Media Compiler v1.0
This software is used in a media optimization pipeline. It is used to calculate stock concentrations, volumes and instructions for the liquid handler used in ESE (Biomek NX-S8).
Radivojevic, Tijana↗
SEARCH · Engineering Papers
Results for “Software pipelines”
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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"Reducing Detailed Vehicle Energy Dynamics to Physics-Like Models"
The energy demand of vehicles, particularly in unsteady drive cycles, is affected by complex dynamics internal to the engine and other powertrain components. Yet, in many applications, particularly macroscopic traffic flow modeling and optimization, structurally simple approximations to the complex vehicle dynamics are needed that nevertheless reproduce the correct effective energy behavior. This work presents a systematic model reduction pipeline that starts from complex vehicle models based on the Autonomie software and derives a hierarchy of simplified models that are fast to evaluate, easy to disseminate in open-source frameworks, and compatible with optimization frameworks. The pipeline, based on a virtual chassis dynamometer and subsequent approximation strategies, is reproducible and is applied to six different vehicle classes to produce concrete explicit energy models that represent an average vehicle in each class and leverage the accuracy and validation work of the Autonomie software.
Khoudari, Nour↗
Face Recognition Oak Ridge (FaRO): A Framework for Distributed and Scalable Biometrics Applications
The facial biometrics community has seen a recent abundance of high-accuracy facial analytic models become freely available. Although these models' capabilities in facial detection, landmark detection, attribute analysis, and recognition are ever-increasing, they aren't always straightforward to deploy in a real-world environment. In reality, the use of the field's ever growing collection of models is becoming exceedingly difficult as library dependencies update and deprecate. Researchers often encounter headaches when attempting to utilize multiple models requiring different or conflicting software packages. Face Recognition Oak Ridge (FaRO) is an open-source project designed to provide a highly modular, flexible framework for unifying facial analytic models through a compartmentalized plug-and-play paradigm built on top of the gRPC (Google Remote Procedure Call) protocol. FaRO's server-client architecture and flexible portability allows easy construction of modularized and heterogeneous face analysis pipelines, distributed over many machines with differing hardware and software resources. This paper outlines FaRO's architecture and current capabilities, along with some experiments in model testing and distributed scaling through FaRO.
Bolme, David↗
Fisher Forecasting for the DESC with $\texttt{Augur}$
The Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST) has begun its ten-year survey of the entire visible southern hemisphere. To ensure robust cosmological measurements, computationally inexpensive investigations of modeling choices must be made to gauge the performance of proposed cosmological analyses. In this paper, we introduce the $\texttt{Augur}$ tool of the Dark Energy Science Collaboration (DESC), which provides Fisher forecasts for cosmological inference for the LSST using software frameworks designed for DESC science. We test the pipeline by comparing it to forecasts produced by external code and direct sampling of the posterior via nested sampling methods, finding good agreement between all methods. We additionally investigate a range of modeling and hyperparameter choices for a 3$\times$2pt investigation in harmonic space, providing users with diagnostics to obtain reliable forecasts. $\texttt{Augur}$ will be continually updated to be compatible with the other tools in the DESC software ecosystem as additional probes and functionality become available.
