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NASA NTRSDate not supplied

Small Satellite Reliability Initiative (SSRI) Knowledge Base Tool: Update and Future Direction

NASA’s Small Satellite Reliability Initiative (SSRI), in conjunction with NASA’s Small Spacecraft Systems Virtual Institute (S3VI), has developed the SSRI Knowledge Base to improve mission confidence for small spacecraft. The SSRI Knowledge Base is a comprehensive and searchable online tool that consolidates and organizes resources, best practices, and lessons learned from previous small satellite missions sponsored by NASA, other government agencies, and academia. This free, publicly available tool is available to the entire SmallSat community at: NASA SSRI Knowledge Base | Explore. The SSRI Knowledge Base provides vetted, high-quality sources of information on elements that are key to successful small satellite missions. These resources include SSRI working group generated documents and presentations in addition to existing guides, publications, standards, software tools, websites, and books. The Knowledge Base is fully searchable, offers downloadable content when possible, and otherwise links to or references content directly from within the tool. All 58 of the planned topic pages that comprise the SSRI Knowledge Base have been recently completed and include over 450 unique resources that are now available for review. Over the past several months significant enhancements to the tool’s capabilities have been developed and implemented. These enhancements consist of the completed baseline content; development of an Application Programming Interface (API); improved user interfaces; scalable and searchable Best Practices and Lessons Learned (BPLL) lists with ratings; and custom website analytics. This presentation and paper will discuss the motivation for and development of the SSRI Knowledge Base, demonstrate the existing tool, and outline plans for further development. The SSRI is a collaborative activity with broad participation from civil, Department of Defense, and both national and international commercial space systems providers and stakeholders. The S3VI is jointly sponsored by NASA’s Space Technology Mission Directorate and Science Mission Directorate.

Small Spacecraft↗
NASA NTRSDate not supplied

Small Satellite Reliability Initiative (SSRI) Knowledge Base Tool: Use Case Review and Future Functionality and Content Direction

NASA’s Small Satellite Reliability Initiative (SSRI), in conjunction with NASA’s Small Spacecraft Systems Virtual Institute (S3VI), has developed the SSRI Knowledge Base to improve mission confidence for small spacecraft. The SSRI Knowledge Base is a comprehensive and searchable online tool that consolidates and organizes resources, best practices, and lessons learned from previous small satellite missions sponsored by NASA, other government agencies, and academia. This free, publicly available tool is available to the entire SmallSat community at: NASA SSRI Knowledge Base | Explore. The SSRI Knowledge Base provides vetted, high-quality sources of information on elements that are key to successful small satellite missions. These resources include SSRI working group generated documents and presentations in addition to existing guides, publications, standards, software tools, websites, and books. The Knowledge Base is fully searchable, offers downloadable content when possible, and otherwise links to or references content directly from within the tool. All 58 of the planned topic pages that comprise the SSRI Knowledge Base have been recently completed and include over 450 unique resources that are now available for review. Over the past several months significant enhancements to the tool’s capabilities have been developed and implemented. These enhancements consist of the completed baseline content; development of an Application Programming Interface (API); improved user interfaces; scalable and searchable Best Practices and Lessons Learned (BPLL) lists with ratings; and custom website analytics. This presentation and paper will discuss the motivation for and development of the SSRI Knowledge Base, review of potential use case(s), and outline plans for further development and content generation. The SSRI is a collaborative activity with broad participation from civil, Department of Defense, and both national and international commercial space systems providers and stakeholders. The S3VI is jointly sponsored by NASA’s Space Technology Mission Directorate and Science Mission Directorate.

Small Spacecraft↗
NASA NTRSDate not supplied

Introduction to the JPSS-2 Advanced Technology Microwave Sounder (ATMS) Government Calibration Data Book (GCDB)

