Elaenia: Automated Error Analysis of Numerical Software
DAHCS Demo day poster for LDRD 25-0103
Pollard, Samuel Douglas [Sandia National Laborator↗
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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Progress toward improving accelerator performance and automating operations with advanced analysis software
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DARHT, Adaptive Machine Learning, Linear Induction↗
AEcroscopy: A Software–Hardware Framework Empowering Microscopy Toward Automated and Autonomous Experimentation
Microscopy has been pivotal in improving the understanding of structure-function relationships at the nanoscale and is by now ubiquitous in most characterization labs. However, traditional microscopy operations are still limited largely by a human-centric click-and-go paradigm utilizing vendor-provided software, which limits the scope, utility, efficiency, effectiveness, and at times reproducibility of microscopy experiments. Here, in this work, a coupled software–hardware platform is developed that consists of a software package termed AEcroscopy (short for Automated Experiments in Microscopy), along with a field-programmable-gate-array device with LabView-built customized acquisition scripts, which overcome these limitations and provide the necessary abstractions toward full automation of microscopy platforms. The platform works across multiple vendor devices on scanning probe microscopes and electron microscopes. It enables customized scan trajectories, processing functions that can be triggered locally or remotely on processing servers, user-defined excitation waveforms, standardization of data models, and completely seamless operation through simple Python commands to enable a plethora of microscopy experiments to be performed in a reproducible, automated manner. This platform can be readily coupled with existing machine-learning libraries and simulations, to provide automated decision-making and active theory-experiment optimization to turn microscopes from characterization tools to instruments capable of autonomous model refinement and physics discovery.
47 OTHER INSTRUMENTATION↗
Automated Vulnerability Detection (AVUD) for Compiled Smart Grid Software
This project developed and implemented a system for conducting cybersecurity vulnerability detection of smart grid components and systems by performing static analysis of compiled software (“firmware”). The resulting system for automated vulnerability detection (AVUD) was implemented as part of Oak Ridge National Laboratory’s existing test bed for smart meters, the Sustainable Campus Initiative. The work consisted of two phases: the first phase implemented the necessary software and computational models to perform the analysis, and the second phase demonstrated the system on example firmware in partnership with smart meter manufacturer Sensus USA, Inc. The resulting system won an R&D 100 award and has been successfully commercialized, winning a National Laboratory Consortium Commercialization Award.
97 MATHEMATICS AND COMPUTING↗
AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry–mass spectrometry
Abstract Motivation Ion mobility spectrometry (IMS) separations are increasingly used in conjunction with mass spectrometry (MS) for separation and characterization of ionized molecular species. Information obtained from IMS measurements includes the ion’s collision cross section (CCS), which reflects its size and structure and constitutes a descriptor for distinguishing similar species in mixtures that cannot be separated using conventional approaches. Incorporating CCS into MS-based workflows can improve the specificity and confidence of molecular identification. At present, there is no automated, open-source pipeline for determining CCS of analyte ions in both targeted and untargeted fashion, and intensive user-assisted processing with vendor software and manual evaluation is often required. Results We present AutoCCS, an open-source software to rapidly determine CCS values from IMS-MS measurements. We conducted various IMS experiments in different formats to demonstrate the flexibility of AutoCCS for automated CCS calculation: (i) stepped-field methods for drift tube-based IMS (DTIMS), (ii) single-field methods for DTIMS (supporting two calibration methods: a standard and a new enhanced method) and (iii) linear calibration for Bruker timsTOF and non-linear calibration methods for traveling wave based-IMS in Waters Synapt and Structures for Lossless Ion Manipulations. We demonstrated that AutoCCS offers an accurate and reproducible determination of CCS for both standard and unknown analyte ions in various IMS-MS platforms, IMS-field methods, ionization modes and collision gases, without requiring manual processing. Availability and implementation https://github.com/PNNL-Comp-Mass-Spec/AutoCCS. Supplementary information Supplementary data are available at Bioinformatics online. Demo datasets are publicly available at MassIVE (Dataset ID: MSV000085979).