Rogozenski, Paul [Carnegie Mellon U.; Arizona U.] ↗
Cosmic Frontier Project at SMU
The SMU group led by Professor Robert Kehoe continued to work to constrain dark energy measurements of the Dark Energy Spectroscopic Instrument (DESI). These constraints are obtained by measuring the expected peak in characteristic distance scale between galaxies, the ‘BAO peak’, as a function of redshift for four different types of galaxy. DESI will cover the redshift range to z<3.5 with approximately 40 million galaxy spectra. SMU’s primary emphasis during the funding period was on the early DESI data, including the development of software that would allow the measurement of the impact of incomplete targeting of galaxies in the survey. We provided software to calculate the weights that are critical to permit us to correctly compare data to the theoretical calculations of dark matter halos. SMU also began development of software that can be integrated into the analysis pipeline that uses alternate targeting to generate these weights. Baryonic physics has a critical impact on galaxy development and placement within dark matter halos. SMU also increased its efforts in the area of modeling this galaxy-halo connection in two areas. The primary emphasis was to work on a sub-halo abundance matching scheme using dark matter simulation with very fine mass resolution (‘Uchuu’). Our effort here is to produce models for use by DESI that more correctly account for the subhalo structure of dark matter distribution, and its manifestation in satellite galaxies. Our initial effort had been for emission line galaxies. In the funding period, we were able to produce first halo-occupation distribution models. This work is slated to contribute to DESI Key Project papers. We also furthered our ongoing effort to study galaxy placement in halos using semi-analytic methods. Kehoe’s group also continued to maintain its strong role in DESI Operations, with SMU postdoc serving as a Lead Observing Scientist.
79 ASTRONOMY AND ASTROPHYSICS↗
PROTOCALC, a W -band Polarized Calibrator for Cosmic Microwave Background Telescopes: Application to Simons Observatory and CLASS
Current- and next-generation cosmic microwave background (CMB) experiments will measure polarization anisotropies with unprecedented sensitivities. The need for high precision in these measurements underscores the importance of gaining a comprehensive understanding of instrument properties, with a particular emphasis on the study of the beam properties, and especially their polarization characteristics and the measurement of the polarization angle. In this context, a major challenge lies in the scarcity of millimeter polarized astrophysical sources with sufficient brightness and calibration knowledge to meet the stringent accuracy requirements of future CMB missions. This led to the development of a drone-borne calibration source designed for the frequency band centered on approximately 90 GHz, matching a commonly used channel in ground-based CMB measurements. The Prototype Calibrator for Cosmology, PROTOCALC, has undergone thorough in-lab testing, and its properties have been subsequently modeled through simulation software integrated into the standard Simons Observatory analysis pipeline. Moreover, the PROTOCALC system has been tested in the field, having been deployed twice on calibration campaigns with CMB telescopes in the Atacama Desert. The data collected constrain the roll angle of the source with a statistical accuracy of 0$^°_•$045.
79 ASTRONOMY AND ASTROPHYSICS↗
The Phenix‐AlphaFold webservice: Enabling AlphaFold predictions for use in Phenix
Abstract Advances in machine learning have enabled sufficiently accurate predictions of protein structure to be used in macromolecular structure determination with crystallography and cryo‐electron microscopy data. The Phenix software suite has AlphaFold predictions integrated into an automated pipeline that can start with an amino acid sequence and data, and automatically perform model‐building and refinement to return a protein model fitted into the data. Due to the steep technical requirements of running AlphaFold efficiently, we have implemented a Phenix‐AlphaFold webservice that enables all Phenix users to run AlphaFold predictions remotely from the Phenix GUI starting with the official 1.21 release. This webservice will be improved based on how it is used by the research community and the future research directions for Phenix.
Poon, Billy K.↗
MPACT Safeguards Modeling: FY25 Update
Sandia National Laboratories develops and maintains several open-source software packages to support material accountancy analyses. This includes the Material Accountancy Performance Indicator Toolkit (MAPIT), the Fissile Facility Flow Modeler (F3M) and the Separation and Safeguards Performance Model Library (SSPM-L). MAPIT is responsible for performing statistical safeguards analyses on bulk and itemized data from nuclear fuel cycle facilities and can operate on real or synthetic data. MAPIT is the only open-source software for such analyses. F3M is a library of modules, built in MATLAB Simulink, that contain pre made blocks to represent different generic fuel cycle processes. These blocks can be used together in a modular fashion to represent and simulate nuclear fuel cycle processes with the goal of improving facility-level accountancy during the design phase. F3M is also an open-source library. Finally, the SSPM-L library is a series of completed models built from F3M. The library includes facility models such as a generic PUREX facility and a fuel fabrication facility. The SSPM-L library is not open source, but is available to collaborators with a relevant use case. These tools include modeling and simulation pipelines to simulate nuclear fuel cycle facilities and the underlying software needed to simulate measurement uncertainty and perform statistical analyses. Together, these tools can perform end-to-end nuclear material accountancy analyses. This report documents the various improvements made to these tools in FY25. Specifically, we added new statistical test, new statistical modeling capabilities, new fuel cycle facility models, and launched a new open-source model component library.
