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All sources NASA NTRS DOE OSTI

DOE OSTI2025

UnigeneFinder: An Automated Pipeline for Gene Calling From Transcriptome Assemblies Without a Reference Genome

ABSTRACT For most species, transcriptome data are much more readily available than genome data. Without a reference genome, gene calling is cumbersome and inaccurate because of the high degree of redundancy in de novo transcriptome assemblies. To simplify and increase the accuracy of de novo transcriptome assembly in the absence of a reference genome, we developed UnigeneFinder. Combining several clustering methods, UnigeneFinder substantially reduces the redundancy typical of raw transcriptome assemblies. This pipeline offers an effective solution to the problem of inflated transcript numbers, achieving a closer representation of the actual underlying genome. UnigeneFinder performs comparably or better, compared with existing tools, on plant species with varying genome complexities. UnigeneFinder is the only available transcriptome redundancy solution that fully automates the generation of primary transcript, coding region, and protein sequences, analogous to those available for high‐quality reference genomes. These features, coupled with the pipeline’s cross‐platform implementation, focus on automation, and an accessible, user‐friendly interface, make UnigeneFinder a useful tool for many downstream sequence‐based analyses in nonmodel organisms lacking a reference genome, including differential gene expression analysis, accurate ortholog identification, functional enrichments, and evolutionary analyses. UnigeneFinder also runs efficiently both on high‐performance computing (HPC) systems and personal computers, further reducing barriers to use.

Xue, Bo [Plant Resilience Institute Michigan State↗

NASA NTRS1982

Land Mobile Satellite Service (LMSS): A conceptual system design and identification of the critical technologies. Part 1: Executive summary

A system design for a satellite aided land mobile service is described. The advanced system is based on a geostationary satellite which employs a large UHF reflector to communicate with small user antennas on mobile vehicles. It is shown that the system through multiple beam antennas and frequency reuse provides for radiotelephone and dispatch channels. It is concluded that the system is technologically feasible to provide service to rural and remote regions.

Naderi, F.↗

NASA NTRS2021

VESIcal Part I: An open-source thermodynamic model engine for mixed volatile (H2O-CO2) solubility in silicate melts

Thermodynamics has been fundamental to the interpretation of geologic data and modeling of geologic systems for decades. However, more recent advancements in computational capabilities and a marked increase in researchers’ accessibility to computing tools has outpaced the functionality and extensibility of currently available modeling tools. Here we present VESIcal (Volatile Equilibria and Saturation Identification calculator): the first comprehensive modeling tool for H 2 O, CO 2 , and mixed (H 2 O-CO 2 ) solubility in silicate melts that: a) allows users access to seven commonly used models, plus easy inter-comparison between models; b) provides universal functionality for all models (e.g., functions for calculating saturation pressures, degassing paths, etc.); c) can process large datasets (1,000’s of samples) automatically; d) can output computed data into an excel spreadsheet for simple post-modeling analysis; e) integrates advanced plotting capabilities directly within the tool; and f) provides all of these within the framework of a python library, making the tool extensible by the user and allowing any of the model functions to be incorporated into any other code capable of calling python. The tool is presented within this manuscript, which is a Jupyter notebook containing worked examples accessible to python users with a range of skill levels. The basic functions of VESIcal can also be access via a web app (https://vesical.anvil.app). The VESIcal python library is open-source and available for download at https://github.com/kaylai/VESIcal.

K. Iacovino↗

NASA NTRS1977

Interactive LORAN-C to geographic and geographic-to-LORAN-C computation

The LORAN program is stored in CMS disk files for use by Avionics Engineering Center terminal users. A CMS EXEC file named LORAN controls program operation. The user types LORAN and the program then prompts for data input and produces output on the terminal. The FORTRAN program refers to a disk file of LORAN master data giving station locations, coding delays, repetition rate and station pair identification letters. For Geographic-to-LORAN conversion, no iterative computations are required; the program is a straightforward coordinate conversion based upon the techniques described by the Navy. For LORAN-to-Geographic conversion, the original Navy program required a dead-reckoned position, near the actual unknown fix, to begin computations. No iteration was performed to obtain the LORAN fix, but internal program errors occurred at execution time if the dead-reckoned fix were displaced from the actual fix by more than a few minutes of latitude or longitude. In order to enhance usefulness of the program for the terminal user, an iterative routine was added which allows a single dead-reckoned position to be entered from the master data file for each LORAN chain. The results compare exactly with the LORAN-C navigation chart, and provide adequate benchmark data for general aviation flight planning and data analysis.

