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At least 1,225 records · Page 68

BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more

Common steps in phylogenomic matrix production include biological sequence concatenation, morphological data concatenation, insertion/deletion (indel) coding, gene content (presence/absence) coding, removing uninformative characters for parsimony analysis, recording with reduced amino acid alphabets, and occupancy filtering. Existing software does not accomplish these tasks on a phylogenomic scale using a single program. BAD2matrix is a Python script that performs the above-mentioned steps in phylogenomic matrix construction for DNA or amino acid sequences as well as morphological data. The script works in UNIX-like environments (e.g., LINUX, MacOS, Windows Subsystem for LINUX).

59 BASIC BIOLOGICAL SCIENCES↗

Data acquisition and slow control interface for the Mu2e experiment

The Mu2e experiment at the Fermilab Muon Campus will search for the coherent neutrinoless conversion of a muon into an electron in the field of an aluminum nucleus with a sensitivity improvement by a factor of 10000 over existing limits. The Mu2e Trigger and Data Acquisition System (TDAQ) uses otsdaq as the online Data Acquisition System (DAQ) solution. Developed at Fermilab, otsdaq integrates both the artdaq DAQ and the art analysis frameworks for event transfer, filtering, and processing. otsdaq is an online DAQ software suite with a focus on flexibility and scalability and provides a multi-user, web-based, interface accessible through a web browser. The data stream from the detector subsystems is read by a software filter algorithm that selects events which are combined with the data flux coming from a cosmic ray veto system. The Detector Control System (DCS) has been developed using the Experimental Physics and Industrial Control System (EPICS) open source platform for monitoring, controlling, alarming, and archiving. The DCS system has been integrated into otsdaq. A prototype of the TDAQ and the DCS systems has been built at Fermilab's Feynman Computing Center. In this study, we report on the progress of the integration of this prototype in the online otsdaq software.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Results from the First Two Flights of the Static Computer Memory Integrity Testing Experiment

This paper details the scientific objectives, experiment design, data collection method, and post flight analysis following the first two flights of the Static Computer Memory Integrity Testing (SCMIT) experiment. SCMIT is designed to detect soft-event upsets in passive magnetic memory. A soft-event upset is a change in the logic state of active or passive forms of magnetic memory, commonly referred to as a "Bitflip". In its mildest form a soft-event upset can cause software exceptions, unexpected events, start spacecraft safeing (ending data collection) or corrupted fault protection and error recovery capabilities. In it's most severe form loss of mission or spacecraft can occur. Analysis after the first flight (in 1991 during STS-40) identified possible soft-event upsets to 25% of the experiment detectors. Post flight analysis after the second flight (in 1997 on STS-87) failed to find any evidence of soft-event upsets. The SCMIT experiment is currently scheduled for a third flight in December 1999 on STS-101.

Hancock, Thomas M., III↗

Ultrasonic Data Display and Analysis System Developed (Including Fuzzy Logic Analysis) for the Windows-Based PC

Post-Scan Interactive Data Display (PSIDD) III is a user-oriented Windows-based system that facilitates the display and comparison of ultrasonic contact measurement data obtained at NASA Glenn Research Center's Ultrasonic Nondestructive Evaluation measurement facility. The system is optimized to compare ultrasonic measurements made at different locations within a material or at different stages of material degradation. PSIDD III provides complete analysis of the primary waveforms in the time and frequency domains along with the calculation of several frequency-dependent properties including phase velocity and attenuation coefficient and several frequency-independent properties, like the cross correlation velocity. The system allows image generation on all the frequency-dependent properties at any available frequency (limited by the bandwidth used in the scans) and on any of the frequency-independent properties. From ultrasonic contact scans, areas of interest on an image can be studied with regard to underlying raw waveforms and derived ultrasonic properties by simply selecting the point on the image. The system offers various modes of indepth comparison between scan points. Up to five scan points can be selected for comparative analysis at once. The system was developed with Borland Delphi software (Visual Pascal) and is based on an SQL data base. It is ideal for the classification of material properties or the location of microstructure variations in materials. Along with the ultrasonic contact measurement software that it is partnered with, this system is technology ready and can be transferred to users worldwide.

Lovelace, Jeffrey J.↗

Analysis and synthesis of abstract data types through generalization from examples

The discovery of general patterns of behavior from a set of input/output examples can be a useful technique in the automated analysis and synthesis of software systems. These generalized descriptions of the behavior form a set of assertions which can be used for validation, program synthesis, program testing, and run-time monitoring. Describing the behavior is characterized as a learning process in which the set of inputs is mapped into an appropriate transform space such that general patterns can be easily characterized. The learning algorithm must chose a transform function and define a subset of the transform space which is related to equivalence classes of behavior in the original domain. An algorithm for analyzing the behavior of abstract data types is presented and several examples are given. The use of the analysis for purposes of program synthesis is also discussed.