97 MATHEMATICS AND COMPUTING↗
Applying the ATOM drug discovery platform to small-molecule antivirals (Annual Report)
The objective of this project is to advance our understanding of the ML approaches needed to find the most potent inhibitor through an AI guided search that simultaneously optimizes for limited off-target safety activity and desirable pharmacokinetics (PK) properties. The methods will be tested for inhibiting SARS-CoV-2 activity through inhibition of the main protease as a demonstration, but the methodology will be developed to apply to any biothreat target using a small-molecule protein binding-based intervention, with limited experimental data. Computational experiments are conducted using our ATOM generative molecular design (GMD) loop software, which is the implementation of our AI/ML drug design pipeline.
59 BASIC BIOLOGICAL SCIENCES↗
High resolution hydrologic routing with machine learning assisted waterbody classification
This software contains the code for a machine learning-based pipeline for creating persistent waterbody databases used in hydrologic routing. It consists of three components, 1) a PyTorch library (TorchWBType) for classifying/labeling arbitrary waterbodies into lakes and non-lakes, 2) a batch processing orchestrator (wbextractor) for delineating waterbodies from remote sensing imagery, and 3) graphing/analysis scripts for reproducing the plots in an associated journal article (LA-UR-24-22590).
Stachelek, Jemma↗
Building a Computational and Experimental Rapid Response Pipeline to Counter the Coronavirus Disease 2019 Outbreak and Emerging Biothreats
The COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs, especially where protective candidates can be rapidly identified or developed for emerging biothreats and escape variants. Current cutting-edge technologies for this purpose still rely on pathogen-exposed convalescent volunteers and a large screening effort to find a proverbial needle in a haystack. Computational design of protective antibodies based on pre-existing templates skips those requirements and allows for greater control over the breadth and target epitope, while also co-optimizing for potency and developability or other biophysical characteristics. We approached this problem by building and expanding an in vitro experimental rapid antibody production and characterization pipeline to support development of an autonomous, closed loop, active learning software system based on structural simulation and ground truth experimental data to design and evaluate antibody antigen interactions. Starting from early in the pandemic, we targeted SARS-CoV-2, the causative agent of COVID-19, by re-purposing neutralizing antibodies against SARS-CoV-1 that had been identified in the wake of that outbreak in the early 2000’s. We successfully re-targeted three different anti-SARS-CoV-1 antibodies to neutralize SARS-CoV-2 in vitro, where the antibodies were generated externally and tested through conventional binding and neutralization assays internally or with collaborators. As antibodies were identified from the blood of humans infected with SARS-CoV-2, we shifted to collaborate with academic partners to develop improved versions of their human-derived antibodies. This work reached its most important stage in rapid response to the emergence of the Omicron variant of concern (VOC) in late 2021. In a matter of weeks, enabled by on demand innovation to our screening pipeline, we computationally designed and experimentally characterized derivative antibodies of COV2-2130, one of two antibodies from Vanderbilt that form the basis of the AstraZeneca Evusheld prophylactic drug product. This drug product suffers a serious loss of efficacy against Omicron BA.1 and BA.1.1, the first Omicron strains. Due to tight integration of computational design and experimental evaluation, we were able to identify a pair of designs with potent neutralization of the main targets Omicron BA.1 and BA.1.1; but also the earlier Delta variant, and subsequent Omicron strains including BA.2, BA.4, BA.5, and BA.2.75, demonstrating that our multi-target design process can, by its nature, produce robust antibody designs that strictly improve over the parental antibody. These results, recognized by a 2022 Director’s Science and Technology award, have enabled the follow-on GUIDE program, to commence in FY23. While earlier design campaigns were substantially outsourced, we have engineered better and faster processes internally to better compliment, calibrate, and speed computational designs. As part of the follow-on GUIDE program, we will stand up a rapid and high-throughput antibody production and characterization facility staffed with the expertise and capabilities to foster our current collaboration across PLS and ENG as well as other partnerships toward computational design of biologics.
