BigDataScript: a scripting language for data pipelines

PubMed Central

Cingolani, Pablo; Sladek, Rob; Blanchette, Mathieu

2015-01-01

Motivation: The analysis of large biological datasets often requires complex processing pipelines that run for a long time on large computational infrastructures. We designed and implemented a simple script-like programming language with a clean and minimalist syntax to develop and manage pipeline execution and provide robustness to various types of software and hardware failures as well as portability. Results: We introduce the BigDataScript (BDS) programming language for data processing pipelines, which improves abstraction from hardware resources and assists with robustness. Hardware abstraction allows BDS pipelines to run without modification on a wide range of computer architectures, from a small laptop to multi-core servers, server farms, clusters and clouds. BDS achieves robustness by incorporating the concepts of absolute serialization and lazy processing, thus allowing pipelines to recover from errors. By abstracting pipeline concepts at programming language level, BDS simplifies implementation, execution and management of complex bioinformatics pipelines, resulting in reduced development and debugging cycles as well as cleaner code. Availability and implementation: BigDataScript is available under open-source license at http://pcingola.github.io/BigDataScript. Contact: pablo.e.cingolani@gmail.com PMID:25189778

78 FR 53751 - Dominion NGL Pipelines, LLC; Notice of Petition for Declaratory Order

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-30

... new ethane pipeline (Natrium Ethane Pipeline) extending from a new natural gas processing and... utilize, or pay for, significant capacity on the Natrium Ethane Pipeline (Committed Shipper); and (3) the...

49 CFR 192.937 - What is a continual process of evaluation and assessment to maintain a pipeline's integrity?

Code of Federal Regulations, 2010 CFR

2010-10-01

... Relating to Transportation (Continued) PIPELINE AND HAZARDOUS MATERIALS SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) PIPELINE SAFETY TRANSPORTATION OF NATURAL AND OTHER GAS BY PIPELINE: MINIMUM FEDERAL SAFETY STANDARDS Gas Transmission Pipeline Integrity Management § 192.937 What is a...

75 FR 5167 - Office of Hazardous Materials Safety; Notice of Delays In Processing of Special Permits Applications

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-01

... DEPARTMENT OF TRANSPORTATION Pipeline and Hazardous Materials Safety Administration Office of Hazardous Materials Safety; Notice of Delays In Processing of Special Permits Applications AGENCY: Pipeline..., Office of Hazardous Materials Special Permits and Approvals, Pipeline and Hazardous Materials Safety...

75 FR 78800 - Office of Hazardous Materials Safety; Notice of Delays in Processing of Special Permits Applications

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-16

... DEPARTMENT OF TRANSPORTATION Pipeline and Hazardous Materials Safety Administration Office of Hazardous Materials Safety; Notice of Delays in Processing of Special Permits Applications AGENCY: Pipeline..., Office of Hazardous Materials Special Permits and Approvals, Pipeline and Hazardous Materials Safety...

The ALMA Science Pipeline: Current Status

NASA Astrophysics Data System (ADS)

Humphreys, Elizabeth; Miura, Rie; Brogan, Crystal L.; Hibbard, John; Hunter, Todd R.; Indebetouw, Remy

2016-09-01

The ALMA Science Pipeline is being developed for the automated calibration and imaging of ALMA interferometric and single-dish data. The calibration Pipeline for interferometric data was accepted for use by ALMA Science Operations in 2014, and for single-dish data end-to-end processing in 2015. However, work is ongoing to expand the use cases for which the Pipeline can be used e.g. for higher frequency and lower signal-to-noise datasets, and for new observing modes. A current focus includes the commissioning of science target imaging for interferometric data. For the Single Dish Pipeline, the line finding algorithm used in baseline subtraction and baseline flagging heuristics have been greately improved since the prototype used for data from the previous cycle. These algorithms, unique to the Pipeline, produce better results than standard manual processing in many cases. In this poster, we report on the current status of the Pipeline capabilities, present initial results from the Imaging Pipeline, and the smart line finding and flagging algorithm used in the Single Dish Pipeline. The Pipeline is released as part of CASA (the Common Astronomy Software Applications package).

SUPRA: open-source software-defined ultrasound processing for real-time applications : A 2D and 3D pipeline from beamforming to B-mode.

PubMed

Göbl, Rüdiger; Navab, Nassir; Hennersperger, Christoph

2018-06-01

Research in ultrasound imaging is limited in reproducibility by two factors: First, many existing ultrasound pipelines are protected by intellectual property, rendering exchange of code difficult. Second, most pipelines are implemented in special hardware, resulting in limited flexibility of implemented processing steps on such platforms. With SUPRA, we propose an open-source pipeline for fully software-defined ultrasound processing for real-time applications to alleviate these problems. Covering all steps from beamforming to output of B-mode images, SUPRA can help improve the reproducibility of results and make modifications to the image acquisition mode accessible to the research community. We evaluate the pipeline qualitatively, quantitatively, and regarding its run time. The pipeline shows image quality comparable to a clinical system and backed by point spread function measurements a comparable resolution. Including all processing stages of a usual ultrasound pipeline, the run-time analysis shows that it can be executed in 2D and 3D on consumer GPUs in real time. Our software ultrasound pipeline opens up the research in image acquisition. Given access to ultrasound data from early stages (raw channel data, radiofrequency data), it simplifies the development in imaging. Furthermore, it tackles the reproducibility of research results, as code can be shared easily and even be executed without dedicated ultrasound hardware.

Development of Protective Coatings for Co-Sequestration Processes and Pipelines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bierwagen, Gordon; Huang, Yaping

2011-11-30

The program, entitled Development of Protective Coatings for Co-Sequestration Processes and Pipelines, examined the sensitivity of existing coating systems to supercritical carbon dioxide (SCCO2) exposure and developed new coating system to protect pipelines from their corrosion under SCCO2 exposure. A literature review was also conducted regarding pipeline corrosion sensors to monitor pipes used in handling co-sequestration fluids. Research was to ensure safety and reliability for a pipeline involving transport of SCCO2 from the power plant to the sequestration site to mitigate the greenhouse gas effect. Results showed that one commercial coating and one designed formulation can both be supplied asmore » potential candidates for internal pipeline coating to transport SCCO2.« less

An integrated SNP mining and utilization (ISMU) pipeline for next generation sequencing data.

PubMed

Azam, Sarwar; Rathore, Abhishek; Shah, Trushar M; Telluri, Mohan; Amindala, BhanuPrakash; Ruperao, Pradeep; Katta, Mohan A V S K; Varshney, Rajeev K

2014-01-01

Open source single nucleotide polymorphism (SNP) discovery pipelines for next generation sequencing data commonly requires working knowledge of command line interface, massive computational resources and expertise which is a daunting task for biologists. Further, the SNP information generated may not be readily used for downstream processes such as genotyping. Hence, a comprehensive pipeline has been developed by integrating several open source next generation sequencing (NGS) tools along with a graphical user interface called Integrated SNP Mining and Utilization (ISMU) for SNP discovery and their utilization by developing genotyping assays. The pipeline features functionalities such as pre-processing of raw data, integration of open source alignment tools (Bowtie2, BWA, Maq, NovoAlign and SOAP2), SNP prediction (SAMtools/SOAPsnp/CNS2snp and CbCC) methods and interfaces for developing genotyping assays. The pipeline outputs a list of high quality SNPs between all pairwise combinations of genotypes analyzed, in addition to the reference genome/sequence. Visualization tools (Tablet and Flapjack) integrated into the pipeline enable inspection of the alignment and errors, if any. The pipeline also provides a confidence score or polymorphism information content value with flanking sequences for identified SNPs in standard format required for developing marker genotyping (KASP and Golden Gate) assays. The pipeline enables users to process a range of NGS datasets such as whole genome re-sequencing, restriction site associated DNA sequencing and transcriptome sequencing data at a fast speed. The pipeline is very useful for plant genetics and breeding community with no computational expertise in order to discover SNPs and utilize in genomics, genetics and breeding studies. The pipeline has been parallelized to process huge datasets of next generation sequencing. It has been developed in Java language and is available at http://hpc.icrisat.cgiar.org/ISMU as a standalone free software.

A distributed pipeline for DIDSON data processing

USGS Publications Warehouse

Li, Liling; Danner, Tyler; Eickholt, Jesse; McCann, Erin L.; Pangle, Kevin; Johnson, Nicholas

2018-01-01

Technological advances in the field of ecology allow data on ecological systems to be collected at high resolution, both temporally and spatially. Devices such as Dual-frequency Identification Sonar (DIDSON) can be deployed in aquatic environments for extended periods and easily generate several terabytes of underwater surveillance data which may need to be processed multiple times. Due to the large amount of data generated and need for flexibility in processing, a distributed pipeline was constructed for DIDSON data making use of the Hadoop ecosystem. The pipeline is capable of ingesting raw DIDSON data, transforming the acoustic data to images, filtering the images, detecting and extracting motion, and generating feature data for machine learning and classification. All of the tasks in the pipeline can be run in parallel and the framework allows for custom processing. Applications of the pipeline include monitoring migration times, determining the presence of a particular species, estimating population size and other fishery management tasks.

The Kepler Science Data Processing Pipeline Source Code Road Map

NASA Technical Reports Server (NTRS)

Wohler, Bill; Jenkins, Jon M.; Twicken, Joseph D.; Bryson, Stephen T.; Clarke, Bruce Donald; Middour, Christopher K.; Quintana, Elisa Victoria; Sanderfer, Jesse Thomas; Uddin, Akm Kamal; Sabale, Anima;

Risk Analysis using Corrosion Rate Parameter on Gas Transmission Pipeline

NASA Astrophysics Data System (ADS)

Sasikirono, B.; Kim, S. J.; Haryadi, G. D.; Huda, A.

2017-05-01

In the oil and gas industry, the pipeline is a major component in the transmission and distribution process of oil and gas. Oil and gas distribution process sometimes performed past the pipeline across the various types of environmental conditions. Therefore, in the transmission and distribution process of oil and gas, a pipeline should operate safely so that it does not harm the surrounding environment. Corrosion is still a major cause of failure in some components of the equipment in a production facility. In pipeline systems, corrosion can cause failures in the wall and damage to the pipeline. Therefore it takes care and periodic inspections or checks on the pipeline system. Every production facility in an industry has a level of risk for damage which is a result of the opportunities and consequences of damage caused. The purpose of this research is to analyze the level of risk of 20-inch Natural Gas Transmission Pipeline using Risk-based inspection semi-quantitative based on API 581 associated with the likelihood of failure and the consequences of the failure of a component of the equipment. Then the result is used to determine the next inspection plans. Nine pipeline components were observed, such as a straight pipes inlet, connection tee, and straight pipes outlet. The risk assessment level of the nine pipeline’s components is presented in a risk matrix. The risk level of components is examined at medium risk levels. The failure mechanism that is used in this research is the mechanism of thinning. Based on the results of corrosion rate calculation, remaining pipeline components age can be obtained, so the remaining lifetime of pipeline components are known. The calculation of remaining lifetime obtained and the results vary for each component. Next step is planning the inspection of pipeline components by NDT external methods.

Methodology for reducing energy and resource costs in construction of trenchless crossover of pipelines

NASA Astrophysics Data System (ADS)

Toropov, V. S.

2018-05-01

The paper suggests a set of measures to select the equipment and its components in order to reduce energy costs in the process of pulling the pipeline into the well in the constructing the trenchless pipeline crossings of various materials using horizontal directional drilling technology. A methodology for reducing energy costs has been developed by regulating the operation modes of equipment during the process of pulling the working pipeline into a drilled and pre-expanded well. Since the power of the drilling rig is the most important criterion in the selection of equipment for the construction of a trenchless crossover, an algorithm is proposed for calculating the required capacity of the rig when operating in different modes in the process of pulling the pipeline into the well.

DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation sequencing data.

PubMed

Nagasaki, Hideki; Mochizuki, Takako; Kodama, Yuichi; Saruhashi, Satoshi; Morizaki, Shota; Sugawara, Hideaki; Ohyanagi, Hajime; Kurata, Nori; Okubo, Kousaku; Takagi, Toshihisa; Kaminuma, Eli; Nakamura, Yasukazu

2013-08-01

High-performance next-generation sequencing (NGS) technologies are advancing genomics and molecular biological research. However, the immense amount of sequence data requires computational skills and suitable hardware resources that are a challenge to molecular biologists. The DNA Data Bank of Japan (DDBJ) of the National Institute of Genetics (NIG) has initiated a cloud computing-based analytical pipeline, the DDBJ Read Annotation Pipeline (DDBJ Pipeline), for a high-throughput annotation of NGS reads. The DDBJ Pipeline offers a user-friendly graphical web interface and processes massive NGS datasets using decentralized processing by NIG supercomputers currently free of charge. The proposed pipeline consists of two analysis components: basic analysis for reference genome mapping and de novo assembly and subsequent high-level analysis of structural and functional annotations. Users may smoothly switch between the two components in the pipeline, facilitating web-based operations on a supercomputer for high-throughput data analysis. Moreover, public NGS reads of the DDBJ Sequence Read Archive located on the same supercomputer can be imported into the pipeline through the input of only an accession number. This proposed pipeline will facilitate research by utilizing unified analytical workflows applied to the NGS data. The DDBJ Pipeline is accessible at http://p.ddbj.nig.ac.jp/.

DDBJ Read Annotation Pipeline: A Cloud Computing-Based Pipeline for High-Throughput Analysis of Next-Generation Sequencing Data

PubMed Central

Nagasaki, Hideki; Mochizuki, Takako; Kodama, Yuichi; Saruhashi, Satoshi; Morizaki, Shota; Sugawara, Hideaki; Ohyanagi, Hajime; Kurata, Nori; Okubo, Kousaku; Takagi, Toshihisa; Kaminuma, Eli; Nakamura, Yasukazu

2013-01-01

High-performance next-generation sequencing (NGS) technologies are advancing genomics and molecular biological research. However, the immense amount of sequence data requires computational skills and suitable hardware resources that are a challenge to molecular biologists. The DNA Data Bank of Japan (DDBJ) of the National Institute of Genetics (NIG) has initiated a cloud computing-based analytical pipeline, the DDBJ Read Annotation Pipeline (DDBJ Pipeline), for a high-throughput annotation of NGS reads. The DDBJ Pipeline offers a user-friendly graphical web interface and processes massive NGS datasets using decentralized processing by NIG supercomputers currently free of charge. The proposed pipeline consists of two analysis components: basic analysis for reference genome mapping and de novo assembly and subsequent high-level analysis of structural and functional annotations. Users may smoothly switch between the two components in the pipeline, facilitating web-based operations on a supercomputer for high-throughput data analysis. Moreover, public NGS reads of the DDBJ Sequence Read Archive located on the same supercomputer can be imported into the pipeline through the input of only an accession number. This proposed pipeline will facilitate research by utilizing unified analytical workflows applied to the NGS data. The DDBJ Pipeline is accessible at http://p.ddbj.nig.ac.jp/. PMID:23657089

Text-based Analytics for Biosurveillance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Charles, Lauren E.; Smith, William P.; Rounds, Jeremiah

The ability to prevent, mitigate, or control a biological threat depends on how quickly the threat is identified and characterized. Ensuring the timely delivery of data and analytics is an essential aspect of providing adequate situational awareness in the face of a disease outbreak. This chapter outlines an analytic pipeline for supporting an advanced early warning system that can integrate multiple data sources and provide situational awareness of potential and occurring disease situations. The pipeline, includes real-time automated data analysis founded on natural language processing (NLP), semantic concept matching, and machine learning techniques, to enrich content with metadata related tomore » biosurveillance. Online news articles are presented as an example use case for the pipeline, but the processes can be generalized to any textual data. In this chapter, the mechanics of a streaming pipeline are briefly discussed as well as the major steps required to provide targeted situational awareness. The text-based analytic pipeline includes various processing steps as well as identifying article relevance to biosurveillance (e.g., relevance algorithm) and article feature extraction (who, what, where, why, how, and when). The ability to prevent, mitigate, or control a biological threat depends on how quickly the threat is identified and characterized. Ensuring the timely delivery of data and analytics is an essential aspect of providing adequate situational awareness in the face of a disease outbreak. This chapter outlines an analytic pipeline for supporting an advanced early warning system that can integrate multiple data sources and provide situational awareness of potential and occurring disease situations. The pipeline, includes real-time automated data analysis founded on natural language processing (NLP), semantic concept matching, and machine learning techniques, to enrich content with metadata related to biosurveillance. Online news articles are presented as an example use case for the pipeline, but the processes can be generalized to any textual data. In this chapter, the mechanics of a streaming pipeline are briefly discussed as well as the major steps required to provide targeted situational awareness. The text-based analytic pipeline includes various processing steps as well as identifying article relevance to biosurveillance (e.g., relevance algorithm) and article feature extraction (who, what, where, why, how, and when).« less

75 FR 35632 - Transparency Provisions of Section 23 of the Natural Gas Act

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-23

... pipeline- quality natural gas. For instance, some Respondents questioned whether pipeline-quality natural gas that is sold directly into an interstate or intrastate natural gas pipeline without processing... reported transactions of pipeline-quality gas under the assumption that ``unprocessed natural gas'' was...

Development and Applications of Pipeline Steel in Long-Distance Gas Pipeline of China

NASA Astrophysics Data System (ADS)

Chunyong, Huo; Yang, Li; Lingkang, Ji

In past decades, with widely utilizing of Microalloying and Thermal Mechanical Control Processing (TMCP) technology, the good matching of strength, toughness, plasticity and weldability on pipeline steel has been reached so that oil and gas pipeline has been greatly developed in China to meet the demand of strong domestic consumption of energy. In this paper, development history of pipeline steel and gas pipeline in china is briefly reviewed. The microstructure characteristic and mechanical performance of pipeline steel used in some representative gas pipelines of china built in different stage are summarized. Through the analysis on the evolution of pipeline service environment, some prospective development trend of application of pipeline steel in China is also presented.