Wild, Christian↗

Performance analysis of a generalized concurrent error detection procedure

A general procedure for error detection in complex systems, called the data block capture and analysis monitoring process, is described and analyzed. It is assumed that, in addition to being exposed to potential external fault sources, a complex system will in general always contain embedded hardware and software fault mechanisms which can cause the system to perform incorrect computations and/or produce incorrect output. Thus, in operation, the system continuously moves back and forth between error and no-error states. These external fault sources or internal fault mechanisms are extremely difficult to detect. The data block capture and analysis monitoring process is concerned with detecting deviations from the normal performance of the system, known as errors, which are symptomatic of fault conditions. The process consists of repeatedly recording a fixed amount of data from a set of predetermined observation lines of the system being monitored (i.e., capturing a block of data) and then analyzing the captured block in an attempt to determine whether the system is functioning correctly. The performances of linear, quadratic, and logarithmic data analysis algorithms are rigorously characterized in terms of the probability of correctly detecting an error, the expectation and variance of the number of false alarms per error, and the expectation and variance of the latency in detection of errors. Insight into the nature of the general problem of error detection is obtained.

Blough, Douglas M.↗

Dark Energy Survey Year 6 Results: Point-Spread Function Modeling

We present the point-spread function (PSF) modeling for weak lensing shear measurement using the full six years of the Dark Energy Survey (DES Y6) data. We review the PSF estimation procedure using the PIFF (PSFs In the Full FOV) software package and describe the key improvements made to PIFF and modeling diagnostics since the DES year three (Y3) analysis: (i) use of external Gaia and infrared photometry catalogs to ensure higher purity of the stellar sample used for model fitting, (ii) addition of color-dependent PSF modeling, the first for any weak lensing analysis, and (iii) inclusion of model diagnostics inspecting fourth-order moments, which can bias weak lensing measurements to a similar degree as second-order modeling errors. Through a comprehensive set of diagnostic tests, we demonstrate the improved accuracy of the Y6 models evident in significantly smaller systematic errors than those of the Y3 analysis, in which all g band data were excluded due to insufficiently accurate PSF models. For the Y6 weak lensing analysis, we include g band photometry data in addition to the riz bands, providing a fourth band for photometric redshift estimation. Looking forward to the next generation of wide-field surveys, we describe several ongoing improvements to PIFF, which will be the default PSF modeling software for weak lensing analyses for the Vera C. Rubin Observatory’s Legacy Survey of Space and Time.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

GIDEP Batching Tool

This software provides internal, automated search mechanics of GIDEP (Government- Industry Data Exchange Program) Alert data imported from the GIDEP government Web site. The batching tool allows the import of a single parts list in tab-delimited text format into the local JPL GIDEP database. Delimiters from every part number are removed. The original part numbers with delimiters are compared, as well as the newly generated list without the delimiters. The two lists run against the GIDEP imports, and output any matches. This feature only works with Netscape 2.0 or greater, or Internet Explorer 4.0 or greater. The user selects the browser button to choose a text file to import. When the submit button is pressed, this script will import alerts from the text file into the local JPL GIDEP database. This batch tool provides complete in-house control over exported material and data for automated batch match abilities. The batching tool has the ability to match capabilities of the parts list to tables, and yields results that aid further research and analysis. This provides more control over GIDEP information for metrics and reports information not provided by the government site. This software yields results quickly and gives more control over external data from the government site in order to generate other reports not available from the external source. There is enough space to store years of data. The program relates to risk identification and management with regard to projects and GIDEP alert information encompassing flight parts for space exploration.

