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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

rcsb-api : Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs

The Protein Data Bank (PDB) was founded in 1971 as the first open-access digital data resource in biology to serve as the single global archive for three-dimensional (3D) macromolecular structure data. Current PDB holdings exceed 230,000 experimentally determined structures of proteins, nucleic acids, viruses, and macromolecular machines. The RCSB Protein Data Bank RCSB.org research-focused web portal facilitates search, analyses, and visualization of every PDB structure along with more than one million Computed Structure Models from AlphaFold DB and the ModelArchive. It is powered by a set of publicly available Application Programming Interfaces (APIs) that both support RCSB.org users and provide programmatic access to PDB data. Given the breadth and levels of granularity encompassed in this rich data collection, efficiently accessing the information programmatically may be challenging for new users. RCSB PDB has developed a Python software package, rcsb-api , that facilitates easy and efficient use of RCSB PDB APIs within a Python environment. This software tool is designed to streamline access to the extensive corpus of data housed within the PDB, enabling researchers to search, retrieve, and analyze 3D biostructure data seamlessly. Its use will accelerate research in structural biology, molecular biology and biochemistry, drug discovery, and bioinformatics by providing more efficient tools for data integration and analysis. The new toolkit is available on GitHub (github.com/rcsb/py-rcsb-api) and published to the public Python package repository (PyPI) to foster wider usage and support basic and applied research in fundamental biology, biomedicine, and the energy sciences.

FAIR principles↗
DOE OSTI2025

Accelerated data-driven materials science with the Materials Project

The Materials Project was launched formally in 2011 to drive materials discovery forwards through high-throughput computation and open data. More than a decade later, the Materials Project has become an indispensable tool used by more than 600,000 materials researchers around the world. This Perspective describes how the Materials Project, as a data platform and a software ecosystem, has helped to shape research in data-driven materials science. We cover how sustainable software and computational methods have accelerated materials design while becoming more open source and collaborative in nature. Next, we present cases where the Materials Project was used to understand and discover functional materials. We then describe our efforts to meet the needs of an expanding user base, through technical infrastructure updates ranging from data architecture and cloud resources to interactive web applications. Finally, we discuss opportunities to better aid the research community, with the vision that more accessible and easy-to-understand materials data will result in democratized materials knowledge and an increasingly collaborative community.

Horton, Matthew K↗
DOE OSTI2025

Extraction and Analysis of Time Series Data from Building Automation Systems Using Large Language Models

Semantic schemas like Haystack 4, Brick and ASHRAE standard 223 enable the structured, standardized, and machine-readable representation of building data, facilitating interoperability, data integration, and advanced analytics. However, extracting information from these models requires specialized expertise in SPARQL and other programming languages, skills that are not commonly found among building professionals. Recent advancements in Large Language Models (LLMs), such as ChatGPT, enable the construction of queries using natural language, making it easier for individuals to interact with these systems in a manner that resembles everyday speech. However, these methods have not yet been tested on building semantic ontologies. This paper introduces a novel workflow and tool for enabling users to ask questions about a specific building's data, using natural language and receive answers automatically generated by GPT-4o. Our approach integrates semantic ontologies with advanced LLM capabilities to automate three critical steps: (1) generating SPARQL queries to retrieve time series references from ontological models, (2) extracting the corresponding time series data from the Building Automation System, and (3) performing computations and visualizations tailored to the user's query. The proposed method simplifies access to BAS data, allowing both domain experts and non-specialists to conduct sophisticated analyses without needing extensive technical knowledge of semantic web technologies. By demonstrating this pipeline, we facilitate more accessible and scalable data-driven decision-making in building operations and management.

Mulayim, Ozan Baris↗
DOE OSTI2025

Extraction and Analysis of Time Series Data from Building Automation Systems Using Large Language Models

Semantic schemas like Haystack 4, Brick and ASHRAE standard 223 enable the structured, standardized, and machine-readable representation of building data, facilitating interoperability, data integration, and advanced analytics. However, extracting information from these models requires specialized expertise in SPARQL and other programming languages, skills that are not commonly found among building professionals. Recent advancements in Large Language Models (LLMs), such as ChatGPT, enable the construction of queries using natural language, making it easier for individuals to interact with these systems in a manner that resembles everyday speech. However, these methods have not yet been tested on building semantic ontologies. This paper introduces a novel workflow and tool for enabling users to ask questions about a specific building's data, using natural language and receive answers automatically generated by GPT-4o. Our approach integrates semantic ontologies with advanced LLM capabilities to automate three critical steps: (1) generating SPARQL queries to retrieve time series references from ontological models, (2) extracting the corresponding time series data from the Building Automation System, and (3) performing computations and visualizations tailored to the user's query. The proposed method simplifies access to BAS data, allowing both domain experts and non-specialists to conduct sophisticated analyses without needing extensive technical knowledge of semantic web technologies. By demonstrating this pipeline, we facilitate more accessible and scalable data-driven decision-making in building operations and management.

