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DOE OSTI2021

Rapid Automated Annotation and Analysis of N-Glycan Mass Spectrometry Imaging Data Sets Using NGlycDB in METASPACE

Imaging N-glycan spatial distribution in tissues using mass spectrometry imaging (MSI) is emerging as a promising tool in biological and clinical applications. However, there is currently no high throughput tool for visualization and molecular annotation of N-glycans in MSI data, which significantly slows down data processing and hampers the applicability of this approach. In this work, we present how METASPACE, an open-source cloud engine for molecular annotation of MSI data, can be used to automatically annotate, visualize, analyze, and interpret high-resolution mass spectrometry-based spatial N-glycomics data. METASPACE is an emerging tool in spatial metabolomics, but the lack of compatible glycan databases has limited its application for comprehensive N-glycan annotations from MSI datasets. We created NGlycDB, a public database of N-glycans, by adapting available glycan databases. We demonstrate the applicability of NGlycDB in METASPACE by analyzing MALDI-MSI data from formalin-fixed paraffin-embedded (FFPE) human kidney and mouse lung tissue sections. We added NGlycDB to METASPACE for public use, thus facilitating applications of MSI in glycobiology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Invited: Bambu: an Open-Source Research Framework for the High-Level Synthesis of Complex Applications

This paper presents the open-source High-Level Synthesis research framework Bambu. The framework provides an open-source starting point to experiment with new ideas across High-Level Synthesis, high-level verification and debugging, FPGA/ASIC design, design flow space exploration, and parallel hardware accelerator design. The tool accepts as input standard C/C++ specifications and compiler intermediate representations (IRs) coming from the well-known Clang/LLVM and GCC com- pilers. The broad spectrum and flexibility of input formats allow the electronic design automation (EDA) research community to explore and integrate new transformations and optimizations. The easily extendable modular framework already includes many op- timizations and HLS benchmarks. The integration with synthesis and verification backends (commercial and open-source) allows researchers to quickly test any new finding and easily obtain performance and resource usage metrics for a given application. Different FPGA devices are supported from several different vendors: AMD/XILINX, Intel/Altera, Lattice Semiconductor, and NanoXplore. Finally, integration with the OpenRoad open-source end-to-end silicon compiler perfectly fits with the recent push towards open-source EDA.

Ferrandi, Fabrizio↗

DOE OSTI2026

DTLMod: A simulation framework for in situ workflow optimization

In situ processing workflows have become essential for coping with the explosion in data volume and velocity in large-scale scientific computing, providing domain scientists with early insights at runtime. Multiple frameworks implement this paradigm through a data transport layer (DTL), offering different data access modes and deployment schemes, but researchers currently lack the appropriate tools to assess design and deployment options before committing to costly real experiments. We introduce DTLMod, an open-source simulated DTL that enables performance evaluation of in situ workflow configurations at scale. Built on SimGrid, it links into any SimGrid-based simulator and is available in C++ and Python. We evaluate DTLMod along four axes: scalability (tens of thousands of simulated processes across interconnected clusters in seconds, with linear memory scaling), versatility (three implementation variants trading fidelity for speed), accuracy (simulated times faithfully reflecting real behavior), and practical utility (two use cases demonstrating evidence-based workflow design decisions).

Suter, Fred [ORNL] (ORCID:0000000319021955)↗

DOE OSTI2025

STREAM: A technology planning and capacity expansion model for the industrial sector

The Strategic Technology Roadmapping and Energy, Environmental, and Economic Analysis Model—STREAM—is an optimization-based modeling tool and analysis framework to assist with strategic planning and technology investments of the industrial sector. This open-source framework is written in Julia using the JuMP package, which enables users to model future “pathways” for incumbent and future production technologies, costs, fuels and energy carriers, and energy and non-energy environmental impacts from industries as they transform in pursuit of a robust and competitive manufacturing sector. The model starts with an initial stock of industrial production technologies and assets at a facility level and then determines pathways that minimize cost, subject to an array of possible constraints on demand, market shares, environmental flows, and other exogenously specified operational considerations such as capacity utilization rates or regional energy costs. Key features of the framework include flexibility to model a wide range of industries and industrial technologies/processes at varying levels of granularity, ability to perform parametric sensitivity analyses, and ability to visualize model results using visualization objects.

