Results for “web portal” — Page 4

DOE OSTI2024

Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.org research-focused web portal. We report substantial additions to the tools and visualization features available at RCSB.org, which now delivers more than 227000 experimentally determined atomic-level three-dimensional (3D) biostructures stored in the global PDB archive alongside more than 1 million Computed Structure Models (CSMs) of proteins (including models for human, model organisms, select human pathogens, crop plants and organisms important for addressing climate change). In addition to providing support for 3D structure motif searches with user-provided coordinates, new features highlighted herein include query results organized by redundancy-reduced Groups and summary pages that facilitate exploration of groups of similar proteins. Newly released programmatic tools are also described, as are enhanced training opportunities.

Burley, Stephen K.↗

DOE OSTI2026

VirJenDB: a FAIR (meta)data and bioinformatics platform for all viruses

High-throughput sequencing has generated an unprecedented volume of data. However, researcher-submitted data in repositories requires extensive curation and quality control for reuse. These tasks are hindered by the multiplicity of repositories, the sheer volume of the data, and the complexity of virus (meta)data curation. To address these challenges, VirJenDB offers a user-friendly platform to facilitate versioned, community-driven curation, and ontology development. Virus sequences were ingested from 16 sources, including ~200 fields of metadata or standards, covering taxonomy, sample, and host information. Up to 85 metadata fields have undergone at least one round of curation, and are linked to 15.4 million virus sequences, with 88 % from those infecting eukaryotes and the remaining infecting prokaryotes. Subsets were created, including a novel collection of 0.91 million viral operational taxonomic unit (vOTU) sequences across all viruses, while keeping the original sequences from each vOTU to facilitate downstream analyses, e.g. sequence variation. The VirJenDB web portal (https://www.virjendb.org) provides HTTPS and Application Programming Interface (API) access to the sequence datasets and metadata, offering a search engine, filtering, download, visualizations, and documentation. VirJenDB aims to connect the phage and eukaryotic virus research communities by supporting webtool integration, meta-analyses, and metadata schema extensions.

Saghaei, Shahram↗

DOE OSTI2024

RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures

The Protein Data Bank (PDB) was established as the first open-access digital data resource in biology and medicine in 1971 with seven X-ray crystal structures of proteins. Today, the PDB houses >210 000 experimentally determined, atomic level, 3D structures of proteins and nucleic acids as well as their complexes with one another and small molecules ( e.g. approved drugs, enzyme cofactors). These data provide insights into fundamental biology, biomedicine, bioenergy and biotechnology. They proved particularly important for understanding the SARS-CoV-2 global pandemic. The US-funded Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) and other members of the Worldwide Protein Data Bank (wwPDB) partnership jointly manage the PDB archive and support >60 000 `data depositors' (structural biologists) around the world. wwPDB ensures the quality and integrity of the data in the ever-expanding PDB archive and supports global open access without limitations on data usage. The RCSB PDB research-focused web portal at https://www.rcsb.org/ (RCSB.org) supports millions of users worldwide, representing a broad range of expertise and interests. In addition to retrieving 3D structure data, PDB `data consumers' access comparative data and external annotations, such as information about disease-causing point mutations and genetic variations. RCSB.org also provides access to >1 000 000 computed structure models (CSMs) generated using artificial intelligence/machine-learning methods. To avoid doubt, the provenance and reliability of experimentally determined PDB structures and CSMs are identified. Related training materials are available to support users in their RCSB.org explorations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

IPPOG: a global network for particle physics outreach and education

We present the International Particle Physics Outreach Group (IPPOG), a global network dedicated to connecting students, educators, and the general public with the world of particle physics. In this paper, we outline the need to bridge the existing gap between the particle physics community and the wider audience, and we present the solutions that IPPOG has implemented to overcome it through three pillar Activities: the International Masterclasses and the Global Cosmics hands-on activities network, which have engaged together over 200,000 high-school students to date, and the curation of an Outreach Resource Database and web portal.

Abreu, Pedro [University of Lisboa (Portugal); IPP↗

DOE OSTI2026

Baseline vs. DER Scenario

Projections and associated uncertainty estimates are generated for a variety of user-selectable EV charging sessions, electricity tariffs, subsidy levels, revenue schemes, charging station configurations, and on-site solar and/or storage options. The outputs are presented in CHIP's web portal browser in the form of easily interpretable graphics (interactive graphs and bar charts) that facilitate convenient comparison among different scenarios to aid decision-making. The user should bring assumptions for modeling on simulation planning horizon, number of EV charging sessions per year, electricity costs (energy and demand charge rates; flat versus time-of-use rate), site capital costs (equipment for EV chargers and transformer), solar PV, and battery energy storage (kW).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2023

PACE

Performance Analytics for Computational Experiments (PACE) is an end-to-end performance monitoring infrastructure to summarize performance data collected from Department of Energy’s (DOE) climate model experiments to derive insights and present them through a web portal. PACE automatically captures provenance/timing data from simulations run on DOE supercomputers.