TESS Data Processing and Quick-look Pipeline

NASA Astrophysics Data System (ADS)

Fausnaugh, Michael; Huang, Xu; Glidden, Ana; Guerrero, Natalia; TESS Science Office

2018-01-01

We describe the data analysis procedures and pipelines for the Transiting Exoplanet Survey Satellite (TESS). We briefly review the processing pipeline developed and implemented by the Science Processing Operations Center (SPOC) at NASA Ames, including pixel/full-frame image calibration, photometric analysis, pre-search data conditioning, transiting planet search, and data validation. We also describe data-quality diagnostic analyses and photometric performance assessment tests. Finally, we detail a "quick-look pipeline" (QLP) that has been developed by the MIT branch of the TESS Science Office (TSO) to provide a fast and adaptable routine to search for planet candidates in the 30 minute full-frame images.

ARTIP: Automated Radio Telescope Image Processing Pipeline

NASA Astrophysics Data System (ADS)

Sharma, Ravi; Gyanchandani, Dolly; Kulkarni, Sarang; Gupta, Neeraj; Pathak, Vineet; Pande, Arti; Joshi, Unmesh

2018-02-01

The Automated Radio Telescope Image Processing Pipeline (ARTIP) automates the entire process of flagging, calibrating, and imaging for radio-interferometric data. ARTIP starts with raw data, i.e. a measurement set and goes through multiple stages, such as flux calibration, bandpass calibration, phase calibration, and imaging to generate continuum and spectral line images. Each stage can also be run independently. The pipeline provides continuous feedback to the user through various messages, charts and logs. It is written using standard python libraries and the CASA package. The pipeline can deal with datasets with multiple spectral windows and also multiple target sources which may have arbitrary combinations of flux/bandpass/phase calibrators.

77 FR 26760 - Kinder Morgan, Inc.; Analysis of Proposed Agreement Containing Consent Orders To Aid Public Comment

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-07

... to as natural gas liquids or NGLs. Interstate pipelines have a limit on how much NGLs natural gas can... gas processing plant to remove those liquids before it can be transported on interstate pipelines... Gas Transmission, and Trailblazer pipelines, as well as associated processing and storage capacity. On...

Data as a Service: A Seismic Web Service Pipeline

NASA Astrophysics Data System (ADS)

Martinez, E.

2016-12-01

Publishing data as a service pipeline provides an improved, dynamic approach over static data archives. A service pipeline is a collection of micro web services that each perform a specific task and expose the results of that task. Structured request/response formats allow micro web services to be chained together into a service pipeline to provide more complex results. The U.S. Geological Survey adopted service pipelines to publish seismic hazard and design data supporting both specific and generalized audiences. The seismic web service pipeline starts at source data and exposes probability and deterministic hazard curves, response spectra, risk-targeted ground motions, and seismic design provision metadata. This pipeline supports public/private organizations and individual engineers/researchers. Publishing data as a service pipeline provides a variety of benefits. Exposing the component services enables advanced users to inspect or use the data at each processing step. Exposing a composite service enables new users quick access to published data with a very low barrier to entry. Advanced users may re-use micro web services by chaining them in new ways or injecting new micros services into the pipeline. This allows the user to test hypothesis and compare their results to published results. Exposing data at each step in the pipeline enables users to review and validate the data and process more quickly and accurately. Making the source code open source, per USGS policy, further enables this transparency. Each micro service may be scaled independent of any other micro service. This ensures data remains available and timely in a cost-effective manner regardless of load. Additionally, if a new or more efficient approach to processing the data is discovered, this new approach may replace the old approach at any time, keeping the pipeline running while not affecting other micro services.

Significantly reducing the processing times of high-speed photometry data sets using a distributed computing model

NASA Astrophysics Data System (ADS)

Doyle, Paul; Mtenzi, Fred; Smith, Niall; Collins, Adrian; O'Shea, Brendan

2012-09-01

The scientific community is in the midst of a data analysis crisis. The increasing capacity of scientific CCD instrumentation and their falling costs is contributing to an explosive generation of raw photometric data. This data must go through a process of cleaning and reduction before it can be used for high precision photometric analysis. Many existing data processing pipelines either assume a relatively small dataset or are batch processed by a High Performance Computing centre. A radical overhaul of these processing pipelines is required to allow reduction and cleaning rates to process terabyte sized datasets at near capture rates using an elastic processing architecture. The ability to access computing resources and to allow them to grow and shrink as demand fluctuates is essential, as is exploiting the parallel nature of the datasets. A distributed data processing pipeline is required. It should incorporate lossless data compression, allow for data segmentation and support processing of data segments in parallel. Academic institutes can collaborate and provide an elastic computing model without the requirement for large centralized high performance computing data centers. This paper demonstrates how a base 10 order of magnitude improvement in overall processing time has been achieved using the "ACN pipeline", a distributed pipeline spanning multiple academic institutes.

Numerical research on the lateral global buckling characteristics of a high temperature and pressure pipeline with two initial imperfections

PubMed Central

Liu, Wenbin; Liu, Aimin

2018-01-01

With the exploitation of offshore oil and gas gradually moving to deep water, higher temperature differences and pressure differences are applied to the pipeline system, making the global buckling of the pipeline more serious. For unburied deep-water pipelines, the lateral buckling is the major buckling form. The initial imperfections widely exist in the pipeline system due to manufacture defects or the influence of uneven seabed, and the distribution and geometry features of initial imperfections are random. They can be divided into two kinds based on shape: single-arch imperfections and double-arch imperfections. This paper analyzed the global buckling process of a pipeline with 2 initial imperfections by using a numerical simulation method and revealed how the ratio of the initial imperfection’s space length to the imperfection’s wavelength and the combination of imperfections affects the buckling process. The results show that a pipeline with 2 initial imperfections may suffer the superposition of global buckling. The growth ratios of buckling displacement, axial force and bending moment in the superposition zone are several times larger than no buckling superposition pipeline. The ratio of the initial imperfection’s space length to the imperfection’s wavelength decides whether a pipeline suffers buckling superposition. The potential failure point of pipeline exhibiting buckling superposition is as same as the no buckling superposition pipeline, but the failure risk of pipeline exhibiting buckling superposition is much higher. The shape and direction of two nearby imperfections also affects the failure risk of pipeline exhibiting global buckling superposition. The failure risk of pipeline with two double-arch imperfections is higher than pipeline with two single-arch imperfections. PMID:29554123

76 FR 54531 - Pipeline Safety: Potential for Damage to Pipeline Facilities Caused by the Passage of Hurricanes

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-01

... production and processing is prone to disruption by hurricanes. In 2005, Hurricanes Katrina and Rita caused... Hurricanes AGENCY: Pipeline and Hazardous Materials Safety Administration (PHMSA), DOT. ACTION: Notice... the passage of Hurricanes. ADDRESSES: This document can be viewed on the Office of Pipeline Safety...

75 FR 17397 - Hydrogen Energy California's Integrated Gasification Combined Cycle Project, Kern County, CA...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-06

... and potable water pipelines, a transmission line, a natural gas supply pipeline, a CO 2 pipeline... line. HECA would also construct an approximately 8-mile natural gas supply pipeline extending southeast... produce synthesis gas (syngas), which would then be processed and purified to produce a hydrogen-rich fuel...

Assessing fugitive emissions of CH4 from high-pressure gas pipelines

NASA Astrophysics Data System (ADS)

Worrall, Fred; Boothroyd, Ian; Davies, Richard

2017-04-01

The impact of unconventional natural gas production using hydraulic fracturing methods from shale gas basins has been assessed using life-cycle emissions inventories, covering areas such as pre-production, production and transmission processes. The transmission of natural gas from well pad to processing plants and its transport to domestic sites is an important source of fugitive CH4, yet emissions factors and fluxes from transmission processes are often based upon ver out of date measurements. It is important to determine accurate measurements of natural gas losses when compressed and transported between production and processing facilities so as to accurately determine life-cycle CH4 emissions. This study considers CH4 emissions from the UK National Transmission System (NTS) of high pressure natural gas pipelines. Mobile surveys of CH4 emissions using a Picarro Surveyor cavity-ring-down spectrometer were conducted across four areas in the UK, with routes bisecting high pressure pipelines and separate control routes away from the pipelines. A manual survey of soil gas measurements was also conducted along one of the high pressure pipelines using a tunable diode laser. When wind adjusted 92 km of high pressure pipeline and 72 km of control route were drive over a 10 day period. When wind and distance adjusted CH4 fluxes were significantly greater on routes with a pipeline than those without. The smallest leak detectable was 3% above ambient (1.03 relative concentration) with any leaks below 3% above ambient assumed ambient. The number of leaks detected along the pipelines correlate to the estimated length of pipe joints, inferring that there are constant fugitive CH4 emissions from these joints. When scaled up to the UK's National Transmission System pipeline length of 7600 km gives a fugitive CH4 flux of 4700 ± 2864 kt CH4/yr - this fugitive emission from high pressure pipelines is 0.016% of the annual gas supply.

An Integrated SNP Mining and Utilization (ISMU) Pipeline for Next Generation Sequencing Data

PubMed Central

Azam, Sarwar; Rathore, Abhishek; Shah, Trushar M.; Telluri, Mohan; Amindala, BhanuPrakash; Ruperao, Pradeep; Katta, Mohan A. V. S. K.; Varshney, Rajeev K.

2014-01-01

Open source single nucleotide polymorphism (SNP) discovery pipelines for next generation sequencing data commonly requires working knowledge of command line interface, massive computational resources and expertise which is a daunting task for biologists. Further, the SNP information generated may not be readily used for downstream processes such as genotyping. Hence, a comprehensive pipeline has been developed by integrating several open source next generation sequencing (NGS) tools along with a graphical user interface called Integrated SNP Mining and Utilization (ISMU) for SNP discovery and their utilization by developing genotyping assays. The pipeline features functionalities such as pre-processing of raw data, integration of open source alignment tools (Bowtie2, BWA, Maq, NovoAlign and SOAP2), SNP prediction (SAMtools/SOAPsnp/CNS2snp and CbCC) methods and interfaces for developing genotyping assays. The pipeline outputs a list of high quality SNPs between all pairwise combinations of genotypes analyzed, in addition to the reference genome/sequence. Visualization tools (Tablet and Flapjack) integrated into the pipeline enable inspection of the alignment and errors, if any. The pipeline also provides a confidence score or polymorphism information content value with flanking sequences for identified SNPs in standard format required for developing marker genotyping (KASP and Golden Gate) assays. The pipeline enables users to process a range of NGS datasets such as whole genome re-sequencing, restriction site associated DNA sequencing and transcriptome sequencing data at a fast speed. The pipeline is very useful for plant genetics and breeding community with no computational expertise in order to discover SNPs and utilize in genomics, genetics and breeding studies. The pipeline has been parallelized to process huge datasets of next generation sequencing. It has been developed in Java language and is available at http://hpc.icrisat.cgiar.org/ISMU as a standalone free software. PMID:25003610

The PREP pipeline: standardized preprocessing for large-scale EEG analysis.

PubMed

Bigdely-Shamlo, Nima; Mullen, Tim; Kothe, Christian; Su, Kyung-Min; Robbins, Kay A

2015-01-01

The technology to collect brain imaging and physiological measures has become portable and ubiquitous, opening the possibility of large-scale analysis of real-world human imaging. By its nature, such data is large and complex, making automated processing essential. This paper shows how lack of attention to the very early stages of an EEG preprocessing pipeline can reduce the signal-to-noise ratio and introduce unwanted artifacts into the data, particularly for computations done in single precision. We demonstrate that ordinary average referencing improves the signal-to-noise ratio, but that noisy channels can contaminate the results. We also show that identification of noisy channels depends on the reference and examine the complex interaction of filtering, noisy channel identification, and referencing. We introduce a multi-stage robust referencing scheme to deal with the noisy channel-reference interaction. We propose a standardized early-stage EEG processing pipeline (PREP) and discuss the application of the pipeline to more than 600 EEG datasets. The pipeline includes an automatically generated report for each dataset processed. Users can download the PREP pipeline as a freely available MATLAB library from http://eegstudy.org/prepcode.

78 FR 56268 - Pipeline Safety: Public Workshop on Integrity Verification Process, Comment Extension

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-12

.... PHMSA-2013-0119] Pipeline Safety: Public Workshop on Integrity Verification Process, Comment Extension... public workshop on ``Integrity Verification Process'' which took place on August 7, 2013. The notice also sought comments on the proposed ``Integrity Verification Process.'' In response to the comments received...

Data processing pipeline for Herschel HIFI

NASA Astrophysics Data System (ADS)

Shipman, R. F.; Beaulieu, S. F.; Teyssier, D.; Morris, P.; Rengel, M.; McCoey, C.; Edwards, K.; Kester, D.; Lorenzani, A.; Coeur-Joly, O.; Melchior, M.; Xie, J.; Sanchez, E.; Zaal, P.; Avruch, I.; Borys, C.; Braine, J.; Comito, C.; Delforge, B.; Herpin, F.; Hoac, A.; Kwon, W.; Lord, S. D.; Marston, A.; Mueller, M.; Olberg, M.; Ossenkopf, V.; Puga, E.; Akyilmaz-Yabaci, M.

2017-12-01

Context. The HIFI instrument on the Herschel Space Observatory performed over 9100 astronomical observations, almost 900 of which were calibration observations in the course of the nearly four-year Herschel mission. The data from each observation had to be converted from raw telemetry into calibrated products and were included in the Herschel Science Archive. Aims: The HIFI pipeline was designed to provide robust conversion from raw telemetry into calibrated data throughout all phases of the HIFI missions. Pre-launch laboratory testing was supported as were routine mission operations. Methods: A modular software design allowed components to be easily added, removed, amended and/or extended as the understanding of the HIFI data developed during and after mission operations. Results: The HIFI pipeline processed data from all HIFI observing modes within the Herschel automated processing environment as well as within an interactive environment. The same software can be used by the general astronomical community to reprocess any standard HIFI observation. The pipeline also recorded the consistency of processing results and provided automated quality reports. Many pipeline modules were in use since the HIFI pre-launch instrument level testing. Conclusions: Processing in steps facilitated data analysis to discover and address instrument artefacts and uncertainties. The availability of the same pipeline components from pre-launch throughout the mission made for well-understood, tested, and stable processing. A smooth transition from one phase to the next significantly enhanced processing reliability and robustness. Herschel was an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.

The JCSG high-throughput structural biology pipeline.

PubMed

Elsliger, Marc André; Deacon, Ashley M; Godzik, Adam; Lesley, Scott A; Wooley, John; Wüthrich, Kurt; Wilson, Ian A

2010-10-01

The Joint Center for Structural Genomics high-throughput structural biology pipeline has delivered more than 1000 structures to the community over the past ten years. The JCSG has made a significant contribution to the overall goal of the NIH Protein Structure Initiative (PSI) of expanding structural coverage of the protein universe, as well as making substantial inroads into structural coverage of an entire organism. Targets are processed through an extensive combination of bioinformatics and biophysical analyses to efficiently characterize and optimize each target prior to selection for structure determination. The pipeline uses parallel processing methods at almost every step in the process and can adapt to a wide range of protein targets from bacterial to human. The construction, expansion and optimization of the JCSG gene-to-structure pipeline over the years have resulted in many technological and methodological advances and developments. The vast number of targets and the enormous amounts of associated data processed through the multiple stages of the experimental pipeline required the development of variety of valuable resources that, wherever feasible, have been converted to free-access web-based tools and applications.

Rapid Processing of Radio Interferometer Data for Transient Surveys

NASA Astrophysics Data System (ADS)

Bourke, S.; Mooley, K.; Hallinan, G.

2014-05-01

We report on a software infrastructure and pipeline developed to process large radio interferometer datasets. The pipeline is implemented using a radical redesign of the AIPS processing model. An infrastructure we have named AIPSlite is used to spawn, at runtime, minimal AIPS environments across a cluster. The pipeline then distributes and processes its data in parallel. The system is entirely free of the traditional AIPS distribution and is self configuring at runtime. This software has so far been used to process a EVLA Stripe 82 transient survey, the data for the JVLA-COSMOS project, and has been used to process most of the EVLA L-Band data archive imaging each integration to search for short duration transients.

Study of sleeper’s impact on the deep-water pipeline lateral global buckling

NASA Astrophysics Data System (ADS)

Liu, Wenbin; Li, Bin

2017-08-01

Pipelines are the most important transportation way for offshore oil and gas, and the lateral buckling is the main global buckling form for deep-water pipelines. The sleeper is an economic and efficient device to trigger the lateral buckling in preset location. This paper analyzed the lateral buckling features for on-bottom pipeline and pipeline with sleeper. The stress and strain variation during buckling process is shown to reveal the impact of sleeper on buckling.

Integration of a neuroimaging processing pipeline into a pan-canadian computing grid

NASA Astrophysics Data System (ADS)

Lavoie-Courchesne, S.; Rioux, P.; Chouinard-Decorte, F.; Sherif, T.; Rousseau, M.-E.; Das, S.; Adalat, R.; Doyon, J.; Craddock, C.; Margulies, D.; Chu, C.; Lyttelton, O.; Evans, A. C.; Bellec, P.

2012-02-01

The ethos of the neuroimaging field is quickly moving towards the open sharing of resources, including both imaging databases and processing tools. As a neuroimaging database represents a large volume of datasets and as neuroimaging processing pipelines are composed of heterogeneous, computationally intensive tools, such open sharing raises specific computational challenges. This motivates the design of novel dedicated computing infrastructures. This paper describes an interface between PSOM, a code-oriented pipeline development framework, and CBRAIN, a web-oriented platform for grid computing. This interface was used to integrate a PSOM-compliant pipeline for preprocessing of structural and functional magnetic resonance imaging into CBRAIN. We further tested the capacity of our infrastructure to handle a real large-scale project. A neuroimaging database including close to 1000 subjects was preprocessed using our interface and publicly released to help the participants of the ADHD-200 international competition. This successful experiment demonstrated that our integrated grid-computing platform is a powerful solution for high-throughput pipeline analysis in the field of neuroimaging.

