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

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

FAIR principles

Python wrapper library and analysis functions for Geotab Altitude API [SWR-24-77]

This software library serves as a Python wrapper for Geotab's Altitude API. It streamlines querying of the API, converts loosely structured API outputs into a standardized tabular data format, and enables analysis of the resulting data tables. It also includes example notebooks showing how to use the library.

Bruchon, Matthew

Standardized Protocol for Real-Time APIs as Required by Title 23 CFR 680.116(c)

Improving the ability of drivers to easily locate working and available chargers is key to improving the public charging experience. Electric vehicle charging providers who are recipients of federal funds through the National Electric Vehicle Infrastructure (NEVI) Formula Program, Charging and Fueling Infrastructure (CFI) Discretionary Grant Program, and other funding programs as identified under Title 23 of the U.S. Code must deploy and maintain an application programming interface (API) to access information about charging stations they operate.1 This includes information about individual charging ports, pricing, and availability in accordance with the Federal Highway Administration’s National Electric Vehicle Infrastructure Standards and Requirements, 23 CFR 680.116(c), herein referred to as the minimum standards (Federal Highway Administration 2023). Specifically outlined in the minimum standards, states and other designated recipients are required to ensure that charging station information including location, connector type, power level, real-time status, and real-time price to charge are available free of charge to third-party software developers through an API. These requirements are intended to enable effective communication with consumers about available charging stations and help consumers make informed decisions about trip planning, including when and where to charge. This document provides a standardized protocol for how to structure data, data update frequency, and practices for making the data required to be shared via API usable for improving public transparency and the customer experience. These are recommendations only and do not modify the Federal Highway Administration’s minimum standards in any way.

33 ADVANCED PROPULSION SYSTEMS

Evaluation of Maximum Allowable Working Pressure and Svensson Burst Pressure Recommended in API 579-1 2021 Edition

Abstract API 579-1/ASME FFS-1 2021 Edition provides the minimum wall thickness, the maximum allowable working pressure (MAWP), and the membrane stress equations for thin and thick-walled cylindrical shells subject to internal pressure in Section 2C.3.3.1 of Appendix 2C – Thickness, MAWP, and Stress Equations for an FFS Assessment. The minimum wall thickness and MAWP are determined using the hoop stress and the Tresca yield criterion. Section 2C.7 – Estimation of Burst Pressure newly added the Svensson method for calculating burst pressure of cylindrical shells under internal pressure, where the plastic yielding is characterized by the von Mises yield criterion. For thin-walled cylinders, the von Mises flow solution of burst pressure in Equation (2C.179) was recommended. For thick-walled cylinders, an implicit burst pressure solution in an integral equation (2C.176) was recommended. But this integral equation is inconvenient to use in practice. It is well known that the classic plasticity theory includes the Tresca and von Mises yield criteria, with the Tresca criterion predicting a lower bound solution and the von Mises criteria predicting an upper bound solution. In addition, the present author developed an average shear stress yield criterion that can determine more accurate limit and burst pressures for thin and thick-walled cylinders. This work uses these three yield criteria to evaluate the minimum required wall thickness, MAWP and Svensson burst pressure recommended in the API 579 code.

burst pressure

hybridlane (fka CV-DV Quantum Circuit API)

This software package will abstract building a CV-DV quantum circuit for simulation and running on hardware. Existing simulation software each has their own API. This software intends to define a common API to be executed on several simulation and physical hardware backends.

Stavenger, Tim [Pacific Northwest National Laborat

RouteE API

This is the API endpoint for RouteE energy prediction, which can be used to get both single vehicle link or route energy estimates and transportation network-wide energy consumption estimates for a variety of vehicles. This enables external researchers and transportation engineers to access and utilize NLR's growing library of pre-trained vehicle models for prediction of transportation energy consumption. This API provides three endpoints: - /route: Energy estimation of a vehicle over a planning link or sequence of links (route). - /network: Network-wide estimation of energy consumption for all vehicle traffic in the desired area. - /compass: Energy-optimal “eco-routing” between input origin and destination coordinates (Currently in beta for Denver metro area only).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI

Evaluation of Maximum Allowable Working Pressure and Svensson Burst Pressure Recommended in API 579-1 2021 Edition

