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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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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Automating Software Productivity Planning: Lightweight Tools for Upgrading Team Practices

A lightweight iterative workflow, called Productivity and Sustainability Improvement Planning (PSIP) has been developed to assist software teams with employing good software engineering practices. Three PSIP tools automate practice summarization, self-assessment, and progress tracking to enhance team engagement around software process improvement: Reposcanner, RateYourProject (RYP) and Progress Tracking Cards (PTCs) respectively. Reposcanner is a data analysis tool. RYP is an interactive self-assessment tool that provides an easy-to-use entry point to the PSIP process. Once process improvements are identified, PTCs are created by teams to measure outcomes and progression toward their goals. We present an exemplifying case study with a software team where these tools have been put to use, along with a description of the tools, and future plans for further improvements.

Raybourn, Elaine↗
DOE OSTI2022

Pit depth analysis using automated software for three containers with complete imaging

The 3013 surveillance program is tasked with ensuring the long term safety of plutonium storage in 3013-compliant containers. One component of this task is to understand corrosion features found on the interior sidewall of the inner container closure weld region (ICCWR). To this end, three containers were selected to have laser confocal microscope (LCM) 20X imaging of the entire ICCWR. This report describes the analysis of the LCM pit depth data using the automated corrosion analysis software. The analysis included determining maximum pit depths and distributions of pit depths, volumes, and diameters for all pit features identified on the three containers. Results provided insight into possible corrosion mechanisms and were consistent with previous pit growth model predictions.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Development of an Automated Software Reliability Tester for Digital I and C

Existing nuclear facilities are in the process of upgrading analog systems to new, software- based digital components; however, the qualification of these new systems has been a significant hurdle for their implementation in the United States. This paper describes the development of a Software Reliability Tester (SRT) that will provide a means to quantify the reliability and fault tolerance of digital instrumentation and control (I and C) systems used in nuclear facilities. The SRT is comprised of hardware and software that exercise digital equipment inputs and compare the outputs to expected values to quantify system reliability. Incorporation of fault injection techniques enables the SRT to evaluate the robustness of digital I and C in the presence of abnormal conditions. The integration of both quantitative reliability and fault tolerance measures will provide the nuclear industry with an automated and systematic approach to digital I and C qualification. This will enable safer, more reliable, and more cost effective implementations of a broad spectrum of digital I and C equipment in existing and next generation nuclear facilities. This paper includes a description of the design of the SRT, including software modules and the hardware interface. In addition, an example of using the SRT to automate functional testing of a digital timer relay is presented. The SRT described in this paper provides a means to conduct efficient and robust testing for a variety of digital devices. Future plans for the SRT include integrating fault injection testing so that devices can be evaluated in the presence of off-normal conditions. (authors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2014

Development of Automated Software Program for the Analysis of Alzheimer's Disease Scans: Evaluation of PET imaging with PBR-111 in HV and AD subjects