Bioinformatic pipelines in Python with Leaf

PubMed Central

2013-01-01

Background An incremental, loosely planned development approach is often used in bioinformatic studies when dealing with custom data analysis in a rapidly changing environment. Unfortunately, the lack of a rigorous software structuring can undermine the maintainability, communicability and replicability of the process. To ameliorate this problem we propose the Leaf system, the aim of which is to seamlessly introduce the pipeline formality on top of a dynamical development process with minimum overhead for the programmer, thus providing a simple layer of software structuring. Results Leaf includes a formal language for the definition of pipelines with code that can be transparently inserted into the user’s Python code. Its syntax is designed to visually highlight dependencies in the pipeline structure it defines. While encouraging the developer to think in terms of bioinformatic pipelines, Leaf supports a number of automated features including data and session persistence, consistency checks between steps of the analysis, processing optimization and publication of the analytic protocol in the form of a hypertext. Conclusions Leaf offers a powerful balance between plan-driven and change-driven development environments in the design, management and communication of bioinformatic pipelines. Its unique features make it a valuable alternative to other related tools. PMID:23786315

The PREP pipeline: standardized preprocessing for large-scale EEG analysis

PubMed Central

Bigdely-Shamlo, Nima; Mullen, Tim; Kothe, Christian; Su, Kyung-Min; Robbins, Kay A.

2015-01-01

The technology to collect brain imaging and physiological measures has become portable and ubiquitous, opening the possibility of large-scale analysis of real-world human imaging. By its nature, such data is large and complex, making automated processing essential. This paper shows how lack of attention to the very early stages of an EEG preprocessing pipeline can reduce the signal-to-noise ratio and introduce unwanted artifacts into the data, particularly for computations done in single precision. We demonstrate that ordinary average referencing improves the signal-to-noise ratio, but that noisy channels can contaminate the results. We also show that identification of noisy channels depends on the reference and examine the complex interaction of filtering, noisy channel identification, and referencing. We introduce a multi-stage robust referencing scheme to deal with the noisy channel-reference interaction. We propose a standardized early-stage EEG processing pipeline (PREP) and discuss the application of the pipeline to more than 600 EEG datasets. The pipeline includes an automatically generated report for each dataset processed. Users can download the PREP pipeline as a freely available MATLAB library from http://eegstudy.org/prepcode. PMID:26150785

Remaining Sites Verification Package for the 100-F-26:12, 1.8-m (72-in.) Main Process Sewer Pipeline, Waste Site Reclassification Form 2007-034

DOE Office of Scientific and Technical Information (OSTI.GOV)

J. M. Capron

2008-04-29

The 100-F-26:12 waste site was an approximately 308-m-long, 1.8-m-diameter east-west-trending reinforced concrete pipe that joined the North Process Sewer Pipelines (100-F-26:1) and the South Process Pipelines (100-F-26:4) with the 1.8-m reactor cooling water effluent pipeline (100-F-19). In accordance with this evaluation, the verification sampling results support a reclassification of this site to Interim Closed Out. The results of verification sampling show that residual contaminant concentrations do not preclude any future uses and allow for unrestricted use of shallow zone soils. The results also demonstrate that residual contaminant concentrations are protective of groundwater and the Columbia River.

From Pipelines to Tasting Lemonade: Reconceptualizing College Access

ERIC Educational Resources Information Center

Pitcher, Erich N.; Shahjahan, Riyad A.

2017-01-01

Pipeline metaphors are ubiquitous in theorizing and interpreting college access processes. In this conceptual article, we explore how a lemonade metaphor can open new possibilities to reimagining higher education access and going processes. We argue that using food metaphors, particularly the processes of mixing, tasting, and digesting lemonade,…

Integrating the ODI-PPA scientific gateway with the QuickReduce pipeline for on-demand processing

NASA Astrophysics Data System (ADS)

Young, Michael D.; Kotulla, Ralf; Gopu, Arvind; Liu, Wilson

2014-07-01

As imaging systems improve, the size of astronomical data has continued to grow, making the transfer and processing of data a significant burden. To solve this problem for the WIYN Observatory One Degree Imager (ODI), we developed the ODI-Portal, Pipeline, and Archive (ODI-PPA) science gateway, integrating the data archive, data reduction pipelines, and a user portal. In this paper, we discuss the integration of the QuickReduce (QR) pipeline into PPA's Tier 2 processing framework. QR is a set of parallelized, stand-alone Python routines accessible to all users, and operators who can create master calibration products and produce standardized calibrated data, with a short turn-around time. Upon completion, the data are ingested into the archive and portal, and made available to authorized users. Quality metrics and diagnostic plots are generated and presented via the portal for operator approval and user perusal. Additionally, users can tailor the calibration process to their specific science objective(s) by selecting custom datasets, applying preferred master calibrations or generating their own, and selecting pipeline options. Submission of a QuickReduce job initiates data staging, pipeline execution, and ingestion of output data products all while allowing the user to monitor the process status, and to download or further process/analyze the output within the portal. User-generated data products are placed into a private user-space within the portal. ODI-PPA leverages cyberinfrastructure at Indiana University including the Big Red II supercomputer, the Scholarly Data Archive tape system and the Data Capacitor shared file system.

The Chandra Source Catalog 2.0: Data Processing Pipelines

NASA Astrophysics Data System (ADS)

Miller, Joseph; Allen, Christopher E.; Budynkiewicz, Jamie A.; Gibbs, Danny G., II; Paxson, Charles; Chen, Judy C.; Anderson, Craig S.; Burke, Douglas; Civano, Francesca Maria; D'Abrusco, Raffaele; Doe, Stephen M.; Evans, Ian N.; Evans, Janet D.; Fabbiano, Giuseppina; Glotfelty, Kenny J.; Graessle, Dale E.; Grier, John D.; Hain, Roger; Hall, Diane M.; Harbo, Peter N.; Houck, John C.; Lauer, Jennifer L.; Laurino, Omar; Lee, Nicholas P.; Martínez-Galarza, Juan Rafael; McCollough, Michael L.; McDowell, Jonathan C.; McLaughlin, Warren; Morgan, Douglas L.; Mossman, Amy E.; Nguyen, Dan T.; Nichols, Joy S.; Nowak, Michael A.; Plummer, David A.; Primini, Francis Anthony; Rots, Arnold H.; Siemiginowska, Aneta; Sundheim, Beth A.; Tibbetts, Michael; Van Stone, David W.; Zografou, Panagoula

2018-01-01

With the construction of the Second Chandra Source Catalog (CSC2.0), came new requirements and new techniques to create a software system that can process 10,000 observations and identify nearly 320,000 point and compact X-ray sources. A new series of processing pipelines have been developed to allow for deeper more complete exploration of the Chanda observations. In CSC1.0 there were 4 general pipelines, whereas in CSC2.0 there are 20 data processing pipelines that have been organized into 3 distinct phases of operation - detection, master matching and source property characterization.With CSC2.0, observations within one arcminute of each other are stacked before searching for sources. The detection phase of processing combines the data, adjusts for shifts in fine astrometry, detects sources, and assesses the likelihood that sources are real. During the master source phase, detections across stacks of observations are analyzed for coverage of the same source to produce a master source. Finally, in the source property phase, each source is characterized with aperture photometry, spectrometry, variability and other properties at theobservation, stack and master levels over several energy bands.We present how these pipelines were constructed and the challenges we faced in how we processed data ranging from virtually no counts to millions of counts, how pipelines were tuned to work optimally on a computational cluster, and how we ensure the data produced was correct through various quality assurance steps.This work has been supported by NASA under contract NAS 8-03060 to the Smithsonian Astrophysical Observatory for operation of the Chandra X-ray Center.

Improved coal-slurry pipeline

NASA Technical Reports Server (NTRS)

Dowler, W. L.

1979-01-01

High strength steel pipeline carries hot mixture of powdered coal and coal derived oil to electric-power-generating station. Slurry is processed along way to remove sulfur, ash, and nitrogen and to recycle part of oil. System eliminates hazards and limitations associated with anticipated coal/water-slurry pipelines.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hansen, E.A.; Smed, P.F.; Bryndum, M.B.

The paper describes the numerical program, PIPESIN, that simulates the behavior of a pipeline placed on an erodible seabed. PIPEline Seabed INteraction from installation until a stable pipeline seabed configuration has occurred is simulated in the time domain including all important physical processes. The program is the result of the joint research project, ``Free Span Development and Self-lowering of Offshore Pipelines`` sponsored by EU and a group of companies and carried out by the Danish Hydraulic Institute and Delft Hydraulics. The basic modules of PIPESIN are described. The description of the scouring processes has been based on and verified throughmore » physical model tests carried out as part of the research project. The program simulates a section of the pipeline (typically 500 m) in the time domain, the main input being time series of the waves and current. The main results include predictions of the onset of free spans, their length distribution, their variation in time, and the lowering of the pipeline as function of time.« less

Lateral instability of high temperature pipelines, the 20-in. Sleipner Vest pipeline

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saevik, S.; Levold, E.; Johnsen, O.K.

1996-12-01

The present paper addresses methods to control snaking behavior of high temperature pipelines resting on a flat sea bed. A case study is presented based on the detail engineering of the 12.5 km long 20 inch gas pipeline connecting the Sleipner Vest wellhead platform to the Sleipner T processing platform in the North Sea. The study includes screening and evaluation of alternative expansion control methods, ending up with a recommended method. The methodology and philosophy, used as basis to ensure sufficient structural strength throughout the lifetime of the pipeline, are thereafter presented. The results show that in order to findmore » the optimum technical solution to control snaking behavior, many aspects need to be considered such as process requirements, allowable strain, hydrodynamic stability, vertical profile, pipelay installation and trawlboard loading. It is concluded that by proper consideration of all the above aspects, the high temperature pipeline can be designed to obtain sufficient safety level.« less

Enhancement of Hydrodynamic Processes in Oil Pipelines Considering Rheologically Complex High-Viscosity Oils

NASA Astrophysics Data System (ADS)

Konakhina, I. A.; Khusnutdinova, E. M.; Khamidullina, G. R.; Khamidullina, A. F.

2016-06-01

This paper describes a mathematical model of flow-related hydrodynamic processes for rheologically complex high-viscosity bitumen oil and oil-water suspensions and presents methods to improve the design and performance of oil pipelines.

Natural language processing pipelines to annotate BioC collections with an application to the NCBI disease corpus

PubMed Central

Comeau, Donald C.; Liu, Haibin; Islamaj Doğan, Rezarta; Wilbur, W. John

2014-01-01

BioC is a new format and associated code libraries for sharing text and annotations. We have implemented BioC natural language preprocessing pipelines in two popular programming languages: C++ and Java. The current implementations interface with the well-known MedPost and Stanford natural language processing tool sets. The pipeline functionality includes sentence segmentation, tokenization, part-of-speech tagging, lemmatization and sentence parsing. These pipelines can be easily integrated along with other BioC programs into any BioC compliant text mining systems. As an application, we converted the NCBI disease corpus to BioC format, and the pipelines have successfully run on this corpus to demonstrate their functionality. Code and data can be downloaded from http://bioc.sourceforge.net. Database URL: http://bioc.sourceforge.net PMID:24935050

77 FR 58217 - Notice of Delays in Processing of Special Permits Applications

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-19

... DEPARTMENT OF TRANSPORTATION Pipeline and Hazardous Materials Safety Administration Notice of Delays in Processing of Special Permits Applications AGENCY: Pipeline and Hazardous Materials Safety.... FOR FURTHER INFORMATION CONTACT: Ryan Paquet, Director, Office of Hazardous Materials Special Permits...

77 FR 64846 - Notice of Delays in Processing of Special Permits Applications

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-23

... DEPARTMENT OF TRANSPORTATION Pipeline and Hazardous Materials Safety Administration Notice of Delays in Processing of Special Permits Applications AGENCY: Pipeline and Hazardous Materials Safety.... FOR FURTHER INFORMATION CONTACT: Ryan Paquet, Director, Office of Hazardous Materials Special Permits...

HiCUP: pipeline for mapping and processing Hi-C data.

PubMed

Wingett, Steven; Ewels, Philip; Furlan-Magaril, Mayra; Nagano, Takashi; Schoenfelder, Stefan; Fraser, Peter; Andrews, Simon

2015-01-01

HiCUP is a pipeline for processing sequence data generated by Hi-C and Capture Hi-C (CHi-C) experiments, which are techniques used to investigate three-dimensional genomic organisation. The pipeline maps data to a specified reference genome and removes artefacts that would otherwise hinder subsequent analysis. HiCUP also produces an easy-to-interpret yet detailed quality control (QC) report that assists in refining experimental protocols for future studies. The software is freely available and has already been used for processing Hi-C and CHi-C data in several recently published peer-reviewed studies.

Natural language processing pipelines to annotate BioC collections with an application to the NCBI disease corpus.

PubMed

Comeau, Donald C; Liu, Haibin; Islamaj Doğan, Rezarta; Wilbur, W John

2014-01-01

BioC is a new format and associated code libraries for sharing text and annotations. We have implemented BioC natural language preprocessing pipelines in two popular programming languages: C++ and Java. The current implementations interface with the well-known MedPost and Stanford natural language processing tool sets. The pipeline functionality includes sentence segmentation, tokenization, part-of-speech tagging, lemmatization and sentence parsing. These pipelines can be easily integrated along with other BioC programs into any BioC compliant text mining systems. As an application, we converted the NCBI disease corpus to BioC format, and the pipelines have successfully run on this corpus to demonstrate their functionality. Code and data can be downloaded from http://bioc.sourceforge.net. Database URL: http://bioc.sourceforge.net. © The Author(s) 2014. Published by Oxford University Press.

Kepler Science Operations Center Architecture

NASA Technical Reports Server (NTRS)

Middour, Christopher; Klaus, Todd; Jenkins, Jon; Pletcher, David; Cote, Miles; Chandrasekaran, Hema; Wohler, Bill; Girouard, Forrest; Gunter, Jay P.; Uddin, Kamal;

A Pipeline Tool for CCD Image Processing

NASA Astrophysics Data System (ADS)

Bell, Jon F.; Young, Peter J.; Roberts, William H.; Sebo, Kim M.

MSSSO is part of a collaboration developing a wide field imaging CCD mosaic (WFI). As part of this project, we have developed a GUI based pipeline tool that is an integrated part of MSSSO's CICADA data acquisition environment and processes CCD FITS images as they are acquired. The tool is also designed to run as a stand alone program to process previously acquired data. IRAF tasks are used as the central engine, including the new NOAO mscred package for processing multi-extension FITS files. The STScI OPUS pipeline environment may be used to manage data and process scheduling. The Motif GUI was developed using SUN Visual Workshop. C++ classes were written to facilitate launching of IRAF and OPUS tasks. While this first version implements calibration processing up to and including flat field corrections, there is scope to extend it to other processing.

76 FR 56009 - Mandatory Reporting of Greenhouse Gases: Technical Revisions to the Electronics Manufacturing and...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-09

... Pipeline transportation of natural gas. 221210 Natural gas distribution facilities. 211 Extractors of crude... natural gas processing facilities in transmission pipelines or into storage. 40 CFR Sec. 98.230(a)(4). A... and inaccuracies in reporting''. Pipeline Quality Yes. Natural Gas. CEC/ AXPC asserted that ``[t]here...

76 FR 60478 - Record of Decision, Texas Clean Energy Project

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-29

... the plant with one or both of the nearby power grids; process water supply pipelines; a natural gas... per year. The CO 2 will be delivered through a regional pipeline network to existing oil fields in the... proposed Fort Stockton Holdings water supply pipeline; Possible changes in discharges to Monahans Draw and...

Relationship between Pipeline Wall Thickness (Gr. X60) and Water Depth towards Avoiding Failure during Installation

NASA Astrophysics Data System (ADS)

Razak, K. Abdul; Othman, M. I. H.; Mat Yusuf, S.; Fuad, M. F. I. Ahmad; yahaya, Effah

2018-05-01

Oil and gas today being developed at different water depth characterized as shallow, deep and ultra-deep waters. Among the major components involved during the offshore installation is pipelines. Pipelines are a transportation method of material through a pipe. In oil and gas industry, pipeline come from a bunch of line pipe that welded together to become a long pipeline and can be divided into two which is gas pipeline and oil pipeline. In order to perform pipeline installation, we need pipe laying barge or pipe laying vessel. However, pipe laying vessel can be divided into two types: S-lay vessel and J-lay vessel. The function of pipe lay vessel is not only to perform pipeline installation. It also performed installation of umbilical or electrical cables. In the simple words, pipe lay vessel is performing the installation of subsea in all the connecting infrastructures. Besides that, the installation processes of pipelines require special focus to make the installation succeed. For instance, the heavy pipelines may exceed the lay vessel’s tension capacities in certain kind of water depth. Pipeline have their own characteristic and we can group it or differentiate it by certain parameters such as grade of material, type of material, size of diameter, size of wall thickness and the strength. For instances, wall thickness parameter studies indicate that if use the higher steel grade of the pipelines will have a significant contribution in pipeline wall thickness reduction. When running the process of pipe lay, water depth is the most critical thing that we need to monitor and concern about because of course we cannot control the water depth but we can control the characteristic of the pipe like apply line pipe that have wall thickness suitable with current water depth in order to avoid failure during the installation. This research will analyse whether the pipeline parameter meet the requirements limit and minimum yield stress. It will overlook to simulate pipe grade API 5L X60 which size from 8 to 20mm thickness with a water depth of 50 to 300m. Result shown that pipeline installation will fail from the wall thickness of 18mm onwards since it has been passed the critical yield percentage.

Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses.

