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NASA NTRSDate not supplied

Towards A Better Measurement of eta-Earth and Beyond Via Modernizing the Kepler Pipeline: An Update

The measurement of the occurrence of rocky habitable-zone planets orbiting Sun-like stars (eta-Earth), is a fundamental quantity for guiding our search for habitable exoplanets. Despite being launched 15 years ago, NASA’s Kepler mission remains responsible for finding the majority of all known exoplanet candidates relevant to eta-Earth, ushering in a new era of exoplanet demographics studies and continuing to drive planet occurrence rate calculations. However, the paucity of detections of likely rocky planets in the habitable zones of their host stars remains a limiting factor for estimating eta-Earth. We describe our five-year project for modernizing the Kepler planet detection and vetting pipeline in order to produce a more complete and reliable exoplanet catalog, which will lead to more accurate and precise measurements of eta-Earth. First, we are currently porting the original Kepler pipeline code from MATLAB to Python. We will then describe new stellar catalogs based on Gaia and ground-based imaging data, and ways to improve the pipeline detection and vetting algorithms. We will provide an update on the current state of this work. When completed, we will use this new pipeline and catalog to calculate updated estimates of eta-Earth. The full, updated pipeline code in Python, as well as all our inputs and results, will be made available to the public for detailed exoplanet occurrence-rate and demographics studies.

kepler↗
NASA NTRS2012

The HEASARC Swift Gamma-Ray Burst Archive: The Pipeline and the Catalog

Since its launch in late 2004, the Swift satellite triggered or observed an average of one gamma-ray burst (GRB) every 3 days, for a total of 771 GRBs by 2012 January. Here, we report the development of a pipeline that semi automatically performs the data-reduction and data-analysis processes for the three instruments on board Swift (BAT, XRT, UVOT). The pipeline is written in Perl, and it uses only HEAsoft tools and can be used to perform the analysis of a majority of the point-like objects (e.g., GRBs, active galactic nuclei, pulsars) observed by Swift. We run the pipeline on the GRBs, and we present a database containing the screened data, the output products, and the results of our ongoing analysis. Furthermore, we created a catalog summarizing some GRB information, collected either by running the pipeline or from the literature. The Perl script, the database, and the catalog are available for downloading and querying at the HEASARC Web site.

BURST ARCHIVE↗
NASA NTRS2016

The Kepler Science Data Processing Pipeline Source Code Road Map

We give an overview of the operational concepts and architecture of the Kepler Science Processing Pipeline. Designed, developed, operated, and maintained by the Kepler Science Operations Center (SOC) at NASA Ames Research Center, the Science Processing Pipeline is a central element of the Kepler Ground Data System. The SOC consists of an office at Ames Research Center, software development and operations departments, and a data center which hosts the computers required to perform data analysis. The SOC's charter is to analyze stellar photometric data from the Kepler spacecraft and report results to the Kepler Science Office for further analysis. We describe how this is accomplished via the Kepler Science Processing Pipeline, including, the software algorithms. We present the high-performance, parallel computing software modules of the pipeline that perform transit photometry, pixel-level calibration, systematic error correction, attitude determination, stellar target management, and instrument characterization.

Kepler pipeline software↗
NASA NTRS1990

Optimal pipelining

An effort is made to characterize the tradeoffs and overheads limiting the speedup potential theoretically projected for pipeline-incorporating computer architectures, using a mathematical model of the roles played by the various parameters. Pipeline optimization proceeds by a partitioning of the pipeline into an optimum number of segments so that maximization of throughput is obtained. Inferences are drawn from the model, and potential improvements to it are identified. Substantial agreement is obtained with Kunkel and Smith's (1986) CRAY-1S simulations of pipelining.

Dubey, Pradeep K.↗
NASA NTRS1992

A bipolar population counter using wave pipelining to achieve 2.5 x normal clock frequency

Wave pipelining is a technique for pipelining digital systems that can increase clock frequency in practical circuits without increasing the number of storage elements. In wave pipelining, multiple coherent waves of data are sent through a block of combinational logic by applying new inputs faster than the delay through the logic. The throughput of a 63-b CML population counter was increased from 97 to 250 MHz using wave pipelining. The internal circuit is flowthrough combinational logic. Novel CAD methods have balanced all input-to-output paths to about the same delay. This allows multiple data waves to propagate in sequence when the circuit is clocked faster than its propagation delay.