Study goal: A Phase 1 evaluation of the kinetics, clearance and cerebral distribution of one novel peripheral benzodiazepine receptors(PBR)positron emission tomography (PET) imaging agent, 18F-PBR-111 following intravenous administration in healthy volunteers and Alzheimer's disease (AD) patients. Short title: Evaluation of PET imaging with PBR-111 in HV and AD subjects Proof of Mechanism. Primary Objective: To evaluate the cerebral distribution of PBR-111 positron emission tomography (PET) for detection/exclusion of microglial activation in patients with Alzheimer's disease subjects compared to healthy volunteers. Secondary objectives: - To assess the dynamic uptake and washout of [18F]PBR-111, a potential imaging bio-marker for inflammatory changes in brain, using positron emission tomography in subjects with Alzheimer's disease (AD) and healthy volunteers (HV). - To perform blood metabolite characterization of [18F]PBR-111 in subjects with AD and HV to determine the nature of metabolites in assessment of [18F]-PBR-111 as a PET brain imaging agent. Name of radioactive drug substance: PBR-111 Dose(s): The applied PBR-111 radioactive dose will be up to 5.0 mCi, diluted in a maximum of 10 ml of saline. The radioligand will be administered as a slow intravenous bolus injection (i.e., 6 sec/ml) into a large vein (e.g., antecubital vein). Route of administration: Intravenous injection Duration of treatment: Single administration of a diagnostic agent Indication: PBR-111 positron emission tomography (PET) imaging has the potential to detect microglial activation. In the presence of PBR-111 uptake (representative of microglial activation), inflammation in the brain can be detected. Diagnosis and main criteria for inclusion: Study participants will be HVs and patients diagnosed with probable AD. HVs must be 18 years of age (at least four subjects 50 years of age) and have no evidence of cognitive impairment or other neurologic disease by medical history. The lack of cognitive impairment will also be based on a Clinical Dementia Rating (CDR) of 0. Patients with probable AD must be 50 years of age and must fulfill the National Institute of Neurological and Communicative Disorders and Stroke, Alzheimer's Disease and Related Disorders Association [NINCDS-ADRDA] criteria for probable AD. The CDR score must be 1.0 and 2.0 and have a modified Hachinski of 4. All HVs and all patients with probable AD must be able to comply with all study procedures. Study design: This is a Phase 1, open-label, single-center, non-randomized single dose study to assess the kinetics, clearance and cerebral distribution of PBR-111 PET imaging in detecting microglial activation in the brain in patients with probable AD compared to HVs. All aspects related to image acquisition, processing, and visual as well as quantitative evaluation will be developed, optimized, and validated (where required). Each subject will be required to visit the study center during the screening phase and on the PBR-111 PET imaging day (baseline). A telephone follow-up visit will be performed 7 days (± 3 days) after PBR-111 PET administration. At the screening visit, each subject (or caregiver in the case of AD subjects) will be asked to provide written informed consent or assent. During the screening phase (maximum duration of 60 days) subject medical, neurological, and surgical history, clinical assessments, and a neuro-psychiatric evaluation will be performed on all eligible subjects. Subjects will be allowed to leave the center after all evaluations have been completed. During this period an MRI of the brain will be performed during the screening period. If an MRI of the brain has been performed within six months of the imaging visit using the methods described in the protocol, and there has been no medically significant events in the interim, the previous MRI may be used. During the PBR-111 PET imaging day, all subjects will receive a single intravenous injection of PBR-111 and scanning will be performed over a 3.5 hour period. Each subject will have a telephone follow-up 7 days (± 3 days) thereafter to assess for adverse events. Methodology: - Assessments to provide clinical characterization of the AD subjects will be performed. - After administration of PBR-111, images will be generated with state-of-the-art PET imaging. Images will be assessed quantitatively for the presence of microglial activation by a nuclear physician blinded to clinical data. - Total radioactivity and estimation of the fraction of radioactivity associated to the un-metabolized tracer will be determined. In addition, the metabolite patterns of PBR-111 are determined in venous plasma and arterial samples based on high-performance liquid chromatography (HPLC) analyses. - Arterial sampling will be acquired in the initial two AD and two HV subjects and modeling will be assessed to determine if additional arterial sampling is necessary.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Automated Data Acquisition Software for National Instruments Hardware with Timed Acquisition, Real-Time Display and Spectrogram, and Data Redundancy. Current version is Version 7 of DataAcq.exe.RElease1.2.4.26.

This software automates the collection of waveform data on a timed schedule so that an operator does not need to be at the computer to initiate the collection of data sets.It provides real time display of up to 16 channels of data as a time display, frequency display, or frequency vs time (spectrogram) display. The software provides the ability to collect data sets of a user selected time length at a selected interval. This operation can be set to occur during a selected time interval during the day. This software provides the capability to write two copies of the data files simultaneously so that the data is backed up as collected. This software automates the collection of waveform data on a timed schedule so that an operator does not need to be at the computer to initiate the collection of data sets. It provides real time display of up to 16 channels of data as a time display, frequency display, or frequency vs time (spectrogram) display. The software provides the ability to collect data sets of a user selected time length at a selected interval. This operation can be set to occur during a selected time interval during the day. This software provides the capability to write two copies of the data files simultaneously so that the data is backed up as collected.