47 OTHER INSTRUMENTATION↗
Implementation of Plot File Testing in the DYNA3D/ParaDyn Software Quality Assurance Suite
Automated testing of DYNA3D/ParaDyn plot files was added to the DYNA3D/ParaDyn software quality assurance (SQA) test suite. The new capability extracts select data from the plot files generated during each verification run and compares it to the same baseline answers used to verify the problem. Deviations between baseline answers and plot file values are reported in the same manner as solution discrepancies, and differences in precision levels between the baseline answers and plot file results are accounted for. The new testing leverages the existing SQA test suite framework and test problems and the Python Mili reader and minimally increases the overall run time (< 5%) of the SQA test suite. This new capability provides incremental end-toend testing of the most common DYNA3D/ParaDyn simulation workflows.
42 ENGINEERING↗
Automated Credibility Assessments of User Features in Scientific Software
Scientific software (SciSoft) is complex, often containing a mixture of production capabilities co-mingled with features under active research and development. Furthermore, SciSoft is often developed over decades by non-computer scientists who may not have a strong background in or prioritize software architecture design, testing, and quality (e.g., test coverage). These conditions lead to difficulty in understanding which software components or functions implement what user-facing features and therefore those features’ software quality pedigree. This lack of understanding poses challenges in assessing readiness and credibility of user features, and often relies on a SciSoft subject matter expert’s (SME) laborious investigation and assertion. This final report of a one-year Computing and Information Sciences Lab Directed Research and Development project presents a general framework for modeling SciSoft architecture as a direct relationship between user features and the software components/functions that implement them. Our approach leverages automated labeling of the SciSoft’s regression test suite and employs machine learning algorithms to construct the architecture model. We demonstrate this framework on the Solid Mechanics component of the SIERRA multi-physics engineering analysis suite developed at Sandia National Laboratories.
97 MATHEMATICS AND COMPUTING↗
Optical emissivity dataset of multi-material heterogeneous designs generated with automated figure extraction
Optical device design is typically an iterative optimization process based on a good initial guess from prior reports. Optical properties databases are useful in this process but difficult to compile because their parsing requires finding relevant papers and manually converting graphical emissivity curves to data tables. Here, we present two contributions: one is a dataset of thermal emissivity records with design-related parameters, and the other is a software tool for automated colored curve data extraction from scientific plots. We manually collected 64 papers with 176 figures reporting thermal emissivity and automatically retrieved 153 colored curve data records. The automated figure analysis software pipeline uses Faster R-CNN for axes and legend object detection, EasyOCR for axes numbering recognition, and k-means clustering for colored curve retrieval. Additionally, we manually extracted geometry, materials, and method information from the text to add necessary metadata to each emissivity curve. Finally, we analyzed the dataset to determine the dominant classes of emissivity curves and determine the underlying design parameters leading to a type of emissivity profile.
47 OTHER INSTRUMENTATION↗
A Python Instrument Control and Data Acquisition Suite for Reproducible Research
Tools that standardize and automate experimental data collection are needed for greater confidence in research results. The National Synchrotron Light Source-II (NSLS-II) has generated an open-source Python data acquisition, management, and analysis software suite that automates X-ray experiments and collects an experimental record that facilitates complete reproducibility. Here, we show that the NSLS-II tools are not only useful for X-ray science at large-scale facilities by presenting an add-on package that adapts these tools for use in a small laboratory with common physics and electrical engineering instruments. The composite software suite eases and automates the execution of experiments, records extensive metadata, stores data in portable containers, and speeds up the analysis through tools for comprehensive searches. In total, this software suite increases the reproducibility of laboratory experiments. We demonstrate the software via the evaluation of two lock-in amplifiers-the miniature ADA2200 and the ubiquitous Stanford Research Systems (SRS) SR810. The frequency resolution, signal-to-noise ratio, and dynamic reserve of the lock-in amplifiers are measured and presented. The usage of the software suite is described throughout these measurements so that the reader can implement the tools in their lab.