PubMed

Golosova, Olga; Henderson, Ross; Vaskin, Yuriy; Gabrielian, Andrei; Grekhov, German; Nagarajan, Vijayaraj; Oler, Andrew J; Quiñones, Mariam; Hurt, Darrell; Fursov, Mikhail; Huyen, Yentram

2014-01-01

The advent of Next Generation Sequencing (NGS) technologies has opened new possibilities for researchers. However, the more biology becomes a data-intensive field, the more biologists have to learn how to process and analyze NGS data with complex computational tools. Even with the availability of common pipeline specifications, it is often a time-consuming and cumbersome task for a bench scientist to install and configure the pipeline tools. We believe that a unified, desktop and biologist-friendly front end to NGS data analysis tools will substantially improve productivity in this field. Here we present NGS pipelines "Variant Calling with SAMtools", "Tuxedo Pipeline for RNA-seq Data Analysis" and "Cistrome Pipeline for ChIP-seq Data Analysis" integrated into the Unipro UGENE desktop toolkit. We describe the available UGENE infrastructure that helps researchers run these pipelines on different datasets, store and investigate the results and re-run the pipelines with the same parameters. These pipeline tools are included in the UGENE NGS package. Individual blocks of these pipelines are also available for expert users to create their own advanced workflows.

The Dark Energy Survey Image Processing Pipeline

NASA Astrophysics Data System (ADS)

Morganson, E.; Gruendl, R. A.; Menanteau, F.; Carrasco Kind, M.; Chen, Y.-C.; Daues, G.; Drlica-Wagner, A.; Friedel, D. N.; Gower, M.; Johnson, M. W. G.; Johnson, M. D.; Kessler, R.; Paz-Chinchón, F.; Petravick, D.; Pond, C.; Yanny, B.; Allam, S.; Armstrong, R.; Barkhouse, W.; Bechtol, K.; Benoit-Lévy, A.; Bernstein, G. M.; Bertin, E.; Buckley-Geer, E.; Covarrubias, R.; Desai, S.; Diehl, H. T.; Goldstein, D. A.; Gruen, D.; Li, T. S.; Lin, H.; Marriner, J.; Mohr, J. J.; Neilsen, E.; Ngeow, C.-C.; Paech, K.; Rykoff, E. S.; Sako, M.; Sevilla-Noarbe, I.; Sheldon, E.; Sobreira, F.; Tucker, D. L.; Wester, W.; DES Collaboration

2018-07-01

The Dark Energy Survey (DES) is a five-year optical imaging campaign with the goal of understanding the origin of cosmic acceleration. DES performs a ∼5000 deg2 survey of the southern sky in five optical bands (g, r, i, z, Y) to a depth of ∼24th magnitude. Contemporaneously, DES performs a deep, time-domain survey in four optical bands (g, r, i, z) over ∼27 deg2. DES exposures are processed nightly with an evolving data reduction pipeline and evaluated for image quality to determine if they need to be retaken. Difference imaging and transient source detection are also performed in the time domain component nightly. On a bi-annual basis, DES exposures are reprocessed with a refined pipeline and coadded to maximize imaging depth. Here we describe the DES image processing pipeline in support of DES science, as a reference for users of archival DES data, and as a guide for future astronomical surveys.

The Kepler Science Operations Center Pipeline Framework Extensions

NASA Technical Reports Server (NTRS)

Klaus, Todd C.; Cote, Miles T.; McCauliff, Sean; Girouard, Forrest R.; Wohler, Bill; Allen, Christopher; Chandrasekaran, Hema; Bryson, Stephen T.; Middour, Christopher; Caldwell, Douglas A.;

Practical Approach for Hyperspectral Image Processing in Python

NASA Astrophysics Data System (ADS)

Annala, L.; Eskelinen, M. A.; Hämäläinen, J.; Riihinen, A.; Pölönen, I.

2018-04-01

Python is a very popular programming language among data scientists around the world. Python can also be used in hyperspectral data analysis. There are some toolboxes designed for spectral imaging, such as Spectral Python and HyperSpy, but there is a need for analysis pipeline, which is easy to use and agile for different solutions. We propose a Python pipeline which is built on packages xarray, Holoviews and scikit-learn. We have developed some of own tools, MaskAccessor, VisualisorAccessor and a spectral index library. They also fulfill our goal of easy and agile data processing. In this paper we will present our processing pipeline and demonstrate it in practice.

UOE Pipe Numerical Model: Manufacturing Process And Von Mises Residual Stresses Resulted After Each Technological Step

NASA Astrophysics Data System (ADS)

Delistoian, Dmitri; Chirchor, Mihael

2017-12-01

Fluid transportation from production areas to final customer is effectuated by pipelines. For oil and gas industry, pipeline safety and reliability represents a priority. From this reason, pipe quality guarantee directly influence pipeline designed life, but first of all protects environment. A significant number of longitudinally welded pipes, for onshore/offshore pipelines, are manufactured by UOE method. This method is based on cold forming. In present study, using finite element method is modeled UOE pipe manufacturing process and is obtained von Mises stresses for each step. Numerical simulation is performed for L415 MB (X60) steel plate with 7,9 mm thickness, length 30 mm and width 1250mm, as result it is obtained a DN 400 pipe.

An image processing pipeline to detect and segment nuclei in muscle fiber microscopic images.

PubMed

Guo, Yanen; Xu, Xiaoyin; Wang, Yuanyuan; Wang, Yaming; Xia, Shunren; Yang, Zhong

2014-08-01

Muscle fiber images play an important role in the medical diagnosis and treatment of many muscular diseases. The number of nuclei in skeletal muscle fiber images is a key bio-marker of the diagnosis of muscular dystrophy. In nuclei segmentation one primary challenge is to correctly separate the clustered nuclei. In this article, we developed an image processing pipeline to automatically detect, segment, and analyze nuclei in microscopic image of muscle fibers. The pipeline consists of image pre-processing, identification of isolated nuclei, identification and segmentation of clustered nuclei, and quantitative analysis. Nuclei are initially extracted from background by using local Otsu's threshold. Based on analysis of morphological features of the isolated nuclei, including their areas, compactness, and major axis lengths, a Bayesian network is trained and applied to identify isolated nuclei from clustered nuclei and artifacts in all the images. Then a two-step refined watershed algorithm is applied to segment clustered nuclei. After segmentation, the nuclei can be quantified for statistical analysis. Comparing the segmented results with those of manual analysis and an existing technique, we find that our proposed image processing pipeline achieves good performance with high accuracy and precision. The presented image processing pipeline can therefore help biologists increase their throughput and objectivity in analyzing large numbers of nuclei in muscle fiber images. © 2014 Wiley Periodicals, Inc.

A pipeline for comprehensive and automated processing of electron diffraction data in IPLT.

PubMed

Schenk, Andreas D; Philippsen, Ansgar; Engel, Andreas; Walz, Thomas

2013-05-01

Electron crystallography of two-dimensional crystals allows the structural study of membrane proteins in their native environment, the lipid bilayer. Determining the structure of a membrane protein at near-atomic resolution by electron crystallography remains, however, a very labor-intense and time-consuming task. To simplify and accelerate the data processing aspect of electron crystallography, we implemented a pipeline for the processing of electron diffraction data using the Image Processing Library and Toolbox (IPLT), which provides a modular, flexible, integrated, and extendable cross-platform, open-source framework for image processing. The diffraction data processing pipeline is organized as several independent modules implemented in Python. The modules can be accessed either from a graphical user interface or through a command line interface, thus meeting the needs of both novice and expert users. The low-level image processing algorithms are implemented in C++ to achieve optimal processing performance, and their interface is exported to Python using a wrapper. For enhanced performance, the Python processing modules are complemented with a central data managing facility that provides a caching infrastructure. The validity of our data processing algorithms was verified by processing a set of aquaporin-0 diffraction patterns with the IPLT pipeline and comparing the resulting merged data set with that obtained by processing the same diffraction patterns with the classical set of MRC programs. Copyright © 2013 Elsevier Inc. All rights reserved.

A pipeline for comprehensive and automated processing of electron diffraction data in IPLT

PubMed Central

Schenk, Andreas D.; Philippsen, Ansgar; Engel, Andreas; Walz, Thomas

2013-01-01

Electron crystallography of two-dimensional crystals allows the structural study of membrane proteins in their native environment, the lipid bilayer. Determining the structure of a membrane protein at near-atomic resolution by electron crystallography remains, however, a very labor-intense and time-consuming task. To simplify and accelerate the data processing aspect of electron crystallography, we implemented a pipeline for the processing of electron diffraction data using the Image Processing Library & Toolbox (IPLT), which provides a modular, flexible, integrated, and extendable cross-platform, open-source framework for image processing. The diffraction data processing pipeline is organized as several independent modules implemented in Python. The modules can be accessed either from a graphical user interface or through a command line interface, thus meeting the needs of both novice and expert users. The low-level image processing algorithms are implemented in C++ to achieve optimal processing performance, and their interface is exported to Python using a wrapper. For enhanced performance, the Python processing modules are complemented with a central data managing facility that provides a caching infrastructure. The validity of our data processing algorithms was verified by processing a set of aquaporin-0 diffraction patterns with the IPLT pipeline and comparing the resulting merged data set with that obtained by processing the same diffraction patterns with the classical set of MRC programs. PMID:23500887

The connectome mapper: an open-source processing pipeline to map connectomes with MRI.

PubMed

Daducci, Alessandro; Gerhard, Stephan; Griffa, Alessandra; Lemkaddem, Alia; Cammoun, Leila; Gigandet, Xavier; Meuli, Reto; Hagmann, Patric; Thiran, Jean-Philippe

2012-01-01

Researchers working in the field of global connectivity analysis using diffusion magnetic resonance imaging (MRI) can count on a wide selection of software packages for processing their data, with methods ranging from the reconstruction of the local intra-voxel axonal structure to the estimation of the trajectories of the underlying fibre tracts. However, each package is generally task-specific and uses its own conventions and file formats. In this article we present the Connectome Mapper, a software pipeline aimed at helping researchers through the tedious process of organising, processing and analysing diffusion MRI data to perform global brain connectivity analyses. Our pipeline is written in Python and is freely available as open-source at www.cmtk.org.

77 FR 48112 - Pipeline Safety: Administrative Procedures; Updates and Technical Corrections

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-13

...This Notice of Proposed Rulemaking updates the administrative civil penalty maximums for violation of the pipeline safety regulations to conform to current law, updates the informal hearing and adjudication process for pipeline enforcement matters to conform to current law, amends other administrative procedures used by PHMSA personnel, and makes other technical corrections and updates to certain administrative procedures. The proposed amendments do not impose any new operating, maintenance, or other substantive requirements on pipeline owners or operators.

78 FR 50087 - Notice of Intent To Prepare a Supplemental Environmental Impact Statement for the Alpine...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-16

... the majority of the infield road and pipeline route. CPAI proposes placement of fill material on 73.1..., gas, and water produced from the reservoir would be carried via pipeline to CD-1 for processing. Sales... construct, operate, and maintain a drill site, access road, pipelines, and ancillary facilities to support...

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data

Treesearch

Jonathan M. Palmer; Michelle A. Jusino; Mark T. Banik; Daniel L. Lindner

2018-01-01

High-throughput amplicon sequencing (HTAS) of conserved DNA regions is a powerful technique to characterize microbial communities. Recently, spike-in mock communities have been used to measure accuracy of sequencing platforms and data analysis pipelines. To assess the ability of sequencing platforms and data processing pipelines using fungal internal transcribed spacer...

Generation of ethylene tracer by noncatalytic pyrolysis of natural gas at elevated pressure

USGS Publications Warehouse

Lu, Y.; Chen, S.; Rostam-Abadi, M.; Ruch, R.; Coleman, D.; Benson, L.J.

2005-01-01

There is a critical need within the pipeline gas industry for an inexpensive and reliable technology to generate an identification tag or tracer that can be added to pipeline gas to identify gas that may escape and improve the deliverability and management of gas in underground storage fields. Ethylene is an ideal tracer, because it does not exist naturally in the pipeline gas, and because its physical properties are similar to the pipeline gas components. A pyrolysis process, known as the Tragen process, has been developed to continuously convert the ???2%-4% ethane component present in pipeline gas into ethylene at common pipeline pressures of 800 psi. In our studies of the Tragen process, pyrolysis without steam addition achieved a maximum ethylene yield of 28%-35% at a temperature range of 700-775 ??C, corresponding to an ethylene concentration of 4600-5800 ppm in the product gas. Coke deposition was determined to occur at a significant rate in the pyrolysis reactor without steam addition. The ?? 13C isotopic analysis of gas components showed a ?? 13C value of ethylene similar to ethane in the pipeline gas, indicating that most of the ethylene was generated from decomposition of the ethane in the raw gas. However, ?? 13C isotopic analysis of the deposited coke showed that coke was primarily produced from methane, rather than from ethane or other heavier hydrocarbons. No coke deposition was observed with the addition of steam at concentrations of > 20% by volume. The dilution with steam also improved the ethylene yield. ?? 2005 American Chemical Society.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reggio, R.; Haun, R.

This paper reviews the engineering and design work along with the installation procedures for a Persian Gulf natural gas pipeline. OPMI Ltd., a joint venture of Offshore Pipelines, Inc., Houston, and Maritime Industrial Services Co., Ltd., United Arab Emirates (UAE), successfully completed this 57.4 mile, 16-inch gas export pipeline for Consolidated Transmissions Inc. The pipeline begins at a platform in the Mubarek field offshore Sharjah, UAE, and runs to a beach termination at the Dugas treatment plant, Jebel Ali, Dubai. The paper describes the site preparation required for installation of the pipeline along with the specific design of the pipelinemore » itself to deal with corrosion, welding processes, condensate dropout, and temperature gradients.« less

Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family.

PubMed

Song, Jia; Zheng, Sisi; Nguyen, Nhung; Wang, Youjun; Zhou, Yubin; Lin, Kui

2017-10-03

Because phylogenetic inference is an important basis for answering many evolutionary problems, a large number of algorithms have been developed. Some of these algorithms have been improved by integrating gene evolution models with the expectation of accommodating the hierarchy of evolutionary processes. To the best of our knowledge, however, there still is no single unifying model or algorithm that can take all evolutionary processes into account through a stepwise or simultaneous method. On the basis of three existing phylogenetic inference algorithms, we built an integrated pipeline for inferring the evolutionary history of a given gene family; this pipeline can model gene sequence evolution, gene duplication-loss, gene transfer and multispecies coalescent processes. As a case study, we applied this pipeline to the STIMATE (TMEM110) gene family, which has recently been reported to play an important role in store-operated Ca 2+ entry (SOCE) mediated by ORAI and STIM proteins. We inferred their phylogenetic trees in 69 sequenced chordate genomes. By integrating three tree reconstruction algorithms with diverse evolutionary models, a pipeline for inferring the evolutionary history of a gene family was developed, and its application was demonstrated.

The visual and radiological inspection of a pipeline using a teleoperated pipe crawler

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fogle, R.F.; Kuelske, K.; Kellner, R.

1995-01-01

In the 1950s, the Savannah River Site built an open, unlined retention basin to temporarily store potentially radionuclide contaminated cooling water from a chemical separations process and storm water drainage from a nearby waste management facility that stored large quantities of nuclear fission byproducts in carbon steel tanks. The retention basin was retired from service in 1972 when a new, lined basin was completed. In 1978, the old retention basin was excavated, backfilled with uncontaminated dirt, and covered with grass. At the same time, much of the underground process pipeline leading to the basin was abandoned. Since the closure ofmore » the retention basin, new environmental regulations require that the basin undergo further assessment to determine whether additional remediation is required. A visual and radiological inspection of the pipeline was necessary to aid in the remediation decision making process for the retention basin system. A teleoperated pipe crawler inspection system was developed to survey the abandoned sections of underground pipelines leading to the retired retention basin. This paper will describe the background to this project, the scope of the investigation, the equipment requirements, and the results of the pipeline inspection.« less

The inspection of a radiologically contaminated pipeline using a teleoperated pipe crawler

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fogle, R.F.; Kuelske, K.; Kellner, R.A.

1995-08-01

In the 1950s, the Savannah River Site built an open, unlined retention basin to temporarily store potentially radionuclide contaminated cooling water from a chemical separations process and storm water drainage from a nearby waste management facility that stored large quantities of nuclear fission byproducts in carbon steel tanks. The retention basin was retired from service in 1972 when a new, lined basin was completed. In 1978, the old retention basin was excavated, backfilled with uncontaminated dirt, and covered with grass. At the same time, much of the underground process pipeline leading to the basin was abandoned. Since the closure ofmore » the retention basin, new environmental regulations require that the basin undergo further assessment to determine whether additional remediation is required. A visual and radiological inspection of the pipeline was necessary to aid in the remediation decision making process for the retention basin system. A teleoperated pipe crawler inspection system was developed to survey the abandoned sections of underground pipelines leading to the retired retention basin. This paper will describe the background to this project, the scope of the investigation, the equipment requirements, and the results of the pipeline inspection.« less

Multinode reconfigurable pipeline computer

NASA Technical Reports Server (NTRS)

Nosenchuck, Daniel M. (Inventor); Littman, Michael G. (Inventor)

1989-01-01

A multinode parallel-processing computer is made up of a plurality of innerconnected, large capacity nodes each including a reconfigurable pipeline of functional units such as Integer Arithmetic Logic Processors, Floating Point Arithmetic Processors, Special Purpose Processors, etc. The reconfigurable pipeline of each node is connected to a multiplane memory by a Memory-ALU switch NETwork (MASNET). The reconfigurable pipeline includes three (3) basic substructures formed from functional units which have been found to be sufficient to perform the bulk of all calculations. The MASNET controls the flow of signals from the memory planes to the reconfigurable pipeline and vice versa. the nodes are connectable together by an internode data router (hyperspace router) so as to form a hypercube configuration. The capability of the nodes to conditionally configure the pipeline at each tick of the clock, without requiring a pipeline flush, permits many powerful algorithms to be implemented directly.

