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At least 595 records · Page 33
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Mondo: integrating disease terminology across communities

Precision medicine aims to enhance diagnosis, treatment, and prognosis by integrating multimodal data at the point of care. However, challenges arise due to the vast number of diseases, differing methods of classification, and conflicting terminological coding systems and practices used to represent molecular definitions of disease. This lack of interoperability artificially constrains the potential for diagnosis, clinical decision support, care outcome analysis, as well as data linkage across research domains to support the development or repurposing of therapeutics. There is a clear and pressing need for a unified system for managing disease entities⁠—including identifiers, synonyms, and definitions. To address these issues, we created the Mondo disease ontology—a community-driven, open-source, unified disease classification system that harmonizes diverse terminologies into a consistent, computable framework. Mondo integrates key medical and biomedical terminologies, including Online Mendelian Inheritance in Man (OMIM), Orphanet, Medical Subject Headings (MeSH), National Cancer Institute Thesaurus (NCIt), and more, to provide a comprehensive and accurate representation of disease concepts with fully provenanced and attributed links back to the sources. Mondo can be used as the handle for curation of gene–disease associations utilized in diagnostic applications, research applications such as computational phenotyping, and in clinical coding systems in clinical decision support by pointing the clinician to the numerous knowledge resources linked to the Mondo identifier. Mondo's community-centric approach, stewarded by the Monarch Initiative's expertise in ontologies, ensures that the ontology remains adaptable to the evolving needs of biomedical research and clinical communities, as well as the knowledge providers.

biomedical informatics↗
DOE OSTI2025

MolViewSpec: a Mol* extension for describing and sharing molecular visualizations

Data visualization is a pivotal component of a structural biologist’s arsenal. The Mol* Viewer makes molecular visualizations available to broader audiences via most web browsers. While Mol* provides a wide range of functionality, it has a steep learning curve and is only available via a JavaScript interface. To enhance the accessibility and usability of web-based molecular visualization, we introduce MolViewSpec (molstar.org/mol-view-spec), a standardized approach for defining molecular visualizations that decouples the definition of complex molecular scenes from their rendering. Scene definition can include references to commonly used structural, volumetric, and annotation data formats together with a description of how the data should be visualized and paired with optional annotations specifying colors, labels, measurements, and custom 3D geometries. Developed as an open standard, this solution paves the way for broader interoperability and support across different programming languages and molecular viewers, enabling more streamlined, standardized, and reproducible visual molecular analyses. MolViewSpec is freely available as a Mol* extension and a standalone Python package.

Midlik, Adam [European Bioinformatics Institute (U↗
DOE OSTI2025

BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies

Abstract BioPortal (https://bioportal.bioontology.org) is the world’s most comprehensive repository of biomedical ontologies. It provides infrastructure for finding, sharing, searching, and utilizing biomedical ontologies. Launched in 2005, BioPortal now includes 1549 ontologies (1182 of them public). Its open, freely accessible website enables anyone (i) to browse the ontology library, (ii) to search for terms across ontologies, (iii) to browse mappings between terms, (iv) to see popularity ratings and recommendations on which ontologies are most relevant to their use cases, (v) to annotate text with ontology terms, (vi) to submit an ontology, and (vii) to request ontology changes. The library of ontologies can be accessed programmatically via a REST application programming interface (API). Recent enhancements include a BioPortal knowledge graph that integrates knowledge from multiple ontologies; a unified data model for interoperability with other knowledge sources; ontology popularity ratings and recommendations for relevant ontologies; and the ability to request ontology changes via a simple user interface that automatically converts user change requests to GitHub Pull Requests that specify the edits that will be made to the ontology upon approval.

Vendetti, Jennifer↗
DOE OSTI2020

Spectroscopic factors, overlaps, and isospin symmetry from an R -matrix point of view

Background: Spectroscopic factors, overlaps, and isospin symmetry are often used in conjunction with single-particle wave functions for the phenomenological analysis of nuclear structure and reactions. Many differing prescriptions for connecting these quantities to physically relevant asymptotic normalization constants or widths are available in the literature, but their relationship and degree of validity are not always clear. Purpose: This paper derives relationships among the above quantities of interest using well-defined methodology and starting assumptions. Method: R -matrix theory is used as the primary tool to interoperate among the quantities of interest to this work. Particular attention is paid to effects arising from beyond the nuclear surface, where isospin symmetry is strongly violated. Results: Relationships between the quantities of interest are derived. Example applications of these methods to mirror levels in nucleon + 12 C, nucleon + 16 O, and nucleon + 26 Al are presented. A new approach to multilevel mirror symmetry is derived and applied to the first three 2 + states of 18 O and 18 Ne. Conclusions: In this work, the relationship between the quantities of interest is clarified and certain procedures are recommended. It is found that the asymptotic normalization constant of the second 2 + state in 18 Ne deduced from the mirror state in 18 O is significantly larger than found in previous work. This finding has the effect of increasing the 17 F($\textit{p,γ}$) 18 Ne reaction rate in novae.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2026