Wong, Derek C.↗
NASA NTRS2009

Implementation and Comparison of Acoustic Travel-Time Measurement Procedures for the Helioseismic and Magnetic Imager Time-Distance Helioseismology Pipeline

The Helioseismic and Magnetic Imager (HMI) instrument on board the Solar Dynamics Observatory (SDO) satellite is designed to produce high-resolution Doppler velocity maps of oscillations at the solar surface with high temporal cadence. To take advantage of these high-quality oscillation data, a time-distance helioseismology pipeline has been implemented at the Joint Science Operations Center (JSOC) at Stanford University. The aim of this pipeline is to generate maps of acoustic travel times from oscillations on the solar surface, and to infer subsurface 3D flow velocities and sound-speed perturbations. The wave travel times are measured from cross covariances of the observed solar oscillation signals. For implementation into the pipeline we have investigated three different travel-time definitions developed in time-distance helioseismology: a Gabor wavelet fitting (Kosovichev and Duvall, 1997), a minimization relative to a reference cross-covariance function (Gizon and Birch, 2002), and a linearized version of the minimization method (Gizon and Birch, 2004). Using Doppler velocity data from the Michelson Doppler Imager (MDI) instrument on board SOHO, we tested and compared these definitions for the mean and difference travel-time perturbations measured from reciprocal signals. Although all three procedures return similar travel times in a quiet Sun region, the method of Gizon and Birch (2004) gives travel times that are significantly different from the others in a magnetic (active) region. Thus, for the pipeline implementation we chose the procedures of Kosovichev and Duvall (1997) and Gizon and Birch (2002). We investigated the relationships among these three travel-time definitions, their sensitivities to fitting parameters, and estimated the random errors they produce

Couvidat, S.↗
NASA NTRS2010

Implementation and Comparison of Acoustic Travel-Time Measurement Procedures for the Solar Dynamics Observatory-Helioseismic and Magnetic Imager Time-Distance Helioseismology Pipeline

The Helioseismic and Magnetic Imager (HMI) instrument onboard the Solar Dynamics Observatory (SDO) satellite is designed to produce high-resolution Doppler-velocity maps of oscillations at the solar surface with high temporal cadence. To take advantage of these high-quality oscillation data, a time - distance helioseismology pipeline (Zhao et al., Solar Phys. submitted, 2010) has been implemented at the Joint Science Operations Center (JSOC) at Stanford University. The aim of this pipeline is to generate maps of acoustic travel times from oscillations on the solar surface, and to infer subsurface 3D flow velocities and sound-speed perturbations. The wave travel times are measured from cross-covariances of the observed solar oscillation signals. For implementation into the pipeline we have investigated three different travel-time definitions developed in time - distance helioseismology: a Gabor-wavelet fitting (Kosovichev and Duvall, SCORE'96: Solar Convection and Oscillations and Their Relationship, ASSL, Dordrecht, 241, 1997), a minimization relative to a reference cross-covariance function (Gizon and Birch, Astrophys. J. 571, 966, 2002), and a linearized version of the minimization method (Gizon and Birch, Astrophys. J. 614, 472, 2004). Using Doppler-velocity data from the Michelson Doppler Imager (MDI) instrument onboard SOHO, we tested and compared these definitions for the mean and difference traveltime perturbations measured from reciprocal signals. Although all three procedures return similar travel times in a quiet-Sun region, the method of Gizon and Birch (Astrophys. J. 614, 472, 2004) gives travel times that are significantly different from the others in a magnetic (active) region. Thus, for the pipeline implementation we chose the procedures of Kosovichev and Duvall (SCORE'96: Solar Convection and Oscillations and Their Relationship, ASSL, Dordrecht, 241, 1997) and Gizon and Birch (Astrophys. J. 571, 966, 2002). We investigated the relationships among these three travel-time definitions, their sensitivities to fitting parameters, and estimated the random errors that they produce.