capacity expansion↗

DOE OSTI2021

Highly Extensible X-ray Diffraction Toolkit

This code has been previous released as open source under LLNL-CODE-529294. The HEXRD program comprises a library of X-ray diffraction analysis tools and a stand-alone GUI application. While there are many software packages that provide similar capabilities, HEXRD was designed to provide an extremely flexible and extensible basis for describing a broad array of X-ray diffraction instruments; this includes both mono- and poly-chromatic modalities as well as poly- and single-crystal samples. The high-level objects include Material: an abstraction for defining crystalline materials, including unit cell parameters and anisotropic elastic moduli Imageseries: an interface for series of diffraction images containing one or more frames, including provisions for metadata. Instrument: an abstraction of an X-ray diffraction instrument including support for the definition of multiple detector elements as well as powder, Laue, and mono-chromatic single/multi-grain diffraction analysis modalities (including attendant calibration routines). The hexrdgui package is a standalone PySide2/Qt5 GUI built on top of hexrd. The 0.8.1 release includes various bug fixes as well as some new functionality in the GUI, including: o Enhancements to the import tools for LLNL diffraction instruemtns (PXRDIP and TARDIS) o The ability to save 1-d LeBail fits of integrated diffraction spectra.

Barton, NathanR.↗

DOE OSTI2024

datacenterCoolingModel

ExaDigiT is a framework for developing comprehensive digital twins of liquid-cooled supercomputers, which has three main modules: (1) a python-based Resource Allocator and Power Simulator (RAPS), (2) a Modelica-based Thermo-Fluidic cooling model, and (3) a C++-based augmented reality model built on Unreal Engine 5. The Modelica-based cooling model is primarily built-on the open-source Transient Simulation Framework of Reconfigurable Models (TRANSFORM) library and the open-source autocsm library. The library follows the templating architecture developed in the TRANSFORM and the autocsm libraries. This tool can be easily extended to model other Frontier-like liquid cooled supercomputers.

Kumar, Vineet [Oak Ridge National Laboratory (ORNL↗

DOE OSTI2025

OPET Control (Open PV Electrical Tool Control Software) [SWR-25-44]

Software interface for controlling and collecting data from the Open PV Electrical Tool (OPET) device. This repository contains everything relating to the control of the OPET device including source code. If you are looking for the hardware or firmware software repositories, links are below: https://github.com/NREL/opet-hardware https://github.com/NREL/opet-firmware

McDanold, Byron [National Renewable Energy Laborat↗

DOE OSTI2025

Ghidra Galore

SAND2025-00232O Ghidra Galore is a software tool that provides a test harness for running an analysis script in multiple versions of Ghidra, an open-source binary disassembler, using Docker. It allows users to understand how different versions of Ghidra evolve over time by analyzing a corpus of input files. The software includes a Python script that wraps the Docker functionality, simplifying the process of running the analysis script across different Ghidra versions. 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.

Crussell, Jonathan [Sandia National Lab. (SNL-CA),↗

DOE OSTI2021

Review of WEC-Sim Development and Applications

WEC-Sim (Wave Energy Converter Simulator) is an open-source code for simulating wave energy converters that has been actively developed and applied to simulate a wide variety of device archetypes, and has become a popular tool since its release. This paper reviews the development efforts and usage of WEC-Sim. The publications considered in this study have been broken down into six topic areas, namely, feature development, experimental validation, device modelling, control modelling, powertake-off (PTO) and grid modelling, and novel applications, which includes some non-wave energy applications. This review paper also recognizes the contributions of academic researchers and technology developers from around the world toward the broader WEC-Sim development effort. The growing number of external applications of WEC-Sim demonstrates a broader acceptance of the open-source code, and the ways WEC-Sim has been used in certain topic areas also highlight potential future development needs.

applications↗

DOE OSTI2021

PBjam: A Python Package for Automating Asteroseismology of Solar-like Oscillators