59 BASIC BIOLOGICAL SCIENCES↗
IGRINS RV: A Precision Radial Velocity Pipeline for IGRINS Using Modified Forward Modeling in the Near-infrared
Application of the radial velocity (RV) technique in the near-infrared is valuable because of the diminished impact of stellar activity at longer wavelengths, making it particularly advantageous for the study of late-type stars but also for solar-type objects. In this paper, we present the IGRINS RV open-source python pipeline for computing infrared RV measurements from reduced spectra taken with IGRINS, an R ≡ λ/Δλ ∼ 45,000 spectrograph with simultaneous coverage of the H band (1.49–1.80 μm) and K band (1.96–2.46 μm). Using a modified forward-modeling technique, we construct high-resolution telluric templates from A0 standard observations on a nightly basis to provide a source of common-path wavelength calibration while mitigating the need to mask or correct for telluric absorption. Telluric standard observations are also used to model the variations in instrumental resolution across the detector, including a yearlong period when the K band was defocused. Without any additional instrument hardware, such as a gas cell or laser frequency comb, we are able to achieve precisions of 26.8 m s{sup −1} in the K band and 31.1 m s{sup −1} in the H band for narrow-line hosts. These precisions are empirically determined by a monitoring campaign of two RV standard stars, as well as the successful retrieval of planet-induced RV signals for both HD 189733 and τ Boo A; furthermore, our results affirm the presence of the Rossiter–McLaughlin effect for HD 189733. The IGRINS RV pipeline extends another important science capability to IGRINS, with publicly available software designed for widespread use.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NSRDB (National Solar Radiation Database Software) [SWR-23-77]
This repository contains all of the methods for the NSRDB data processing pipeline. The NSRDB is a serially complete collection of hourly and half-hourly values of meteorological data and the three most common measurements of solar radiation: global horizontal, direct normal and diffuse horizontal irradiance.
Benton, Brandon↗
Hydrogen Extremely Low Probability of Rupture Version 1
SAND2024-08511O The Hydrogen Extremely Low Probability of Rupture (HELPR) software toolkit provides probabilistic fracture assessments of natural gas infrastructure for transporting hydrogen. Using probabilistic sampling and sensitivity analysis—along with engineering fatigue and fracture mechanics— the software develops models that can predict structural integrity measures for natural gas pipelines under stress. 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.
Schroeder, Benjamin↗
Detecting Dwarf Galaxies Around NGC 55
In order to improve our understanding of the satellite populations of low-mass galaxies, the DECam Local Volume Exploration (DELVE) – DEEP Survey is performing a search for satellites around the isolated, low-mass galaxy, NGC 55. As part of this search, we characterize our dwarf galaxy detection sensitivity by injecting artificial dwarf galaxies into our data set and measuring the fraction that we can recover. Additionally, we inject and recover artificial dwarfs to test how the blending of resolved stars affects the detection of dwarf galaxies. We inject 650 artificial dwarfs across 26 DELVE-DEEP coadded images of the NGC 55 halo and use the software tool, Source Extractor, to perform source recovery. A dwarf-search pipeline is then run on our dwarf-injected catalogs, utilizing the photutils function, find peaks, and detections are recorded as a function of dwarf size and luminosity. Our results demonstrate that we are most sensitive to large, bright dwarf galaxies, and our sensitivity begins to decrease as we approach DELVE-DEEP’s detection limit or blending causes significant reductions in recovered magnitude. We also find that our results are hindered by the limitations of star-galaxy separation applied to distant, faint sources, which is possibly a consequence of the blending of small star clusters within dwarf galaxies.