Piecuch, L. M.↗

DOE OSTI2025

The CHIMERAS project: design framework for the Collisionless HIgh-beta Magnetized Experiment Researching Astrophysical Systems

From the near-Earth solar wind to the intracluster medium of galaxy clusters, collisionless, high-beta, magnetized plasmas pervade our universe. Energy and momentum transport from large-scale fields and flows to small-scale motions of plasma particles is ubiquitous in these systems, but a full picture of the underlying physical mechanisms remains elusive. The transfer is often mediated by a turbulent cascade of Alfvénic fluctuations as well as a variety of kinetic instabilities; these processes tend to be multi-scale and/or multi-dimensional, which makes them difficult to study using spacecraft missions and numerical simulations alone. Meanwhile, existing laboratory devices struggle to produce the collisionless, high ion beta (β i ≳ 1), magnetized plasmas across the range of scales necessary to address these problems. As envisioned in recent community planning documents, it is therefore important to build a next generation laboratory facility to create a β i ≳ 1, collisionless, magnetized plasma in the laboratory for the first time. A working group has been formed and is actively defining the necessary technical requirements to move the facility towards a construction-ready state. Recent progress includes the development of target parameters and diagnostic requirements as well as the identification of a need for source-target device geometry. As the working group is already leading to new synergies across the community, we anticipate a broad community of users funded by a variety of federal agencies (including National Aeronautics and Space Administration, Department of Energy and National Science Foundation) to make copious use of the future facility.

astrophysical plasmas↗

DOE OSTI2022

Guiding the choice of informatics software and tools for lipidomics research applications

Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Machine Learning and Social Media to Mine and Disseminate Big Scientific Data

One of the challenges in supplying the communities with wider access to scientific databases is the need for knowledge of database languages like Structured Query Language (SQL). Although the SQL language has been published in many forms, not everybody is able to write SQL queries. Another challenge is that it might not be practical to make the public aware of the structure of databases. There is a need for novice users to query relational databases using their natural language. To solve this problem, many natural language interfaces to structured databases have been developed. The goal is to provide a more intuitive method for generating database queries and delivering responses. Through social media, which makes it possible to interact with a wide section of the population, and with the help of natural language processing, researchers at the Atmospheric Radiation Measurement (ARM) Data Center at Oak Ridge National Laboratory (ORNL) have developed a concept to enable easy search and retrieval of data from several environmental data centers for the scientific community through social media.Using a machine learning framework that maps natural language text to thousands of datasets, instruments, variables, and data streams, the prototype system would allow users to request data through Twitter and receive a link (via tweet) to applicable data results on the project's search catalog tailored to their key words. This automated identification of relevant data from various petascale archives at ORNL could increase convenience, access, and use of the project's data by the broader community. In this paper we discuss how some data-intensive projects at ORNL are using innovative ways to help in data discovery.

Devarakonda, Ranjeet↗

NASA NTRS1972

Identification of specific requirements for a NASA aerospace law information system and identification of the acquisition requirements for an aerospace law collection for the NASA law library

The study to develop, implement, and maintain a space law library and information system is summarized. The survey plan; major interviews with individuals representative of potential sources, users and producers of information related to aerospace law; and system trade-off analyses are discussed along with the NASA/RECON system capability. The NASA publications of STAR and IAA are described, and the NASA legal micro-thesaurus is included.

Morenoff, J.↗

DOE OSTI2020

Jefferson Laboratory C100 Superconducting Radio-Frequency Cavity Fault Data, 2020