Asteroseismology is an exceptional tool for studying stars using the properties of observed modes of oscillation. So far the process of performing an asteroseismic analysis of a star has remained somewhat esoteric and inaccessible to nonexperts. In this software paper we describe PBjam, an open-source Python package for analyzing the frequency spectra of solar-like oscillators in a simple but principled and automated way. The aim of PBjam is to provide a set of easy-to-use tools to extract information about the radial and quadropole oscillations in stars that oscillate like the Sun, which may then be used to infer bulk properties such as stellar mass, radius, age, or even structure. Asteroseismology and its data analysis methods are becoming increasingly important as space-based photometric observatories are producing a wealth of new data, allowing asteroseismology to be applied in a wide range of contexts such as exoplanet, stellar structure and evolution, and Galactic population studies.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Large-Eddy Simulations of Idealized Atmospheric Boundary Layers Using Nalu-Wind

Accurate prediction of wind-plant performance relies, in part, on properly characterizing the turbulent atmospheric boundary layer (ABL) flow in which wind turbines operate. Large-eddy simulation (LES) is a powerful tool for simulating ABLs because it resolves the largest, most energetic scales of three-dimensional turbulent motions. Yet LES predictions are well known to depend on modeling choices such as grid resolution, numerical discretization schemes, and closures for unresolved scales of turbulence. Here, we evaluate how these choices influence predictions of ABL winds using Nalu-Wind, a wind-specific fork of the open-source, generalized, unstructured, massively parallel flow solver NaluCFD/Nalu.

17 WIND ENERGY↗

DOE OSTI2026

rustpix

rustpix is a high-performance, open-source Rust library with first-class Python bindings (via PyO3) for processing pixel-detector data in neutron imaging. It targets time-stamping detectors such as Timepix3 (TPX3) at ORNL's Spallation Neutron Source (VENUS beamline), where each detected neutron deposits charge across a cluster of pixels within a very high-rate event stream (96M+ hits/sec). rustpix parses TPX3 event data in parallel using memory-mapped I/O, offers four interchangeable clustering algorithms (ABS adjacency-based search, DBSCAN, graph/union-find connected components, and a parallel grid method), and extracts weighted, super-resolved centroids to produce neutron-event lists. A streaming architecture lets it process files larger than available memory. rustpix is distributed as a pip-installable Python package (with NumPy integration), Rust crates, a command-line tool, and an interactive GUI; it writes HDF5, Apache Arrow, and CSV; and it is designed to extend to TPX4 and other detector types. Released as open-source under the MIT License.

Zhang, Chen [Oak Ridge National Laboratory (ORNL),↗

DOE OSTI2022

Cooperative Research and Development Agreement between National Energy Technology Laboratory and Gas Technology Institute (Abstract)

Hydrogen has the potential to play an important role in decarbonizing energy-intensive sectors, and credible and open-source protocols are needed to vet the environmental credibility of a specific production pathway, given the variability even among the same technologies. Stakeholders and markets lack consistent, transparent, technical tools and protocols to assess the carbon intensity of hydrogen production at the asset level. Gas Technology Institute (GTI) and S&P Global Platts have launched the Open Hydrogen Initiative (OHI), a new collaboration focused on brining industry within the hydrogen marketplace together to provide further transparency into the environmental greenhouse gas (GHG) impact of hydrogen production. As part of this initiative, GTI has invited NETL to participate in the effort because of NETL’s deep expertise and capabilities in Life Cycle Analysis. Therefore, NETL is joining forces with the Gas Technology Institute (GTI) to build a measurement tool, accompanying protocols, and confidence score of the quality of the measurement. This CRADA effort provides the technical research collaboration support with GTI that will be used in the broader Open Hydrogen Initiative that can provide stakeholders the technical tools and protocols to decarbonize energyintensive sectors.

08 HYDROGEN↗

DOE OSTI2021

A systems engineering framework for the optimization of food supply chains under circular economy considerations

