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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Foldy: An open-source web application for interactive protein structure analysis

Foldy is a cloud-based application that allows non-computational biologists to easily utilize advanced AI-based structural biology tools, including AlphaFold and DiffDock. With many deployment options, it can be employed by individuals, labs, universities, and companies in the cloud without requiring hardware resources, but it can also be configured to utilize locally available computers. Foldy enables scientists to predict the structure of proteins and complexes up to 6000 amino acids with AlphaFold, visualize Pfam annotations, and dock ligands with AutoDock Vina and DiffDock. In our manuscript, we detail Foldy’s interface design, deployment strategies, and optimization for various user scenarios. We demonstrate its application through case studies including rational enzyme design and analyzing proteins with domains of unknown function. Furthermore, we compare Foldy’s interface and management capabilities with other open and closed source tools in the field, illustrating its practicality in managing complex data and computation tasks. Our manuscript underlines the benefits of Foldy as a day-to-day tool for life science researchers, and shows how Foldy can make modern tools more accessible and efficient.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

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↗
DOE OSTI2025

Hypermut 3: identifying specific mutational patterns in a defined nucleotide context that allows multistate characters

Abstract Motivation The detection of APOBEC3F- and APOBEC3G-induced mutations in virus sequences is useful for identifying hypermutated sequences. These sequences are not representative of viral evolution and can therefore alter the results of downstream sequence analyses if included. We previously published the software Hypermut, which detects hypermutation events in sequences relative to a reference. Two versions of this method are available as a webtool. Neither of these methods consider multistate characters or gaps in the sequence alignment. Results Here, we present an updated, user-friendly web and command-line version of Hypermut with functionality to handle multistate characters and gaps in the sequence alignment. This tool allows for straightforward integration of hypermutation detection into sequence analysis pipelines. As with the previous tool, while the main purpose is to identify G to A hypermutation events, any mutational pattern and context can be specified. Availability and implementation Hypermut 3 is written in Python 3. It is available as a command-line tool at https://github.com/MolEvolEpid/hypermut3 and as a webtool at https://www.hiv.lanl.gov/content/sequence/HYPERMUT/hypermutv3.html.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Nuclear Science User Facilities High Performance Computing: Provide a Science Gateway for HPC Users

Idaho National Laboratory (INL), supported by the Department of Energy Office of Nuclear Energy (DOE-NE) through the Nuclear Science User Facilities (NSUF), provides direct access to the Barracuda Virtual Reactor and 18 Multiphysics Object-Oriented Simulation Environment (MOOSE) applications via a web-based science gateway developed using Open Ondemand on the INL high performance computing (HPC) systems. This gateway features the computational tools of the Nuclear Computational Resource Center (NCRC) and the computing resources of the INL high performance computing systems. These computational tools are a key foundation of collaboration and innovation in nuclear energy systems research. High performance computing resources and INL staff directly support the mission and objectives of DOE-NE. The Barracuda Virtual Reactor was the first science gateway deployed in Jan 2021 to support NSUF users. In July 2021, the science gateway was expanded to support access to NCRC codes for use across all supported INL HPC systems. The HPC science gateway currently supports 20 total applications. The gateway also includes access to training resources specific to NCRC tools.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2021

Scoreboard

Emerging HPC machines have given rise to enhanced compute power that far outstrips the machine's ability to save large scale results for post-processing. To combat this, in situ data analysis techniques are slowly being adopted. With in situ data management favoring workflows composed of multiple simulations and analyses connected in transit on heterogeneous machines, scientists and engineers need a tool that enables them to create data extracts, visualizations, and interactively monitor and steer their simulations. Scoreboard Phase II is a next generation analysis software that supports composite in transit workflows on heterogeneous architectures and restores interactivity to in situ data analysis through simulation monitoring and computational steering. Scoreboard provides a simulation dashboard with graphs of metrics over time, controls for setting custom simulation steering parameters, controls for managing the set of data extracts being produced in the simulation, as well as the ability to explore data extracts, all from a web browser. Realizing the vision outlined in this project required research into making a system that integrates end to end from simulations all the way to the user. In situ tools generally suffer from complexity and excessive software dependencies. Scoreboard, by contrast, is easy to build and integrate into simulation codes and it provides first class FORTRAN support. The Scoreboard library is capable of in situ and in transit data analysis that can produce data extracts commonly needed for Computational Fluid Dynamics (CFD) analysis. Simulations can transparently stage data in transit to a Scoreboard Endpoint program, which can accept their data and produce the requested data extracts. This lets simulations return to their work while the Endpoint works on the analysis. Efficiently staging the data at scale was a topic of this research. Scoreboard provides the means to let the user manage data extracts and monitor/steer many simulations from a web browser. This area of the research focused on discovery of in transit network components to expose and control their steering parameters within an interactive browser-based user interface that includes: system topology, gathered metrics, notifications, dynamically-generated steering controls, and exploration of visualization data products.