Fong, Danny↗

Software Released by LEWICE 2.0 Ice Accretion Software Development Project

Computational icing simulation methods are making the transition from the realm of research to commonplace use in design and certification. As such, standards of software management, design, validation, and documentation must be adjusted to accommodate the increased expectations of the user community with respect to accuracy, reliability, capability, and usability. With this in mind, in collaboration with Glenn's Engineering Design and Analysis Division, the Icing Branch of the NASA Glenn Research Center at Lewis Field began a software improvement project focused on the two-dimensional ice accretion simulation tool LEWICE. This project is serving as an introduction to the concepts of software management and is intended to serve as a pilot project for future icing simulation code development. The LEWICE 2.0 Software Development Project consisted of two major elements: software management and software validation. The software management element consisted of identifying features of well-designed and well-managed software that are appropriate for an analytical prediction tool such as LEWICE and applying them to a revised version of the code. This element included tasks such as identification of software requirements, development and implementation of coding standards, and implementation of software revision control practices. With the application of these techniques, the LEWICE ice accretion code became a more stable and reliable software product. In addition, the lessons learned about software development and maintenance can be factored into future software projects at the outset. The software validation activity was an integral part of our effort to make LEWICE a more accurate and reliable analysis tool. Because of the efforts taken to extensively validate this software, LEWICE 2.0 is more robust than previous releases and can reproduce results accurately across several computing platforms. It also differs from previous versions in the extensive quantitative comparisons of its results with a data base of ice shapes that were generated in Glenn's Icing Research Tunnel. The results of the shape comparisons were analyzed to determine the range of meteorological conditions under which LEWICE 2.0 is within the repeatability found for ice shapes obtained from experiments. These comparisons show that the average variation of LEWICE 2.0 from experimental data is 7.2 percent, whereas the overall variability of the experimental data is 2.5 percent. The LEWICE 2.0 Software Development Project resulted in the release, at the recent Icing Branch LEWICE Workshop, of a more useful and robust analysis tool than was previously available to the icing community. The lessons learned from this project will be applied to the Icing Branch s future software development efforts.

Potapczuk, Mark G.↗

Structural Analysis and Test Comparison of a 20-Meter Inflation-Deployed Solar Sail

Under the direction of the NASA In-Space Propulsion Technology Office, the team of L Garde, NASA Jet Propulsion Laboratory, Ball Aerospace, and NASA Langley Research Center has been developing a scalable solar sail configuration to address NASA s future space propulsion needs. Prior to a flight experiment of a full-scale solar sail, a comprehensive test program was implemented to advance the technology readiness level of the solar sail design. These tests consisted of solar sail component, subsystem, and sub-scale system ground tests that simulated the aspects of the space environment such as vacuum and thermal conditions. In July 2005, a 20-m four-quadrant solar sail system test article was tested in the NASA Glenn Research Center s Space Power Facility to measure its static and dynamic structural responses. Key to the maturation of solar sail technology is the development of validated finite element analysis (FEA) models that can be used for design and analysis of solar sails. A major objective of the program was to utilize the test data to validate the FEA models simulating the solar sail ground tests. The FEA software, ABAQUS, was used to perform the structural analyses to simulate the ground tests performed on the 20-m solar sail test article. This paper presents the details of the FEA modeling, the structural analyses simulating the ground tests, and a comparison of the pretest and post-test analysis predictions with the ground test results for the 20-m solar sail system test article. The structural responses that are compared in the paper include load-deflection curves and natural frequencies for the beam structural assembly and static shape, natural frequencies, and mode shapes for the solar sail membrane. The analysis predictions were in reasonable agreement with the test data. Factors that precluded better correlation of the analyses and the tests were unmeasured initial conditions in the test set-up.

Sleight, David W.↗

Statistical Analysis of an Infrared Thermography Inspection of Reinforced Carbon-Carbon

Each piece of flight hardware being used on the shuttle must be analyzed and pass NASA requirements before the shuttle is ready for launch. One tool used to detect cracks that lie within flight hardware is Infrared Flash Thermography. This is a non-destructive testing technique which uses an intense flash of light to heat up the surface of a material after which an Infrared camera is used to record the cooling of the material. Since cracks within the material obstruct the natural heat flow through the material, they are visible when viewing the data from the Infrared camera. We used Ecotherm, a software program, to collect data pertaining to the delaminations and analyzed the data using Ecotherm and University of Dayton Log Logistic Probability of Detection (POD) Software. The goal was to reproduce the statistical analysis produced by the University of Dayton software, by using scatter plots, log transforms, and residuals to test the assumption of normality for the residuals.