The dataset was created to train machine learning models for the task of identifying the (1) cavity and (2) fault type from C100-type cryomodules at the Thomas Jefferson National Accelerator Facility (Jefferson Lab), thereby replacing the time-consuming efforts of a subject matter expert. Superconducting radio-frequency (SRF) cavity trips represent a significant source of accelerator downtime. Real-time – rather than post-mortem – identification of the offending cavity and classification of the fault type would give control room operators valuable feedback for corrective action planning. The anticipated benefit is increased beam-on-target time for users and provides performance metrics that can be used to improve future cavity designs. A series of 17 RF signals are recorded for each of the 8 cavities in a C100 cryomodule every time a cavity trips. These time-series signals are written to file using a specially designed data acquisition system. The dataset represents fault events recorded during Continuous Electron Beam Accelerator Facility (CEBAF) beam operations between January 18, 2019 and March 9, 2020. The following filtering steps were applied to collected data; (1) only 4 of the 17 signals per cavity are retained (GMES, GASK, CRFP, DETA2) (2) only events with data from each of the eight cavities in the cryomodule are kept, (3) only events that were sampled at 5 kHz were kept, (4) events from cryomodule 0L04 were neglected, (5) events occurring between February 4, 3PM and February 5, 12PM were neglected. As a result of preprocessing, the dataset is comprised of 2,375 unique events. The full dataset is comprised of three files: features.csv, cavity_labels.csv, fault_labels.csv. Each instance in faults.csv includes a timestamp (“date_time”), a label for the cryomodule which experienced the trip (“zone_label”), and 192 features (“feature_1”, “feature_2”... “feature_192”). The features correspond to 6 autoregressive features for each of 4 signals per cavity for each of the 8 cavities (6 × 4 signals/cavity × 8 cavities/cryomodule = 192). To deal with the large variation of signal amplitudes, time-series standardization via the z-score (standard score) function was applied prior to computing the features. For each instance, there is an associated label for the (1) cavity which faulted first (cavity_labels.csv) and (2) the type of fault that caused the trip (fault_labels.csv). The cavity identification can take values of [0, 1, 2, 3, 4, 5, 6, 7, 8] and the fault type can take values of [‘Microphonics’, ‘Quench_100ms’, ‘Controls_Fault’, ‘E_Quench’, ‘Quench_3ms’, ‘Single_Cav_Turn_Off’ , ‘Heat_Riser_Choke’, ‘Multi_Cav_Turn_Off’].

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

Transmission Data-Driven User-Defined Model for Inverter-based and Conventional Power Plants

Recent events in Odessa [1], [2] have shed light on the complexities of integrating large Inverter-Based Resource (IBR) plants with the transmission system, prompting NERC to stress continuous performance monitoring by transmission operators. Challenges such as plant control updates, IBR model revisions, Phase-locked loop loss of synchronism, and protection events have been identified, underscoring the need for enhanced monitoring protocols by regulatory bodies. The recent FERC 901 order underscores the importance of accurate data exchange regarding IBRs for reliability studies. However, limited access to IBR plant-related data hampers effective decision-making for transmission operators (TOP). This paper proposes a method for constructing data-driven User-Defined dynamic Models (UDM) for power plants for validating multiple-event data using field measurements from interconnection bus locations. The problem is formulated as a power plant model identification problem and a multi-task learning approach under partial input observability assumptions is proposed in this work. This approach aims to predict aggregated responses of conventional and IBR power plants during various dynamic physical events which is useful for planning studies under diverse disturbance conditions. Ultimately, this methodology emphasizes the importance of plant visibility to operators in addressing power system challenges, facilitating improved planning and operational studies.

Mahapatra, Kaveri [BATTELLE (PACIFIC NW LAB)]↗

NASA NTRS1981

Large modal survey testing using the Ibrahim time domain /ITD/ identification technique

The ability of the ITD identification algorithm in identifying a complete set of structural modal parameters using a large number of free-response time histories simultaneously in one analysis, assuming a math model with a high number of degrees-of-freedom, has been studied. Identification results using simulated free responses of a uniform rectangular plate, with 225 measurement stations, and experimental responses from a ground vibration test of the Long Duration Exposure Facility (LDEF) Space Shuttle payload, with 142 measurement stations, are presented. As many as 300 degrees-of-freedom were allowed in analyzing these data. In general, the use of a significantly oversized math model in the identification process was found to maintain or increase identification accuracy and to identify modes of low response level that are not identified with smaller math model sizes. The concept of a Mode Shape Correlation Constant is introduced for use when more than one identification analysis of the same structure are conducted. This constant quantifies the degree of correlation between any two sets of complex mode shapes identified using different excitation conditions, different user-selectable algorithm constants, or overlapping sets of measurements.

