Results for “Website” — Page 2

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), ↗

DOE OSTI2026

Pioneer WEC Dashboard

SAND2026-18911O The Pioneer WEC (Wave Energy Converter) Dashboard tool visualizes real-time data from the Pioneer WEC v1 prototype, which supplies power to a mooring in the Coastal Pioneer Array. It offers up-to-date information, performance metrics, and graphical plots that enable users to monitor the prototype's efficiency. Developed using Python and Jekyll, this static website is updated daily and hosted on GitHub. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.

Michelen Strofer, Carlos [Sandia National Lab. (SN↗

DOE OSTI2025

An HPC benchmark survey and taxonomy for characterization

The field of High-Performance Computing (HPC) is defined by providing computing devices with highest performance for a variety of demanding scientific users. The tight co-design relationship between HPC providers and users propels the field forward, paired with technological improvements, achieving continuously higher performance and resource utilization. A key device for system architects, architecture researchers, and scientific users are benchmarks, allowing for well-defined assessment of hardware, software, and algorithms. Many benchmarks exist in the community, from individual niche benchmarks testing specific features, to large-scale benchmark suites for whole procurements. We survey the available HPC benchmarks, summarizing them in table form with key details and concise categorization, also through an interactive website. For categorization, we present a benchmark taxonomy for well-defined characterization of benchmarks.

Benchmarking↗

DOE OSTI2024

Road Lidar Dataset for the TxDOT Austin District

This is a road lidar data collection for developing road elevation models and road inundation mapping methodologies, a joint work between ORNL and The University of Texas at Austin. This dataset is generated as part of the flood transportation infrastructure, partly funded by the NOAA CIROH project. ORNL is a project partner for high-performance computing-empowered flood inundation mapping methodology R&D. The dataset is computed using a GPU-accelerated lidar data processing workflow developed at ORNL. The lidar data source is from TxGIO, the state lidar data collection site. The output dataset is in two formats: laz and copc. It is organized by TxDOT's maintenance sections, covering the Austin District. Data size: 3.86 billion road lidar points, 1.67% of the entire lidar data input Projection: EPSG:32614 (WGS84/UTM zone 14N) Website: https://web.corral.tacc.utexas.edu/nfiedata/road3d/austin_district/AustinMaintenanceSections_H_epsg6343_V_epsg5703/ LICENSE FOR USE -- MAPS AND DATA DISCLAIMER This resource is shared under the Creative Commons Attribution CC BY, http://creativecommons.org/licenses/by/4.0/ MAPS AND DATA DISCLAIMER The Oak Ridge National Laboratory (ORNL) shall not be held liable for improper or incorrect use of the data described or information contained on this map or associated series of maps. The data and related map graphics are not legal, land survey or engineering documents and are not intended to be used as such. ORNL gives no warranty, express or implied, as to the accuracy, reliability, utility or completeness of this information. The user of these maps and data assumes all responsibility and risk for the use of the maps and data. ORNL disclaims all warranties, representations or endorsements either express or implied, with regard to the information contained in this map product, including, but not limited to, all implied warranties of merchantability, fitness for a particular purpose or non-infringement. This preliminary map product is for research and review purposes only. It is not intended to be used for emergency management operational or life safety decisions at the local or regional governmental level or by the general public. Users requiring information regarding hazardous conditions or meteorological conditions for specific geographic areas should consult directly with their city or county emergency management office.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