Comeaux, Kayla↗

SMAnalytics Automated Shape Memory Test Analysis Software User's Manual: UCFTC, UPER, and DSC Test Methods, Version 1.0.2

Over the course of 60 years of shape memory alloy research and development, the properties of these alloys have been measured using various testing methods, which are often customized by the organization performing the test. However, commercial adoption of shape memory alloys in aeronautic actuator applications requires reducing property uncertainty through standardizing test methods. Historically, differential scanning calorimetry (DSC) has been used to measure transformation temperatures under stress-free conditions. This testing method is well established, and tests are run under the applicable standard, ASTM F2004-17: Standard Test Method for Transformation Temperature of Nickel-Titanium Alloys by Thermal Analysis. Two other test methods for measuring strains and transformation temperatures under constant load or free recovery after prestraining have only recently been standardized—ASTM E3097: Standard Test Method for Mechanical Uniaxial Constant Force Thermal Cycling of SMAs (UCFTC) and ASTM E3098: Standard Test Method for Mechanical Uniaxial Pre-Strain and Thermal Free Recovery of SMAs (UPFR). These standards represent a critical step forward in producing reliable material property data for the use of these alloys in aeronautics and other commercial areas. However, no standard programs or software packages were previously available for postprocessing UCFTC- and UPFR-type test data to extract property data. Each organization that performed the testing analyzed data using its own custom manual methods, such as using a plot and a straight edge, spreadsheet plotting methods, or custom code routines, to extract the required values for strains, stresses, and transformation temperatures. SMAnalytics represents the first publicly available uniform software package for processing data generated using the DSC, UCFTC, and UPFR test methods, as well as many modifications of these methods, including loading in martensite versus austenite and performing multiple thermal cycles at stress. In doing so, it provides a tool for reducing potential error or variability in the measured values due to the precision of the technique used and person-to-person variability. It is also expected that this automated data-parsing tool can accelerate the data analysis phase of the test campaign, especially for large data files. This User’s Manual describes how the SMAnalytics software works and the method for its use.

Shape Memory Alloy↗

Data acquisition and analysis on a Macintosh

The introduction of inexpensive analog-to-digital boards for the Macintosh opens the way for its use in areas that have previously been filled by either specialized, dedicated or more expensive mainframe based systems. Two such Macintosh-based systems are the Acoustic Laboratory Data Acquisition System (ALDAS) and the Jet Calibration and Hover Test Facility (JCAHT) data acquisition system. ALDAS provides an inexpensive, transportable means to digitize four channels at up to 50,000 samples per second and analyze this data. The ALDAS software package was written for use with rotorcraft acoustics and performs automatic acoustic calibration of channels, data display, and various types of data analysis. The program can use data obtained either from internal analog-to-digital conversion or discrete external data imported in ASCII format. All aspects of ALDAS can be improved as new hardware becomes available and new features are introduced into the code. The JCAHT data acquisition system was built as not only an analysis program but also to act as the online safety monitoring system. This paper will provide an overview of these systems.

Watts, Michael E.↗

[MODIS Investigation]

The objectives of the last six months were: Continue analysis of Hawaii Ocean Time-series (HOT) bio-optical mooring data, Recover instrumentation from JGOFS cruises in the Southern Ocean and analyze data Maintain documentation of MOCEAN algorithms and software for use by MOCEAN and GLI teams Continue chemostat experiments on the relationship of fluorescence quantum yield to environmental factors. Continue to develop and expand browser-based information system for in situ bio-optical data Work Analysis of Field Data from Hawaii We are continuing to analyze bio-optical data collected at the Hawaii Ocean Time Series mooring. The HOT bio-optical mooring was recovered in May 1998. After retrieving the data, the sensor package was serviced and redeployed. We now have over 18 months of data. These are being analyzed as part of a larger study of mesoscale processes at this JGOFS time series site. We have had some failures in the data logger which have affected the fluorescence channels. These are being repaired. We also had an instrument housing failure, and minor modifications have been made to avoid subsequent problems. In addition, Ricardo Letelier is funded as part of the SeaWiFS calibrator/validation effort (through a subcontract from the University of Hawaii, Dr. John Porter), and he is collecting bio-optical and fluorescence data as part of the HOT activity.