Mulayim, Ozan Baris↗
NASA NTRS2002

Quick Fix for Managing Risks

Under a Phase II SBIR contract, Kennedy and Lumina Decision Systems, Inc., jointly developed the Schedule and Cost Risk Analysis Modeling (SCRAM) system, based on a version of Lumina's flagship software product, Analytica(R). Acclaimed as "the best single decision-analysis program yet produced" by MacWorld magazine, Analytica is a "visual" tool used in decision-making environments worldwide to build, revise, and present business models, minus the time-consuming difficulty commonly associated with spreadsheets. With Analytica as their platform, Kennedy and Lumina created the SCRAM system in response to NASA's need to identify the importance of major delays in Shuttle ground processing, a critical function in project management and process improvement. As part of the SCRAM development project, Lumina designed a version of Analytica called the Analytica Design Engine (ADE) that can be easily incorporated into larger software systems. ADE was commercialized and utilized in many other developments, including web-based decision support.

Source record↗
DOE OSTI2026

ACDC (Automated Campbell Diagram Code) [SWR-26-042]

This application provides a web-based graphical user interface to generating Campbell Diagrams and visualizing mode shapes for OpenFAST turbine models. Determining the aeroelastic stability and dynamic characteristics of wind turbines is a critical step in turbine design and analysis. Historically, extracting natural frequencies and mode shapes from OpenFAST—the industry-standard whole-turbine simulation code—has been a fragmented and tedious process. It required manual model configuration, command-line linearization execution, and complex post-processing via proprietary scripts to handle rotating-frame dynamics. To address these workflow bottlenecks, we present the Automated Campbell Diagram Code (ACDC), an open-source graphical software tool developed by the National Laboratory of the Rockies (NLR) under the DOE-funded Distributed Wind Aeroelastic Modeling (dWAM) project. ACDC streamlines the end-to-end linearization and stability analysis workflow into a single, intuitive cross-platform application. The software guides users through OpenFAST model configuration, definition of operating points, and the automated execution of steady-state trim and linearization simulations. Under the hood, ACDC automates the complex mathematical post-processing steps required for rotating systems, including Multi-Blade Coordinate (MBC) transformations, eigenanalysis, and advanced modal tracking utilizing the Modal Assurance Criterion (MAC) and spectral clustering. Finally, ACDC processes these results to automatically generate Campbell diagrams and features a robust 3D visualization engine to animate full-system mode shapes. By eliminating the reliance on external post-processing environments and manual data manipulation, ACDC significantly accelerates dynamic analysis and lowers the barrier to entry for wind energy researchers and engineers.

Summerville, Brent [National Laboratory of the Roc↗
NASA NTRS2001

XML-Based Visual Specification of Multidisciplinary Applications

The advancements in the Internet and Web technologies have fueled a growing interest in developing a web-based distributed computing environment. We have designed and developed Arcade, a web-based environment for designing, executing, monitoring, and controlling distributed heterogeneous applications, which is easy to use and access, portable, and provides support through all phases of the application development and execution. A major focus of the environment is the specification of heterogeneous, multidisciplinary applications. In this paper we focus on the visual and script-based specification interface of Arcade. The web/browser-based visual interface is designed to be intuitive to use and can also be used for visual monitoring during execution. The script specification is based on XML to: (1) make it portable across different frameworks, and (2) make the development of our tools easier by using the existing freely available XML parsers and editors. There is a one-to-one correspondence between the visual and script-based interfaces allowing users to go back and forth between the two. To support this we have developed translators that translate a script-based specification to a visual-based specification, and vice-versa. These translators are integrated with our tools and are transparent to users.