The third Advanced Technology Microwave Sounder (ATMS) is an instrument onboard the Joint Polar Satellite System (JPSS), JPSS-2 (renamed NOAA-21 in orbit) mission. This report is to introduce the JPSS-2 Government Calibration Data Book (J2 GCDB) for ATMS, SN 304. This J2 GCDB document contains key information generated during the calibration testing campaign that is driving parameters for radiometric performance. This document also contains supporting data that augments the calibration results. The values in this document are utilized by ATMS’s calibration packet which is, in turn, an integral component in the interpretation of science data. The calibration data in this report was collected from tests such as shelf-level testing, antenna testing, instrument thermal vacuum (TVAC) testing; satellite TVAC testing; and JPSS-2 post-launch tests. JPSS-2 was launched on November 10, 2022. In the subsequent years, the Government will release an ATMS GCDB for each JPSS mission. We expect that all public users can download these ATMS GCDBs from the NOAA operational Integrated Calibration and Validation System (ICVS) website, see more discussions below. The goal of this GCDB is to demonstrate how to characterize ATMS measurements using JPSS-2 ATMS on-orbit operational data and to provide relevant explanations. This document serves as a primary public domain reference for calibrating operational ATMS Raw Data Records (RDR) science data, as used in the current operational Interface Data Processing Segment (IDPS) system. This same RDR science data is distributed through direct broadcast (DB) to DB users for use in their ground processing systems. This J2 GCDB provides the results of the ATMS system radiometric calibration, the antenna flat reflector emissivity [1], the antenna pattern measurements, the antenna pattern corrected brightness temperature [2], the brightness temperature of the lunar disk [3], Lunar Intrusion (LI) correction algorithm [4], receiver spectral parameters, and mechanical alignment on-orbit pointing results, and the striping effect appeared significantly in S-NPP on-orbit radiance data when the data are compared to the Radiative Transfer Model (RTM) simulation in numerical weather prediction (NWP) system [5]. It also provides the parameters required for conversion of telemetry counts to engineering units, for radiometric calibration, and for antenna beam geo-location. Moreover, it provides JPSS-2 ATMS Spectral Response Functions data, some additional information related to ATMS on-orbit performance, on-orbit lunar intrusion correction parameters and Earth contamination bias, and on how to derive ATMS RDR, antenna Temperature Data Records (TDR), and Sensor Data Records (SDR). Furthermore, an introduction of NOAA operational Integrated Calibration and Validation System (ICVS) website and services is added in this J2 GCDB. This ICVS hosts a long-term monitoring system which allows to visualization and comparison of data from JPSS missions, NOAA legacy Polar Operational Environmental Satellites (POES), and Geostationary Operational Environmental Satellites (GOES). From NOAA Comprehensive Large Array-data Stewardship System (CLASS), the public users can download all JPSS ATMS data products for all JPSS missions.

Microwave Sounder↗
DOE OSTI2025

Automation of Vulnerability and Patch Management: Information Extraction, Association, and Optimization

Vulnerability and patch management is an integral part of a robust cybersecurity program, yet it grows increasingly complex due to the sheer amount of data that must be analyzed. Particularly in Operational Technology (OT) environments, analysis must be done manually because of the lack of automated solutions. Additionally, there are many steps in this process, from the initial discovery of the vulnerability to the implementation of its remediation, and each step in the process requires different data in order to be performed effectively. In this work, we provide approaches and strategies to assist operators in industrial or OT environments throughout the vulnerability management cycle. Security advisories provide key information about mitigation strategies, or actions that can be taken when a patch is unavailable or cannot be installed. Details of these strategies are not shared in public vulnerability databases and must be found manually. We approach this problem by designing a solution to automatically identify that information within vendor security advisories and retrieve it for operator use. We start with an approach that requires domain-specific knowledge of certain frequently-seen reference websites. Next, an approach that can work on an arbitrary website but relies on certain keywords. Finally, an approach that uses Natural Language Processing (NLP) methods and does not require specific knowledge or keywords. Each of these approaches is more general than its predecessor; we demonstrate high accuracy for all approaches Advisories also often contain details of affected products in non-standard or natural language formats. While this information can be easily understood when read by an operator, the non-standard format acts as a barrier to effective automation. We provide an approach for the first step in this process: identifying vendors in security advisories and mapping them to a standard framework for representing digital assets and software products. We evaluate five established string similarity algorithms, plus one of our own design that combines string similarity and information theory, on the task of mapping vendors to their corresponding entries in the Common Platform Enumeration (CPE) repository. Our results show that our proposed metric outperforms all others. Due to the constraints on time, finances, and personnel for organizations, Large Language Models (LLMs) may seem like attractive opportunities for security operators to speed up information gathering; however, it is still not clear whether LLMs can handle vulnerability management tasks well. To answer this question, we perform an empirical study of LLMs’ ability to provide consistent, accurate information about vulnerabilities in order to guide organizations in their adoption of LLMs. We observe poor performance for all models tested, suggesting that these models are not well-suited to the consistent retrieval of accurate vulnerability information. Finally, once vulnerabilities have been identified and any additional information has been obtained, operators must decide which remediation actions to implement based on their available resources. This already-complex problem becomes even more so when we consider that a vulnerability may have multiple avenues for remediation. We formulate this scenario as two knapsack problems and provide solutions, which we then compare against several existing strategies for vulnerability prioritization seen in real operational environments.