97 MATHEMATICS AND COMPUTING↗
TranSyT , an innovative framework for identifying transport systems
The importance and rate of development of genome-scale metabolic models have been growing for the last few years, increasing the demand for software solutions that automate several steps of this process. However, since TRIAGE’s release, software development for the automatic integration of transport reactions into models has stalled. Here, in this paper, we present the Transport Systems Tracker (TranSyT). Unlike other transport systems annotation software, TranSyT does not rely on manual curation to expand its internal database, which is derived from highly curated records retrieved from the Transporters Classification Database and complemented with information from other data sources. TranSyT compiles information regarding transporter families and proteins, and derives reactions into its internal database, making it available for rapid annotation of complete genomes. All transport reactions have GPR associations and can be exported with identifiers from four different metabolite databases. TranSyT is currently available as a plugin for merlin v4.0 and an app for KBase.
59 BASIC BIOLOGICAL SCIENCES↗
Autosampler software
control software for an automated liquid chromatography sample injection and separation system. It is related to a PNNL invention report 31630-E, Method for direct delivering trace samples from smallsize wells to liquid chromatography and mass spectrometry. The main purpose of the control software is to enable automated sample injection from a nanowell device.
Liyu, Andrey↗
Automated reaction kinetics and network exploration (Arkane): A statistical mechanics, thermodynamics, transition state theory, and master equation software
The open-source statistical mechanics software described here, Arkane–Automated Reaction Kinetics and Network Exploration–facilitates computations of thermodynamic properties of chemical species, high-pressure limit reaction rate coefficients, and pressure-dependent rate coefficient over multi-well molecular potential energy surfaces (PES) including the effects of collisional energy transfer on phenomenological kinetics. Arkane can use estimates to fill in information for molecules or reactions where quantum chemistry information is missing. The software solves the internal energy master equation for complex unimolecular reaction systems. Inputs to the software include converged electronic structure computations performed by the user using a variety of supported software packages (Gaussian, Molpro, Orca, TeraChem, Q-Chem, Psi4). The software outputs high-pressure limit rate coefficients and pressure-dependent phenomenological rate coefficients, as well as computed thermodynamic properties (enthalpy, entropy, and constant pressure heat capacity) with added energy corrections. Some of the key features of Arkane include treatment of 1D, 2D or ND hindered internal rotation modes, treatment of free internal rotation modes, quantum tunneling effect consideration, transition state theory (TST) and Rice-Ramsperger-Kassel-Marcus (RRKM) rate coefficient computations, master equation solution with four implemented methods, inverse-Laplace transform of high-pressure limit rate coefficients into the energy domain, energy corrections based on bond-additivity or isodesmic reactions, automated and efficient PES exploration, and PES sensitivity analysis. The present work describes the design of Arkane, how it should be used, and refers to the theory that it employs. Arkane is distributed via the RMG-Py software suite (https://github.com/ReactionMechanismGenerator/RMG-Py).
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Numerical Modeling and Optimization of the iProTech Pitching Inertial Pump (PIP) Wave Energy Converter (WEC) (Cooperative Research and Development Final Report, CRADA Number: CRD-22-22968)
This work generated a first-of-its-kind automated workflow to couple time-domain simulations of wave energy converters written in one software language with a set of design generation and evaluation scripts written in another software language. This automated workflow used an existing optimization package to analyze the sensitivity of different design parameters on the power output of a specific WEC, iProTech’s Pitching Inertial Pump (PIP). Geometric, inertial, and power take-off variables were all varied and optimized to find values that produced the highest amount of power generated over varying wave conditions. The findings on these parameter sensitivity studies are used to inform future design iterations of the PIP WEC. Including more design variables in the optimizations will only increase computational run time and further software development is needed to analyze a larger optimization.
