybersecurity best practices identified by technical research and site visits where the framework was used to assess the cybersecurity posture of DER systems.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Data Needs for Modeling Low-Temperature Non-Equilibrium Plasmas: The LXCat Project, History, Perspectives and a Tutorial

Technologies based on non-equilibrium, low-temperature plasmas are ubiquitous in today’s society. Plasma modeling plays an essential role in their understanding, development and optimization. An accurate description of electron and ion collisions with neutrals and their transport is required to correctly describe plasma properties as a function of external parameters. LXCat is an open-access, web-based platform for storing, exchanging and manipulating data needed for modeling the electron and ion components of non-equilibrium, low-temperature plasmas. The data types supported by LXCat are electron- and ion-scattering cross-sections with neutrals (total and differential), interaction potentials, oscillator strengths, and electron- and ion-swarm/transport parameters. Online tools allow users to identify and compare the data through plotting routines, and use the data to generate swarm parameters and reaction rates with the integrated electron Boltzmann solver. In this review, the historical evolution of the project and some perspectives on its future are discussed together with a tutorial review for using data from LXCat.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