Sreepathi, Sarat [Oak Ridge National Lab. (ORNL), ↗

DOE OSTI2025

bmdrc: Python package for quantifying phenotypes from chemical exposures with benchmark dose modeling

Though chemical exposures are known to potentially have negative impacts on health, including contributing to chronic diseases such as cancer, the quantitative contribution of risk is not fully understood for every chemical. A commonly used approach to quantify levels of risk is to measure the proportion of organisms (such as a total number of zebrafish on a plate or mice in a cage) with abnormal behavioral responses or morphology at increasing concentrations of chemical exposure. A particular challenge with processing the proportional data from these assays is the appropriate estimation of chemical concentration levels that result in malformations or acute toxicity, as these values typically vary between experimental measurements. The recommended approach by the Environmental Protection Agency (EPA) is to fit benchmark dose curves with specific filters and model fitting steps, which are crucial to properly processing the proportional data. Several tools exist for the fitting of benchmark dose response curves, but none are standalone Python libraries built to process both morphological and behavioral data as proportions with all the EPA recommended filters, filter parameters, models, and model parameters. Thus, here we present the benchmark dose response curve (bmdrc) Python library, which was built to closely follow these EPA guidelines with helpful visualizations of filters and fitted model curves, and reports for reproducibility purposes. bmdrc is open-source and has demonstrated utility as a support package to an existing web portal for information on chemicals (https://srp.pnnl.gov). Our package will support any toxicology analysis where the response is a proportional value at increasing levels of a concentration of a chemical or chemical mixture.

Superfund↗

DOE OSTI2026

DOE EV Data Collection - Vehicle Data

Vehicle data consist of electric vehicle performance data collected directly from the vehicle during standard operations. Data were collected using onboard data loggers that were either installed by the project team or preinstalled by the original equipment manufacturer. Data recorded by the data loggers were made accessible via an online web portal or an application programming interface. Different data loggers were used (HEM, ViriCiti, and Geotab), and the method for each vehicle is defined in the vehicle attributes file. Some systems collected data on a “trip-level” basis, in which each row of a table represents a single trip (the period between a key-on and key-off event), whereas other data were collected on a per-day basis, in which each row represents a single day of operation. Data were collected over a range of data collection periods, depending on the project. Data have been anonymized by removing information or decreasing information resolution as necessary so that fleets are not identifiable. Due to the wide range of vehicle types represented and variation in data collection, data parameters and frequencies differ between vehicles and fleets The **Performance Data Daily/Trip Data Dictionaries** contain definitions for each available parameter associated with a vehicle’s operations, aggregated at either a daily or trip level. The parameters available will vary from vehicle to vehicle, but every possible parameter will be defined. The **Vehicle Attributes Data Dictionary** contains definitions for each available parameter associated with a vehicle’s physical and functional attributes and fleet context. The **Vehicle Attributes** table contains specific vehicle characteristics, coded to an anonymous Vehicle ID. This Vehicle ID can be used as a key between vehicle data and vehicle attribute tables. The **Vehicle Data** tables contain the data from each vehicle’s operations, aggregated at either a daily or trip level, coded to an anonymous Vehicle ID. This Vehicle ID can be used as a key between vehicle data and vehicle attribute tables. Data is being uploaded quarterly through 2023 and subject to change until the conclusion of the project.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

Baseline vs. DER Scenario

Projections and associated uncertainty estimates are generated for a variety of user-selectable EV charging sessions, electricity tariffs, subsidy levels, revenue schemes, charging station configurations, and on-site solar and/or storage options. The outputs are presented in CHIP's web portal browser in the form of easily interpretable graphics (interactive graphs and bar charts) that facilitate convenient comparison among different scenarios to aid decision-making. The user should bring assumptions for modeling on simulation planning horizon, number of EV charging sessions per year, electricity costs (energy and demand charge rates; flat versus time-of-use rate), site capital costs (equipment for EV chargers and transformer), solar PV, and battery energy storage (kW).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

Baseline vs. DER Scenario

Projections and associated uncertainty estimates are generated for a variety of user-selectable EV charging sessions, electricity tariffs, subsidy levels, revenue schemes, charging station configurations, and on-site solar and/or storage options. The outputs are presented in CHIP's web portal browser in the form of easily interpretable graphics (interactive graphs and bar charts) that facilitate convenient comparison among different scenarios to aid decision-making. The user should bring assumptions for modeling on simulation planning horizon, number of EV charging sessions per year, electricity costs (energy and demand charge rates; flat versus time-of-use rate), site capital costs (equipment for EV chargers and transformer), solar PV, and battery energy storage (kW).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