Natural Language Processing Accurately Calculates Adenoma and Sessile Serrated Polyp Detection Rates.

PubMed

Nayor, Jennifer; Borges, Lawrence F; Goryachev, Sergey; Gainer, Vivian S; Saltzman, John R

2018-07-01

ADR is a widely used colonoscopy quality indicator. Calculation of ADR is labor-intensive and cumbersome using current electronic medical databases. Natural language processing (NLP) is a method used to extract meaning from unstructured or free text data. (1) To develop and validate an accurate automated process for calculation of adenoma detection rate (ADR) and serrated polyp detection rate (SDR) on data stored in widely used electronic health record systems, specifically Epic electronic health record system, Provation ® endoscopy reporting system, and Sunquest PowerPath pathology reporting system. Screening colonoscopies performed between June 2010 and August 2015 were identified using the Provation ® reporting tool. An NLP pipeline was developed to identify adenomas and sessile serrated polyps (SSPs) on pathology reports corresponding to these colonoscopy reports. The pipeline was validated using a manual search. Precision, recall, and effectiveness of the natural language processing pipeline were calculated. ADR and SDR were then calculated. We identified 8032 screening colonoscopies that were linked to 3821 pathology reports (47.6%). The NLP pipeline had an accuracy of 100% for adenomas and 100% for SSPs. Mean total ADR was 29.3% (range 14.7-53.3%); mean male ADR was 35.7% (range 19.7-62.9%); and mean female ADR was 24.9% (range 9.1-51.0%). Mean total SDR was 4.0% (0-9.6%). We developed and validated an NLP pipeline that accurately and automatically calculates ADRs and SDRs using data stored in Epic, Provation ® and Sunquest PowerPath. This NLP pipeline can be used to evaluate colonoscopy quality parameters at both individual and practice levels.

Fast parallel algorithm for slicing STL based on pipeline

NASA Astrophysics Data System (ADS)

Ma, Xulong; Lin, Feng; Yao, Bo

2016-05-01

In Additive Manufacturing field, the current researches of data processing mainly focus on a slicing process of large STL files or complicated CAD models. To improve the efficiency and reduce the slicing time, a parallel algorithm has great advantages. However, traditional algorithms can't make full use of multi-core CPU hardware resources. In the paper, a fast parallel algorithm is presented to speed up data processing. A pipeline mode is adopted to design the parallel algorithm. And the complexity of the pipeline algorithm is analyzed theoretically. To evaluate the performance of the new algorithm, effects of threads number and layers number are investigated by a serial of experiments. The experimental results show that the threads number and layers number are two remarkable factors to the speedup ratio. The tendency of speedup versus threads number reveals a positive relationship which greatly agrees with the Amdahl's law, and the tendency of speedup versus layers number also keeps a positive relationship agreeing with Gustafson's law. The new algorithm uses topological information to compute contours with a parallel method of speedup. Another parallel algorithm based on data parallel is used in experiments to show that pipeline parallel mode is more efficient. A case study at last shows a suspending performance of the new parallel algorithm. Compared with the serial slicing algorithm, the new pipeline parallel algorithm can make full use of the multi-core CPU hardware, accelerate the slicing process, and compared with the data parallel slicing algorithm, the new slicing algorithm in this paper adopts a pipeline parallel model, and a much higher speedup ratio and efficiency is achieved.

Planck 2015 results. II. Low Frequency Instrument data processings

NASA Astrophysics Data System (ADS)

Planck Collaboration; Ade, P. A. R.; Aghanim, N.; Ashdown, M.; Aumont, J.; Baccigalupi, C.; Ballardini, M.; Banday, A. J.; Barreiro, R. B.; Bartolo, N.; Basak, S.; Battaglia, P.; Battaner, E.; Benabed, K.; Benoît, A.; Benoit-Lévy, A.; Bernard, J.-P.; Bersanelli, M.; Bielewicz, P.; Bock, J. J.; Bonaldi, A.; Bonavera, L.; Bond, J. R.; Borrill, J.; Bouchet, F. R.; Bucher, M.; Burigana, C.; Butler, R. C.; Calabrese, E.; Cardoso, J.-F.; Castex, G.; Catalano, A.; Chamballu, A.; Christensen, P. R.; Colombi, S.; Colombo, L. P. L.; Crill, B. P.; Curto, A.; Cuttaia, F.; Danese, L.; Davies, R. D.; Davis, R. J.; de Bernardis, P.; de Rosa, A.; de Zotti, G.; Delabrouille, J.; Dickinson, C.; Diego, J. M.; Dole, H.; Donzelli, S.; Doré, O.; Douspis, M.; Ducout, A.; Dupac, X.; Efstathiou, G.; Elsner, F.; Enßlin, T. A.; Eriksen, H. K.; Fergusson, J.; Finelli, F.; Forni, O.; Frailis, M.; Franceschet, C.; Franceschi, E.; Frejsel, A.; Galeotta, S.; Galli, S.; Ganga, K.; Giard, M.; Giraud-Héraud, Y.; Gjerløw, E.; González-Nuevo, J.; Górski, K. M.; Gratton, S.; Gregorio, A.; Gruppuso, A.; Hansen, F. K.; Hanson, D.; Harrison, D. L.; Henrot-Versillé, S.; Herranz, D.; Hildebrandt, S. R.; Hivon, E.; Hobson, M.; Holmes, W. A.; Hornstrup, A.; Hovest, W.; Huffenberger, K. M.; Hurier, G.; Jaffe, A. H.; Jaffe, T. R.; Juvela, M.; Keihänen, E.; Keskitalo, R.; Kiiveri, K.; Kisner, T. S.; Knoche, J.; Krachmalnicoff, N.; Kunz, M.; Kurki-Suonio, H.; Lagache, G.; Lähteenmäki, A.; Lamarre, J.-M.; Lasenby, A.; Lattanzi, M.; Lawrence, C. R.; Leahy, J. P.; Leonardi, R.; Lesgourgues, J.; Levrier, F.; Liguori, M.; Lilje, P. B.; Linden-Vørnle, M.; Lindholm, V.; López-Caniego, M.; Lubin, P. M.; Macías-Pérez, J. F.; Maggio, G.; Maino, D.; Mandolesi, N.; Mangilli, A.; Maris, M.; Martin, P. G.; Martínez-González, E.; Masi, S.; Matarrese, S.; Mazzotta, P.; McGehee, P.; Meinhold, P. R.; Melchiorri, A.; Mendes, L.; Mennella, A.; Migliaccio, M.; Mitra, S.; Montier, L.; Morgante, G.; Morisset, N.; Mortlock, D.; Moss, A.; Munshi, D.; Murphy, J. A.; Naselsky, P.; Nati, F.; Natoli, P.; Netterfield, C. B.; Nørgaard-Nielsen, H. U.; Novikov, D.; Novikov, I.; Oppermann, N.; Paci, F.; Pagano, L.; Paoletti, D.; Partridge, B.; Pasian, F.; Patanchon, G.; Pearson, T. J.; Peel, M.; Perdereau, O.; Perotto, L.; Perrotta, F.; Pettorino, V.; Piacentini, F.; Pierpaoli, E.; Pietrobon, D.; Pointecouteau, E.; Polenta, G.; Pratt, G. W.; Prézeau, G.; Prunet, S.; Puget, J.-L.; Rachen, J. P.; Rebolo, R.; Reinecke, M.; Remazeilles, M.; Renzi, A.; Rocha, G.; Romelli, E.; Rosset, C.; Rossetti, M.; Roudier, G.; Rubiño-Martín, J. A.; Rusholme, B.; Sandri, M.; Santos, D.; Savelainen, M.; Scott, D.; Seiffert, M. D.; Shellard, E. P. S.; Spencer, L. D.; Stolyarov, V.; Sutton, D.; Suur-Uski, A.-S.; Sygnet, J.-F.; Tauber, J. A.; Tavagnacco, D.; Terenzi, L.; Toffolatti, L.; Tomasi, M.; Tristram, M.; Tucci, M.; Tuovinen, J.; Türler, M.; Umana, G.; Valenziano, L.; Valiviita, J.; Van Tent, B.; Vassallo, T.; Vielva, P.; Villa, F.; Wade, L. A.; Wandelt, B. D.; Watson, R.; Wehus, I. K.; Wilkinson, A.; Yvon, D.; Zacchei, A.; Zonca, A.

2016-09-01

We present an updated description of the Planck Low Frequency Instrument (LFI) data processing pipeline, associated with the 2015 data release. We point out the places where our results and methods have remained unchanged since the 2013 paper and we highlight the changes made for the 2015 release, describing the products (especially timelines) and the ways in which they were obtained. We demonstrate that the pipeline is self-consistent (principally based on simulations) and report all null tests. For the first time, we present LFI maps in Stokes Q and U polarization. We refer to other related papers where more detailed descriptions of the LFI data processing pipeline may be found if needed.

30 CFR 250.1003 - Installation, testing, and repair requirements for DOI pipelines.

Code of Federal Regulations, 2011 CFR

2011-07-01

... installed in water depths of less than 200 feet shall be buried to a depth of at least 3 feet unless they... damage potential exists. (b)(1) Pipelines shall be pressure tested with water at a stabilized pressure of... repair, the pipeline shall be pressure tested with water or processed natural gas at a minimum stabilized...

A Mitigation Process for Impacts of the All American Pipeline on Oak Woodlands in Santa Barbara County

Treesearch

Germaine Reyes-French; Timothy J. Cohen

1991-01-01

This paper outlines a mitigation program for pipeline construction impacts to oak tree habitat by describing the requirements for the Offsite Oak Mitigation Program for the All American Pipeline (AAPL) in Santa Barbara County, California. After describing the initial environmental analysis, the County regulatory structure is described under which the plan was required...

ORAC-DR: Astronomy data reduction pipeline

NASA Astrophysics Data System (ADS)

Jenness, Tim; Economou, Frossie; Cavanagh, Brad; Currie, Malcolm J.; Gibb, Andy

2013-10-01

ORAC-DR is a generic data reduction pipeline infrastructure; it includes specific data processing recipes for a number of instruments. It is used at the James Clerk Maxwell Telescope, United Kingdom Infrared Telescope, AAT, and LCOGT. This pipeline runs at the JCMT Science Archive hosted by CADC to generate near-publication quality data products; the code has been in use since 1998.

Open source pipeline for ESPaDOnS reduction and analysis

NASA Astrophysics Data System (ADS)

Martioli, Eder; Teeple, Doug; Manset, Nadine; Devost, Daniel; Withington, Kanoa; Venne, Andre; Tannock, Megan

2012-09-01

OPERA is a Canada-France-Hawaii Telescope (CFHT) open source collaborative software project currently under development for an ESPaDOnS echelle spectro-polarimetric image reduction pipeline. OPERA is designed to be fully automated, performing calibrations and reduction, producing one-dimensional intensity and polarimetric spectra. The calibrations are performed on two-dimensional images. Spectra are extracted using an optimal extraction algorithm. While primarily designed for CFHT ESPaDOnS data, the pipeline is being written to be extensible to other echelle spectrographs. A primary design goal is to make use of fast, modern object-oriented technologies. Processing is controlled by a harness, which manages a set of processing modules, that make use of a collection of native OPERA software libraries and standard external software libraries. The harness and modules are completely parametrized by site configuration and instrument parameters. The software is open- ended, permitting users of OPERA to extend the pipeline capabilities. All these features have been designed to provide a portable infrastructure that facilitates collaborative development, code re-usability and extensibility. OPERA is free software with support for both GNU/Linux and MacOSX platforms. The pipeline is hosted on SourceForge under the name "opera-pipeline".

VizieR Online Data Catalog: New Kepler planetary candidates (Ofir+, 2013)

NASA Astrophysics Data System (ADS)

Ofir, A.; Dreizler, S.

2013-10-01

We present first results of our efforts to re-analyze the Kepler photometric dataset, searching for planetary transits using an alternative processing pipeline to the one used by the Kepler mission The SARS pipeline was tried and tested extensively by processing all available CoRoT mission data. For this first paper of the series we used this pipeline to search for (additional) planetary transits only in a small subset of stars - the Kepler objects of interest (KOIs), which are already known to include at least one promising planet candidate. (2 data files).

Nine Years of XMM-Newton Pipeline: Experience and Feedback

NASA Astrophysics Data System (ADS)

Michel, Laurent; Motch, Christian

2009-05-01

The Strasbourg Astronomical Observatory is member of the Survey Science Centre (SSC) of the XMM-Newton satellite. Among other responsibilities, we provide a database access to the 2XMMi catalogue and run the part of the data processing pipeline performing the cross-correlation of EPIC sources with archival catalogs. These tasks were all developed in Strasbourg. Pipeline processing is flawlessly in operation since 1999. We describe here the work load and infrastructure setup in Strasbourg to support SSC activities. Our nine year long SSC experience could be used in the framework of the Simbol-X ground segment.

The Dark Energy Survey Image Processing Pipeline

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morganson, E.; et al.

The Dark Energy Survey (DES) is a five-year optical imaging campaign with the goal of understanding the origin of cosmic acceleration. DES performs a 5000 square degree survey of the southern sky in five optical bands (g,r,i,z,Y) to a depth of ~24th magnitude. Contemporaneously, DES performs a deep, time-domain survey in four optical bands (g,r,i,z) over 27 square degrees. DES exposures are processed nightly with an evolving data reduction pipeline and evaluated for image quality to determine if they need to be retaken. Difference imaging and transient source detection are also performed in the time domain component nightly. On amore » bi-annual basis, DES exposures are reprocessed with a refined pipeline and coadded to maximize imaging depth. Here we describe the DES image processing pipeline in support of DES science, as a reference for users of archival DES data, and as a guide for future astronomical surveys.« less

Quantification technology study on flaws in steam-filled pipelines based on image processing

NASA Astrophysics Data System (ADS)

Sun, Lina; Yuan, Peixin

2009-07-01

Starting from exploiting the applied detection system of gas transmission pipeline, a set of X-ray image processing methods and pipeline flaw quantificational evaluation methods are proposed. Defective and non-defective strings and rows in gray image were extracted and oscillogram was obtained. We can distinguish defects in contrast with two gray images division. According to the gray value of defects with different thicknesses, the gray level depth curve is founded. Through exponential and polynomial fitting way to obtain the attenuation mathematical model which the beam penetrates pipeline, thus attain flaw deep dimension. This paper tests on the PPR pipe in the production of simulated holes flaw and cracks flaw, 135KV used the X-ray source on the testing. Test results show that X-ray image processing method, which meet the needs of high efficient flaw detection and provide quality safeguard for thick oil recovery, can be used successfully in detecting corrosion of insulated pipe.

Quantification technology study on flaws in steam-filled pipelines based on image processing

NASA Astrophysics Data System (ADS)

Yuan, Pei-xin; Cong, Jia-hui; Chen, Bo

2008-03-01

Starting from exploiting the applied detection system of gas transmission pipeline, a set of X-ray image processing methods and pipeline flaw quantificational evaluation methods are proposed. Defective and non-defective strings and rows in gray image were extracted and oscillogram was obtained. We can distinguish defects in contrast with two gray images division. According to the gray value of defects with different thicknesses, the gray level depth curve is founded. Through exponential and polynomial fitting way to obtain the attenuation mathematical model which the beam penetrates pipeline, thus attain flaw deep dimension. This paper tests on the PPR pipe in the production of simulated holes flaw and cracks flaw. The X-ray source tube voltage was selected as 130kv and valve current was 1.5mA.Test results show that X-ray image processing methods, which meet the needs of high efficient flaw detection and provide quality safeguard for thick oil recovery, can be used successfully in detecting corrosion of insulated pipe.

sTools - a data reduction pipeline for the GREGOR Fabry-Pérot Interferometer and the High-resolution Fast Imager at the GREGOR solar telescope

NASA Astrophysics Data System (ADS)

Kuckein, C.; Denker, C.; Verma, M.; Balthasar, H.; González Manrique, S. J.; Louis, R. E.; Diercke, A.

2017-10-01

A huge amount of data has been acquired with the GREGOR Fabry-Pérot Interferometer (GFPI), large-format facility cameras, and since 2016 with the High-resolution Fast Imager (HiFI). These data are processed in standardized procedures with the aim of providing science-ready data for the solar physics community. For this purpose, we have developed a user-friendly data reduction pipeline called ``sTools'' based on the Interactive Data Language (IDL) and licensed under creative commons license. The pipeline delivers reduced and image-reconstructed data with a minimum of user interaction. Furthermore, quick-look data are generated as well as a webpage with an overview of the observations and their statistics. All the processed data are stored online at the GREGOR GFPI and HiFI data archive of the Leibniz Institute for Astrophysics Potsdam (AIP). The principles of the pipeline are presented together with selected high-resolution spectral scans and images processed with sTools.

Seqping: gene prediction pipeline for plant genomes using self-training gene models and transcriptomic data.

PubMed

Chan, Kuang-Lim; Rosli, Rozana; Tatarinova, Tatiana V; Hogan, Michael; Firdaus-Raih, Mohd; Low, Eng-Ti Leslie

2017-01-27

Gene prediction is one of the most important steps in the genome annotation process. A large number of software tools and pipelines developed by various computing techniques are available for gene prediction. However, these systems have yet to accurately predict all or even most of the protein-coding regions. Furthermore, none of the currently available gene-finders has a universal Hidden Markov Model (HMM) that can perform gene prediction for all organisms equally well in an automatic fashion. We present an automated gene prediction pipeline, Seqping that uses self-training HMM models and transcriptomic data. The pipeline processes the genome and transcriptome sequences of the target species using GlimmerHMM, SNAP, and AUGUSTUS pipelines, followed by MAKER2 program to combine predictions from the three tools in association with the transcriptomic evidence. Seqping generates species-specific HMMs that are able to offer unbiased gene predictions. The pipeline was evaluated using the Oryza sativa and Arabidopsis thaliana genomes. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis showed that the pipeline was able to identify at least 95% of BUSCO's plantae dataset. Our evaluation shows that Seqping was able to generate better gene predictions compared to three HMM-based programs (MAKER2, GlimmerHMM and AUGUSTUS) using their respective available HMMs. Seqping had the highest accuracy in rice (0.5648 for CDS, 0.4468 for exon, and 0.6695 nucleotide structure) and A. thaliana (0.5808 for CDS, 0.5955 for exon, and 0.8839 nucleotide structure). Seqping provides researchers a seamless pipeline to train species-specific HMMs and predict genes in newly sequenced or less-studied genomes. We conclude that the Seqping pipeline predictions are more accurate than gene predictions using the other three approaches with the default or available HMMs.