McClanahan, Kylie↗
DOE OSTI2025

The neurobench framework for benchmarking neuromorphic computing algorithms and systems

Neuromorphic computing shows promise for advancing computing efficiency and capabilities of AI applications using brain-inspired principles. However, the neuromorphic research field currently lacks standardized benchmarks, making it difficult to accurately measure technological advancements, compare performance with conventional methods, and identify promising future research directions. This article presents NeuroBench, a benchmark framework for neuromorphic algorithms and systems, which is collaboratively designed from an open community of researchers across industry and academia. NeuroBench introduces a common set of tools and systematic methodology for inclusive benchmark measurement, delivering an objective reference framework for quantifying neuromorphic approaches in both hardware-independent and hardware-dependent settings. For latest project updates, visit the project website (neurobench.ai).

Yik, Jason [Harvard Univ., Cambridge, MA (United S↗
DOE OSTI2025

Emerging protein sequencing technologies: proteomics without mass spectrometry?

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been a leading method for proteomics for 30 years. Advantages provided by LC-MS/MS are offset by significant disadvantages, including cost. Recently, several non-mass spectrometric methods have emerged, but little information is available about their capacity to analyze the complex mixtures routine for mass spectrometry. Areas Covered: We review recent non-mass-spectrometric methods for sequencing proteins and peptides, including those using nanopores, sequencing by degradation, reverse translation, and short-epitope mapping, with comments on bioinformatics challenges, fundamental limitations, and areas where new technologies will be more or less competitive with LC-MS/MS. In addition to conventional literature searches, instrument vendor websites, patents, webinars, and preprints were also consulted to give a more up-to-date picture. Expert Opinion: Many new technologies are promising. However, demonstrations that they outperform mass spectrometry in terms of peptides and proteins identified have not yet been published, and astute observers note important disadvantages, especially relating to the dynamic range of single-molecule measurements of complex mixtures. Still, even if the performance of emerging methods proves inferior to LC-MS/MS, their low cost could create a different kind of revolution: a dramatic increase in the number of biology laboratories engaging in new forms of proteomics research.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

GenomeDepot: data management system for microbial comparative genomics

Summary GenomeDepot is an open-source web-based platform for annotation, management, and comparative analysis of microbial genomic sequences and associated data including ortholog families, protein domains, operons, regulatory interactions, strain taxonomy, and sample metadata. GenomeDepot supports rapid creation of websites for user-defined genome collections that include bioinformatic tools for interactive genome browsing, Basic Local Alignment Search Tool (BLAST) search, annotation search, comparative genomic neighborhood visualization, and sequence download. Gene function annotations are generated by a customizable annotation pipeline. The pipeline runs annotation tools in Conda environments and can be easily extended with additional user-specified tools. Availability and implementation GenomeDepot is open source and distributed under the GNU General Public License via GitHub (https://github.com/aekazakov/genome-depot). GenomeDepot is implemented in Python and was tested in Ubuntu Linux. Full installation instructions and documentation are available at https://aekazakov.github.io/genome-depot/. GenomeDepot demo server is freely accessible at https://iseq.lbl.gov/demogd/.

Kazakov, Alexey [Lawrence Berkeley National Labora↗
DOE OSTI2024

The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters

Secondary metabolites are small molecules produced by all corners of life, often with specialized bioactive functions with clinical and environmental relevance. Secondary metabolite biosynthetic gene clusters (BGCs) can often be identified within DNA sequences by various sequence similarity tools, but determining the exact functions of genes in the pathway and predicting their chemical products can often only be done by careful, manual comparative analysis. To facilitate this, we report the first release of the secondary metabolism collaboratory (SMC), which aims to provide a comprehensive, tool-agnostic repository of BGC sequence data drawn from all publicly available and user-submitted bacterial and archaeal genome and contig sources. On the website, users are provided a searchable catalog of putative BGCs identified from each source, along with visualizations of gene and domain annotations derived from multiple sequence analysis tools. SMC’s data is also available through publicly-accessible application programming interface (API) endpoints to facilitate programmatic access. Users are encouraged to share their findings (and search for others’) through comment posts on BGC and source pages. At the time of writing, SMC is the largest repository of BGC information, holding 13.1M BGC regions from 1.3M source sequences and growing, and can be found at https://smc.jgi.doe.gov.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data

