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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↗

Catalyst Revised: Rethinking the ParaView in Situ Analysis and Visualization API

As in situ analysis goes mainstream, ease of development, deployment, and maintenance becomes essential, perhaps more so than raw capabilities. In this paper, we present the design and implementation of Catalyst, an API for in situ analysis using ParaView, which we refactored with these objectives in mind. Furthermore, our implementation combines design ideas from in situ frameworks and HPC tools like Ascent and MPICH.

97 MATHEMATICS AND COMPUTING↗

Building Performance Database API (BPD API) v2.1

The Building Performance Database (BPD) is the largest publicly-available source of measured energy performance data for buildings in the United States. It contains information about the building's energy use, location, and physical and operational characteristics. The BPD can be used by building owners, operators, architects and engineers to compare a building's energy efficiency against customized peer groups, identify energy efficiency opportunities, and set energy efficiency targets. It can also be used by energy efficiency program implementers and policymakers to analyze energy efficiency features and trends in the building stock. The BPD compiles data from various data sources, converts it into a standard format, cleanses and quality checks the data, and provides users with access to the data in a way that maintains anonymity for data providers. This software is the database and the Application Programming Interface (API). Users can utilize the BPD's data to develop their own applications using the API. Version 2.1 included a major update for multiple years of data and refactoring of code for faster queries.

Mathew, Paul↗

Building Efficiency Targeting Tool for Energy Retrofits (BETTER) Application Programing Interface (API) (BETTER API) v1.0

The BETTER API allows advanced users and developers to access BETTER's analytical functionalities via HTTP requests from their own software platform without using the BETTER web-interface. API users prepare the input data and analysis configurations in a JSON format and send it to the web application via an HTTP request. The web application runs the analytical workflow on the back end and returns an HTTP response in JSON format. The user can then decide to render the results or further process it.

Szum, Carolyn↗

A verification study of fatigue-based methods in API RP 1183 for estimating fatigue life of pipeline dents

Pipeline dents are mechanical damage caused by a third party in buried pipelines during construction or maintenance repair. Dents are recognized as a leading cause of pipeline failures for both liquid and gas transmission lines, and their assessment and management are critical to pipeline integrity. To meet the industry need, American Institute of Petroleum (API) in 2020 published a recommended practice (RP) 1183 – Assessment and Management of Pipeline Dents. This API code provides the pipeline industry “standard methods” for evaluating severity and fatigue life of pipeline dents with a single peak. This paper performed an initial verification study of fatigue-based methods prescribed in API RP 1183 for estimating fatigue life of pipeline dents. A brief review was first given to the dent fatigue-based methods, including three dent screening methods for estimating dent fatigue life in Sections 7.4.1, 7.4.2, and 7.4.3 of API 1183 and one dent assessment method for predicting fatigue life in Section 8.3.4. In order to verify these fatigue life prediction methods, a set of “standard examples” of dents provided in Annexes A.1 to A.5 of API RP 1183 were utilized in this study to calculate fatigue life, to determine restraint condition, and to evaluate both screening and assessment methods for single-peak dents. Through detailed calculations and comparisons, this study confirmed some specifications of API RP 1183, but also found some self-inconsistences and errors existing in this new API code. Furthermore, this includes the self-inconsistences between three screening methods and the self-inconsistence between the screening and assessment methods. On this basis, recommendations were made on how the operators should use API RP 1183, and what actions API should take to improve this code.

42 ENGINEERING↗

Domain-Specific Type-Safe APIs for Hierarchical Scientific Data with Modern C++

General-purpose library application programming interfaces (APIs) for self-describing hierarchical scientific data storage, such as the HDF5 and NetCDF libraries, are traditionally of runtime nature. Runtime errors for entry existence and data types are typically caught later in the development process of higher-level application-specific APIs. In this paper, we propose exploiting modern C++ metaprogramming features to add compile-time type-safety to improve the interaction with a well-defined metadata-rich scientific schema in domain-specific hierarchical datasets. We tackle two aspects of common use: (i) direct data access, (ii) flexible “in-memory” index models for efficient search and data processing. The proposed APIs use C++17’s template type auto deduction features, C++11’s enum class for type-safety and C-style preprocessor macros for generative templated code. We showcase the pros and cons of our initial work on the standard NeXus schema used for annotating and storing experimental neutron scattering data at several facilities around the world on top of HDF5. Extendable compile-time type-safe APIs are a desirable feature that could be indexed by any modern integrated development environment (IDE). Hence, such APIs can help ease the learning curve for domain scientists using a less error-prone software interaction to enhance the findability of their data without resorting to a domain-specific language (DSL).