Whitlock, BradJoseph [Intelligent Light] (00000001↗
DOE OSTI2025

Updating the Building Science Advisor (BSA): A Tool to Assist in the Design of Durable Building Envelopes

Predicting the moisture durability of building envelope components remains challenging due to multiple influencing factors, including material selection, assembly positioning, local climate conditions, air tightness, interior environment, and construction quality. Building codes increasingly emphasize energy efficiency through enhanced insulation and tighter envelopes but offer limited guidance on moisture durability considerations. Consequently, builders face uncertainty, particularly as new materials and assemblies enter the market.The Building Science Advisor (BSA) is a free, web-based expert system developed to address these challenges by providing actionable insights into the moisture durability and energy efficiency of both new and retrofit wall designs. Recently updated, we are now providing version 3.0 of the tool. BSA features significant user interface improvements, enhancing navigation and user interaction through a refreshed, intuitive design. Additionally, the tool incorporates a newly developed database containing pre-simulated wall assembly cases, significantly reducing response times and improving the accuracy of moisture durability assessments. Furthermore, the updated BSA includes moisture content as a performance criterion, providing users with a more comprehensive understanding of moisture-related durability risks. These enhancements enable rapid, reliable assessments tailored to specific climate zones and local building practices. BSA continues to offer targeted guidance on wall retrofit scenarios and delivers access to an expanded library of location-specific building science resources.This paper describes these key updates, highlighting the enhanced features, expanded capabilities, and overall improvements to user experience and educational content. The paper includes a demonstration that illustrates how the revised BSA effectively supports practitioners in designing durable, energy-efficient building envelope assemblies.

Salonvaara, Mikael [ORNL] (ORCID:0000000318991554)↗
DOE OSTI2020

WindWatts Computational Framework and Web UI [SWR-20-100]

This software provides a collection of algorithms, an API, and a functional Web UI for the Distributed Wind’s WindWatts project. DW WindWatts is a DOE WETO-funded project aimed at the development of tools to supporting the distributed wind industry, particularly with respect to siting and resource assessment. The computational framework and the back-end API are powering the easy to use front-end services available at: https://windwatts.nrel.gov. https://github.com/NREL/dw-tap-api; https://github.com/NREL/dw-tap; https://github.com/NREL/windwatts-data For reference, this software was previously known as DW TAP Computational Framework.

Phillips, Caleb↗
DOE OSTI2026

MCP-eGridGPT (MCP-Enabled Chatbot with Electrical Power System Analysis and Interactive Visualization Tool) [SWR-25-126]

This software is an advanced chatbot system that integrates the Model Context Protocol (MCP) to provide intelligent electrical power system analysis and automated visualization generation. The system enables users to interact with complex electrical engineering tools through natural language, automatically analyzes power system data for voltage violations and grid health assessment, and generates professional interactive HTML dashboards and reports. Key features include dynamic tool discovery from MCP servers, multi-LLM provider support, intelligent data interpretation using large language models, automated chart generation, and a web-based interface for real-time analysis. The software bridges sophisticated electrical engineering analysis with user-friendly interfaces, making power system diagnostics accessible through conversational AI.