2019 and 2022 Twin Cities Travel Behavior Inventory Surveys

# 2019 and 2022 Twin Cities Travel Behavior Inventory Surveys To help local and regional planning agencies understand shifting demographics and travel patterns, surveys were conducted in Minnesota’s greater Twin Cities region in 2019 and 2022. Survey results aided the Metropolitan Council in proposing practical transportation investments, preparing competitive grant applications, and prioritizing improvements to best fit regional needs. ## Data Collection Agency RSG conducted the surveys for the Metropolitan Council. ## Survey Methodology These mixed-mode surveys focused on bus, rail, car, micromobility, ride-hailing, and walking. Designed as household travel surveys, they were carried out in English, Spanish, Karen, Oromo, Somali, and Hmong during two timeframes: Oct. 1, 2018—Sept. 30, 2019 and June 22, 2021—Feb. 5, 2022. Participants accessed the surveys using a smartphone-based app, website, or call center. A questionnaire captured data about demographics, daily travel activities, and typical transportation patterns to inform model updates and gain information about emerging behavioral changes such as electric vehicle adoption and teleworking frequency. It also addressed the impacts of COVID-19 on participants’ typical travel behavior. ## Survey Records, Data, and Documentation Survey records include a total of 31,251 participants—16,152 participants from 7,837 households during the 2019 survey and 15,099 participants from 7,952 households during the 2022 survey.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

2022 Kauai Ground Transportation Survey

# 2022 Kauai Ground Transportation Survey The 2022 Kauai Ground Transportation Survey was designed to improve understanding of the transportation preferences of residents and visitors of the Hawaiian island of Kauai. For residents of Kauai, the survey focused on mode-choice decisions for commute, leisure, and shopping activities and whether they would consider using alternative modes instead of driving if such options were available. For visitors, the survey focused on whether they would consider alternatives to rental cars if such options were available. Ultimately, survey results will inform the development of sustainable transportation strategies for the island. ## Data Collection Agency NREL and the Kauai Office of Economic Development conducted the study as part of the U.S. Department of Energy's Energy Transitions Initiative Partnership Project. ## Survey Methodology The survey was conducted July—October 2022. Respondents were recruited via direct email invitation, a press release on the Kauai County website and Facebook page, and posters at community outreach events. ## Survey Records, Data, and Documentation Survey records include 1,437 participants.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

2019 and 2022 Twin Cities Travel Behavior Inventory Surveys

# 2019 and 2022 Twin Cities Travel Behavior Inventory Surveys To help local and regional planning agencies understand shifting demographics and travel patterns, surveys were conducted in Minnesota’s greater Twin Cities region in 2019 and 2022. Survey results aided the Metropolitan Council in proposing practical transportation investments, preparing competitive grant applications, and prioritizing improvements to best fit regional needs. ## Data Collection Agency RSG conducted the surveys for the Metropolitan Council. ## Survey Methodology These mixed-mode surveys focused on bus, rail, car, micromobility, ride-hailing, and walking. Designed as household travel surveys, they were carried out in English, Spanish, Karen, Oromo, Somali, and Hmong during two timeframes: Oct. 1, 2018—Sept. 30, 2019 and June 22, 2021—Feb. 5, 2022. Participants accessed the surveys using a smartphone-based app, website, or call center. A questionnaire captured data about demographics, daily travel activities, and typical transportation patterns to inform model updates and gain information about emerging behavioral changes such as electric vehicle adoption and teleworking frequency. It also addressed the impacts of COVID-19 on participants’ typical travel behavior. ## Survey Records, Data, and Documentation Survey records include a total of 31,251 participants—16,152 participants from 7,837 households during the 2019 survey and 15,099 participants from 7,952 households during the 2022 survey.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

2022 Kauai Ground Transportation Survey

# 2022 Kauai Ground Transportation Survey The 2022 Kauai Ground Transportation Survey was designed to improve understanding of the transportation preferences of residents and visitors of the Hawaiian island of Kauai. For residents of Kauai, the survey focused on mode-choice decisions for commute, leisure, and shopping activities and whether they would consider using alternative modes instead of driving if such options were available. For visitors, the survey focused on whether they would consider alternatives to rental cars if such options were available. Ultimately, survey results will inform the development of sustainable transportation strategies for the island. ## Data Collection Agency NREL and the Kauai Office of Economic Development conducted the study as part of the U.S. Department of Energy's Energy Transitions Initiative Partnership Project. ## Survey Methodology The survey was conducted July—October 2022. Respondents were recruited via direct email invitation, a press release on the Kauai County website and Facebook page, and posters at community outreach events. ## Survey Records, Data, and Documentation Survey records include 1,437 participants.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