Historical analysis of US pipeline accidents triggered by natural hazards

NASA Astrophysics Data System (ADS)

Girgin, Serkan; Krausmann, Elisabeth

2015-04-01

Natural hazards, such as earthquakes, floods, landslides, or lightning, can initiate accidents in oil and gas pipelines with potentially major consequences on the population or the environment due to toxic releases, fires and explosions. Accidents of this type are also referred to as Natech events. Many major accidents highlight the risk associated with natural-hazard impact on pipelines transporting dangerous substances. For instance, in the USA in 1994, flooding of the San Jacinto River caused the rupture of 8 and the undermining of 29 pipelines by the floodwaters. About 5.5 million litres of petroleum and related products were spilled into the river and ignited. As a results, 547 people were injured and significant environmental damage occurred. Post-incident analysis is a valuable tool for better understanding the causes, dynamics and impacts of pipeline Natech accidents in support of future accident prevention and mitigation. Therefore, data on onshore hazardous-liquid pipeline accidents collected by the US Pipeline and Hazardous Materials Safety Administration (PHMSA) was analysed. For this purpose, a database-driven incident data analysis system was developed to aid the rapid review and categorization of PHMSA incident reports. Using an automated data-mining process followed by a peer review of the incident records and supported by natural hazard databases and external information sources, the pipeline Natechs were identified. As a by-product of the data-collection process, the database now includes over 800,000 incidents from all causes in industrial and transportation activities, which are automatically classified in the same way as the PHMSA record. This presentation describes the data collection and reviewing steps conducted during the study, provides information on the developed database and data analysis tools, and reports the findings of a statistical analysis of the identified hazardous liquid pipeline incidents in terms of accident dynamics and consequences.

The developing human connectome project: A minimal processing pipeline for neonatal cortical surface reconstruction.

PubMed

Makropoulos, Antonios; Robinson, Emma C; Schuh, Andreas; Wright, Robert; Fitzgibbon, Sean; Bozek, Jelena; Counsell, Serena J; Steinweg, Johannes; Vecchiato, Katy; Passerat-Palmbach, Jonathan; Lenz, Gregor; Mortari, Filippo; Tenev, Tencho; Duff, Eugene P; Bastiani, Matteo; Cordero-Grande, Lucilio; Hughes, Emer; Tusor, Nora; Tournier, Jacques-Donald; Hutter, Jana; Price, Anthony N; Teixeira, Rui Pedro A G; Murgasova, Maria; Victor, Suresh; Kelly, Christopher; Rutherford, Mary A; Smith, Stephen M; Edwards, A David; Hajnal, Joseph V; Jenkinson, Mark; Rueckert, Daniel

2018-06-01

The Developing Human Connectome Project (dHCP) seeks to create the first 4-dimensional connectome of early life. Understanding this connectome in detail may provide insights into normal as well as abnormal patterns of brain development. Following established best practices adopted by the WU-MINN Human Connectome Project (HCP), and pioneered by FreeSurfer, the project utilises cortical surface-based processing pipelines. In this paper, we propose a fully automated processing pipeline for the structural Magnetic Resonance Imaging (MRI) of the developing neonatal brain. This proposed pipeline consists of a refined framework for cortical and sub-cortical volume segmentation, cortical surface extraction, and cortical surface inflation, which has been specifically designed to address considerable differences between adult and neonatal brains, as imaged using MRI. Using the proposed pipeline our results demonstrate that images collected from 465 subjects ranging from 28 to 45 weeks post-menstrual age (PMA) can be processed fully automatically; generating cortical surface models that are topologically correct, and correspond well with manual evaluations of tissue boundaries in 85% of cases. Results improve on state-of-the-art neonatal tissue segmentation models and significant errors were found in only 2% of cases, where these corresponded to subjects with high motion. Downstream, these surfaces will enhance comparisons of functional and diffusion MRI datasets, supporting the modelling of emerging patterns of brain connectivity. Copyright © 2018 Elsevier Inc. All rights reserved.

Automated processing pipeline for neonatal diffusion MRI in the developing Human Connectome Project.

PubMed

Bastiani, Matteo; Andersson, Jesper L R; Cordero-Grande, Lucilio; Murgasova, Maria; Hutter, Jana; Price, Anthony N; Makropoulos, Antonios; Fitzgibbon, Sean P; Hughes, Emer; Rueckert, Daniel; Victor, Suresh; Rutherford, Mary; Edwards, A David; Smith, Stephen M; Tournier, Jacques-Donald; Hajnal, Joseph V; Jbabdi, Saad; Sotiropoulos, Stamatios N

2018-05-28

The developing Human Connectome Project is set to create and make available to the scientific community a 4-dimensional map of functional and structural cerebral connectivity from 20 to 44 weeks post-menstrual age, to allow exploration of the genetic and environmental influences on brain development, and the relation between connectivity and neurocognitive function. A large set of multi-modal MRI data from fetuses and newborn infants is currently being acquired, along with genetic, clinical and developmental information. In this overview, we describe the neonatal diffusion MRI (dMRI) image processing pipeline and the structural connectivity aspect of the project. Neonatal dMRI data poses specific challenges, and standard analysis techniques used for adult data are not directly applicable. We have developed a processing pipeline that deals directly with neonatal-specific issues, such as severe motion and motion-related artefacts, small brain sizes, high brain water content and reduced anisotropy. This pipeline allows automated analysis of in-vivo dMRI data, probes tissue microstructure, reconstructs a number of major white matter tracts, and includes an automated quality control framework that identifies processing issues or inconsistencies. We here describe the pipeline and present an exemplar analysis of data from 140 infants imaged at 38-44 weeks post-menstrual age. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Microcomputers, software combine to provide daily product, movement inventory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cable, T.

1985-06-01

This paper describes the efforts of Sante Fe Pipelines Inc. in keeping track of product inventory on the 810 mile, 12-in. Chapparal Pipeline and the 1,913 mile, 8- and 10-in. Gulf Central Pipeline. The decision to use a PC for monitoring the inventory was significant. The application was completed by TRON, Inc. The system is actually two major subsystems. The pipeline system accounts for injections into the pipeline and deliveries of product. This feeds the storage and the terminal inventory system where inventories are maintained at storage locations by shipper and supplier account. The paper further explains the inventory monitoringmore » process in detail. Communications software is described as well.« less

Neuroimaging Study Designs, Computational Analyses and Data Provenance Using the LONI Pipeline

PubMed Central

Dinov, Ivo; Lozev, Kamen; Petrosyan, Petros; Liu, Zhizhong; Eggert, Paul; Pierce, Jonathan; Zamanyan, Alen; Chakrapani, Shruthi; Van Horn, John; Parker, D. Stott; Magsipoc, Rico; Leung, Kelvin; Gutman, Boris; Woods, Roger; Toga, Arthur

2010-01-01

Modern computational neuroscience employs diverse software tools and multidisciplinary expertise to analyze heterogeneous brain data. The classical problems of gathering meaningful data, fitting specific models, and discovering appropriate analysis and visualization tools give way to a new class of computational challenges—management of large and incongruous data, integration and interoperability of computational resources, and data provenance. We designed, implemented and validated a new paradigm for addressing these challenges in the neuroimaging field. Our solution is based on the LONI Pipeline environment [3], [4], a graphical workflow environment for constructing and executing complex data processing protocols. We developed study-design, database and visual language programming functionalities within the LONI Pipeline that enable the construction of complete, elaborate and robust graphical workflows for analyzing neuroimaging and other data. These workflows facilitate open sharing and communication of data and metadata, concrete processing protocols, result validation, and study replication among different investigators and research groups. The LONI Pipeline features include distributed grid-enabled infrastructure, virtualized execution environment, efficient integration, data provenance, validation and distribution of new computational tools, automated data format conversion, and an intuitive graphical user interface. We demonstrate the new LONI Pipeline features using large scale neuroimaging studies based on data from the International Consortium for Brain Mapping [5] and the Alzheimer's Disease Neuroimaging Initiative [6]. User guides, forums, instructions and downloads of the LONI Pipeline environment are available at http://pipeline.loni.ucla.edu. PMID:20927408

From Pixels to Planets

NASA Technical Reports Server (NTRS)

Brownston, Lee; Jenkins, Jon M.

2015-01-01

The Kepler Mission was launched in 2009 as NASAs first mission capable of finding Earth-size planets in the habitable zone of Sun-like stars. Its telescope consists of a 1.5-m primary mirror and a 0.95-m aperture. The 42 charge-coupled devices in its focal plane are read out every half hour, compressed, and then downlinked monthly. After four years, the second of four reaction wheels failed, ending the original mission. Back on earth, the Science Operations Center developed the Science Pipeline to analyze about 200,000 target stars in Keplers field of view, looking for evidence of periodic dimming suggesting that one or more planets had crossed the face of its host star. The Pipeline comprises several steps, from pixel-level calibration, through noise and artifact removal, to detection of transit-like signals and the construction of a suite of diagnostic tests to guard against false positives. The Kepler Science Pipeline consists of a pipeline infrastructure written in the Java programming language, which marshals data input to and output from MATLAB applications that are executed as external processes. The pipeline modules, which underwent continuous development and refinement even after data started arriving, employ several analytic techniques, many developed for the Kepler Project. Because of the large number of targets, the large amount of data per target and the complexity of the pipeline algorithms, the processing demands are daunting. Some pipeline modules require days to weeks to process all of their targets, even when run on NASA's 128-node Pleiades supercomputer. The software developers are still seeking ways to increase the throughput. To date, the Kepler project has discovered more than 4000 planetary candidates, of which more than 1000 have been independently confirmed or validated to be exoplanets. Funding for this mission is provided by NASAs Science Mission Directorate.

Data processing pipeline for serial femtosecond crystallography at SACLA.

PubMed

Nakane, Takanori; Joti, Yasumasa; Tono, Kensuke; Yabashi, Makina; Nango, Eriko; Iwata, So; Ishitani, Ryuichiro; Nureki, Osamu

2016-06-01

A data processing pipeline for serial femtosecond crystallography at SACLA was developed, based on Cheetah [Barty et al. (2014). J. Appl. Cryst. 47 , 1118-1131] and CrystFEL [White et al. (2016). J. Appl. Cryst. 49 , 680-689]. The original programs were adapted for data acquisition through the SACLA API, thread and inter-node parallelization, and efficient image handling. The pipeline consists of two stages: The first, online stage can analyse all images in real time, with a latency of less than a few seconds, to provide feedback on hit rate and detector saturation. The second, offline stage converts hit images into HDF5 files and runs CrystFEL for indexing and integration. The size of the filtered compressed output is comparable to that of a synchrotron data set. The pipeline enables real-time feedback and rapid structure solution during beamtime.

Proposal and design of a natural gas liquefaction process recovering the energy obtained from the pressure reducing stations of high-pressure pipelines

NASA Astrophysics Data System (ADS)

Tan, Hongbo; Zhao, Qingxuan; Sun, Nannan; Li, Yanzhong

2016-12-01

Taking advantage of the refrigerating effect in the expansion at an appropriate temperature, a fraction of high-pressure natural gas transported by pipelines could be liquefied in a city gate station through a well-organized pressure reducing process without consuming any extra energy. The authors proposed such a new process, which mainly consists of a turbo-expander driven booster, throttle valves, multi-stream heat exchangers and separators, to yield liquefied natural gas (LNG) and liquid light hydrocarbons (LLHs) utilizing the high-pressure of the pipelines. Based on the assessment of the effects of several key parameters on the system performance by a steady-state simulation in Aspen HYSYS, an optimal design condition of the proposed process was determined. The results showed that the new process is more appropriate to be applied in a pressure reducing station (PRS) for the pipelines with higher pressure. For the feed gas at the pressure of 10 MPa, the maximum total liquefaction rate (ytot) of 15.4% and the maximum exergy utilizing rate (EUR) of 21.7% could be reached at the optimal condition. The present process could be used as a small-scale natural gas liquefying and peak-shaving plant at a city gate station.

Jenkins-CI, an Open-Source Continuous Integration System, as a Scientific Data and Image-Processing Platform.

PubMed

Moutsatsos, Ioannis K; Hossain, Imtiaz; Agarinis, Claudia; Harbinski, Fred; Abraham, Yann; Dobler, Luc; Zhang, Xian; Wilson, Christopher J; Jenkins, Jeremy L; Holway, Nicholas; Tallarico, John; Parker, Christian N

2017-03-01

High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an "off-the-shelf," open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS). Jenkins-CI provides numerous plugins for standard compute tasks, and its design allows the quick integration of external scientific applications. Using Jenkins-CI, we integrated CellProfiler, an open-source image-processing platform, with various HCS utilities and a high-performance Linux cluster. The platform is web-accessible, facilitates access and sharing of high-performance compute resources, and automates previously cumbersome data and image-processing tasks. Imaging pipelines developed using the desktop CellProfiler client can be managed and shared through a centralized Jenkins-CI repository. Pipelines and managed data are annotated to facilitate collaboration and reuse. Limitations with Jenkins-CI (primarily around the user interface) were addressed through the selection of helper plugins from the Jenkins-CI community.

Jenkins-CI, an Open-Source Continuous Integration System, as a Scientific Data and Image-Processing Platform

PubMed Central

Moutsatsos, Ioannis K.; Hossain, Imtiaz; Agarinis, Claudia; Harbinski, Fred; Abraham, Yann; Dobler, Luc; Zhang, Xian; Wilson, Christopher J.; Jenkins, Jeremy L.; Holway, Nicholas; Tallarico, John; Parker, Christian N.

2016-01-01

High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an “off-the-shelf,” open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS). Jenkins-CI provides numerous plugins for standard compute tasks, and its design allows the quick integration of external scientific applications. Using Jenkins-CI, we integrated CellProfiler, an open-source image-processing platform, with various HCS utilities and a high-performance Linux cluster. The platform is web-accessible, facilitates access and sharing of high-performance compute resources, and automates previously cumbersome data and image-processing tasks. Imaging pipelines developed using the desktop CellProfiler client can be managed and shared through a centralized Jenkins-CI repository. Pipelines and managed data are annotated to facilitate collaboration and reuse. Limitations with Jenkins-CI (primarily around the user interface) were addressed through the selection of helper plugins from the Jenkins-CI community. PMID:27899692

Tajikistan Country Profile

DTIC Science & Technology

2009-07-01

light industry and therefore was largely an agricultural support base for the economy. Aluminum and uranium production and processing were the major...Tajikistan is not a producer/exporter of energy resources although has oil and natural gas reserves. The country has a pipeline importing natural gas from...Uzbekistan. The country also imports gas from Uzbekistan. The total length of gas pipeline is 549 km and 38 km of oil pipelines. Railroads

Forecasting and Evaluation of Gas Pipelines Geometric Forms Breach Hazard

NASA Astrophysics Data System (ADS)

Voronin, K. S.

2016-10-01

Main gas pipelines during operation are under the influence of the permanent pressure drops which leads to their lengthening and as a result, to instability of their position in space. In dynamic systems that have feedback, phenomena, preceding emergencies, should be observed. The article discusses the forced vibrations of the gas pipeline cylindrical surface under the influence of dynamic loads caused by pressure surges, and the process of its geometric shape deformation. Frequency of vibrations, arising in the pipeline at the stage preceding its bending, is being determined. Identification of this frequency can be the basis for the development of a method of monitoring the technical condition of the gas pipeline, and forecasting possible emergency situations allows planning and carrying out in due time reconstruction works on sections of gas pipeline with a possible deviation from the design position.

16 CFR 802.3 - Acquisitions of carbon-based mineral reserves.

Code of Federal Regulations, 2014 CFR

2014-01-01

... gas, shale or tar sands, or rights to reserves of oil, natural gas, shale or tar sands together with... gas, shale or tar sands, or rights to reserves of oil, natural gas, shale or tar sands and associated... pipeline and pipeline system or processing facility which transports or processes oil and gas after it...

16 CFR 802.3 - Acquisitions of carbon-based mineral reserves.

Code of Federal Regulations, 2010 CFR

2010-01-01

... gas, shale or tar sands, or rights to reserves of oil, natural gas, shale or tar sands together with... gas, shale or tar sands, or rights to reserves of oil, natural gas, shale or tar sands and associated... pipeline and pipeline system or processing facility which transports or processes oil and gas after it...

16 CFR 802.3 - Acquisitions of carbon-based mineral reserves.

Code of Federal Regulations, 2013 CFR

2013-01-01

... gas, shale or tar sands, or rights to reserves of oil, natural gas, shale or tar sands together with... gas, shale or tar sands, or rights to reserves of oil, natural gas, shale or tar sands and associated... pipeline and pipeline system or processing facility which transports or processes oil and gas after it...

16 CFR 802.3 - Acquisitions of carbon-based mineral reserves.

Code of Federal Regulations, 2012 CFR

2012-01-01

... gas, shale or tar sands, or rights to reserves of oil, natural gas, shale or tar sands together with... gas, shale or tar sands, or rights to reserves of oil, natural gas, shale or tar sands and associated... pipeline and pipeline system or processing facility which transports or processes oil and gas after it...