ABSTRACT API 579-1/ASME FFS-1 2021 Edition provides the minimum wall thickness, the maximum allowable working pressure (MAWP), and the membrane stress equations for thin and thick-walled cylindrical shells subject to internal pressure in Section 2C.3.3.1 of Appendix 2C – Thickness, MAWP, and Stress Equations for an FFS Assessment. The minimum wall thickness and MAWP are determined using the hoop stress and the Tresca yield criterion. Section 2C.7 – Estimation of Burst Pressure newly added the Svensson method for calculating burst pressure of cylindrical shells under internal pressure, where the plastic yielding is characterized by the von Mises yield criterion. For thin-walled cylinders, the von Mises flow solution of burst pressure in Equation (2C.179) was recommended. For thick-walled cylinders, an implicit burst pressure solution in an integral equation (2C.176) was recommended. But this integral equation is inconvenient to use in practice. It is well known that the classic plasticity theory includes the Tresca and von Mises yield criteria, with the Tresca criterion predicting a lower bound solution and the von Mises criteria predicting an upper bound solution. In addition, the present author developed an average shear stress yield criterion that can determine more accurate limit and burst pressures for thin and thick-walled cylinders. This work uses these three yield criteria to evaluate the minimum required wall thickness, MAWP and Svensson burst pressure recommended in the API 579 code.

burst pressure

Reinforcement expectation in the honeybee ( Apis mellifera ): Can downshifts in reinforcement show conditioned inhibition?

When animals learn the association of a conditioned stimulus (CS) with an unconditioned stimulus (US), later presentation of the CS invokes a representation of the US. When the expected US fails to occur, theoretical accounts predict that conditioned inhibition can accrue to any other stimuli that are associated with this change in the US. Empirical work with mammals has confirmed the existence of conditioned inhibition. But the way it is manifested, the conditions that produce it, and determining whether it is the opposite of excitatory conditioning are important considerations. Invertebrates can make valuable contributions to this literature because of the well-established conditioning protocols and access to the central nervous system (CNS) for studying neural underpinnings of behavior. Nevertheless, although conditioned inhibition has been reported, it has yet to be thoroughly investigated in invertebrates. Here, we evaluate the role of the US in producing conditioned inhibition by using proboscis extension response conditioning of the honeybee (Apis mellifera). Specifically, using variations of a “feature-negative” experimental design, we use downshifts in US intensity relative to US intensity used during initial excitatory conditioning to show that an odorant in an odor–odor mixture can become a conditioned inhibitor. We argue that some alternative interpretations to conditioned inhibition are unlikely. However, we show variation across individuals in how strongly they show conditioned inhibition, with some individuals possibly revealing a different means of learning about changes in reinforcement. We discuss how the resolution of these differences is needed to fully understand whether and how conditioned inhibition is manifested in the honeybee, and whether it can be extended to investigate how it is encoded in the CNS. It is also important for extension to other insect models. In particular, work like this will be important as more is revealed of the complexity of the insect brain from connectome projects.

60 APPLIED LIFE SCIENCES

Secure API-Driven Research Automation to Accelerate Scientific Discovery

The Secure Scientific Service Mesh (S3M) provides API-driven infrastructure to accelerate scientific discovery through automated research workflows. By integrating near real-time streaming capabilities, intelligent workflow orchestration, and fine-grained authorization within a service mesh architecture, S3M enables secure and flexible programmatic access to high performance computing (HPC) resources. This framework allows intelligent agents and experimental facilities to dynamically provision resources and execute complex workflows, accelerating experimental lifecycles, and enabling AI-augmented autonomous science. S3M establishes a modern foundation for scientific computing infrastructure that significantly reduces traditional barriers between researchers, computational resources, and experimental facilities.

Skluzacek, Tyler [ORNL] (ORCID:0000000322424931)

Risks Associated with Sharing the MOSSAIC APIs

The MOSSAIC APIs contain two files which, in theory, could be used to discover information about the pathology report data from the SEER registries on which the AI models were trained. In this document, we explain the contents of these files and assess the associated risk. APPENDIX A contains a set of slides to aid in the dissemination of this information.