Wysor, Robert W↗
DOE OSTI2019

Ultra-low-dose limited renal CT for volumetric stone surveillance: advantages over standard unenhanced CT

Purpose: To describe and validate a novel CT approach using volumetric analysis for renal stone surveillance. Materials and methods: This prospective trial consisted of a standard low-dose non-contrast CT (SLD) of the abdomen and pelvis, immediately followed by an ultra-low-dose non-contrast CT (ULD) with reconstruction limited to the kidneys. A novel dedicated software tool was applied that automates stone volume, density, and maximum linear size. Manual linear stone size was measured by a radiology fellow and urology resident for comparison. CT dose and clinical charges were considered. Results: Twenty-eight stones in 16 patients were analyzed. Mean effective dose of ULD CT was 0.57 mSv, an average 92% lower than the SLD CT dose. For SLD, mean size ± SD (range) (mm) was 7.9 ± 6.2 (2.6–30.5) for Reader 1, 7.3 ± 6 (2.4–30.7) for Reader 2, and 9.3 ± 6.4 (3.7–33.1) for the automated software. For ULD, mean size ± SD (range) (mm) was 7.3 ± 6 (2.5–30.5) for Reader 1, 7.2 ± 6.1 (2.1–30.7) for Reader 2, and 9.1 ± 6.4 (4.2–32.8) for the automated software. Automated stone diameters were larger than manual diameters for 27/28 stones (mean difference, 23%); difference was ≥ 2 mm in 30%. Average variability between manual measurements was 8.6% (SLD) and 7.8% (ULD), but was 0% for the automated technique. Our institutional charge for ULD renal CT is slightly less than renal US, and > 4× less than SLD CT. The Medicare global fee for the ULD renal CT is less than the SLD CT of the abdomen and pelvis. Conclusions: This focused stone surveillance CT protocol is lower cost and lower dose compared to the standard CT approach. Automated assessment of stone burden provides improved reproducibility over manual linear measurement and offers the advantages of 3D measurements and volumetry. We now offer and perform this protocol in routine clinical practice for stone surveillance.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2024

PeakQC: A Software Tool for Omics-Agnostic Automated Quality Control of Mass Spectrometry Data

Mass spectrometry is broadly employed to study complex molecular mechanisms in various biological and environmental fields, enabling 'omics' research such as proteomics, metabolomics, and lipidomics. As study cohorts grow larger and more complex with dozens to hundreds of samples, the need for robust quality control (QC) measures through automated software tools becomes paramount to ensure the integrity, high quality, and validity of scientific conclusions from downstream analyses and minimize the waste of resources. Since existing QC tools are mostly dedicated to proteomics, automated solutions supporting metabolomics are needed. To address this need, we developed the software PeakQC, a tool for automated QC of MS data that is independent of omics molecular types (i.e., omics-agnostic). It allows automated extraction and inspection of peak metrics of precursor ions (e.g., errors in mass, retention time, arrival time) and supports various instrumentations and acquisition types, from infusion experiments or using liquid chromatography and/or ion mobility spectrometry front-end separations and with/without fragmentation spectra from data-dependent or independent acquisition analyses. Diagnostic plots for fragmentation spectra are also generated. Here, in this paper, we describe and illustrate PeakQC’s functionalities using different representative data sets, demonstrating its utility as a valuable tool for enhancing the quality and reliability of omics mass spectrometry analyses.

47 OTHER INSTRUMENTATION↗
DOE OSTI2026

Vision and Development of a Design, Implementation, and Verification Automation (DIVA) Software Platform for DNA Construction

Abstract DNA construction, while a prerequisite to many biological endeavors, is often a time-consuming distraction from an individual’s primary research objectives. We envisioned that with the right software infrastructure and cultural mindset, a single person could execute in parallel the batched DNA construction tasks of an entire research institute, at scales realizing efficiency gains through process and laboratory automation. In pursuit of this vision, we developed the Design, Implementation, and Verification Automation (DIVA) software platform. DIVA’s web interface enables researchers to design DNA constructs (using visual biological computer-aided design tools and biological parts repositories), submit designs for construction to dedicated staff, and track DNA construction as it progresses. DIVA supports the dedicated staff through the DNA construction process and records both successful and unsuccessful attempts toward improving the overall process. The platform is publicly available at public-diva.jbei.org and its open-source code through github.com/JBEI/DIVA.

Plahar, Hector [DOE Agile BioFoundry , , ,; DOE Jo↗
DOE OSTI2014

Turbo FRMAC 2011

The Turbo FRMAC (TF) software automates the calculations described in volumes 1-3 of "The Federal Manual for Assessing Environmental Data During a Radiological Emergency" (2010 version). This software automates the process of assessing radiological data during a Federal Radiological Emergency. The manual upon which the software is based is unclassified and freely available on the Internet. TF takes values generated by field samples or computer dispersion models and assesses the data in a way which is meaningful to a decision maker at a radiological emergency; such as, do radiation values exceed city, state, or federal limits; should the crops be destroyed or can they be utilized; do residents need to be evacuated, sheltered in place, or should another action taken. The software also uses formulas generated by the EPA, FDA, and other federal agencies to generate field observable values specific to the radiological event that can be used to determine where regulatory limit values are exceeded. In addition to these calculations, TF calculates values which indicate how long an emergency worker can work in the contaminated area during a radiological emergency, the dose received from drinking contaminated water or milk, the dose from eating contaminated food, the does expected down or upwind of a given field sample, along with a significant number of other similar radiological health values.