Abstract BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, training of artificial intelligence models and computational chemistry methods development. This update reports significant growth and enhancements since our last review in 2016. Of note, the database now contains 2.9 million binding measurements spanning 1.3 million compounds and thousands of protein targets. This growth is largely attributable to our unique focus on curating data from US patents, which has yielded a substantial influx of novel binding data. Recent improvements include a remake of the website following responsive web design principles, enhanced search and filtering capabilities, new data download options and webservices and establishment of a long-term data archive replicated across dispersed sites. We also discuss BindingDB’s positioning relative to related resources, its open data sharing policies, insights gleaned from the dataset and plans for future growth and development.

Liu, Tiqing↗
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 OSTI2024

Development of learning objectives to support undergraduate virology curriculum guidelines

It has become increasingly important for microbiology educators to help students learn critical concepts of the discipline. This is particularly true in virology, where current challenges include increasing rates of vaccine hesitancy, misinformation about the COVID-19 pandemic, and controversy surrounding research on pathogens with pandemic potential. Having students learn virology can attract more people to the field and increase the number of people who can engage in meaningful discourse about issues relating to the discipline. However, the limited number of virologists who teach undergraduates, combined with the fact that many institutions lack stand-alone virology courses, results in virology often being taught as a limited number of lectures within an undergraduate microbiology course (if it is covered at all), which may or may not be taught by an individual trained as a virologist. To provide a framework to teach virology to undergraduate students, a team of virology educators, with support from the American Society for Virology (ASV), developed curriculum guidelines for use in a stand-alone undergraduate virology course or a virology section within another course. These guidelines are available at the ASV website (https://asv.org/curriculum-guidelines/). To assist educators in implementing these guidelines, we created examples of measurable learning objectives. This perspective provides details about the virology curriculum guidelines and learning objectives and accompanies the perspective by Boury et al. in this issue of the Journal of Microbiology & Biology Education about the recent revision of the microbiology curriculum guidelines overseen by the American Society for Microbiology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Scintillator Library

This website provides measured scintillation properties of many inorganic and organic materials and citations to published papers in which the original measurements were reported. It is intended for two main uses: a web-accessible reference to useful scintillation detector materials and properties; an aid in developing fundamental theories or empirical relations between basic material properties and scintillation performance. To this end, both strong and weak scintillators have been included as well as those where sensitive measurements have not detected any scintillation emissions.

Shook, L. [University of California, Berkeley, CA ↗
DOE OSTI2024

Chemical Webscraper [SWR-24-105]

Chemical Webscraper uses the chrome web browser to search for and collect cost data for chemicals from specified distribution websites.

Cordell, Jacob↗
DOE OSTI2025

Bioenergy Research Centers Data Sharing Portal

The bioenergy.org website is the end product of the Data Sharing Shared Research objective for the Bioenergy Centers. The objective is to Enhance BRC data legacy through the development and use of shared software tools to make previously published datasets more findable and accessible through the Inter-BRC Data Products Portal, and to explore the use of generative AI to assist in the exploration of published datasets. The software repository is released per the license information below.

Thrower, Nicholas↗
DOE OSTI2025

multiBreath.py

This is a research code which is intended to be made available to researchers to the password-protected simtk.org website which hosts the lung deposition simulation project "In-silico LADDER: Lung Aerosol Dosimetry for Drug and Environmental Research" headed by NIH PI Prof. Chantal Darquenne (UCSD). Industrial applications are more accurate deposition predictions of medical aerosols, including potentially subject-specific exposures. Accessing the code requires registration.

Kuprat, Andrew [Pacific Northwest National Laborat↗
DOE OSTI2025

EverBESS

SF-25-113 This software is a website for the EverBESS model. This model examines the cost and environmental impacts related to end-of-life management of battery energy storage systems. Users input their system's specifications and the model returns estimates for the costs of decommissioning, transporting, and recycling the system.