Al-Theneyan, Ahmed↗
NASA NTRS2013

ISTP CDF Skeleton Editor

Basic Common Data Format (CDF) tools (e.g., cdfedit) provide no specific support for creating International Solar-Terrestrial Physics/Space Physics Data Facility (ISTP/SPDF) standard files. While it is possible for someone who is familiar with the ISTP/SPDF metadata guidelines to create compliant files using just the basic tools, the process is error-prone and unreasonable for someone without ISTP/SPDF expertise. The key problem is the lack of a tool with specific support for creating files that comply with the ISTP/SPDF guidelines. There are basic CDF tools such as cdfedit and skeletoncdf for creating CDF files, but these have no specific support for creating ISTP/ SPDF compliant files. The SPDF ISTP CDF skeleton editor is a cross-platform, Java-based GUI editor program that allows someone with only a basic understanding of the ISTP/SPDF guidelines to easily create compliant files. The editor is a simple graphical user interface (GUI) application for creating and editing ISTP/SPDF guideline-compliant skeleton CDF files. The SPDF ISTP CDF skeleton editor consists of the following components: A swing-based Java GUI program, JavaHelp-based manual/ tutorial, Image/Icon files, and HTML Web page for distribution. The editor is available as a traditional Java desktop application as well as a Java Network Launching Protocol (JNLP) application. Once started, it functions like a typical Java GUI file editor application for creating/editing application-unique files.

Chimiak, Reine↗
NASA NTRS1997

Archiving of Wideband Plasma Wave Data

Beginning with the third year of funding, we began a more ambitious archiving production effort, minimizing work on new software and concentrating on building representative archives of the missions mentioned above, recognizing that only a small percentage of the data from any one mission can be archived with reasonable effort. We concentrated on data from Dynamics Explorer and ISEE 1, archiving orbits or significant fractions of orbits which attempt to capture the essence of the mission and provide data which will hopefully be sufficient for ongoing and new research as well as to provide a reference to upcoming and current ISTP missions which will not fly in the same regions of space as the older missions and which will not have continuous wideband data. We archived approximately 181 Gigabytes of data, accounting for some 1582 hours of data. Included in these data are all of the AMPTE chemical releases, all of the Spacelab 2/PDP data obtained during the free-flight portion of its mission, as well as significant portions of the S3, DE-1, Imp-6, Hawkeye, Injun 5, and ISEE 1 and 2 data sets. Table 1 summarizes these data. All of the data archived are summarized in gif-formatted images of frequency-time spectrograms which are directly accessible via the internet. Each of the gif files are identified by year, day, and time as described in the Web page. This provides a user with a specific date/time in mind a way of determining very quickly if there is data for the interval in question and, by clicking on the file name, browsing the data. Alternately, a user can browse the data for interesting features and events simply by viewing each of the gif files. When a user finds data of interest, he/she can notify us by email of the time period involved. Based on the user's needs, we can provide data on a convenient medium or by ftp, or we can mount the appropriate data and provide access to our analysis tools via the network. We can even produce products such as plots or spectrograms in hardcopy form based on the specific request of the user.

Kurth, William S.↗
DOE OSTI2020

BioHackathon 2015: Semantics of data for life sciences and reproducible research

We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Reinspection of a Clinical Proteomics Tumor Analysis Consortium (CPTAC) Dataset with Cloud Computing Reveals Abundant Post-Translational Modifications and Protein Sequence Variants

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has provided some of the most in-depth analyses of the phenotypes of human tumors ever constructed. Today, the majority of proteomic data analysis is still performed using software housed on desktop computers which limits the number of sequence variants and post-translational modifications that can be considered. The original CPTAC studies limited the search for PTMs to only samples that were chemically enriched for those modified peptides. Similarly, the only sequence variants considered were those with strong evidence at the exon or transcript level. In this multi-institutional collaborative reanalysis, we utilized unbiased protein databases containing millions of human sequence variants in conjunction with hundreds of common post-translational modifications. Using these tools, we identified tens of thousands of high-confidence PTMs and sequence variants. We identified 4132 phosphorylated peptides in nonenriched samples, 93% of which were confirmed in the samples which were chemically enriched for phosphopeptides. In addition, our results also cover 90% of the high-confidence variants reported by the original proteogenomics study, without the need for sample specific next-generation sequencing. Finally, we report fivefold more somatic and germline variants that have an independent evidence at the peptide level, including mutations in ERRB2 and BCAS1. In this reanalysis of CPTAC proteomic data with cloud computing, we present an openly available and searchable web resource of the highest-coverage proteomic profiling of human tumors described to date.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2000