16 TIDAL AND WAVE POWER↗
American-Made Solar Prize: Edgeli Enables DER Integration (CRADA 615) (Final Report)
The purpose of this project was to demonstrate how granular time series data and automated data transformation, and impact assessment tools could speed interconnection approvals for distributed energy resource projects of various types and sizes. Types included community solar, rooftop solar, and EV charging projects. Using software routines to automate the transformation of data (e.g. GIS) to a network database and power flow model then applying scenarios to create hourly (8760) hosting capacity values and voltage and thermal impacts for specific projects, we were able to demonstrate the feasibility of quickly assembling and analyzing key utility data sets for interconnection purposes. The outcomes of this effort will become the foundation for future work that will enhance and encapsulate the software components developed as part of this project, into web services (e.g. APIs) that can be integrated into queue management systems and automate interconnection screening processes.
14 SOLAR ENERGY↗
R3IT, Rapid Rural Resilient Interconnection Toolkit, Final Technical Report
Utilities nationwide are beginning to experience multiple solar interconnection requests per day. This request volume will soon overwhelm utility engineers, especially at smaller utilities which serve the majority of the landmass of the United States. In this project, we developed open-source software tool that automates the interconnection approval process and removes 80% of the time required to approve an interconnection and hence allow more solar to be quickly and safely integrated with the grid. This software is accompanied by a guidebook detailing interconnection best practices and utility lessons learned. Competing solar interconnection software is extremely expensive at ten times the cost of typical distribution engineering tools, it’s closed source which makes it hard to integrate into utility workflows, and it doesn’t address the hardest power flow modeling challenges of interconnection screening. Our solution was built built with our utility partners who are already experiencing multiple interconnection requests per day and integrates best practices from our past work with DOE and the cooperative community on solar integration. The resulting free and open-source solution has been disseminated through our media channels and conferences that engage over 1,900 utilities nationwide.
14 SOLAR ENERGY↗
DIVA/DeviceEditor v6.1.2
DIVA is an end-to-end DNA design and construction management platform that streamlines how researchers design, build, and receive sequence-verified DNA constructs. Through a web-based BioCAD interface (DeviceEditor), researchers independently design DNA constructs and submit them to a centralized queue with a single action. Designs progress transparently through standardized states which allow researchers to track status and access finished constructs via a central DNA repository. Submitted designs are reviewed by dedicated staff for feasibility and optimization, reducing costly failures and improving downstream execution. Automated DNA assembly software optimizes construction strategies by reusing existing parts where possible and sourcing synthetic DNA only when needed. Standardized, sequence-agnostic assembly methods enable many independent constructs to be built in parallel using lab automation, dramatically increasing throughput. High-throughput next-generation sequencing is used to verify construct accuracy, with flexible platforms selected based on task requirements. Throughout the process, detailed success and failure data are captured and analyzed, enabling continuous improvement of assembly protocols. Compared to traditional, manual DNA construction workflows, DIVA offers higher scalability, transparency, reproducibility, and data-driven optimization.
Plahar, Hector [Lawrence Berkeley National Laborat↗
SparcleQC: Automated Input File Creation for QM/MM Studies of Protein:Ligand Complexes
SparcleQC is a Python package that, given a protein:ligand complex in the Protein Data Bank (PDB) file format, can create quantum mechanics/molecular mechanics (QM/MM)-like input files for the electronic structure theory packages PSI4, QChem, and NWChem. The resulting input files include quantum mechanical representations of the ligand and a small section of the protein, surrounded by point charges that represent the rest of the protein. Creation of these QM/MM input files includes cutting and capping the QM subregion, obtaining point charges for the protein, and adjusting charges at the QM/MM boundary; and each of these tasks are automated by the software. In this article, we describe the details of SparcleQC’s procedure, show examples of the Python API, and explain additional features that are helpful in protein:ligand interaction studies. Finally, we show that SparcleQC enables automated preparation of input files for QM/MM calculations, which can return can return accurate interaction energies in minutes, while a fully quantum mechanical computation on the protein:ligand complex could take days, if it is even possible.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Automation Study For Airworthiness and Program Protection Software
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Computer science↗