Fulton, John↗
DOE OSTI2023

IsoMatchMS : Open-Source Software for Automated Annotation and Visualization of High Resolution MALDI-MS Spectra

Due to its speed, accuracy, and adaptability to various sample types, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has become a popular method to identify molecular isotope profiles from biological samples. Often MALDI-MS data do not include tandem MS fragmentation data, and thus the identification of compounds in samples requires external databases so that the accurate mass of detected signals can be matched to known molecular compounds. Most relevant MALDI-MS software tools developed to confirm compound identifications are focused on small molecules (e.g., metabolites, lipids) and cannot be easily adapted to protein data due to their more complex isotopic distributions. Here, we present an R package called IsoMatchMS for the automated annotation of MALDI-MS data for multiple datatypes: intact proteins, peptides, and glycans. This tool accepts already derived molecular formulas or, for proteomics applications, can derive molecular formulas from a list of input peptides or proteins including proteins with post-translational modifications. In conclusion, visualization of all matched isotopic profiles is provided in a highly accessible HTML format called a trelliscope display, which allows users to filter and sort by several parameters such as match scores and the number of peaks matched. IsoMatchMS simplifies the annotation and visualization of MALDI-MS data for downstream analyses.

47 OTHER INSTRUMENTATION↗
DOE OSTI2013

DIVA V1.0

The DIVA software interfaces a process in which researchers design their DNA with a web-based graphical user interface, submit their designs to a central queue, and a few weeks later receive their sequence-verified clonal constructs. Each researcher independently designs the DNA to be constructed with a web-based BioCAD tool, and presses a button to submit their designs to a central queue. Researchers have web-based access to their DNA design queues, and can track the progress of their submitted designs as they progress from "evaluation", to "waiting for reagents", to "in progress", to "complete". Researchers access their completed constructs through the central DNA repository. Along the way, all DNA construction success/failure rates are captured in a central database. Once a design has been submitted to the queue, a small number of dedicated staff evaluate the design for feasibility and provide feedback to the responsible researcher if the design is either unreasonable (e.g., encompasses a combinatorial library of a billion constructs) or small design changes could significantly facilitate the downstream implementation process. The dedicated staff then use DNA assembly design automation software to optimize the DNA construction process for the design, leveraging existing parts from the DNA repository where possible and ordering synthetic DNA where necessary. SynTrack software manages the physical locations and availability of the various requisite reagents and process inputs (e.g., DNA templates). Once all requisite process inputs are available, the design progresses from "waiting for reagents" to "in progress" in the design queue. Human-readable and machine-parseable DNA construction protocols output by the DNA assembly design automation software are then executed by the dedicated staff exploiting lab automation devices wherever possible. Since the all employed DNA construction methods are sequence-agnostic, standardized (utilize the same enzymatic master mixes and reaction conditions), completely independent DNA construction tasks can be aggregated into the same multi-well plates and pursued in parallel. The resulting sets of cloned constructs can then be screened by high-throughput next-gen sequencing platforms for sequence correctness. A combination of long read-length (e.g., PacBio) and paired-end read platforms (e.g., Illumina) would be exploited depending the particular task at hand (e.g., PacBio might be sufficient to screen a set of pooled constructs with significant gene divergence). Post sequence verification, designs for which at least one correct clone was identified will progress to a "complete" status, while designs for which no correct clones wereidentified will progress to a "failure" status. Depending on the failure mode (e.g., no transformants), and how many prior attempts/variations of assembly protocol have been already made for a given design, subsequent attempts may be made or the design can progress to a "permanent failure" state. All success and failure rate information will be captured during the process, including at which stage a given clonal construction procedure failed (e.g., no PCR product) and what the exact failure was (e.g. assembly piece 2 missing). This success/failure rate data can be leveraged to refine the DNA assembly design process.

Source record↗