A Distributed Multi-Agent System for Collaborative Information Management and Learning

In this paper, we present DIAMS, a system of distributed, collaborative agents to help users access, manage, share and exchange information. A DIAMS personal agent helps its owner find information most relevant to current needs. It provides tools and utilities for users to manage their information repositories with dynamic organization and virtual views. Flexible hierarchical display is integrated with indexed query search-to support effective information access. Automatic indexing methods are employed to support user queries and communication between agents. Contents of a repository are kept in object-oriented storage to facilitate information sharing. Collaboration between users is aided by easy sharing utilities as well as automated information exchange. Matchmaker agents are designed to establish connections between users with similar interests and expertise. DIAMS agents provide needed services for users to share and learn information from one another on the World Wide Web.

Chen, James R.↗
NASA NTRS2009

Integrating and Visualizing Tropical Cyclone Data Using the Real Time Mission Monitor

The Real Time Mission Monitor (RTMM) is a visualization and information system that fuses multiple Earth science data sources, to enable real time decision-making for airborne and ground validation experiments. Developed at the NASA Marshall Space Flight Center, RTMM is a situational awareness, decision-support system that integrates satellite imagery, radar, surface and airborne instrument data sets, model output parameters, lightning location observations, aircraft navigation data, soundings, and other applicable Earth science data sets. The integration and delivery of this information is made possible using data acquisition systems, network communication links, network server resources, and visualizations through the Google Earth virtual globe application. RTMM is extremely valuable for optimizing individual Earth science airborne field experiments. Flight planners, scientists, and managers appreciate the contributions that RTMM makes to their flight projects. A broad spectrum of interdisciplinary scientists used RTMM during field campaigns including the hurricane-focused 2006 NASA African Monsoon Multidisciplinary Analyses (NAMMA), 2007 NOAA-NASA Aerosonde Hurricane Noel flight, 2007 Tropical Composition, Cloud, and Climate Coupling (TC4), plus a soil moisture (SMAP-VEX) and two arctic research experiments (ARCTAS) in 2008. Improving and evolving RTMM is a continuous process. RTMM recently integrated the Waypoint Planning Tool, a Java-based application that enables aircraft mission scientists to easily develop a pre-mission flight plan through an interactive point-and-click interface. Individual flight legs are automatically calculated "on the fly". The resultant flight plan is then immediately posted to the Google Earth-based RTMM for interested scientists to view the planned flight track and subsequently compare it to the actual real time flight progress. We are planning additional capabilities to RTMM including collaborations with the Jet Propulsion Laboratory in the joint development of a Tropical Cyclone Integrated Data Exchange and Analysis System (TC IDEAS) which will serve as a web portal for access to tropical cyclone data, visualizations and model output.

Goodman, H. Michael↗
DOE OSTI2023

Hydropower Cybersecurity Value-at-Risk Framework

Hydropower remains one of the strongest forms of renewable energy generation methods. It is crucial to address the increasing risks associated with the rapid digitization. The push towards decarbonization also factors in the need to ensure security and resilience for grid-connected renewable energy resources. This report summarizes the U.S. Department of Energy's Water Power Technologies Office's effort to develop a cybersecurity valuation methodology that assists hydropower stakeholders in assessing risks associated with plan operations and gathers valuation guidance through a web-based application. The Hydropower Cybersecurity Value-at-Risk Framework delivers a platform for industry members to perform self-assessments and make informed decisions on their cybersecurity investments.

13 HYDRO ENERGY↗
DOE OSTI2020

Integrated Dynamic Facade Control with an Agent-based Architecture for Commercial Buildings