Elias, Jakob [Argonne National Laboratory (ANL), A↗
DOE OSTI2025

EV-ELM (Electric Vehicle Policies with the Energy Language Model) [SWR-25-156]

Electric Vehicle Policies with the Energy Language Model (EV-ELM) leverages previous work using Large Language Models (LLMs) to find, download, and parse policy information related to energy infrastructure. In this application, we use LLMs to find policy documents related to the permitting and installation of electric vehicle charging infrastructure. This software contains the code to find, download, and parse these documents, while a related data record in the Open Energy Data Initiative (OEDI) will include the resulting output dataset that can be used for downstream analysis. The EV-ELM repository contains code for the EV-ELM project, which focuses on retrieving and processing EV permitting processes using large language models. The project is composed of two pipelines: (1) a web scraping pipeline for discovering and downloading EV permitting documents, and (2) a document parsing and extraction pipeline that processes the downloaded files to produce structured data. The web scraping pipeline is designed to extract relevant information from various websites, while the document parsing pipeline processes and analyzes the extracted documents to derive meaningful insights. Both pipelines depend on the NLR elm repository, which provides essential tools and functionalities for handling and processing the data. The web scraping pipeline is a modified version of the ordinance_gpt example within the elm repository. It has been adapted to fit the specific requirements of the EV-ELM project, ensuring that it effectively captures and processes the necessary information related to EV permitting.

Olson, Reid [National Laboratory of the Rockies (N↗
DOE OSTI2025

A Data Processing Pipeline To Extract A Knowledge Graph From Heterogeneous Data For Socio-technical Analysis Of Critical Infrastructure Influence

The code is written in Python and consists of the following pipeline that is implemented in Apache Airflow. This pipeline intends to understand the companies that are directly or indirectly involved with a type of critical infrastructure system at some point in that system's lifecycle. The pipeline takes a configuration file that specifies a list of initial companies to consider, a geographic region of interest, and a set of SEC form types as well as other data sources (e.g. CrunchBase) from which to extract entities and relations. There are four main components to this pipeline as currently implemented: Entity Extraction, Network Construction, Analysis, and Visualization. First, Entity Extraction, is implemented as the `topear-extract_organizations` Apache Airflow workflow. Given an initial query that specifies a geographic region of interest and a time interval, the software will extract CI facilities of interest and organizations that have a direct influence relationship to those facilities (e.g. ownership). During the course of the LDRD, we focused on Electric Vehicle charging stations and this information is available via the Department of Energy (DOE) database on fueling stations maintained by NREL. Within the context of the DOE CESER project, we have focused on Battery Energy Storage Systems (BESS). Second, the Network Extraction component will iteratively construct a social network graph given the set of organizations and people extracted in the previous step. Organizations (and eventually People if desired) are then fed as a query to the `topgear-construct_social_network` Apache Airflow workflow which given a set of initial companies and data sets (e.g. SEC EDGAR form types, OpenCorporates, Crunchbase). This Airflow workflow will iteratively query such data sources to discover relationships with new organizations and people. For example, this module can iteratively query SEC EDGAR for metadata that documents the number of each type of form for the given set of companies and their location. This forms metadata represents a catalog of data sources from SEC EDGAR for the extracted social network knowledge graph. The pipeline then downloads these forms from the website and saves them in a build directory for further processing. These documents are then parsed for entities and relations. Again, we note that in additional to SEC data sources, this step can also pull in information on organizations via API services such as CrunchBase and OpenCorporates or bulk data sources. At the end of this step, the resultant social network, the Critical Infrastructure network, and the edges that encode relationships between organizations and CI facilities, form the Adversarial Socio-Technical Network (ASTN) that informs the analysis. Third, the Analysis component processes these generated ASTN. Previously, that has included the ability to compare prevalence of different vendors for a given infrastructure component type across different regions as well as identify common public and private investors across those vendors. This was demonstrated for EV Charging Stations across several different metropolitan areas within an IEEE PES GridEdge publication. More recently, we have looked at ways to identify infrastructure owners and operators of BESS with the most nameplate capacity across different states as well as other indictors of risk resulting from changes in ownership over time. Finally, the Visualization component consists of an HTML/CSS/JS framework by which users can interact geospatial, operational, and organizational relationships across a given portfolio of Critical Infrastructure facilities. The objective is to provide a library of UI/UX modules that can be repurposed for stakeholder-specific dashboards. All of the modules are related via a common event model that enables UI actions in one view to percolate across the other views.

Weaver, Gabriel [Idaho National Laboratory (INL), ↗