Ibrahim, S. R.↗

NASA NTRS1985

Large Modal Survey Testing Using the Ibrahim Time Domain Identification Technique

Ibrahim, S. R.↗

NASA NTRS2005

An Automated Flying-Insect-Detection System

An automated flying-insect-detection system (AFIDS) was developed as a proof-of-concept instrument for real-time detection and identification of flying insects. This type of system has use in public health and homeland security decision support, agriculture and military pest management, and/or entomological research. Insects are first lured into the AFIDS integrated sphere by insect attractants. Once inside the sphere, the insect's wing beats cause alterations in light intensity that is detected by a photoelectric sensor. Following detection, the insects are encouraged (with the use of a small fan) to move out of the sphere and into a designated insect trap where they are held for taxonomic identification or serological testing. The acquired electronic wing beat signatures are preprocessed (Fourier transformed) in real-time to display a periodic signal. These signals are sent to the end user where they are graphically displayed. All AFIDS data are pre-processed in the field with the use of a laptop computer equipped with LABVIEW. The AFIDS software can be programmed to run continuously or at specific time intervals when insects are prevalent. A special DC-restored transimpedance amplifier reduces the contributions of low-frequency background light signals, and affords approximately two orders of magnitude greater AC gain than conventional amplifiers. This greatly increases the signal-to-noise ratio and enables the detection of small changes in light intensity. The AFIDS light source consists of high-intensity Al GaInP light-emitting diodes (LEDs). The AFIDS circuitry minimizes brightness fluctuations in the LEDs and when integrated with an integrating sphere, creates a diffuse uniform light field. The insect wing beats isotropically scatter the diffuse light in the sphere and create wing beat signatures that are detected by the sensor. This configuration minimizes variations in signal associated with insect flight orientation.

Vann, Timi↗

NASA NTRS2007

An Automated Flying-Insect Detection System

An automated flying-insect detection system (AFIDS) was developed as a proof-of-concept instrument for real-time detection and identification of flying insects. This type of system has use in public health and homeland-security decision support, agriculture and military pest management, and/or entomological research. Insects are first lured into the AFIDS integrated sphere by insect attractants. Once inside the sphere, the insect s wing beats cause alterations in light intensity that is detected by a photoelectric sensor. Following detection, the insects are encouraged (with the use of a small fan) to move out of the sphere and into a designated insect trap where they are held for taxonomic identification or serological testing. The acquired electronic wing-beat signatures are preprocessed (Fourier transformed) in real time to display a periodic signal. These signals are sent to the end user where they are graphically. All AFIDS data are preprocessed in the field with the use of a laptop computer equipped with LabVIEW. The AFIDS software can be programmed to run continuously or at specific time intervals when insects are prevalent. A special DC-restored transimpedance amplifier reduces the contributions of low-frequency background light signals, and affords approximately two orders of magnitude greater AC gain than conventional amplifiers. This greatly increases the signal-to-noise ratio and enables the detection of small changes in light intensity. The AFIDS light source consists of high-intensity Al-GaInP light-emitting diodes (LEDs). The AFIDS circuitry minimizes brightness fluctuations in the LEDs and when integrated with an integrating sphere, creates a diffuse uniform light field. The insect wing beats isotropically scatter the diffuse light in the sphere and create wing-beat signatures that are detected by the sensor. This configuration minimizes variations in signal associated with insect flight orientation. Preliminary data indicate that AFIDS has sufficient sensitivity and frequency measuring capability to differentiate between male and female mosquitoes (Figure 1, bottom panel) and fruit flies (data not shown). Similar studies show that AFIDS can be utilized to detect discrete differences between two mosquito species, Aedes aegypti and Aedes albopictus. When fully deployable, a wireless network of AFIDS monitors could be used in combination with other remotely sensed data and visually displayed in a geographic information system (GIS) to provide real-time surveillance (see Figure 2). More accurate and sensitive insect population forecasts and effective rapid response and mitigation of insect issues would then be possible.

Vann, Timi↗

NASA NTRS2011

Computer-Aided Parallelizer and Optimizer

The Computer-Aided Parallelizer and Optimizer (CAPO) automates the insertion of compiler directives (see figure) to facilitate parallel processing on Shared Memory Parallel (SMP) machines. While CAPO currently is integrated seamlessly into CAPTools (developed at the University of Greenwich, now marketed as ParaWise), CAPO was independently developed at Ames Research Center as one of the components for the Legacy Code Modernization (LCM) project. The current version takes serial FORTRAN programs, performs interprocedural data dependence analysis, and generates OpenMP directives. Due to the widely supported OpenMP standard, the generated OpenMP codes have the potential to run on a wide range of SMP machines. CAPO relies on accurate interprocedural data dependence information currently provided by CAPTools. Compiler directives are generated through identification of parallel loops in the outermost level, construction of parallel regions around parallel loops and optimization of parallel regions, and insertion of directives with automatic identification of private, reduction, induction, and shared variables. Attempts also have been made to identify potential pipeline parallelism (implemented with point-to-point synchronization). Although directives are generated automatically, user interaction with the tool is still important for producing good parallel codes. A comprehensive graphical user interface is included for users to interact with the parallelization process.