The current linear “take-make-waste-extractive” model leads to the depletion of natural resources and environmental degradation. Circular Economy (CE) aims to address these impacts by building supply chains that are restorative, regenerative, and environmentally benign. This can be achieved through the re-utilization of products and materials, the extensive usage of renewable energy sources, and ultimately by closing any open material loops. Such a transition towards environmental, economic and social advancements requires analytical tools for quantitative evaluation of the alternative pathways. Here, in this work, we present a novel CE system engineering framework and decision-making tool for the modeling and optimization of food supply chains. First, the alternative pathways for the production of the desired product and the valorization of wastes and by-products are identified. Then, a Resource-Task-Network representation that captures all these pathways is utilized, based on which a mixed-integer linear programming model is developed. This approach allows the holistic modeling and optimization of the entire food supply chain, taking into account any of its special characteristics, potential constraints as well as different objectives. Considering that typically CE introduces multiple, often conflicting objectives, we deploy here a multi-objective optimization strategy for trade-off analysis. A representative case study for the supply chain of coffee is discussed, illustrating the steps and the applicability of the framework. Single and multi-objective optimization formulations under five different coffee-product demand scenarios are presented. The production of instant coffee as the only final product is shown to be the least energy and environmental efficient scenario. On the contrary, the production solely of whole beans sets a hypothetical upper bound on the optimal energy and environmental utilization. In both problems presented, the amount of energy generated is significant due to the utilization of waste generated for the production of excess energy.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2023

Software Citation in HEP: Current State and Recommendations for the Future

In November 2022, the HEP Software Foundation and the Institute for Research and Innovation for Software in High-Energy Physics organized a workshop on the topic of Software Citation and Recognition in HEP. The goal of the workshop was to bring together different types of stakeholders whose roles relate to software citation, and the associated credit it provides, in order to engage the community in a discussion on: the ways HEP experiments handle citation of software, recognition for software efforts that enable physics results disseminated to the public, and how the scholarly publishing ecosystem supports these activities. Reports were given from the publication board leadership of the ATLAS, CMS, and LHCb experiments and HEP open source software community organizations (ROOT, Scikit-HEP, MCnet), and perspectives were given from publishers (Elsevier, JOSS) and related tool providers (INSPIRE, Zenodo). This paper summarizes key findings and recommendations from the workshop as presented at the 26th International Conference on Computing in High Energy and Nuclear Physics (CHEP 2023).

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

STEPS: A Portable Numerical Simulation Toolkit for Electrical Power System Dynamic Studies

Numerical simulation is the key technique for large scale power system analysis. Redistribution of global renewable power via international interconnections requires new simulation tools to study the interconnected systems with different nominal frequencies as a whole. In this paper we introduce an open source simulation toolkit for electrical power systems (STEPS) which is hosted at Github. Its kernel is coded in C++ with major functions of power flow and electro-mechanical dynamic simulation. Flexible options are provided and configurable to improve power flow solution and dynamic simulation. Common devices and models are supported in STEPS for AC/DC hybrid system studies. Studies of interconnected systems with different nominal frequencies is supported in STEPS for research of international interconnection. Application program interfaces are provided and wrapped with Python to enable high-level interfaces for general applications. STEPS is thread safe and parallel computation is supported in both kernel and script levels to accelerate simulation. It is portable and works on Windows and GNU/Linux platforms. Cases from small to large scale systems are thoroughly tested to validate the toolkit with commercial packages as benchmarks.

42 ENGINEERING↗

DOE OSTI2025

Napari-MCP

Napari-MCP connects the open source napari software to modern LLMs. It includes a socket server plugin for napari as well as the MCP tools.

Liu, Shusen [Lawrence Livermore National Laborator↗

DOE OSTI2024

Tools for Water Ingress Testing

The Safety Storage and Engineering Team, as part of the Production Support Services division (PSS-2), is tasked with ensuring the safety of containers used for handling and storage of nuclear materials. As part of this work, water ingress tests are conducted to evaluate the water-tightness of containers intended for in-glovebox use. In collaboration, the statistics group of the Computer and Computational Sciences Division (CCS-6) provided support in developing a statistically defensible approach for determining appropriate sample sizes for water ingress testing. Water ingress testing involves multiple measurements on multiple containers. Our approach uses a simple random effects model to analyze a pilot data set, implementing prediction limits to evaluate the efficacy of collecting additional data. Although this study capitalizes on available data, our approach can be used with estimates of the ratio of between and within variability and average values, often available from past testing or expert knowledge. An interactive Shiny tool was developed as a final user-friendly product for future testing. The Shiny interface is an open-source package providing a framework for building web applications. Raw data exploration and prediction interval-based sample size assessments can quickly be conducted by the engineering team without needing to interact with the underlying code.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