Abbott, Mark R.↗

Use of Machine Learning on PMU Data for Transmission System Fault Analysis

Synchrophasor technology has been used for monitoring, control, and protection of bulk power system for over 10 years. Deployment of phasor measurement units (PMUs) in the USA power system has surpassed 3000 units installed in the transmission substations as stand-alone intelligent electronic devices (IEDs) or as a software add-on to other devices such as digital protective relays (DPRs) or digital fault recorders (DFRs). By now, thousands of terabytes of PMU data may have been captured and stored by various transmission system operators (TSOs) and independent system operators (ISOs). This creates an opportunity to deploy advanced machine learning (ML) techniques to detect and classify faults recorded by PMUs automatically to be used by the system operators for rapid, critical decision-making when manual analysis of the past or unfolding events is not feasible. In this paper we offer a brief background on how the automated fault analysis may be done using DPR and/or DFR data, and compare some of the legacy approaches to the new ML approaches in the context of the system-wide PMU recordings. We then offer insights from developing practical ML solutions that have been applied on field recordings captured by close to 450 PMUs from all three US interconnections (Western, Eastern and ERCOT) over two years (2016-2017). We identify and illustrate ML challenges we addressed: inaccurate data, data with scarce and temporally imprecise fault labels, data recorded by PMUs sparsely located at substations resulting in the fault records taken afar from the ends of the faulted lines, data containing only positive sequence values, and data taken at different voltage levels. We then illustrate the ML model results for fault analysis under different application scenarios. The novelty of this study is not only in the design, implementation, and performance analysis of the ML algorithms, but also in the use of advanced fault modelling and simulation approaches to improve the training results when developing supervised ML models for fault detection and classification. Extensive simulations of faults were conducted on a 14-bus power system to create a training dataset with over 1400 accurately labelled faults. This dataset was applied to enhance the accuracy of fault detection and classification of machine learning-based models trained with small number of labelled faults in large datasets recorded in the grid interconnections ranging from 5,000 to 70,000 buses.

Synchrophasors, Machine Learning, Fault Analysis, ↗

Comparison of Aircraft Icing Growth Assessment Software

A research project is underway to produce computer software that can accurately predict ice growth under any meteorological conditions for any aircraft surface. An extensive comparison of the results in a quantifiable manner against the database of ice shapes that have been generated in the NASA Glenn Icing Research Tunnel (IRT) has been performed, including additional data taken to extend the database in the Super-cooled Large Drop (SLD) regime. The project shows the differences in ice shape between LEWICE 3.2.2, GlennICE, and experimental data. The project addresses the validation of the software against a recent set of ice-shape data in the SLD regime. This validation effort mirrors a similar effort undertaken for previous validations of LEWICE. Those reports quantified the ice accretion prediction capabilities of the LEWICE software. Several ice geometry features were proposed for comparing ice shapes in a quantitative manner. The resulting analysis showed that LEWICE compared well to the available experimental data.

Wright, William↗

Experimental evaluation of the certification-trail method

Certification trails are a recently introduced and promising approach to fault-detection and fault-tolerance. A comprehensive attempt to assess experimentally the performance and overall value of the method is reported. The method is applied to algorithms for the following problems: huffman tree, shortest path, minimum spanning tree, sorting, and convex hull. Our results reveal many cases in which an approach using certification-trails allows for significantly faster overall program execution time than a basic time redundancy-approach. Algorithms for the answer-validation problem for abstract data types were also examined. This kind of problem provides a basis for applying the certification-trail method to wide classes of algorithms. Answer-validation solutions for two types of priority queues were implemented and analyzed. In both cases, the algorithm which performs answer-validation is substantially faster than the original algorithm for computing the answer. Next, a probabilistic model and analysis which enables comparison between the certification-trail method and the time-redundancy approach were presented. The analysis reveals some substantial and sometimes surprising advantages for ther certification-trail method. Finally, the work our group performed on the design and implementation of fault injection testbeds for experimental analysis of the certification trail technique is discussed. This work employs two distinct methodologies, software fault injection (modification of instruction, data, and stack segments of programs on a Sun Sparcstation ELC and on an IBM 386 PC) and hardware fault injection (control, address, and data lines of a Motorola MC68000-based target system pulsed at logical zero/one values). Our results indicate the viability of the certification trail technique. It is also believed that the tools developed provide a solid base for additional exploration.

Sullivan, Gregory F.↗

Lithium-Ion Battery Design for Grid-Scale Energy Storage App

A software that delivers parameters from energy storage system (ESS) to container, rack, module and single cell design, as well as data analysis on arbitrage energy and frequency regulation of ESS in different regions, has been developed. The Lithium-ion Battery Design for Grid-scale Energy Storage App V1.0 has the capability to output the system, module and cell design with the energy, power, capacity, group method, cost of single cell, and single cell test protocol which break down from input energy storage system data in different regions. The default chemistry of the battery is LiFePO4 and graphite. The energy density of the graphite/LiFePO 4 pouch cell ranges from 100 Wh/kg to 200 Wh/Kg in the software. Graphite/LiFePO 4 pouch cell (up to 1Ah in lab) manufacturing line is also built and can be used to evaluate the test protocol, moreover, for electrolyte evaluation in other ESMI seedling projects. The software enables rapid prototyping to accelerate energy storage research, development, and manufacturing.

Liu, Dianying↗