97 MATHEMATICS AND COMPUTING

Petrographic and Advanced Geologic Characterization Report on One Earth Energy #1 (API# 1211325373)

The One Earth Energy #1 (OEE1, API 1211325373) well was drilled to a depth of 7,099 feet from the Pennsylvanian bedrock to the Precambrian granite. In total, 99 thin sections were taken from Rotary Sidewall Core (RSWC) from 2,275 feet to 6,903 feet; 59 thin sections were taken from Whole Core (WC) from 4,311.5 to 6,519.2 feet for this report. This report details specifically thin section point-counting analysis that includes mineralogical and pore space analysis, including grain size analysis annotated thin section photomicrographs, scanning electron microscopy (SEM) with energy dispersive X-ray spectroscopy (EDS), and statistics of grain size analysis on Mount Simon thin sections from OEE1. Characterized units include the St. Peter Sandstone, Eminence Formation, Potosi Dolomite, Franconia Formation, Davis Member, Ironton Sandstone, Galesville Sandstone, Eau Claire Formation, Elmhurst Sandstone, Mt. Simon Sandstone, and Argenta Formation.

09 BIOMASS FUELS

Petrographic and Advanced Geologic Characterization Report on Lively Grove #1 (API# 1218924947)

Lively Grove #1 (LG1 API number 1218924947) well was drilled to a depth of 5,758 feet, from the Glen Dean Limestone to the top of the Precambrian unit. In total, 49 thin sections were taken from Rotary Sidewall Core (RSWC), and one thin section was taken from Whole Core (2,918 feet, New Albany Shale) from 1,700 to 5,872 feet for this report. This report details specifically thin section point-counting analysis that includes mineralogical and pore space analysis, including grain size analysis annotated thin section photomicrographs, scanning electron microscopy (SEM) with Energy Dispersive x-ray Spectroscopy (EDS), X-ray Diffraction (XRD), statistics of grain size analysis on St. Peter Sandstone thin sections, and Argon-Argon (Ar-Ar) dating on Precambrian samples from LG1. Characterized units include the Salem Limestone, New Albany Shale, Trenton Group, Joachim Dolomite, St. Peter Sandstone, Everton Formation, Eminence Formation, Davis Member, Eau Claire Formation, and Precambrian Basement.

01 COAL, LIGNITE, AND PEAT

Redesign of the Timeline Generator at Fermilab using a web-based Flutter Application, GraphQL API and an IOC

Redesign of the Timeline Generator at Fermilab using a web-based Flutter application, GraphQL API and an IOC ABSTRACT = The control system at Fermilab is undergoing an evolution with a shift towards web-based applications with connections to the EPICS infrastructure. The Timeline Generator (TLG) is an application that serves to coordinate events across the lab using different timing links. These links include the Tevatron clock (TCLK), a 10 MHz serial link with events encoded at 20Hz and Ma-chine Data (MDAT), a communication link with states encoded at 720Hz. This paper covers the redesign of the major components of the TLG. This includes a web-based Flutter application for building timelines. A placement service is in use that has a GraphQL interface and uses a timeline input to compute a schedule of events and states. The Flutter application sends this computed schedule to the TLG IOC via a GraphQL interface to the Data Pool Manager (DPM). The TLG IOC runs on an Arria FPGA, the Accelerator Clock Generator (ACLK-GEN), which is responsible for writing the events and states on to the different timing links.

Carmichael, Linden [Fermilab]

Evi-Pro Lite API

This application programing interface provides output from NLR's EVI-Pro model and is used to power the EVI-Pro Lite tool at https://afdc.energy.gov/evi-pro-lite. These endpoints provide daily (24-hour) fleet-level charging load profiles for a variety of customizable scenarios.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI

Redesign of the Timeline Generator at Fermilab using a web-based Flutter application, GraphQL API and an IOC

The control system at Fermilab is undergoing an evolution with a shift towards web-based applications with connections to the EPICS infrastructure. The Timeline Generator (TLG) is an application that serves to coordinate events across the lab using different timing links. These links include the Tevatron clock (TCLK), a 10 MHz serial link with events encoded at 20Hz and Machine Data (MDAT), a communication link with states encoded at 720Hz. This paper covers the redesign of the major components of the TLG. This includes a web-based Flutter application for building timelines. A placement service is in use that has a GraphQL interface and uses a timeline input to compute a schedule of events and states. The Flutter application sends this computed schedule to the TLG IOC via a GraphQL interface to the Data Pool Manager (DPM). The TLG IOC runs on an Arria FPGA, the Accelerator Clock Generator (ACLK-GEN), which is responsible for writing the events and states on to the different timing links.

Carmichael, Linden [Fermilab]