Choi, Seong [National Laboratory of the Rockies (N↗
DOE OSTI2023

Flexible visualization of a 3rd party Intrusion Prevention (Security) tool: A use case with the ELK stack

A difficult aspect of cyber security is the ability to achieve automated real time intrusion prevention across various sets of systems. To this extent, several companies are offering comprehensive solutions that leverage an "accuracy of scale" and moving much of the intelligence and detection on the Cloud, relying on an ever-growing set of data and analytics to increase decision accuracy. Often, they provide tools to visualize the decision workflows in attack prevention (as well as tune the algorithm) but those solutions are not always practical as companies see the problem as "global" that is, from a unified Cyber-security standpoint. However, a key to a successful Cyber-security program is transparency and trust: from an experimental team viewpoint, this specifically means having the ability to immediately see what and from where, who has been blocked and being able to inform the community in case of a revoked access without the need for filing a "ticket" (that may eventually be answered) – in other words, rapid response to their user-base is essential but solutions targeting "sub-groups" in an organization are not often available. We have come up with a versatile solution leveraging the ELK stack (Elasticsearch, Logstash, & Kibana) and an IPS (Intrusion Prevention System) based WAF (Web Application Firewall) from Signal Sciences. Signal Science allows the streaming of detailed logs in a Logstash format suitable for custom solutions for visualization. By combining these two tools, we have strengthened our security posture and enabled individual experiments to monitor their own traffic. Specifically, the IPS WAF provides unique data such as country of origin, protocol, response code, source IP, and paths accessed. In this contribution, we will show how we engineered a visualization solution so experiment groups could access a dashboard with predefined graphs but also, where they can create individual customizable dashboards used to display blocked traffic and troubleshoot latency issues. We will discuss the details and procedures for developing and configuring these tools and how it benefits cyber security postures across our scientific based environment.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Knowledge Beacons: Web services for data harvesting of distributed biomedical knowledge

The continually expanding distributed global compendium of biomedical knowledge is diffuse, heterogeneous and huge, posing a serious challenge for biomedical researchers in knowledge harvesting: accessing, compiling, integrating and interpreting data, information and knowledge. In order to accelerate research towards effective medical treatments and optimizing health, it is critical that efficient and automated tools for identifying key research concepts and their experimentally discovered interrelationships are developed. As an activity within the feasibility phase of a project called “Translator” (https://ncats.nih.gov/translator) funded by the National Center for Advancing Translational Sciences (NCATS) to develop a biomedical science knowledge management platform, we designed a Representational State Transfer (REST) web services Application Programming Interface (API) specification, which we call a Knowledge Beacon. Knowledge Beacons provide a standardized basic API for the discovery of concepts, their relationships and associated supporting evidence from distributed online repositories of biomedical knowledge. This specification also enforces the annotation of knowledge concepts and statements to the NCATS endorsed the Biolink Model data model and semantic encoding standards (https://biolink.github.io/biolink-model/). Implementation of this API on top of diverse knowledge sources potentially enables their uniform integration behind client software which will facilitate research access and integration of biomedical knowledge.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2019

TARDIS. I. A Constrained Reconstruction Approach to Modeling the z ~ 2.5 Cosmic Web Probed by Lyα Forest Tomography

Recent Lyα forest tomography measurements of the intergalactic medium (IGM) have revealed a wealth of cosmic structures at high redshift (z ~ 2.5). In this work, we present the Tomographic Absorption Reconstruction and Density Inference Scheme (TARDIS), a new chronocosmographic analysis tool for understanding the formation and evolution of these observed structures. Here, we use maximum likelihood techniques with a fast nonlinear gravitational model to reconstruct the initial density field of the observed regions. We find that TARDIS allows accurate reconstruction of smaller-scale structures than standard Wiener-filtering techniques. Applying this technique to mock Lyα forest data sets that simulate ongoing and future surveys such as CLAMATO, Subaru PFS, or the ELTs, we are able to infer the underlying matter density field at observed redshift and classify the cosmic web structures. We find good agreement with the underlying truth in both the characteristic eigenvalues and eigenvectors of the pseudo-deformation tensor, with the eigenvalues inferred from 30 m class telescopes correlated at r = 0.95 relative to the truth. As an output of this method, we are able to further evolve the inferred structures to late time (z = 0) and also track the trajectories of coeval z = 2.5 galaxies to their z = 0 cosmic web environments.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Updates to the Alliance of Genome Resources central infrastructure

The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, Caenorhabditis elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and application programming interfaces (APIs). Here, we focus on developments over the last 2 years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific “landing pages” and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse software. We describe our progress toward a central persistent database to support curation, the data modeling that underpins harmonization, and progress toward a state-of-the-art literature curation system with integrated artificial intelligence and machine learning (AI/ML).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

pnnl/simple-building-calculator

The Simple Building Calculator is a web application that estimates annual energy use using regression models that have been fit to simulation results for the DOE Commercial Prototype Building Models. The tool is a single-page application that will allow a user to rapidly analyze the impact of energy efficiency measures and design options on building performance. As it uses linear regression models rather than more complicated machine learning models or physics based simulation, the tool can deploy easily and run client-side.