Integration of Multiple Real-time Simulation Platforms with AIO for Scalability

This paper introduces a practical and scalable approach to extend interoperability of Controller Hardware in the Loop (CHIL) validations for large scale microgrids, networked microgrids, and power electronics-based feeders. The work focuses on integrating multiple real-time simulators using Analog Input/Output (AIO) interface techniques in heterogeneous CHIL environment. It explores interfacing methods, highlighting key challenges related to dynamic accuracy and maintaining bidirectional power balance. A comparative evaluation of the Ideal Transformer Method is presented, assessing its effectiveness in multi-CHIL integration scenarios. The feasibility of this setup is demonstrated through a real-time use case involving multiple Typhoon HIL and Opal-RT platforms, showcasing its applicability for distributed system studies.

Khalid, Mohammad [ORNL] (ORCID:0000000179208805)↗
DOE OSTI2023

Autonomy Loops for Monitoring, Operational Data Analytics, Feedback, and Response in HPC Operations

Many High Performance Computing (HPC) facilities have developed and deployed frameworks in support of continuous monitoring and operational data analytics (MODA) to help improve efficiency and throughput. Because of the complexity and scale of systems and workflows and the need for low-latency response to address dynamic circumstances, automated feedback and response have the potential to be more effective than current human-in-the-loop approaches which are laborious and error prone. Progress has been limited, however, by factors such as the lack of infrastructure and feedback hooks, and successful deployment is often site- and case-specific. In this position paper we report on the outcomes and plans from a recent Dagstuhl Seminar, seeking to carve a path for community progress in the development of autonomous feedback loops for MODA, based on the established formalism of similar (MAPE-K) loops in autonomous computing and self-adaptive systems. By defining and developing such loops for significant cases experienced across HPC sites, we seek to extract commonalities and develop conventions that will facilitate interoperability and interchangeability with system hardware, software, and applications across different sites, and will motivate vendors and others to provide telemetry interfaces and feedback hooks to enable community development and pervasive deployment of MODA autonomy loops.

autonomy loops↗
DOE OSTI2022

Real-time Implementation of Grid Code Compliant Grid Edge Energy Management System

Integrated distributed energy resources (DER) in a distribution system need to follow grid codes to avoid violations that result in DER/circuit segment disconnection. To comply with grid code requirements at the grid edge level, network constrained grid edge energy management system (EMS) can be deployed. The objective of grid edge EMS is to provide economic solution for active and reactive power DER setpoints at each dispatch interval and ensure voltage regulation to support secure interconnection of the grid edge segment to the distribution system with multiple inverter based DER units. In this work, real-time simulation of grid code compliant grid edge EMS is deployed in a realistic feeder circuit segment. For real-time simulation, communication between the grid edge EMS and DERs is done exploiting IEC 61850-7-420. It enables interoperability among different DERs and grid edge EMS. No prior art has deployed IEC 61850-7-420 GOOSE communication protocol for grid edge EMS. Conversion of IEC 61850 GOOSE messages to Modbus communication protocol is also performed to communicate with grid edge EMS in commodity-off the shelf embedded boards in this work. The real-time simulation in OPAL-RT real-time digital simulator shows the out-performance of grid edge EMS by reducing the voltage violation in the distribution circuit.

Energy management system↗
DOE OSTI2025

Development of a Practical Secondary Control for Hardware Microgrids

Practical, vendor-agnostic interoperability guidelines for the secondary control architecture of microgrids (MGs) with multiple grid-forming (GFM) inverter-based resources (IBRs) have not yet been developed. Therefore, this paper proposes a generic and vendor-agnostic secondary control architecture that operates with all GFM IBRs and synchronous generators. This secondary control does not require the use of additional measurement devices in the MG and utilizes the inherent communication systems of the GFM units, such as Modbus TCP/IP. The practical challenges of Modbus registers, such as packet loss and quantization error, and their detrimental impacts on secondary control actions are investigated. The proposed three-stage modification for any secondary control architecture to mitigate these impacts includes: 1) averaging the data read, 2) situational event-triggering of the controller, and 3) finite iteration of the controlling action. The proposed method is validated using a 3-..phi.., 480 V, 60 Hz, 500 kVA laboratory hardware microgrid with commercial two GFM IBRs and one diesel generator. The experimental results corroborates the fact the proposed modification in the secondary control architecture is advantageous for practical usage under erroneous measurements.