16 CFR 802.3 - Acquisitions of carbon-based mineral reserves.

Code of Federal Regulations, 2011 CFR

2011-01-01

... gas, shale or tar sands, or rights to reserves of oil, natural gas, shale or tar sands together with... gas, shale or tar sands, or rights to reserves of oil, natural gas, shale or tar sands and associated... pipeline and pipeline system or processing facility which transports or processes oil and gas after it...

18 CFR 157.21 - Pre-filing procedures and review process for LNG terminal facilities and other natural gas...

Code of Federal Regulations, 2010 CFR

2010-04-01

... the pre-filing review of any pipeline or other natural gas facilities, including facilities not... from the subject LNG terminal facilities to the existing natural gas pipeline infrastructure. (b) Other... and review process for LNG terminal facilities and other natural gas facilities prior to filing of...

Planck 2015 results: II. Low Frequency Instrument data processings

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ade, P. A. R.; Aghanim, N.; Ashdown, M.

In this paper, we present an updated description of the Planck Low Frequency Instrument (LFI) data processing pipeline, associated with the 2015 data release. We point out the places where our results and methods have remained unchanged since the 2013 paper and we highlight the changes made for the 2015 release, describing the products (especially timelines) and the ways in which they were obtained. We demonstrate that the pipeline is self-consistent (principally based on simulations) and report all null tests. For the first time, we present LFI maps in Stokes Q and U polarization. Finally, we refer to other relatedmore » papers where more detailed descriptions of the LFI data processing pipeline may be found if needed.« less

Planck 2015 results: II. Low Frequency Instrument data processings

DOE PAGES

Ade, P. A. R.; Aghanim, N.; Ashdown, M.; ...

2016-09-20

In this paper, we present an updated description of the Planck Low Frequency Instrument (LFI) data processing pipeline, associated with the 2015 data release. We point out the places where our results and methods have remained unchanged since the 2013 paper and we highlight the changes made for the 2015 release, describing the products (especially timelines) and the ways in which they were obtained. We demonstrate that the pipeline is self-consistent (principally based on simulations) and report all null tests. For the first time, we present LFI maps in Stokes Q and U polarization. Finally, we refer to other relatedmore » papers where more detailed descriptions of the LFI data processing pipeline may be found if needed.« less

Comparison of a semi-automatic annotation tool and a natural language processing application for the generation of clinical statement entries.

PubMed

Lin, Ching-Heng; Wu, Nai-Yuan; Lai, Wei-Shao; Liou, Der-Ming

2015-01-01

Electronic medical records with encoded entries should enhance the semantic interoperability of document exchange. However, it remains a challenge to encode the narrative concept and to transform the coded concepts into a standard entry-level document. This study aimed to use a novel approach for the generation of entry-level interoperable clinical documents. Using HL7 clinical document architecture (CDA) as the example, we developed three pipelines to generate entry-level CDA documents. The first approach was a semi-automatic annotation pipeline (SAAP), the second was a natural language processing (NLP) pipeline, and the third merged the above two pipelines. We randomly selected 50 test documents from the i2b2 corpora to evaluate the performance of the three pipelines. The 50 randomly selected test documents contained 9365 words, including 588 Observation terms and 123 Procedure terms. For the Observation terms, the merged pipeline had a significantly higher F-measure than the NLP pipeline (0.89 vs 0.80, p<0.0001), but a similar F-measure to that of the SAAP (0.89 vs 0.87). For the Procedure terms, the F-measure was not significantly different among the three pipelines. The combination of a semi-automatic annotation approach and the NLP application seems to be a solution for generating entry-level interoperable clinical documents. © The Author 2014. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.comFor numbered affiliation see end of article.

Strain-Based Design Methodology of Large Diameter Grade X80 Linepipe

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lower, Mark D.

2014-04-01

Continuous growth in energy demand is driving oil and natural gas production to areas that are often located far from major markets where the terrain is prone to earthquakes, landslides, and other types of ground motion. Transmission pipelines that cross this type of terrain can experience large longitudinal strains and plastic circumferential elongation as the pipeline experiences alignment changes resulting from differential ground movement. Such displacements can potentially impact pipeline safety by adversely affecting structural capacity and leak tight integrity of the linepipe steel. Planning for new long-distance transmission pipelines usually involves consideration of higher strength linepipe steels because theirmore » use allows pipeline operators to reduce the overall cost of pipeline construction and increase pipeline throughput by increasing the operating pressure. The design trend for new pipelines in areas prone to ground movement has evolved over the last 10 years from a stress-based design approach to a strain-based design (SBD) approach to further realize the cost benefits from using higher strength linepipe steels. This report presents an overview of SBD for pipelines subjected to large longitudinal strain and high internal pressure with emphasis on the tensile strain capacity of high-strength microalloyed linepipe steel. The technical basis for this report involved engineering analysis and examination of the mechanical behavior of Grade X80 linepipe steel in both the longitudinal and circumferential directions. Testing was conducted to assess effects on material processing including as-rolled, expanded, and heat treatment processing intended to simulate coating application. Elastic-plastic and low-cycle fatigue analyses were also performed with varying internal pressures. Proposed SBD models discussed in this report are based on classical plasticity theory and account for material anisotropy, triaxial strain, and microstructural damage effects developed from test data. The results are intended to enhance SBD and analysis methods for producing safe and cost effective pipelines capable of accommodating large plastic strains in seismically active arctic areas.« less

Reasons for decision in the matter of Maritimes and Northeast Pipeline Management Ltd. application dated 24 February 1998 for approval of the plan, profile and book of reference respecting the detailed pipeline route from Goldboro, N.S. to St. Stephen, N.B.: MH-3-98

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1998-12-31

In December 1997, Maritimes and Northeast Pipeline Management Ltd. received approval to construct and operate a natural gas pipeline consisting of about 558 kilometers of 762-millimeter pipe to be located within a one-kilometer-wide corridor extending from Goldboro, Nova Scotia to the international border near St. Stephen, New Brunswick. This report covers the second stage of the pipeline approval process where the detailed route is determined. It presents the views of the pipeline company, various landowners and mineral rights holders objecting to the proposed detailed route, and the National Energy Board with regard to two issues: The best possible detailed routemore » for the pipeline, and the most appropriate methods and timing of constructing the pipeline. Specific land/mineral rights owner cases including the nature of the objection, possible alternate routes, and the Board decision in each case are described.« less

PICARD - A PIpeline for Combining and Analyzing Reduced Data

NASA Astrophysics Data System (ADS)

Gibb, Andrew G.; Jenness, Tim; Economou, Frossie

PICARD is a facility for combining and analyzing reduced data, normally the output from the ORAC-DR data reduction pipeline. This document describes an introduction to using PICARD for processing instrument-independent data.

Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics

PubMed Central

Deutsch, Eric W.; Mendoza, Luis; Shteynberg, David; Slagel, Joseph; Sun, Zhi; Moritz, Robert L.

2015-01-01

Democratization of genomics technologies has enabled the rapid determination of genotypes. More recently the democratization of comprehensive proteomics technologies is enabling the determination of the cellular phenotype and the molecular events that define its dynamic state. Core proteomic technologies include mass spectrometry to define protein sequence, protein:protein interactions, and protein post-translational modifications. Key enabling technologies for proteomics are bioinformatic pipelines to identify, quantitate, and summarize these events. The Trans-Proteomics Pipeline (TPP) is a robust open-source standardized data processing pipeline for large-scale reproducible quantitative mass spectrometry proteomics. It supports all major operating systems and instrument vendors via open data formats. Here we provide a review of the overall proteomics workflow supported by the TPP, its major tools, and how it can be used in its various modes from desktop to cloud computing. We describe new features for the TPP, including data visualization functionality. We conclude by describing some common perils that affect the analysis of tandem mass spectrometry datasets, as well as some major upcoming features. PMID:25631240

Leak detection in gas pipeline by acoustic and signal processing - A review

NASA Astrophysics Data System (ADS)

Adnan, N. F.; Ghazali, M. F.; Amin, M. M.; Hamat, A. M. A.

2015-12-01

The pipeline system is the most important part in media transport in order to deliver fluid to another station. The weak maintenance and poor safety will contribute to financial losses in term of fluid waste and environmental impacts. There are many classifications of techniques to make it easier to show their specific method and application. This paper's discussion about gas leak detection in pipeline system using acoustic method will be presented in this paper. The wave propagation in the pipeline is a key parameter in acoustic method when the leak occurs and the pressure balance of the pipe will generated by the friction between wall in the pipe. The signal processing is used to decompose the raw signal and show in time- frequency. Findings based on the acoustic method can be used for comparative study in the future. Acoustic signal and HHT is the best method to detect leak in gas pipelines. More experiments and simulation need to be carried out to get the fast result of leaking and estimation of their location.

Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics.

PubMed

Deutsch, Eric W; Mendoza, Luis; Shteynberg, David; Slagel, Joseph; Sun, Zhi; Moritz, Robert L

2015-08-01

Democratization of genomics technologies has enabled the rapid determination of genotypes. More recently the democratization of comprehensive proteomics technologies is enabling the determination of the cellular phenotype and the molecular events that define its dynamic state. Core proteomic technologies include MS to define protein sequence, protein:protein interactions, and protein PTMs. Key enabling technologies for proteomics are bioinformatic pipelines to identify, quantitate, and summarize these events. The Trans-Proteomics Pipeline (TPP) is a robust open-source standardized data processing pipeline for large-scale reproducible quantitative MS proteomics. It supports all major operating systems and instrument vendors via open data formats. Here, we provide a review of the overall proteomics workflow supported by the TPP, its major tools, and how it can be used in its various modes from desktop to cloud computing. We describe new features for the TPP, including data visualization functionality. We conclude by describing some common perils that affect the analysis of MS/MS datasets, as well as some major upcoming features. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Pipeline for 3D Digital Optical Phenotyping Plant Root System Architecture

NASA Astrophysics Data System (ADS)

Davis, T. W.; Shaw, N. M.; Schneider, D. J.; Shaff, J. E.; Larson, B. G.; Craft, E. J.; Liu, Z.; Kochian, L. V.; Piñeros, M. A.

2017-12-01

This work presents a new pipeline for digital optical phenotyping the root system architecture of agricultural crops. The pipeline begins with a 3D root-system imaging apparatus for hydroponically grown crop lines of interest. The apparatus acts as a self-containing dark room, which includes an imaging tank, motorized rotating bearing and digital camera. The pipeline continues with the Plant Root Imaging and Data Acquisition (PRIDA) software, which is responsible for image capturing and storage. Once root images have been captured, image post-processing is performed using the Plant Root Imaging Analysis (PRIA) command-line tool, which extracts root pixels from color images. Following the pre-processing binarization of digital root images, 3D trait characterization is performed using the next-generation RootReader3D software. RootReader3D measures global root system architecture traits, such as total root system volume and length, total number of roots, and maximum rooting depth and width. While designed to work together, the four stages of the phenotyping pipeline are modular and stand-alone, which provides flexibility and adaptability for various research endeavors.

FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies.

PubMed

Kim, Jiwoong; Kim, Min Soo; Koh, Andrew Y; Xie, Yang; Zhan, Xiaowei

2016-10-10

Given the lack of a complete and comprehensive library of microbial reference genomes, determining the functional profile of diverse microbial communities is challenging. The available functional analysis pipelines lack several key features: (i) an integrated alignment tool, (ii) operon-level analysis, and (iii) the ability to process large datasets. Here we introduce our open-sourced, stand-alone functional analysis pipeline for analyzing whole metagenomic and metatranscriptomic sequencing data, FMAP (Functional Mapping and Analysis Pipeline). FMAP performs alignment, gene family abundance calculations, and statistical analysis (three levels of analyses are provided: differentially-abundant genes, operons and pathways). The resulting output can be easily visualized with heatmaps and functional pathway diagrams. FMAP functional predictions are consistent with currently available functional analysis pipelines. FMAP is a comprehensive tool for providing functional analysis of metagenomic/metatranscriptomic sequencing data. With the added features of integrated alignment, operon-level analysis, and the ability to process large datasets, FMAP will be a valuable addition to the currently available functional analysis toolbox. We believe that this software will be of great value to the wider biology and bioinformatics communities.

CFHT data processing and calibration ESPaDOnS pipeline: Upena and OPERA (optical spectropolarimetry)

NASA Astrophysics Data System (ADS)

Martioli, Eder; Teeple, D.; Manset, Nadine

2011-03-01

CFHT is ESPaDOnS responsible for processing raw images, removing instrument related artifacts, and delivering science-ready data to the PIs. Here we describe the Upena pipeline, which is the software used to reduce the echelle spectro-polarimetric data obtained with the ESPaDOnS instrument. Upena is an automated pipeline that performs calibration and reduction of raw images. Upena has the capability of both performing real-time image-by-image basis reduction and a post observing night complete reduction. Upena produces polarization and intensity spectra in FITS format. The pipeline is designed to perform parallel computing for improved speed, which assures that the final products are delivered to the PIs before noon HST after each night of observations. We also present the OPERA project, which is an open-source pipeline to reduce ESPaDOnS data that will be developed as a collaborative work between CFHT and the scientific community. OPERA will match the core capabilities of Upena and in addition will be open-source, flexible and extensible.

Physical and numerical modeling of hydrophysical proceses on the site of underwater pipelines

NASA Astrophysics Data System (ADS)

Garmakova, M. E.; Degtyarev, V. V.; Fedorova, N. N.; Shlychkov, V. A.

2018-03-01

The paper outlines issues related to ensuring the exploitation safety of underwater pipelines that are at risk of accidents. The performed research is based on physical and mathematical modeling of local bottom erosion in the area of pipeline location. The experimental studies were performed on the basis of the Hydraulics Laboratory of the Department of Hydraulic Engineering Construction, Safety and Ecology of NSUACE (Sibstrin). In the course of physical experiments it was revealed that the intensity of the bottom soil reforming depends on the deepening of the pipeline. The ANSYS software has been used for numerical modeling. The process of erosion of the sandy bottom was modeled under the pipeline. Comparison of computational results at various mass flow rates was made.

Status of the TESS Science Processing Operations Center

NASA Technical Reports Server (NTRS)

Jenkins, Jon M.; Twicken, Joseph D.; Campbell, Jennifer; Tenebaum, Peter; Sanderfer, Dwight; Davies, Misty D.; Smith, Jeffrey C.; Morris, Rob; Mansouri-Samani, Masoud; Girouardi, Forrest;

Kepler Planet Detection Metrics: Pixel-Level Transit Injection Tests of Pipeline Detection Efficiency for Data Release 25

NASA Technical Reports Server (NTRS)

Christiansen, Jessie L.

2017-01-01

This document describes the results of the fourth pixel-level transit injection experiment, which was designed to measure the detection efficiency of both the Kepler pipeline (Jenkins 2002, 2010; Jenkins et al. 2017) and the Robovetter (Coughlin 2017). Previous transit injection experiments are described in Christiansen et al. (2013, 2015a,b, 2016).In order to calculate planet occurrence rates using a given Kepler planet catalogue, produced with a given version of the Kepler pipeline, we need to know the detection efficiency of that pipeline. This can be empirically determined by injecting a suite of simulated transit signals into the Kepler data, processing the data through the pipeline, and examining the distribution of successfully recovered transits. This document describes the results for the pixel-level transit injection experiment performed to accompany the final Q1-Q17 Data Release 25 (DR25) catalogue (Thompson et al. 2017)of the Kepler Objects of Interest. The catalogue was generated using the SOC pipeline version 9.3 and the DR25 Robovetter acting on the uniformly processed Q1-Q17 DR25 light curves (Thompson et al. 2016a) and assuming the Q1-Q17 DR25 Kepler stellar properties (Mathur et al. 2017).

A Comparison between the Decimated Padé Approximant and Decimated Signal Diagonalization Methods for Leak Detection in Pipelines Equipped with Pressure Sensors.

PubMed

Lay-Ekuakille, Aimé; Fabbiano, Laura; Vacca, Gaetano; Kitoko, Joël Kidiamboko; Kulapa, Patrice Bibala; Telesca, Vito

2018-06-04

Pipelines conveying fluids are considered strategic infrastructures to be protected and maintained. They generally serve for transportation of important fluids such as drinkable water, waste water, oil, gas, chemicals, etc. Monitoring and continuous testing, especially on-line, are necessary to assess the condition of pipelines. The paper presents findings related to a comparison between two spectral response algorithms based on the decimated signal diagonalization (DSD) and decimated Padé approximant (DPA) techniques that allow to one to process signals delivered by pressure sensors mounted on an experimental pipeline.

Intermediate Palomar Transient Factory: Realtime Image Subtraction Pipeline

DOE PAGES

Cao, Yi; Nugent, Peter E.; Kasliwal, Mansi M.

2016-09-28

A fast-turnaround pipeline for realtime data reduction plays an essential role in discovering and permitting followup observations to young supernovae and fast-evolving transients in modern time-domain surveys. In this paper, we present the realtime image subtraction pipeline in the intermediate Palomar Transient Factory. By using highperformance computing, efficient databases, and machine-learning algorithms, this pipeline manages to reliably deliver transient candidates within 10 minutes of images being taken. Our experience in using high-performance computing resources to process big data in astronomy serves as a trailblazer to dealing with data from large-scale time-domain facilities in the near future.

Intermediate Palomar Transient Factory: Realtime Image Subtraction Pipeline

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, Yi; Nugent, Peter E.; Kasliwal, Mansi M.

A fast-turnaround pipeline for realtime data reduction plays an essential role in discovering and permitting followup observations to young supernovae and fast-evolving transients in modern time-domain surveys. In this paper, we present the realtime image subtraction pipeline in the intermediate Palomar Transient Factory. By using highperformance computing, efficient databases, and machine-learning algorithms, this pipeline manages to reliably deliver transient candidates within 10 minutes of images being taken. Our experience in using high-performance computing resources to process big data in astronomy serves as a trailblazer to dealing with data from large-scale time-domain facilities in the near future.

