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At least 541 records · Page 30

Enabling Open and Interoperable Science: Multi-Omics Data Processing Platform with NASA GeneLab Standardized Bioinformatics Workflows for Space and Earth Research

Multi-omics biological data continues to be generated at an astounding pace. Genomics, transcriptomics, metabolomics, and proteomics, or collectively known as multi-omics data, are used to assess biological functions, and provide invaluable insights into human, animal, plant, and environmental health both on Earth and in Space. Despite the abundance of these valuable data, the need for bioinformatics expertise, particularly as it relates to the niche filed of space biology, and a lack of accessible resources for processing these data limit their usefulness in deriving biological insights. The NASA Open Science Data Repository (OSDR) provides access to omics data from various spaceflight and analog studies. To enhance the accessibility and reusability of these data, GeneLab (part of OSDR) designs and implements standardized, community-driven, open-source bioinformatics workflows to transform raw omics data into standardized processed data. Currently, GeneLab-processed data from hundreds of space studies have been reused for meta-analyses. This has led to new insights and scientific publications that extend beyond the initial research, thereby enriching our understanding of molecular-scale biological responses to the space environment. To make these bioinformatics workflows open and accessible, GeneLab teamed up with DOE-funded initiatives, including the National Microbiome Data Collaborative (NMDC), to create the NASA EDGE [Empowering the Development of Genomics Expertise] Bioinformatics web-based platform. NASA EDGE utilizes shared compute resources to run the GeneLab standardized bioinformatics workflows, which eliminates the need for researchers to have their own high performance computing cluster. The web-based platform makes complicated biological analyses incredibly easy to perform, thus expanding the reach of these analyses to bioinformatics novices, students, and even citizen scientists enabling them to contribute to scientific discoveries and progress. The authors will demonstrate how the NASA EDGE platform can be used to process microbial omics data hosted on OSDR as well as user-generated omics datasets using GeneLab’s standard workflows.

Amanda M. Saravia-Butler↗

Unsupervised spatial clustering with spectral discrimination

The development of a computer program is reported for extracting features from remotely sensed data presented in digital image form. This computer program requires no human supervision or prejudgment and operates unassisted on the raw digital data. A condensed general background is included on remote sensing of earth features and a short synopsis on some of the most commonly used types of feature extraction techniques. Results obtained from the unsupervised feature extraction computer program along with a description and listing of the computer program are presented.

Jayroe, R. R., Jr.↗

Search and Recovery Efforts for the ALSEP Data Tapes

On NASA's first human lunar landing on Apollo II in July 1969, the astronauts deployed a set of scientific instruments called Early Apollo Science Experiments Package (EASEP). It was powered by a solar panel and operated for -20 earth-days and transmitted data to the Earth. This paved a way for deployment of more expansive instrument packages, powered by radioisotope thermoelectric generators, on Apollo 12, 14, 15, 16, and 17 in November 1969 through December 1972. They were called Apollo Lunar Surface Experiments Packages (ALSEPs). Each ALSEP consisted of a variety of instruments such as seismometers, magnetometers, solar wind spectrometers, heat flow probes, etc. The majority of these instruments kept functioning long after their one-year design lifetime requirement, and they transmitted data to the Earth until September 1977, when the program ended. Over the three decades that followed, users of the NSSDC-archived data have learned that many of the ALSEP instrument data are not complete. The present work is a progress report on the authors' recent effort for restoring the entire raw ALSEP data that were received from the Moon,

Nagihara, S.↗

Discovery of X-ray bursts from two sources in Aquila

Two X-ray burst sources have been discovered in Aquila with the aid of the SAS 3 X-ray Observatory; MXB 1906 + 00 and Aql MXB. The present paper reports on source positions, spectra, time structure, and burst energy. Five bursts were detected from MXB 1906 + 00, and the data are shown to be consistent with the assumption that there was a burst about every 8.9 hr. A comparison of raw counting data for three bursts indicates that the bursts were detected in the energy range from 1.3 to 19 keV and that the spectrum softened during burst decay. The spectrum of the one burst observed from Aql MXB is found not to soften during burst decay. It is suggested that MXB 1906 + 00 and the previously known 'steady' source A 1905 + 00 are very likely to be the same source and that the ratio of time-averaged 'steady' luminosity to time-averaged burst luminosity would be approximately 80.