Godoy, William↗

ThunderBoltz API

The ThunderBoltz application programming interface (API) code is written in Python and is comprised of a set of tools to facilitate compilation of the ThunderBoltz code, as well as fast assembly and formatting of input files for the ThunderBoltz code, post-processing tools of ThunderBoltz results, plotting tools, and runs/schedules the ThunderBoltz code executable for calculations. The ThunderBoltz API code is utilized for importing and manipulating input cross section sets, input conditions, and any other simulation settings made available within the ThunderBoltz input deck via user-defined settings or via automatic generation. The API comes with a set of plotting capabilities of input cross sections, results from ThunderBoltz, and post-processed results carried out with the API.

Park, Ryan↗

Evaluation of radiation hardness of semiconductor materials against alpha particles for an API detector

An Associated Particle Imaging (API) system consists of a high vacuum chamber where deuterium ions are accelerated on a tritium-loaded target, resulting in alpha particles and neutrons emitted back-to-back, the latter escaping the chamber and used, for example, for tomography of a high-Z sample. An accurate determination of the alpha position is crucial to determine the trajectory of the neutron. Existing API systems have several limitations which a semiconductor-based API detector placed inside the vacuum chamber should not present. The semiconductor material can be either silicon or diamond. In particular, large and fast signals are generated by the alpha interactions in these materials. A pixelated API detector will measure the time and hit position of the alphas produced in the reaction. However, during the lifetime of the generator, the semiconductor detector will be exposed to an intense flux of alpha particles that will degrade its performance over time. To assess the radiation hardness of silicon and diamond against the alpha particles, we exposed single diodes made of either of the two materials to a 5 MeV alpha flux generated by an 241Am radioactive source. During irradiation, the diodes were biased and mounted on current-sensitive preamplifier boards. We have therefore been able to measure insitu the evolution of the waveforms as the damage was accumulating in their substrates.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

OPTIMADE, an API for exchanging materials data

Abstract The Open Databases Integration for Materials Design (OPTIMADE) consortium has designed a universal application programming interface (API) to make materials databases accessible and interoperable. We outline the first stable release of the specification, v1.0, which is already supported by many leading databases and several software packages. We illustrate the advantages of the OPTIMADE API through worked examples on each of the public materials databases that support the full API specification.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

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↗

Preliminary API design to access SG-50 database [Slides]

This presentation details the design and use of a rudimentary example API. The example API reads JSON; eventually it needs to operate with the database. It demonstrates ease in applying powerful, publicly available tools.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Evaluating Recursive Blind Forecast Against API and Baseline: A Puerto Rican Case Study on Solar Irradiance for Normal and Extreme Weather

This paper leverages ongoing work in a community microgrid in Adjuntas, Puerto Rico to forecast global horizontal irradiance (GHI) and compare performance in normal and extreme weather. Given a positive correlation of 0.98 between GHI and PV power, forecasting GHI can be an effective, indirect forecast of photovoltaic (PV) power, especially in microgrids where the end-users, owners, operators, or other stakeholders are reluctant to share data for training or validation due to privacy and security concerns. A recursive one-shot (termed as "blind") forecast is, hence, formulated, wherein a gradient-boosted regression tree (GBR) is built to forecast GHI for a 7-day horizon in normal weather, and a 2-day horizon in extreme weather. To demonstrate its resilience, the architecture is trained on normal and hurricane weather GHI from 2002-2022. It is generalized on February 9-16, 2023, and on the landfall of Hurricane Nicole (Nov 4-5, 2022), respectively. Forecasts from GBR are compared against that from a satellite-based API resource and three baselines: persistence, averaging, and exponential smoothing. Results show GBR and persistence outperform sophisticated API in both types of weather for this case study.

Sundararajan, Aditya↗

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↗

Actor API

This package provides a secure transport layer connecting mini-applications run as components of a server infrastructure. The guiding principle is that mini-apps should be "actors" -- able to expose a set of API calls to the network and to have a shared trust model for knowing who is calling which API function and who takes responsibility for the result.

Rogers, DavidM. [Oak Ridge National Lab. (ORNL), O↗

Scribe Network API v.1.0.0

SAND2023-07864O Scribe Network API is an add-on tool for Scribe3D software. Scribe Network API documents tabletop exercises in trainings and plays back simulated videos of the scenarios and responses. Users can apply the software to compiled projects, or to a simple visual studio project solution package. The software runs a web application that relays information between computers using Scribe3D through a web application, or web app. The web app involves a representational state transfer (REST) application programming interface that handles sending and receiving Scribe save files and an SQL server that stores the save files. This follow-on package allows users to facilitate a networked tabletop exercise. 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.

Noel, Todd↗

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 NREL'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↗