79 ASTRONOMY AND ASTROPHYSICS↗
The 200 Gbps Challenge: Imagining HL-LHC analysis facilities
The IRIS-HEP software institute, as a contributor to the broader HEP Python ecosystem, is developing scalable analysis infrastructure and software tools to address the upcoming HL-LHC computing challenges with new approaches and paradigms, driven by our vision of what HL-LHC analysis will require. The institute uses a "Grand Challenge" format, constructing a series of increasingly large, complex, and realistic exercises to show the vision of HL-LHC analysis. Recently, the focus has been demonstrating the IRIS-HEP analysis infrastructure at scale and evaluating technology readiness for production. As a part of the Analysis Grand Challenge activities, the institute executed a "200 Gbps Challenge", aiming to show sustained data rates into the event processing of multiple analysis pipelines. The challenge integrated teams internal and external to the institute, including operations and facilities, analysis software tools, innovative data delivery and management services, and scalable analysis infrastructure. The challenge showcases the prototypes - including software, services, and facilities - built to process around 200 TB of data in both the CMS NanoAOD and ATLAS PHYSLITE data formats with test pipelines. The teams were able to sustain the 200 Gbps target across multiple pipelines. The pipelines focusing on event rate were able to process at over 30 MHz. These target rates are demanding; the activity revealed considerations for future testing at this scale and changes necessary for physicists to work at this scale in the future. The 200 Gbps Challenge has established a baseline on today's facilities, setting the stage for the next exercise at twice the scale.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
BOS Gas Detection Pipeline (Integrated System for Optical Hydrogen Detection Using Background Oriented Schlieren and Machine Learning) [SWR-26-007]
This software is the world's first integrated background oriented schlieren and machine learning-based leak detection system. The system provides real time visualization of gas leaks and machine learning interpenetration of leak severity. The software is supplemented by SWR-25-177, "gpu_piv (Graphics Processing Unit Accelerated Background Oriented Schlieren Algorithm", also developed by the National Laboratory of the Rockies. SEE DOECODE ID 182832.
Palin, Ian [National Laboratory of the Rockies (NL↗
Semi-Automatic Geographic Information System Framework for Creating Photo-Realistic Digital Twin Cities to Support Autonomous Driving Research
Digital twin cities are frequently used in vehicle and traffic simulations to render realistic on-road driving scenarios under various traffic and environmental conditions. These digital twins provide a high-fidelity replica of the physical world (e.g., buildings, roads, infrastructures, traffic) to create three-dimensional (3D) virtual-physical environments to support various emerging vehicle and transportation technologies such as connected and automated vehicles. These virtual environments provide a cost-effective digital proving ground to evaluate, validate, and test emerging technologies that include control algorithms, localization, perception, and sensors. Replicating a real-world traffic scenario in a digital twin using a traditional 3D modeling approach is a time-consuming and labor-intensive effort. Here this paper presents a semi-automated spatial framework to construct realistic 3D digital twin cities to support autonomous driving research using readily available geographic information system (GIS) data and 3D prefabricated (prefab) models. We start with a comprehensive review of geospatial data sources of essential digital entities required in a 3D digital twin city and present an integrated GIS-3D modeling pipeline using customized QGIS/GDAL and Blender scripting in Python. The pipeline outputs are realistic 3D digital twin cities compatible with common vehicle simulation software, such as CARLA and IPG CarMaker. The paper closes with a showcase to demonstrate the quality and usability of a digital twin city created to replicate the Shallowford Road corridor in Chattanooga in both Unity and Unreal engine-based virtual environment. The generated digital twin city can be applied to a hardware-in-the-loop simulation environment with an actual testing vehicle to facilitate autonomous driving research.
33 ADVANCED PROPULSION SYSTEMS↗