HMI↗
NASA NTRS2019

GeneLab Analysis Working Group Pipelines

GeneLab must establish data processing pipelines for common data types including microarray, RNA-sequencing, and metagenomic profiling. Here we give an overview of current microarray and RNA-seq pipelines and discuss future pipelines including metagenomic profiling pipelines

Galazka, Jonathan M.↗
NASA NTRSDate not supplied

Optimizing a Small RNAseq Analysis Pipeline for NASA GeneLab Using Open-Source Tools and Libraries

Small RNA sequencing (small RNAseq) is a powerful tool for studying the regulation of gene expression in various organisms. Small RNAseq has been leveraged in space biology research to study how expression of small RNAs, e.g. micro RNAs (miRNAs), small interfering RNAs (siRNAs), and piwi-interacting RNAs (piRNAs), change upon exposure to the space environment. NASA GeneLab currently hosts small RNAseq raw data derived from space-relevant experiments on the Open Science Data Repository (OSDR). To maximize the accessibility of these data to the scientific community, in addition to hosting raw data, which is only interpretable by bioinformaticians, GeneLab plans to process all small RNAseq datasets and make those processed data available to the scientific community via the OSDR. In this study, we present the development of the GeneLab standardized pipeline for processing small RNAseq datasets. Using human, plant, and synthetic small RNAseq datasets, we interrogate various open-source software and publicly available databases to evaluate their accuracy and reproducibility in each step of the pipeline. For quality control and adapter detection and trimming, we evaluated TrimGalore!, FASTX, SeqKit, and DNApi methods to optimize alignment to reference genomes. We compared BWA, Bowtie, and Bowtie2 to determine the optimal alignment tool. For each alignment tool we also assessed various reference databases, including Ensembl reference genomes and different types of small RNA reference databases, including genome, hairpin, and miRNA references from the miRbase and MirGeneDB databases. To quantify the aligned data, we compared SAMtools, HTSeq, and RSEM for counting alignment events from each alignment tool used. Finally, we evaluated various tools, including DESeq2 and EdgeR, for data normalization and subsequent differential expression analysis. We will present the results from our comparative analyses for each pipeline step and propose a consensus pipeline for processing small RNAseq data derived from various organisms exposed to the space environment.

SmallRNAseq, NASA GeneLab, quality control, adapte↗
NASA NTRSDate not supplied

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↗
NASA NTRS2015

PISCES High Contrast Integral Field Spectrograph Simulations and Data Reduction Pipeline

The PISCES (Prototype Imaging Spectrograph for Coronagraphic Exoplanet Studies) is a lenslet array based integral field spectrograph (IFS) designed to advance the technology readiness of the WFIRST (Wide Field Infrared Survey Telescope)-AFTA (Astrophysics Focused Telescope Assets) high contrast Coronagraph Instrument. We present the end to end optical simulator and plans for the data reduction pipeline (DRP). The optical simulator was created with a combination of the IDL (Interactive Data Language)-based PROPER (optical propagation) library and Zemax (a MatLab script), while the data reduction pipeline is a modified version of the Gemini Planet Imager's (GPI) IDL pipeline. The simulations of the propagation of light through the instrument are based on Fourier transform algorithms. The DRP enables transformation of the PISCES IFS data to calibrated spectral data cubes.

The PISCES (Prototype Imaging Spectrograph for Cor↗
NASA NTRS1978

Prospects for coal slurry pipelines in California

The coal slurry pipeline segment of the transport industry is emerging in the United States. If accepted it will play a vital role in meeting America's urgent energy requirements without public subsidy, tax relief, or federal grants. It is proven technology, ideally suited for transport of an abundant energy resource over thousands of miles to energy short industrial centers and at more than competitive costs. Briefly discussed are the following: (1) history of pipelines; (2) California market potential; (3) slurry technology; (4) environmental benefits; (5) market competition; and (6) a proposed pipeline.

Lynch, J. F.↗
NASA NTRS1979

Induced electric currents in the Alaska oil pipeline measured by gradient, fluxgate, and SQUID magnetometers

The field gradient method for observing the electric currents in the Alaska pipeline provided consistent values for both the fluxgate and SQUID method of observation. These currents were linearly related to the regularly measured electric and magnetic field changes. Determinations of pipeline current were consistent with values obtained by a direct connection, current shunt technique at a pipeline site about 9.6 km away. The gradient method has the distinct advantage of portability and buried- pipe capability. Field gradients due to the pipe magnetization, geological features, or ionospheric source currents do not seem to contribute a measurable error to such pipe current determination. The SQUID gradiometer is inherently sensitive enough to detect very small currents in a linear conductor at 10 meters, or conversely, to detect small currents of one amphere or more at relatively great distances. It is fairly straightforward to achieve imbalance less than one part in ten thousand, and with extreme care, one part in one million or better.