Baseline vs. DER Scenario

Projections and associated uncertainty estimates are generated for a variety of user-selectable EV charging sessions, electricity tariffs, subsidy levels, revenue schemes, charging station configurations, and on-site solar and/or storage options. The outputs are presented in CHIP's web portal browser in the form of easily interpretable graphics (interactive graphs and bar charts) that facilitate convenient comparison among different scenarios to aid decision-making. The user should bring assumptions for modeling on simulation planning horizon, number of EV charging sessions per year, electricity costs (energy and demand charge rates; flat versus time-of-use rate), site capital costs (equipment for EV chargers and transformer), solar PV, and battery energy storage (kW).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

Baseline vs. DER Scenario

Projections and associated uncertainty estimates are generated for a variety of user-selectable EV charging sessions, electricity tariffs, subsidy levels, revenue schemes, charging station configurations, and on-site solar and/or storage options. The outputs are presented in CHIP's web portal browser in the form of easily interpretable graphics (interactive graphs and bar charts) that facilitate convenient comparison among different scenarios to aid decision-making. The user should bring assumptions for modeling on simulation planning horizon, number of EV charging sessions per year, electricity costs (energy and demand charge rates; flat versus time-of-use rate), site capital costs (equipment for EV chargers and transformer), solar PV, and battery energy storage (kW).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

Baseline vs. DER Scenario

Projections and associated uncertainty estimates are generated for a variety of user-selectable EV charging sessions, electricity tariffs, subsidy levels, revenue schemes, charging station configurations, and on-site solar and/or storage options. The outputs are presented in CHIP's web portal browser in the form of easily interpretable graphics (interactive graphs and bar charts) that facilitate convenient comparison among different scenarios to aid decision-making. The user should bring assumptions for modeling on simulation planning horizon, number of EV charging sessions per year, electricity costs (energy and demand charge rates; flat versus time-of-use rate), site capital costs (equipment for EV chargers and transformer), solar PV, and battery energy storage (kW).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

Baseline vs. DER Scenario

Projections and associated uncertainty estimates are generated for a variety of user-selectable EV charging sessions, electricity tariffs, subsidy levels, revenue schemes, charging station configurations, and on-site solar and/or storage options. The outputs are presented in CHIP's web portal browser in the form of easily interpretable graphics (interactive graphs and bar charts) that facilitate convenient comparison among different scenarios to aid decision-making. The user should bring assumptions for modeling on simulation planning horizon, number of EV charging sessions per year, electricity costs (energy and demand charge rates; flat versus time-of-use rate), site capital costs (equipment for EV chargers and transformer), solar PV, and battery energy storage (kW).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

Baseline vs. DER Scenario

Projections and associated uncertainty estimates are generated for a variety of user-selectable EV charging sessions, electricity tariffs, subsidy levels, revenue schemes, charging station configurations, and on-site solar and/or storage options. The outputs are presented in CHIP's web portal browser in the form of easily interpretable graphics (interactive graphs and bar charts) that facilitate convenient comparison among different scenarios to aid decision-making. The user should bring assumptions for modeling on simulation planning horizon, number of EV charging sessions per year, electricity costs (energy and demand charge rates; flat versus time-of-use rate), site capital costs (equipment for EV chargers and transformer), solar PV, and battery energy storage (kW).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

Baseline vs. DER Scenario

Projections and associated uncertainty estimates are generated for a variety of user-selectable EV charging sessions, electricity tariffs, subsidy levels, revenue schemes, charging station configurations, and on-site solar and/or storage options. The outputs are presented in CHIP's web portal browser in the form of easily interpretable graphics (interactive graphs and bar charts) that facilitate convenient comparison among different scenarios to aid decision-making. The user should bring assumptions for modeling on simulation planning horizon, number of EV charging sessions per year, electricity costs (energy and demand charge rates; flat versus time-of-use rate), site capital costs (equipment for EV chargers and transformer), solar PV, and battery energy storage (kW).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

Baseline vs. DER Scenario

Projections and associated uncertainty estimates are generated for a variety of user-selectable EV charging sessions, electricity tariffs, subsidy levels, revenue schemes, charging station configurations, and on-site solar and/or storage options. The outputs are presented in CHIP's web portal browser in the form of easily interpretable graphics (interactive graphs and bar charts) that facilitate convenient comparison among different scenarios to aid decision-making. The user should bring assumptions for modeling on simulation planning horizon, number of EV charging sessions per year, electricity costs (energy and demand charge rates; flat versus time-of-use rate), site capital costs (equipment for EV chargers and transformer), solar PV, and battery energy storage (kW).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

Baseline vs. DER Scenario

Projections and associated uncertainty estimates are generated for a variety of user-selectable EV charging sessions, electricity tariffs, subsidy levels, revenue schemes, charging station configurations, and on-site solar and/or storage options. The outputs are presented in CHIP's web portal browser in the form of easily interpretable graphics (interactive graphs and bar charts) that facilitate convenient comparison among different scenarios to aid decision-making. The user should bring assumptions for modeling on simulation planning horizon, number of EV charging sessions per year, electricity costs (energy and demand charge rates; flat versus time-of-use rate), site capital costs (equipment for EV chargers and transformer), solar PV, and battery energy storage (kW).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