Lewin, W. H. G.↗

Processing AIRS Scientific Data Through Level 2

The Atmospheric Infrared Spectrometer (AIRS) Science Processing System (SPS) is a collection of computer programs, denoted product generation executives (PGEs), for processing the readings of the AIRS suite of infrared and microwave instruments orbiting the Earth aboard NASA s Aqua spacecraft. AIRS SPS at an earlier stage of development was described in "Initial Processing of Infrared Spectral Data' (NPO-35243), NASA Tech Briefs, Vol. 28, No. 11 (November 2004), page 39. To recapitulate: Starting from level 0 (representing raw AIRS data), the PGEs and their data products are denoted by alphanumeric labels (1A, 1B, and 2) that signify the successive stages of processing. The cited prior article described processing through level 1B (the level-2 PGEs were not yet operational). The level-2 PGEs, which are now operational, receive packages of level-1B geolocated radiance data products and produce such geolocated geophysical atmospheric data products such as temperature and humidity profiles. The process of computing these geophysical data products is denoted "retrieval" and is quite complex. The main steps of the process are denoted microwave-only retrieval, cloud detection and cloud clearing, regression, full retrieval, and rapid transmittance algorithm.

Oliphant, Robert↗

Using Quality Attributes to Bridge Systems Engineering Gaps : A Juno Ground Data Systems Case Study

The Juno Mission to Jupiter is the second mission selected by the NASA New Frontiers Program. Juno launched August 2011 and will reach Jupiter July 2016. Juno's payload system is composed of nine instruments plus a gravity science experiment. One of the primary functions of the Juno Ground Data System (GDS) is the assembly and distribution of the CFDP (CCSDS File Delivery Protocol) product telemetry, also referred to as raw science data, for eight out of the nine instruments. The GDS accomplishes this with the Instrument Data Pipeline (IDP). During payload integration, the first attempt to exercise the IDP in a flight like manner revealed that although the functional requirements were well understood, the system was unable to meet latency requirements with the as-is heritage design. A systems engineering gap emerged between Juno instrument data delivery requirements and the assumptions behind the heritage flight-ground interactions. This paper describes the use of quality attributes to measure and overcome this gap by introducing a new systems engineering activity, and a new monitoring service architecture that successfully delivered the performance metrics needed to validate Juno IDP.

Ground Data Systems (GDS)↗

Automated Rock Identification for Future Mars Exploration Missions

A key task for human or robotic explorers on the surface of Mars is choosing which particular rock or mineral samples should be selected for more intensive study. The usual challenges of such a task are compounded by the lack of sensory input available to a suited astronaut or the limited downlink bandwidth available to a rover. Additional challenges facing a human mission include limited surface time and the similarities in appearance of important minerals (e.g. carbonates, silicates, salts). Yet the choice of which sample to collect is critical. To address this challenge we are developing science analysis algorithms to interface with a Geologist's Field Assistant (GFA) device that will allow robotic or human remote explorers to better sense and explore their surroundings during limited surface excursions. We aim for our algorithms to interpret spectral and imaging data obtained by various sensors. The algorithms, for example, will identify key minerals, rocks, and sediments from mid-IR, Raman, and visible/near-IR spectra as well as from high resolution and microscopic images to help interpret data and to provide high-level advice to the remote explorer. A top-level system will consider multiple inputs from raw sensor data output by imagers and spectrometers (visible/near-IR, mid-IR, and Raman) as well as human opinion to identify rock and mineral samples.

Gulick, V. C.↗

The use of airborne imaging spectrometer data to determine experimentally induced variation in coniferous canopy chemistry

It was experimentally determined whether induced differences in forest canopy chemical composition can be detected using data from the Airborne Imaging Spectrometer (AIS). Treatments were applied to an even-aged forest of Douglas fir trees. Work to date has stressed wet chemical analysis of foilage samples and correction of AIS data. Plot treatments were successful in providing a range of foliar N2 concentrations. Much time was spent investigating and correcting problems with the raw AIS data. Initial problems with groups of drop out lines in the AIS data were traced to the tape recorder and the tape drive. Custom adjustment of the tape drive led to recovery of most missing lines. Remaining individual drop out lines were replaced using average of adjacent lines. Application of a notch filter to the Fourier transform of the image in each band satisfactorily removed vertical striping. The aspect ratio was corrected by resampling the image in the line direction using nearest neighbor interpolation.

Swanberg, Nancy A.↗

SAR data compression: Application, requirements, and designs

The feasibility of reducing data volume and data rate is evaluated for the Earth Observing System (EOS) Synthetic Aperture Radar (SAR). All elements of data stream from the sensor downlink data stream to electronic delivery of browse data products are explored. The factors influencing design of a data compression system are analyzed, including the signal data characteristics, the image quality requirements, and the throughput requirements. The conclusion is that little or no reduction can be achieved in the raw signal data using traditional data compression techniques (e.g., vector quantization, adaptive discrete cosine transform) due to the induced phase errors in the output image. However, after image formation, a number of techniques are effective for data compression.