Jin, Haoqiang↗

NASA NTRS2019

NASA GIBS and Worldview: Leveraging FOSS for NASA Earth Science Data Visualizations

The NASA Global Imagery Browse Services (GIBS) and Worldview interactive mapping site leverage scientific and community best practices, open source software, and public standards to provide a scalable, compliant, and authoritative source for NASA Earth Observing System (EOS) Earth science data visualizations. GIBS and Worldview allow end users to easily and quickly interact with more than 800 full resolution pre-generated raster- and vector-based visualizations. This interactive discovery approach relies on visual observation and identification of phenomena that are not as simply identified otherwise. This eLightning presentation will exhibit the broad set of capabilities and visualization layers made possible through the GIBS and Worldview open source software. Specific dependencies on, and contributions to, open source software will be highlighted. Additionally, opportunities for future improvements for better interoperability and reuse through open source software will be discussed.

NASA Global Imagery Browse Services (GIBS)↗

NASA NTRS1977

Millimeter wave satellite concepts, volume 1

The identification of technologies necessary for development of millimeter spectrum communication satellites was examined from a system point of view. Development of methodology based on the technical requirements of potential services that might be assigned to millimeter wave bands for identifying the viable and appropriate technologies for future NASA millimeter research and development programs, and testing of this methodology with selected user applications and services were the goals of the program. The entire communications network, both ground and space subsystems was studied. Cost, weight, and performance models for the subsystems, conceptual design for point-to-point and broadcast communications satellites, and analytic relationships between subsystem parameters and an overall link performance are discussed along with baseline conceptual systems, sensitivity studies, model adjustment analyses, identification of critical technologies and their risks, and brief research and development program scenarios for the technologies judged to be moderate or extensive risks. Identification of technologies for millimeter satellite communication systems, and assessment of the relative risks of these technologies, was accomplished through subsystem modeling and link optimization for both point-to-point and broadcast applications.

Hilsen, N. B.↗

DOE OSTI2014

SU-D-17A-07: Development and Evaluation of a Prototype Ultrasonography Respiratory Monitoring System for 4DCT Reconstruction

Purpose: Respiratory motion artifacts are commonly seen in the abdominal and thoracic CT images. A Real-time Position Management (RPM) system is integrated with CT simulator using abdominal surface as a surrogate for tracking the patient respiratory motion. The respiratory-correlated four-dimensional computed tomography (4DCT) is then reconstructed by GE advantage software. However, there are still artifacts due to inaccurate respiratory motion detecting and sorting methods. We developed an Ultrasonography Respiration Monitoring (URM) system which can directly monitor diaphragm motion to detect respiratory cycles. We also developed a new 4DCT sorting and motion estimation method to reduce the respiratory motion artifacts. The new 4DCT system was compared with RPM and the GE 4DCT system. Methods: Imaging from a GE CT scanner was simultaneously correlated with both the RPM and URM to detect respiratory motion. A radiation detector, Blackcat GM-10, recorded the X-ray on/off and synchronized with URM. The diaphragm images were acquired with Ultrasonix RP system. The respiratory wave was derived from diaphragm images and synchronized with CT scanner. A more precise peaks and valleys detection tool was developed and compared with RPM. The motion is estimated for the slices which are not in the predefined respiratory phases by using block matching and optical flow method. The CT slices were then sorted into different phases and reconstructed, compared with the images reconstructed from GE Advantage software using respiratory wave produced from RPM system. Results: The 4DCT images were reconstructed for eight patients. The discontinuity at the diaphragm level due to an inaccurate identification of phases by the RPM was significantly improved by URM system. Conclusion: Our URM 4DCT system was evaluated and compared with RPM and GE 4DCT system. The new system is user friendly and able to reduce motion artifacts. It also has the potential to monitor organ motion during therapy.

62 RADIOLOGY AND NUCLEAR MEDICINE↗