Campbell, W. H.↗
NASA NTRS1986

Programable Pipelined-Image Processor

Computer serves as pipelined processor for imagery or other two-dimensional digital data. Processor does feature extraction, smoothing, edge detection, texture measurement, and stereoscoptic area correlation. Also plans routes for obstacle avoidance by robots and solves two-dimensional partial differential equations. Image processor consists of modular units: each includes set of computing elements of types particularly useful in pipelined-image processing. Flexible interconnection scheme used to route data to subsequent stages of pipeline.

Gennery, D. B.↗
NASA NTRS1986

A VLSI pipeline design of a fast prime factor DFT on a finite field

A conventional prime factor discrete Fourier transform (DFT) algorithm is used to realize a discrete Fourier-like transform on the finite field, GF(q sub n). A pipeline structure is used to implement this prime factor DFT over GF(q sub n). This algorithm is developed to compute cyclic convolutions of complex numbers and to decode Reed-Solomon codes. Such a pipeline fast prime factor DFT algorithm over GF(q sub n) is regular, simple, expandable, and naturally suitable for VLSI implementation. An example illustrating the pipeline aspect of a 30-point transform over GF(q sub n) is presented.

Truong, T. K.↗
NASA NTRS1986

A study of pipelining in computing arrays

Scheduling considerations in computing arrays are examined. A simple sufficient condition is developed for determining whether a computing array can be pipelined. If the array cannot be pipelined in the form given, the condition also indicates the direction in which to proceed to make it pipelineable. The overall framework and methodology take a good part of the load off the logical architect of the array, and make the translation from the logical to the physical architecture a mechanical process.

Jagadish, H. V.↗
NASA NTRS1997

A Parallel Pipelined Renderer for the Time-Varying Volume Data

This paper presents a strategy for efficiently rendering time-varying volume data sets on a distributed-memory parallel computer. Time-varying volume data take large storage space and visualizing them requires reading large files continuously or periodically throughout the course of the visualization process. Instead of using all the processors to collectively render one volume at a time, a pipelined rendering process is formed by partitioning processors into groups to render multiple volumes concurrently. In this way, the overall rendering time may be greatly reduced because the pipelined rendering tasks are overlapped with the I/O required to load each volume into a group of processors; moreover, parallelization overhead may be reduced as a result of partitioning the processors. We modify an existing parallel volume renderer to exploit various levels of rendering parallelism and to study how the partitioning of processors may lead to optimal rendering performance. Two factors which are important to the overall execution time are re-source utilization efficiency and pipeline startup latency. The optimal partitioning configuration is the one that balances these two factors. Tests on Intel Paragon computers show that in general optimal partitionings do exist for a given rendering task and result in 40-50% saving in overall rendering time.

Chiueh, Tzi-Cker↗
NASA NTRS1998

Parallelization of the Pipelined Thomas Algorithm

In this study the following questions are addressed. Is it possible to improve the parallelization efficiency of the Thomas algorithm? How should the Thomas algorithm be formulated in order to get solved lines that are used as data for other computational tasks while processors are idle? To answer these questions, two-step pipelined algorithms (PAs) are introduced formally. It is shown that the idle processor time is invariant with respect to the order of backward and forward steps in PAs starting from one outermost processor. The advantage of PAs starting from two outermost processors is small. Versions of the pipelined Thomas algorithms considered here fall into the category of PAs. These results show that the parallelization efficiency of the Thomas algorithm cannot be improved directly. However, the processor idle time can be used if some data has been computed by the time processors become idle. To achieve this goal the Immediate Backward pipelined Thomas Algorithm (IB-PTA) is developed in this article. The backward step is computed immediately after the forward step has been completed for the first portion of lines. This enables the completion of the Thomas algorithm for some of these lines before processors become idle. An algorithm for generating a static processor schedule recursively is developed. This schedule is used to switch between forward and backward computations and to control communications between processors. The advantage of the IB-PTA over the basic PTA is the presence of solved lines, which are available for other computations, by the time processors become idle.

Povitsky, A.↗