Curlander, John C.↗

Bayesian Blocks: A New Method to Analyze Photon Counting Data

A Bayesian analysis of photon-counting data leads to a new time-domain algorithm for detecting localized structures (bursts), revealing pulse shapes, and generally characterizing intensity variations. The raw counting data -- time-tag events (TTE), time-to-spill (TTS) data, or binned counts -- is converted to a maximum likelihood segmentation of the observation into time intervals during which the photon arrival rate is perceptibly constant -- i.e. has a fixed intensity without statistically significant variations. The resulting structures, Bayesian Blocks, can be thought of as bins with arbitrary spacing determined by the data. The method itself sets no lower limit to the time scale on which variability can be detected. We have applied the method to RXTE data on Cyg X-1, yielding information on this source's short-time-scale variability.

Scargle, Jeffrey D.↗

Tracking the Martian CO2 Polar Ice Caps in Infrared Images

Researchers at NASA s Jet Propulsion Laboratory have developed a method for automatically tracking the polar caps on Mars as they advance and recede each year (see figure). The seasonal Mars polar caps are composed mainly of CO2 ice and are therefore cold enough to stand out clearly in infrared data collected by the Thermal Emission Imaging System (THEMIS) onboard the Mars Odyssey spacecraft. The Bimodal Image Temperature (BIT) histogram analysis algorithm analyzes raw, uncalibrated data to identify images that contain both "cold" ("polar cap") and "warm" ("not polar cap") pixels. The algorithm dynamically identifies the temperature that separates these two regions. This flexibility is critical, because in the absence of any calibration, the threshold temperature can vary significantly from image to image. Using the identified threshold, the algorithm classifies each pixel in the image as "polar cap" or "not polar cap," then identifies the image row that contains the spatial transition from "polar cap" to "not polar cap." While this method is useful for analyzing data that has already been returned by THEMIS, it has even more significance with respect to data that has not yet been collected. Instead of seeking the polar cap only in specific, targeted images, the simplicity and efficiency of this method makes it feasible for direct, onboard use. That is, THEMIS could continuously monitor its observations for any detections of the polar-cap edge, producing detections over a wide range of spatial and temporal conditions. This effort can greatly contribute to our understanding of long-term climatic change on Mars.

Wagstaff, Kiri L.↗

Processing Of Multispectral Data For Identification Of Rocks

Linear discriminant analysis and supervised classification evaluated. Report discusses processing of multispectral remote-sensing imagery to identify kinds of sedimentary rocks by spectral signatures in geological and geographical contexts. Raw image data are spectra of picture elements in images of seven sedimentary rock units exposed on margin of Wind River Basin in Wyoming. Data acquired by Landsat Thematic Mapper (TM), Thermal Infrared Multispectral Scanner (TIMS), and NASA/JPL airborne synthetic-aperture radar (SAR).

Evans, Diane L.↗

Converting CSV Files to RKSML Files

A computer program converts, into a format suitable for processing on Earth, files of downlinked telemetric data pertaining to the operation of the Instrument Deployment Device (IDD), which is a robot arm on either of the Mars Explorer Rovers (MERs). The raw downlinked data files are in comma-separated- value (CSV) format. The present program converts the files into Rover Kinematics State Markup Language (RKSML), which is an Extensible Markup Language (XML) format that facilitates representation of operations of the IDD and enables analysis of the operations by means of the Rover Sequencing Validation Program (RSVP), which is used to build sequences of commanded operations for the MERs. After conversion by means of the present program, the downlinked data can be processed by RSVP, enabling the MER downlink operations team to play back the actual IDD activity represented by the telemetric data against the planned IDD activity. Thus, the present program enhances the diagnosis of anomalies that manifest themselves as differences between actual and planned IDD activities.

Trebi-Ollennu, Ashitey↗

Study of spectral/radiometric characteristics of the Thematic Mapper for land use applications

Progress during the Environmental Research Institute of Michigan-ERIM's and 5 image data quality assessment program for the thematic mapper is described. Analyses of LANDSAT 5 TM radiometric characteristics were performed. Effects which had earlier been found in LANDSAT 4 TM data were found to be present in LANDSAT 5 data as well, including: (1) scan direction related signal droop; (2) scan correlated level shifts; and (3) low frequency coherent noise. Coincident LANDSAT 4 and 5 raw TM data were analyzed, and band by band relationships between the two sensors were derived. Earlier efforts which developed an information theoretic measure of multispectral information content were continued, comparing TM and MSS information content.

Malila, W. A.↗

More-Precise Calibration Of Polarimetric SAR

Algorithm for calibration of polarimetric synthetic-aperture-radar (SAR) data in Stokes-matrix representation more nearly exact. Present algorithm resembles prior algorithm closely, except requires extraction of one additional parameter from high-resolution raw SAR data in scattering-matrix format before compression and transformation to Stokes-matrix format and slight change in subalgorithm compressing those data.