Xu, Weili↗
DOE OSTI2020

The Web as the Primary Control System User Interface

Fermilab's Control System uses a proprietary application framework written decades ago. Considered state-ofthe- art at one time, the control system now lacks many features we expect from a modern interface and needs to be updated. Our investigation of Web browsers and JavaScript revealed a powerful, rich, and state-of-the-art development environment. We discuss JavaScript frameworks, JavaScript language features, and packaging tools. We also discuss issues we need to resolve before we are confident this can become our primary application platform.

43 PARTICLE ACCELERATORS↗
DOE OSTI2022

Modeling Cosmic Reionization

The transformation of cold neutral intergalactic hydrogen into a highly ionized warm plasma marks the end of the cosmic dark ages and the beginning of the age of galaxies. The details of this process reflect the nature of the early sources of radiation and heat, the statistical characteristics of the large-scale structure of the Universe, the thermodynamics and chemistry of cosmic baryons, and the histories of star formation and black hole accretion. A number of massive data sets from new ground- and space-based instruments and facilities over the next decade are poised to revolutionize our understanding of primeval galaxies, the reionization photon budget, the physics of the intergalactic medium (IGM), and the fine-grained properties of hydrogen gas in the "cosmic web". In this review we survey the physics and key aspects of reionization-era modeling and describe the diverse range of computational techniques and tools currently available in this field.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

FedFleet 2022: Federal Automotive Statistical Tool - FY 2021 Fleet Trends and Data Quality

This presentation presents a brief overview of the collection of information about the US government's fleet of motor vehicles using the Federal Automotive Statistical Tool (FAST), discusses the makeup and operation of the vehicle fleet during FY 2021, discusses quality of the submitted data, and touches on future aspects of fleet data collection and reporting. FAST is a web-based information system sponsored by GSA's Office of Government-wide Policy and DOE's Federal Energy Management Program to collect information about the US federal government's fleet of motor vehicles; FAST is developed, maintained, and supported by DOE's Idaho National Laboratory (INL).

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2021

Guided Resilience Self Assessment Application

Reliable electricity access is vital for everything from hospitals to national security. When grid disturbances occur, it is crucial to minimize the amount of time it takes to recover. Grid resiliency considers both the preparation for and recovery from high-impact low-frequency disturbances (HILF) such as weather events and cyber attacks. The Department of Energy (DOE) Wind Energy Technologies Office (WETO) funds the multi-laboratory Microgrids, Infrastructure Resilience, and Advanced Control Launchpad (MIRACL) project to investigate technologies to support and grow distributed wind. Researchers at Idaho National Laboratory (INL) contribute to resilience and cybersecurity efforts for the project, and have produced a resilience framework to evaluate system resilience based on individual system specifications. In order to make this framework easy for anyone to apply, I have coded a web application that allows users to input their power system qualities, goals, and perceived risks and then receive suggestions on how to improve their grid resiliency. The web application follows the seven steps in the planning stage of the framework process, allowing the user to input information about their grid and select from common goals, metrics, and hazards, as well as add their own. The application currently provides information about how to complete each step, requiring minimal prior knowledge of the framework. Future work for this application will include allowing the user to submit line drawings of their system and incorporate modeling tools so that the hazard simulations of applying the framework is completed for the user.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

CyclusJS: A Distributed Web-based Fuel Cycle Visual Analytics. Research Performance (Final Report)

The overall aim of the CyclusJS project has been to design novel approaches that support fuel cycle simulations and empower decision-makers and researchers with better tools to compare and contrast results from multiple simulations to understand the landscape of potential outcomes better. In particular, nuclear fuel cycle simulations focus on modeling the nuclear industry and ecosystem at a macroscopic level, and the analysis tools connect such simulations with decision support systems. As a demonstration of the novelty and effectiveness of the proposed approach, we study scenarios for transitioning from one technology, Light Water Reactors (LWR), to a newer Sodium-cooled Fast breeder Reactor (SFR) technology.

60 APPLIED LIFE SCIENCES↗