communication systems↗
DOE OSTI2022

Automated Metadata Extraction: Challenges and Opportunities

Proper application of the FAIR data principles is what separates a vibrant data ecosystem, in which research data are frequently shared and reused, from a lifeless data graveyard. Automated metadata extraction systems have been proposed as a means of bolstering the findability, interoperability, and reusabil- ity of data repositories with little or no human intervention. These extraction systems mine metadata by crawling a repository and applying lightweight extractors that, for various types of file (e.g., image, CSV file), extract or synthesize relevant attributes. In practice, however, the automated creation of generally useful metadata is fraught with challenges. Data consumers may have different perspectives as to what metadata representations are useful, the standards for recording metadata tend to change over time, and the software model for processing updates can introduce unnecessary human and computational effort. Thus, generalizing extraction for a broad audience of data consumers is a difficult and relatively unsolved problem.In this work, we explore these challenges faced by extraction systems in the context of constructing our own extraction system for science data. We first define the metadata extraction problem and provide context to the issues faced in generalizing metadata. Additionally, we identify potential research directions to help alleviate many of these challenges for all automated extraction systems. Ultimately, this work represents a first step in designing ubiquitous metadata extraction systems that can maximize the value of research data while minimizing the human efforts required in doing so.

Skluzacek, Tyler↗
DOE OSTI2022

F*** workflows: when parts of FAIR are missing

The FAIR principles for scientific data (Findable, Accessible, Interoperable, Reusable) are also relevant to other digital objects such as research software and scientific workflows that operate on scientific data. The FAIR principles can be applied to the data being handled by a scientific workflow as well as the processes, software, and other infrastructure which are necessary to specify and execute a workflow. The FAIR principles were designed as guidelines, rather than rules, that would allow for differences in standards for different communities and for different degrees of compliance. There are many practical considerations which impact the level of FAIR-ness that can actually be achieved, including policies, traditions, and technologies. Because of these considerations, obstacles are often encountered during the workflow lifecycle that trace directly to shortcomings in the implementation of the FAIR principles. Here, we detail some cases, without naming names, in which data and workflows were Findable but otherwise lacking in areas commonly needed and expected by modern FAIR methods, tools, and users. We describe how some of these problems, all of which were overcome successfully, have motivated us to push on systems and approaches for fully FAIR workflows.

Wilkinson, Sean↗
DOE OSTI2020

A Data Exchange Interface for a Standards Based Data Integration Platform

The modern electrical grid is a complex and a data rich system, requiring several sub-systems to provide the capability and support needed to perform functions such as distributed energy resource management, outage management, and fault location and isolation, to name a few. There is a need to develop software solutions and platforms that provide an integrated infrastructure to allow interoperability between these subsystems, while leveraging the abundant data available from today’s grid. In this paper, we present the development and deployment of an application service to integrate GridAPPS-D which is an open source, standards-based software platform with SurvalentONE, a commonly used DNP3 based ADMS platform that allows operation, monitoring, analysis, restoration, and optimization of network operations. We present details of the integration architecture, including its implementation, and provide results from functional testing of the architecture on a 13 bus IEEE system. The results validate that the integration is successful and is able to provide a two-way exchange of communication and translation between different communication protocols.

Singh, Alka↗
DOE OSTI2020

Enabling Seamless Integration of EV Charging Infrastructure with Weak Electric Grids

Widespread adoption of Electric Vehicles (EVs) for light, medium, and heavy-duty applications has gained significant interest. Based on ownership and user preferences, light duty and local delivery medium-duty EVs are typically connected to grid distribution networks whereas larger medium duty and heavy-duty EVs are typically connected to distribution or even sub-transmission networks. Challenges with at-scale EVs and charging infrastructure supporting them include interoperability, distribution network upgrades, surge in demand charges, power quality issues, voltage stability, etc. Based on real-world data, steady-state and dynamic assessments of light-duty EV charging with a focus on DC Fast Charging (DCFC) for weak distribution grids is presented. Three main areas of contributions in this paper include - steady state and dynamic power quality measurements and assessments using real world data, transient assessments of light duty EV integration with weak distribution networks (IEEE 13 node feeder system) under grid-connected and microgrid modes, and formulation of an intelligent charging decision algorithm to enable an impact-minimal charging.