Dynamic façades have significant technical potential to minimize heating, cooling, and lighting energy use and peak electric demand in the perimeter zone of commercial buildings, but the performance of these systems is reliant on being able to balance complex trade-offs between solar control, daylight admission, comfort, and view over the life of the installation. As the context for controllable energy-efficiency technologies grows more complex with the increased use of intermittent renewable energy resources on the grid, it has become increasingly important to look ahead towards more advanced approaches to integrated systems control in order to achieve optimum life-cycle performance at a lower cost. This study examines the feasibility of a model predictive control system for low-cost autonomous dynamic façades. A system architecture designed around lightweight, simple agents is proposed. The architecture accommodates whole building and grid level demands through its modular, hierarchical approach. Automatically-generated models for computing window heat gains, daylight illuminance, and discomfort glare are described. The open source Modelica and JModelica software tools were used to determine the optimum state of control given inputs of window heat gains and lighting loads for a 24-hour optimization horizon. Penalty functions for glare and view/ daylight quality were implemented as constraints. The control system was tested on a low-power controller (1.4 GHz single core with 2 GB of RAM) to evaluate feasibility. The target platform is a low-cost ($35/unit) embedded controller with 1.2 GHz dual-core cpu and 1 GB of RAM. Configuration and commissioning of the curtainwall unit was designed to be largely plug and play with minimal inputs required by the manufacturer through a web-based user interface. An example application was used to demonstrate optimal control of a three-zone electrochromic window for a south-facing zone. The overall approach was deemed to be promising. Further engineering is required to enable scalable, turnkey solutions.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

American-Made Solar Prize: Edgeli Enables DER Integration (CRADA 615) (Final Report)

The purpose of this project was to demonstrate how granular time series data and automated data transformation, and impact assessment tools could speed interconnection approvals for distributed energy resource projects of various types and sizes. Types included community solar, rooftop solar, and EV charging projects. Using software routines to automate the transformation of data (e.g. GIS) to a network database and power flow model then applying scenarios to create hourly (8760) hosting capacity values and voltage and thermal impacts for specific projects, we were able to demonstrate the feasibility of quickly assembling and analyzing key utility data sets for interconnection purposes. The outcomes of this effort will become the foundation for future work that will enhance and encapsulate the software components developed as part of this project, into web services (e.g. APIs) that can be integrated into queue management systems and automate interconnection screening processes.

14 SOLAR ENERGY↗
NASA NTRSDate not supplied

Enabling Communication Between Astronauts and Ground Teams for Space Exploration Missions

Over the last four years, Playbook’s Mission Log has evolved to become an enabling capability for analog missions that simulate deep space, exploration missions with communication transmission latency. Playbook is a planning and execution web-application for mission operations, aggregating multiple sources of information for astronauts to execute the mission in one place: timeline, procedures, chat interface. Playbook’s Mission Log provides a multimedia chat software interface with unique features and functionalities that support asynchronous communication between analog astronauts and ground support teams. This paper describes the iterative design the Mission Log has undergone based on user observations and solicited feedback. Key features include indicators that help users cope with asynchronous communication as well as aids that assist teams coordinate work. Future work and capabilities are outlined, which build upon the increased use of the Mission Log as a communication and coordination tool for space exploration.

communication↗
DOE OSTI2020

Developing a Decision Support Engine to Enable Irrigation Modernization - Poster

Irrigation systems in the United States are some of the oldest continually utilized infrastructure in existence today, with some systems exceeding 100 years in age. They are operated to meet farming demands but are managed through a balance of varying influence: policies limiting water usage, stakeholder interests, and environmental impacts. Irrigation modernization is defined as a set of activities that update and improve existing irrigation systems, including, but not limited to improving water quantity, development of distributed energy resources for surrounding communities, ecosystem services, and improved agricultural yields. Modernizing an existing irrigation system can enable stakeholders to combat changing environmental and population demands but is difficult because the complexity involved in determining the potential benefits and consequences of irrigation modernization is high. We are combining a large amount of various geospatial, tabular, and temporal data with subject matter expertise into a decision support engine that will enable stakeholders to determine the benefits and consequences of irrigation modernization in their irrigation systems. A web-based GIS will allow the user to construct the modifications out of a palette of modernization options, which will be sent to the analytics engine for computations, and back to the web client for a graphical display and comparison of relevant metrics. Our development process involves four phases: 1) identify mechanisms of modernization, 2) identify data requirements, data streams, first principles and applicable algorithms necessary to quantify modernization mechanisms, 3) create ‘modules’ for each modernization mechanism, these modules will form the decision support engine, each capable of performing independently but can also inform other modules when needed, 4) Merge the decision support engine with a user interface, capable of ingesting user inputs and returning insights into the impacts of a modernization project as they relate to economic, environmental, monetary, and energy generation. Once complete, it is our intention that this tool will be fundamental in irrigation modernization projects, providing a strong analytical basis from which stakeholders can quickly make informed decisions regarding project development.

13 HYDRO ENERGY↗