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DOE OSTI2024

ATCCfinder - Download and Search the ATCC Genome Portal

Much strain-specific sequence data exists in research conducted before the deployment of large sequencing repositories, making it challenging to identify and validate the identity of strains used in these studies through bioinformatics and phenotyping. The American Type Culture Collection (ATCC) is an organization that sells a wide variety of microbes with strain-level taxonomy classification and associated sequenced reference genomes. Currently, ATCC does not provide a method for searching for sequence similarity between a query sequence and their database of reference genomes. Here I propose the software ATCCfinder, which utilizes ATCC application interface software (API) to generate query-able databases from ATCC Genome resources.

Koehler, Samuel↗

DOE OSTI2023

BUTTER-Clarifier [SWR-23-61]

This repository contains a python package of neural network interpretability techniques (interpretability) and a keras callback to easily compute and capture data related to these techniques (values metrics) during training. It was developed to be used with NREL's BUTTER Deep Learning Experimental Framework, but does not depend on this framework and may be useful to projects outside of this framework. The vision for this codebase is to collect algorithms for explainable artificial intelligence (XAI) in a single framework that is easy to use, easy to read, and can be expand upon. Here, we package XAI algorithms into a module called "metrics", which are implemented as python functions. The return type of a metric is typically a dictionary holding data of multiple data types, such as real values and numpy matrices. Callbacks and any other connector code is provided as necessary in a separate module to make these metrics more easily usable. This project depends on Tensorflow's Keras API, although it would be nice to try and support multiple backends one day. Related to: https://github.com/NREL/BUTTER-Empirical-Deep-Learning-Experimental-Framework

Perr-Sauer, Jordan↗

DOE OSTI2024

Database Manager for use with PLEXOS XML files [SWR-24-90]

This software is an API for create and modify XML that are used for Plexos. DISCLAIMER: PLEXOS is a registered trademark of Energy Exemplar Pty Ltd ("Owner"). Owner has no affiliation to or participation in this software. Reference herein to any specific commercial products, process, or service by trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or Alliance for Sustainable Energy, LLC ("Alliance"). The views and opinions of authors expressed in the available or referenced documents do not necessarily state or reflect those of the United States Government or Alliance.

Sanchez Perez, Pedro Andres↗

DOE OSTI2021

Role-Based Access Control for Distributed Energy Resources v.1.0

The Role-Based Access Control (RBAC) for Distributed Energy Resources (DER) software is an automated and transparent stack for RBAC administrators to interact with RBAC policy. The package includes demonstrations of centralized and decentralized RBAC implementation. Both include simulated DER entities that are stored automatically in a centralized Lightweight Directory Access Protocol (LDAP) server. It also includes a REST-API to serve the HTTP requests of the RBAC administrators. A complete front-end is included to serve the users' needs. This software may be used by industry (DER vendors/utilities) as well as the research community to determine if a centralized or decentralized solution fits better the needs of an RBAC model in a DER environment. Additionally, parts of this software may be useful for developing implementations for specific needs. 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. SAND2021-8292 O

Johnson, Jay↗

DOE OSTI2024

Dispatch Optimization Variable Engine

The Dispatch Optimization Variable Engine (DOVE) is software tool written in python, developed at Idaho National Laboratory (INL) that provides an easily accessible application-programming-interface (API) to performing resource dispatch optimization analysis for integrated energy system (IES) configurations. DOVE is an integral part of the Framework for Optimization of Resources and Economics (FORCE) software suite and is leveraged by codes such as the Holistic Energy Resource Optimization Network (HERON) and the Optimization of Real-Time Capacity Allocation (ORCA). The philosophy behind DOVE is to provide a modular software solution to IES planning and operation by utilizing state-of-the-art algorithms and machine learning. The goal is to accurately capture the dispatching behavior of a complex energy system given varying time-dependent signals for demand and commodity pricing.

McDowell, DylanJ. [Idaho National Laboratory (INL)↗

DOE OSTI2024

certified

The missing certificate infrastructure for web APIs.

Rogers, DavidM [Oak Ridge National Laboratory (ORN↗

DOE OSTI2025

PNNL-Predictive-Phenomics/ProCaliper

ProCaliper is a Python library that curates, organizes, and computes protein structure features in a way that easily interfaces with user-provided experimental data. It extracts or computes protein binding site, active site, charge, pLDDT (order/disorder), acid dissociation, protonation, solvent accessible surface area, disulfide bond distance, and protein secondary structure data using precomputed protein structures and publicly available databases. It provides a unified API for integrating additional residue-level data and for visualizing residue features in 3D.

Rozum, Jordan [Pacific Northwest National Lab]↗

DOE OSTI2025

tether

Tether is a python module for benchmarking and assessing large language model (LLMs) performance at generic scientific tasks. The code generates benchmarks, uses the benchmark to prompt LLMs through automatic programming interfaces (APIs), and then logs the number of prompts an LLM correctly answers and presents the results as a completed benchmark.

Kaiser, Bryan [Los Alamos National Laboratory]↗

DOE OSTI2025

NOVA Galaxy Library

The nova-galaxy library provides an abstract API for accessing Galaxy services

Cage, Gregory [Oak Ridge National Laboratory (ORNL↗

DOE OSTI2025

ifbeam

This is a C++ library for acessing the beams database REST api at Fermilab. Example client code is in the demos directory.