actionable intelligence↗
DOE OSTI2023

Introduction to the Special Section on Control and Management of Electric Power Systems With High Shares of Inverter-Based Resources

The growing interest in the integration of variable renewable energy (VRE) and distributed energy resources (DER) on both policy and economic grounds is driving the transformation of electric power systems. The significant deployment of VRE and DER can effectively displace the conventional synchronous generator-based power plants that for decades have been the foundation for power system generation and stability in electric power systems. Inverter-based resources (IBRs) introduce a high-level of uncertainty, variability, and complexity into the operation of electric power networks, and the transformation to IBRs raises a wide range of technical questions and operational challenges. The optimal coordination and control of these resources requires greater interoperability and necessitates significant upgrades of grid automation, including real-time monitoring.

distributed power generation↗
DOE OSTI2021

GPU-based Image Compression for Efficient Compositing in Distributed Rendering Applications

Visualizations of large-scale data sets are often created on graphics clusters that distribute the rendering task amongst many processes. When using real-time GPU-based graphics algorithms, the most time-consuming aspect of distributed rendering is typically the com-positing phase - combining all partial images from each rendering process into the final visualization. Compo siting requires image data to be copied off the GPU and sent over a network to other processes. While compression has been utilized in existing distributed rendering compositors to reduce the data being sent over the network, this compression tends to occur after the raw images are transferred from the GPU to main memory. In this paper, we present work that leverages OpenGL / CUDA interoperability to compress raw images on the GPU prior to transferring the data to main memory. This approach can significantly reduce the device-to-host data transfer time, thus enabling more efficient compositing of images generated by distributed rendering applications.

Lipinksi, Riley↗
DOE OSTI2021

The Kokkos EcoSystem: Comprehensive Performance Portability For High Performance Computing

State of the art Engineering and Science codes have grown in complexity dramatically over the last two decades. As a consequence application teams have adopted more sophisticated development strategies, leveraging third party libraries, deploying comprehensive testing and using advanced debugging and profiling tools. In todays environment of diverse hardware platforms, these applications also desire performance portability - avoiding the need to duplicate work for various platforms - which makes it necessary that these tools and libraries also work across the various systems. The Kokkos EcoSystem provides that portable software stack. Based on the Kokkos Core Programming Model, the EcoSystem provides math libraries, interoperability capabilities with Python and Fortran, and Tools for analysing, debugging, and optimizing applications. In this paper we will provide an overview of the components, discuss some specific use cases, and highlight how co-designing these components enables a more developer friendly experience.

42 ENGINEERING↗
DOE OSTI2024

A Cast of Thousands: How the IDEAS Productivity Project Has Advanced Software Productivity and Sustainability

Computational and data-enabled science and engineering are revolutionizing advances throughout science and society, at all scales of computing. For example, teams in the U.S. Department of Energy’s Exascale Computing Project have been tackling new frontiers in modeling, simulation, and analysis by exploiting unprecedented exascale computing capabilities—building an advanced software ecosystem that supports next-generation applications and addresses disruptive changes in computer architectures. However, concerns are growing about the productivity of the developers of scientific software. Members of the Interoperable Design of Extreme-scale Application Software project serve as catalysts to address these challenges through fostering software communities, incubating and curating methodologies and resources, and disseminating knowledge to advance developer productivity and software sustainability. This article discusses how these synergistic activities are advancing scientific discovery—mitigating technical risks by building a firmer foundation for reproducible, sustainable science at all scales of computing, from laptops to clusters to exascale and beyond.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Then and Now: Improving Software Portability, Productivity, and 100× Performance

The US Exascale Computing Project (ECP) has succeeded in preparing applications to run efficiently on the first reported Exascale supercomputers in the world. To achieve this, it modernized the whole leadership software stack, from libraries to simulation codes. In this article, we contrast selected leadership software before and after ECP. We discuss how sustainable research software development for leadership computing can embrace the conversation with the hardware vendors, the leadership computing facilities, the software community, and the domain scientists who are the application developers and integrators of software products. We elaborate on how software needs to take portability as a central design principle and to benefit from interdependent teams; we also demonstrate how moving to programming languages with high momentum, like modern C++, can help improve the sustainability, interoperability, and performance of research software. Finally, we showcase how cross-institutional efforts can enable algorithm advances that are beyond incremental performance optimization.

97 MATHEMATICS AND COMPUTING↗