Freeman, Anthony↗

Anomaly Detection for the Roman Space Telescope Wide Field Instrument’s Science Data Processing Pipeline

The Roman Space Telescope (RST) Wide Field Instrument (WFI) will be utilizing a preliminary Science Data Processing (SDP) pipeline during its Integration and Test, and to some extent during Operations, to track basic statistics and identify known features such as cosmic rays, snowballs as well as possible anomalies in raw detector data. In our detectors, these anomalies appear as jumps in the ramp of a readout and are classified as cosmic rays if they appear as a streak or snowballs if they’re more circular. The WFI employs an array of 18 H4RG-10 detectors that collect image samples. Each set of raw frames within a non-destructive exposure is packaged by the SDP pipeline into image cubes for each detector. Each cube is a time series of 4096 × 4096 accumulating pixel frames. The preliminary analysis pipeline is used to locate anomalies in these time-series accumulation frames and identify the type of anomaly, either natural phenomena or detector characteristic. To compare different methods, we’ve implemented both heuristic-based and data-driven methods to identify anomalies. For the heuristic-based approach, we identify snowballs and cosmic rays by the size and shape of outlier pixel clusters between consecutive frames. For data driven methods, we evaluated a Convolutional Neural Network (CNN) model, and more traditional methods like Principal Component Analysis (PCA). CNN is a supervised learning/classification method. Thus, we used a labeled dataset of anomalies to perform segmentation of the image and identify anomalies. We used previously identified cosmic rays and snowballs to measure the accuracy and efficiency of the mentioned approaches. In evaluating these methods, we aim to pick the best fit for the SDP pipeline’s anomaly detection in terms of both performance and runtime.

Paul Horton↗

The LATEST Project: Operational Assessment of Total Lightning Data in the U.S.

A government, university, and industry alliance has joined forces to transition total lightning observations from ground-based research networks and NASA satellites (LIS/TRMM) to improve the short range prediction of severe weather. This interest builds on the desire of the U.S Weather Research Program to foster a national Nowcasting Test Bed, with this specific transition activity initiated through the NASA short-term Prediction Research and Transition (SPoRT) Center in Huntsville, AL. A kick-off national workshop sponsored by the SPoRT Center was held in Huntsville April 1-2 to identify the common goals and objectives of the research and operational community, and to assign roles and responsibilities within the alliance. The workshop agenda, presentations, and summary are available at the SPoRT Center Web site ( h h under the "Meetings" tab. The next national workshop is planned for 2005 in Dallas, TX. The NASA North Alabama regional Lightning Mapping Array &MA) has been operational in the Huntsville area for 3 years, and has continuously sampled a variety of severe weather systems during that period. A gridded version of the LMA total lightning data is currently being supplied to National Weather Service offices in Huntsville, Nashville and Birmingham through the NWS AWES decision support system, for the purposes of assessing the utility of the data in the nowcasting of severe weather such as tornadoes, damaging straight line winds, flash flooding and other weather hazards (lightning induced forest fires, microbursts). While the raw LMA data have been useful to NWS forecasters, even greater utility would be realized if higher-order data products could be supplied through AWIPS along with the gridded data over a larger domain. In 2003-2004 additional LMA systems have been deployed across the southern US. from Florida to New Mexico, providing an opportunity for more than 20 NWS forecast offices to evaluate the incremental value of total lightning data in the warning decision making process.

Goodman, Steven↗

Processing CCD Images to Detect Transits of Earth-Sized Planets: Maximizing Sensitivity While Achieving Reasonable Downlink Requirements

We have performed end-to-end laboratory and numerical simulations to demonstrate the capability of differential photometry under realistic operating conditions to detect transits of Earth-sized planets orbiting solar-like stars. Data acquisition and processing were conducted using the same methods planned for the proposed Kepler Mission. These included performing aperture photometry on large-format CCD images of an artificial star fields obtained without a shutter at a readout rate of 1 megapixel/sec, detecting and removing cosmic rays from individual exposures and making the necessary corrections for nonlinearity and shutterless operation in the absence of darks. We will discuss the image processing tasks performed `on-board' the simulated spacecraft, which yielded raw photometry and ancillary data used to monitor and correct for systematic effects, and the data processing and analysis tasks conducted to obtain lightcurves from the raw data and characterize the detectability of transits. The laboratory results are discussed along with the results of a numerical simulation carried out in parallel with the laboratory simulation. These two simulations demonstrate that a system-level differential photometric precision of 10-5 on five- hour intervals can be achieved under realistic conditions.

Earth-size planets↗