Garren, Lynn [Fermi National Accelerator Laborator↗

DOE OSTI2025

libwda

Low level API for IFBeam and other csv data

Mengel, Marc [Fermi National Accelerator Laborator↗

DOE OSTI2025

ChemEcho v1.0

ChemEcho is a tool that converts tandem mass spectra into embeddings used to build machine learning (ML) models with fully explainable predictions. It provides an API for transforming raw tandem mass spectral data into embeddings, along with functions for training and validating ML models. Additionally, it includes utilities for retrieving and cleaning training data. ChemEcho is broadly applicable in ML pipelines that use tandem mass spectra for a variety of tasks, such as chemical classification or bioactivity mining. While there are existing methods to generate embeddings from fragmentation data, ChemEcho's approach ensures that predictions remain interpretable, enabling experts to evaluate results and generate hypotheses about the underlying data.

Harwood, Thomas [Lawrence Berkeley National Labora↗

DOE OSTI2025

BULKI-Store v0.3.2

BULKI-Store is a distributed object storage system optimized for high-performance computing environments. Built with a Rust core and Python bindings, it efficiently manages scientific and machine learning datasets across HPC clusters. The system employs a client-server architecture with MPI integration, enabling seamless scaling on supercomputers like Perlmutter. BULKI-Store's object-oriented approach provides intuitive data organization with rich metadata support, contrasting with traditional file-based solutions. Key optimizations include selective checkpoint loading, unified checkpoint files, and object chunking for large data transfers. For machine learning workloads, BULKI-Store offers advantages through fine-grained access patterns, dynamic data sharing between training instances, and reduced memory pressure. Memory management features include strategic Python GC calls, minimized data copies, and batch processing capabilities. The system leverages Rayon's thread pool for asynchronous data prefetching and supports multiple CPU architectures (ARM64, x86, AMD, RISC-V). By combining performance optimizations with developer-friendly APIs, BULKI-Store addresses the complex data management challenges of modern HPC applications while maintaining compatibility across heterogeneous computing environments.

Zhang, Wei [Lawrence Berkeley National Laboratory ↗

DOE OSTI2021

OpenMC

OpenMC is an open source, community-developed framework for performing Monte Carlo particle transport calculations.It is capable of simulating neutron and photon transport below ~50 MeV and also includes a model for bremsstrahlung production of photons by electrons/positrons. Fixed source, k-eigenvalue, and subcritical multiplication problems can be solved. Problem geometries can be modeled either using constructive solid geometry or a CAD representation. A flexible and efficient tally system enables a wide variety of physical quantities to be tallied and analyzed. OpenMC can run in parallel using a hybrid MPI and OpenMP programming model and has been extensively tested on leadership class supercomputers. A built-in Bateman equation solver enables the modeling of material composition changes due to irradiation. One of the unique features of OpenMC is its rich, extensible Python and C/C++ programming interfaces that enable programming pre- and post-processing, multigroup cross section generation, workflow automation, multiphysics coupling, and the visualization of geometry and tally results. In addition to the core Monte Carlo transport solver and associated APIs, OpenMC includes a Python-based nuclear data interface that enables power users to inspect, modify,and perform various types of nuclear data processing on ENDF, ACE, and OpenMC¿s native HDF5 files

ROMANO, PaulK.↗

DOE OSTI2025

Dirty Word Scanner

SAND2025-09142O Dirty Word Scanner helps prevent the accidental inclusion of sensitive terms by scaning files in repositories to catch "dirty words" before they are committed. While there are existing solutions focused on passwords and API keys, this tool offers additional features tailored to specific security needs. It will function as a standalone tool, incorporating advanced capabilities from similar tools to provide a comprehensive solution. This tool can unpack HDF5 files and examine their contents. It can display image, audio, and visual files to the user and request a manual determination of whether they are safe. It can also detect arbitrary binary files and ask the user to verify that they're safe. The tool enables sophisticated whitelisting of strings and regular expressions for cases where a term is sensitive in certain contexts but not in others. 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.

Gates, Jason [Sandia National Lab. (SNL-CA), Liver↗

DOE OSTI2025

AeroMesh [SWR-25-14]

AeroMesh is a mesher that makes generating finite elements meshes easy. It can accept farm specifications from either a properly formatted YAML file or from an external API call made by another process. It currently supports refinement specifications at the domain, farm, and turbine level in both two and three dimensions.

Allen, Jeffery [National Renewable Energy Laborato↗

DOE OSTI2025

WorkJournalMaker (WJMaker) v0.5

The software generates and maintains daily work journal entries in text format, via a web browser. The journal entries are saved in a structured directory file tree on the system running the software. The software also incorporates a database so that it can track the location of files in the file system and various other metadata. The software allows the users to access their journal entries either through the browser or as discrete text files, facilitating sharing and open science. Additionally, to assist with the yearly PMP process, this tool connects to LLM APIs to provide summarization of the journal entries on a month-by-month or weekly basis. The advantage over similar technologies such as Apple Notes (extremely popular for notetaking) is that the instant software does not force the user to stay inside the Apple ecosystem, since it allows for export of the user's text files. This facilitates open science, so that researchers who use the tool can easily transfer their research notes to any other system. The WebJournalMaker repository is here: https://github.com/lbnl-science-it/WorkJournalMaker The WebJournalMaker repository is forked from the JournalSummarizer: https://github.com/tyfong-lbl/JournalSummarizer and builds on its code. I wrote the code for both of these software repos, using generative AI.

Fong, Timothy [Lawrence Berkeley National Laborato↗

DOE OSTI2025

Responsive Assistant For Navigating And Guiding Engineering With Rigor (ranger)

The bot uses the GitHub API to fetch discussions from a MOOSE repository and store the data in a vector database. When a new discussion is initiated, the algorithm compares the discussion title with the content of all previous discussions (title + discussions) in the database and provides the most relevant posts to the user. The database is updated regularly to include all new posts, potentially on a monthly basis.

Li, Mengnan [Idaho National Laboratory (INL), Idah↗