VPipe: Virtual Pipelining for Scheduling of DAG Stream Query Plans

NASA Astrophysics Data System (ADS)

Wang, Song; Gupta, Chetan; Mehta, Abhay

There are data streams all around us that can be harnessed for tremendous business and personal advantage. For an enterprise-level stream processing system such as CHAOS [1] (Continuous, Heterogeneous Analytic Over Streams), handling of complex query plans with resource constraints is challenging. While several scheduling strategies exist for stream processing, efficient scheduling of complex DAG query plans is still largely unsolved. In this paper, we propose a novel execution scheme for scheduling complex directed acyclic graph (DAG) query plans with meta-data enriched stream tuples. Our solution, called Virtual Pipelined Chain (or VPipe Chain for short), effectively extends the "Chain" pipelining scheduling approach to complex DAG query plans.

DPPP: Default Pre-Processing Pipeline

NASA Astrophysics Data System (ADS)

van Diepen, Ger; Dijkema, Tammo Jan

2018-04-01

DPPP (Default Pre-Processing Pipeline, also referred to as NDPPP) reads and writes radio-interferometric data in the form of Measurement Sets, mainly those that are created by the LOFAR telescope. It goes through visibilities in time order and contains standard operations like averaging, phase-shifting and flagging bad stations. Between the steps in a pipeline, the data is not written to disk, making this tool suitable for operations where I/O dominates. More advanced procedures such as gain calibration are also included. Other computing steps can be provided by loading a shared library; currently supported external steps are the AOFlagger (ascl:1010.017) and a bridge that enables loading python steps.

The visual and radiological inspection of a pipeline using a teleoperated pipe crawler

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fogle, R.F.; Kuelske, K.; Kellner, R.A.

1996-07-01

In the 1950s the Savannah River Site built an open, unlined retention basin for temporary storage of potentially radionuclide-contaminated cooling water form a chemical separations process and storm water drainage from a nearby waste management facility which stored large quantities of nuclear fission by-products in carbon steel tanks. An underground process pipeline lead to the basin. Once the closure of the basin in 1972, further assessment has been required. A visual and radiological inspection of the pipeline was necessary to aid in the decision about further remediation. This article describes the inspection using a teleoperated pipe crawler. 5 figs.

Hardware and software facilities for the J-PAS and J-PLUS surveys archiving, processing and data publication

NASA Astrophysics Data System (ADS)

Cristóbal-Hornillos, D.; Varela, J.; Ederoclite, A.; Vázquez Ramió, H.; López-Sainz, A.; Hernández-Fuertes, J.; Civera, T.; Muniesa, D.; Moles, M.; Cenarro, A. J.; Marín-Franch, A.; Yanes-Díaz, A.

2015-05-01

The Observatorio Astrofísico de Javalambre consists of two main telescopes: JST/T250, a 2.5 m telescope with a FoV of 3 deg, and JAST/T80, a 83 cm with a 2 deg FoV. JST/T250 will be devoted to complete the Javalambre-PAU Astronomical Survey (J-PAS). It is a photometric survey with a system of 54 narrow-band plus 3 broad-band filters covering an area of 8500°^2. The JAST/T80 will perform the J-PLUS survey, covering the same area in a system of 12 filters. This contribution presents the software and hardware architecture designed to store and process the data. The processing pipeline runs daily and it is devoted to correct instrumental signature on the science images, to perform astrometric and photometric calibration, and the computation of individual image catalogs. In a second stage, the pipeline performs the combination of the tile mosaics and the computation of final catalogs. The catalogs are ingested in as Scientific database to be provided to the community. The processing software is connected with a management database to store persistent information about the pipeline operations done on each frame. The processing pipeline is executed in a computing cluster under a batch queuing system. Regarding the storage system, it will combine disk and tape technologies. The disk storage system will have capacity to store the data that is accessed by the pipeline. The tape library will store and archive the raw data and earlier data releases with lower access frequency.

Virtual Instrumentation Corrosion Controller for Natural Gas Pipelines

NASA Astrophysics Data System (ADS)

Gopalakrishnan, J.; Agnihotri, G.; Deshpande, D. M.

2012-12-01

Corrosion is an electrochemical process. Corrosion in natural gas (methane) pipelines leads to leakages. Corrosion occurs when anode and cathode are connected through electrolyte. Rate of corrosion in metallic pipeline can be controlled by impressing current to it and thereby making it to act as cathode of corrosion cell. Technologically advanced and energy efficient corrosion controller is required to protect natural gas pipelines. Proposed virtual instrumentation (VI) based corrosion controller precisely controls the external corrosion in underground metallic pipelines, enhances its life and ensures safety. Designing and development of proportional-integral-differential (PID) corrosion controller using VI (LabVIEW) is carried out. When the designed controller is deployed at field, it maintains the pipe to soil potential (PSP) within safe operating limit and not entering into over/under protection zone. Horizontal deployment of this technique can be done to protect all metallic structure, oil pipelines, which need corrosion protection.

Weld Design, Testing, and Assessment Procedures for High Strength Pipelines

DOT National Transportation Integrated Search

2011-12-20

Long-distance high-strength pipelines are increasingly being constructed for the efficient transportation of energy products. While the high-strength linepipe steels and high productivity welding processes are being applied, the procedures employed f...

ORAC-DR -- SCUBA-2 Pipeline Data Reduction

NASA Astrophysics Data System (ADS)

Gibb, Andrew G.; Jenness, Tim

The ORAC-DR data reduction pipeline is designed to reduce data from many different instruments. This document describes how to use ORAC-DR to process data taken with the SCUBA-2 instrument on the James Clerk Maxwell Telescope.

NGSANE: a lightweight production informatics framework for high-throughput data analysis.

PubMed

Buske, Fabian A; French, Hugh J; Smith, Martin A; Clark, Susan J; Bauer, Denis C

2014-05-15

The initial steps in the analysis of next-generation sequencing data can be automated by way of software 'pipelines'. However, individual components depreciate rapidly because of the evolving technology and analysis methods, often rendering entire versions of production informatics pipelines obsolete. Constructing pipelines from Linux bash commands enables the use of hot swappable modular components as opposed to the more rigid program call wrapping by higher level languages, as implemented in comparable published pipelining systems. Here we present Next Generation Sequencing ANalysis for Enterprises (NGSANE), a Linux-based, high-performance-computing-enabled framework that minimizes overhead for set up and processing of new projects, yet maintains full flexibility of custom scripting when processing raw sequence data. Ngsane is implemented in bash and publicly available under BSD (3-Clause) licence via GitHub at https://github.com/BauerLab/ngsane. Denis.Bauer@csiro.au Supplementary data are available at Bioinformatics online.

Study on Failure of Third-Party Damage for Urban Gas Pipeline Based on Fuzzy Comprehensive Evaluation.

PubMed

Li, Jun; Zhang, Hong; Han, Yinshan; Wang, Baodong

2016-01-01

Focusing on the diversity, complexity and uncertainty of the third-party damage accident, the failure probability of third-party damage to urban gas pipeline was evaluated on the theory of analytic hierarchy process and fuzzy mathematics. The fault tree of third-party damage containing 56 basic events was built by hazard identification of third-party damage. The fuzzy evaluation of basic event probabilities were conducted by the expert judgment method and using membership function of fuzzy set. The determination of the weight of each expert and the modification of the evaluation opinions were accomplished using the improved analytic hierarchy process, and the failure possibility of the third-party to urban gas pipeline was calculated. Taking gas pipelines of a certain large provincial capital city as an example, the risk assessment structure of the method was proved to conform to the actual situation, which provides the basis for the safety risk prevention.

A Model for Oil-Gas Pipelines Cost Prediction Based on a Data Mining Process

NASA Astrophysics Data System (ADS)

Batzias, Fragiskos A.; Spanidis, Phillip-Mark P.

2009-08-01

This paper addresses the problems associated with the cost estimation of oil/gas pipelines during the elaboration of feasibility assessments. Techno-economic parameters, i.e., cost, length and diameter, are critical for such studies at the preliminary design stage. A methodology for the development of a cost prediction model based on Data Mining (DM) process is proposed. The design and implementation of a Knowledge Base (KB), maintaining data collected from various disciplines of the pipeline industry, are presented. The formulation of a cost prediction equation is demonstrated by applying multiple regression analysis using data sets extracted from the KB. Following the methodology proposed, a learning context is inductively developed as background pipeline data are acquired, grouped and stored in the KB, and through a linear regression model provide statistically substantial results, useful for project managers or decision makers.

Applying the vantage PDMS to jack-up drilling ships

NASA Astrophysics Data System (ADS)

Yin, Peng; Chen, Yuan-Ming; Cui, Tong-Kai; Wang, Zi-Shen; Gong, Li-Jiang; Yu, Xiang-Fen

2009-09-01

The plant design management system (PDMS) is an integrated application which includes a database and is useful when designing complex 3-D industrial projects. It could be used to simplify the most difficult part of a subsea oil extraction project—detailed pipeline design. It could also be used to integrate the design of equipment, structures, HVAC, E-ways as well as the detailed designs of other specialists. This article mainly examines the applicability of the Vantage PDMS database to pipeline projects involving jack-up drilling ships. It discusses the catalogue (CATA) of the pipeline, the spec-world (SPWL) of the pipeline, the bolt tables (BLTA) and so on. This article explains the main methods for CATA construction as well as problem in the process of construction. In this article, the authors point out matters needing attention when using the Vantage PDMS database in the design process and discuss partial solutions to these questions.

The application of Mike Urban model in drainage and waterlogging in Lincheng county, China

NASA Astrophysics Data System (ADS)

Luan, Qinghua; Zhang, Kun; Liu, Jiahong; Wang, Dong; Ma, Jun

2018-06-01

Recently, the water disaster in cities especially in Chinese mountainous cities is more serious, due to the coupling influences of waterlogging and regional floods. It is necessary to study the surface runoff process of mountainous cities and examine the regional drainage pipeline network. In this study, the runoff processes of Lincheng county (located in Hebei province, China) in different scenarios were simulated through Mike Urban model. The results show that all of the runoff process of the old town and the new residential area with larger slope, is significant and full flow of these above zones exists in the part of the drainage pipeline network; and the overflow exists in part of the drainage pipeline network when the return period is ten years or twenty years, which illuminates that the waterlogging risk in this zone of Lincheng is higher. Therefore, remodeling drainage pipeline network in the old town of Lincheng and adding water storage ponds in the new residential areas were suggested. This research provides both technical support and decision-making reference to local storm flood management, also give the experiences for the study on the runoff process of similar cities.

Heterogeneous Optimization Framework: Reproducible Preprocessing of Multi-Spectral Clinical MRI for Neuro-Oncology Imaging Research.

PubMed

Milchenko, Mikhail; Snyder, Abraham Z; LaMontagne, Pamela; Shimony, Joshua S; Benzinger, Tammie L; Fouke, Sarah Jost; Marcus, Daniel S

2016-07-01

Neuroimaging research often relies on clinically acquired magnetic resonance imaging (MRI) datasets that can originate from multiple institutions. Such datasets are characterized by high heterogeneity of modalities and variability of sequence parameters. This heterogeneity complicates the automation of image processing tasks such as spatial co-registration and physiological or functional image analysis. Given this heterogeneity, conventional processing workflows developed for research purposes are not optimal for clinical data. In this work, we describe an approach called Heterogeneous Optimization Framework (HOF) for developing image analysis pipelines that can handle the high degree of clinical data non-uniformity. HOF provides a set of guidelines for configuration, algorithm development, deployment, interpretation of results and quality control for such pipelines. At each step, we illustrate the HOF approach using the implementation of an automated pipeline for Multimodal Glioma Analysis (MGA) as an example. The MGA pipeline computes tissue diffusion characteristics of diffusion tensor imaging (DTI) acquisitions, hemodynamic characteristics using a perfusion model of susceptibility contrast (DSC) MRI, and spatial cross-modal co-registration of available anatomical, physiological and derived patient images. Developing MGA within HOF enabled the processing of neuro-oncology MR imaging studies to be fully automated. MGA has been successfully used to analyze over 160 clinical tumor studies to date within several research projects. Introduction of the MGA pipeline improved image processing throughput and, most importantly, effectively produced co-registered datasets that were suitable for advanced analysis despite high heterogeneity in acquisition protocols.

Designing Image Analysis Pipelines in Light Microscopy: A Rational Approach.

PubMed

Arganda-Carreras, Ignacio; Andrey, Philippe

2017-01-01

With the progress of microscopy techniques and the rapidly growing amounts of acquired imaging data, there is an increased need for automated image processing and analysis solutions in biological studies. Each new application requires the design of a specific image analysis pipeline, by assembling a series of image processing operations. Many commercial or free bioimage analysis software are now available and several textbooks and reviews have presented the mathematical and computational fundamentals of image processing and analysis. Tens, if not hundreds, of algorithms and methods have been developed and integrated into image analysis software, resulting in a combinatorial explosion of possible image processing sequences. This paper presents a general guideline methodology to rationally address the design of image processing and analysis pipelines. The originality of the proposed approach is to follow an iterative, backwards procedure from the target objectives of analysis. The proposed goal-oriented strategy should help biologists to better apprehend image analysis in the context of their research and should allow them to efficiently interact with image processing specialists.

Update on the SDSS-III MARVELS data pipeline development

NASA Astrophysics Data System (ADS)

Li, Rui; Ge, J.; Thomas, N. B.; Petersen, E.; Wang, J.; Ma, B.; Sithajan, S.; Shi, J.; Ouyang, Y.; Chen, Y.

2014-01-01

MARVELS (Multi-object APO Radial Velocity Exoplanet Large-area Survey), as one of the four surveys in the SDSS-III program, has monitored over 3,300 stars during 2008-2012, with each being visited an average of 26 times over a 2-year window. Although the early data pipeline was able to detect over 20 brown dwarf candidates and several hundreds of binaries, no giant planet candidates have been reliably identified due to its large systematic errors. Learning from past data pipeline lessons, we re-designed the entire pipeline to handle various types of systematic effects caused by the instrument (such as trace, slant, distortion, drifts and dispersion) and observation condition changes (such as illumination profile and continuum). We also introduced several advanced methods to precisely extract the RV signals. To date, we have achieved a long term RMS RV measurement error of 14 m/s for HIP-14810 (one of our reference stars) after removal of the known planet signal based on previous HIRES RV measurement. This new 1-D data pipeline has been used to robustly identify four giant planet candidates within the small fraction of the survey data that has been processed (Thomas et al. this meeting). The team is currently working hard to optimize the pipeline, especially the 2-D interference-fringe RV extraction, where early results show a 1.5 times improvement over the 1-D data pipeline. We are quickly approaching the survey baseline performance requirement of 10-35 m/s RMS for 8-12 solar type stars. With this fine-tuned pipeline and the soon to be processed plates of data, we expect to discover many more giant planet candidates and make a large statistical impact to the exoplanet study.

Image processing pipeline for synchrotron-radiation-based tomographic microscopy.

PubMed

Hintermüller, C; Marone, F; Isenegger, A; Stampanoni, M

2010-07-01

With synchrotron-radiation-based tomographic microscopy, three-dimensional structures down to the micrometer level can be visualized. Tomographic data sets typically consist of 1000 to 1500 projections of 1024 x 1024 to 2048 x 2048 pixels and are acquired in 5-15 min. A processing pipeline has been developed to handle this large amount of data efficiently and to reconstruct the tomographic volume within a few minutes after the end of a scan. Just a few seconds after the raw data have been acquired, a selection of reconstructed slices is accessible through a web interface for preview and to fine tune the reconstruction parameters. The same interface allows initiation and control of the reconstruction process on the computer cluster. By integrating all programs and tools, required for tomographic reconstruction into the pipeline, the necessary user interaction is reduced to a minimum. The modularity of the pipeline allows functionality for new scan protocols to be added, such as an extended field of view, or new physical signals such as phase-contrast or dark-field imaging etc.

Supply Support of Air Force 463L Equipment: An Analysis of the 463L equipment Spare Parts Pipeline

DTIC Science & Technology

1989-09-01

service; and 4) the order processing system created inherent delays in the pipeline because of outdated and indirect information systems and technology. Keywords: Materials handling equipment, Theses. (AW)

Extraction of UMLS® Concepts Using Apache cTAKES™ for German Language.

PubMed

Becker, Matthias; Böckmann, Britta

2016-01-01

Automatic information extraction of medical concepts and classification with semantic standards from medical reports is useful for standardization and for clinical research. This paper presents an approach for an UMLS concept extraction with a customized natural language processing pipeline for German clinical notes using Apache cTAKES. The objectives are, to test the natural language processing tool for German language if it is suitable to identify UMLS concepts and map these with SNOMED-CT. The German UMLS database and German OpenNLP models extended the natural language processing pipeline, so the pipeline can normalize to domain ontologies such as SNOMED-CT using the German concepts. For testing, the ShARe/CLEF eHealth 2013 training dataset translated into German was used. The implemented algorithms are tested with a set of 199 German reports, obtaining a result of average 0.36 F1 measure without German stemming, pre- and post-processing of the reports.

Kepler: A Search for Terrestrial Planets - SOC 9.3 DR25 Pipeline Parameter Configuration Reports

NASA Technical Reports Server (NTRS)

Campbell, Jennifer R.

2017-01-01

This document describes the manner in which the pipeline and algorithm parameters for the Kepler Science Operations Center (SOC) science data processing pipeline were managed. This document is intended for scientists and software developers who wish to better understand the software design for the final Kepler codebase (SOC 9.3) and the effect of the software parameters on the Data Release (DR) 25 archival products.

Pipeline transport and simultaneous saccharification of corn stover.

PubMed

Kumar, Amit; Cameron, Jay B; Flynn, Peter C

2005-05-01

Pipeline transport of corn stover delivered by truck from the field is evaluated against a range of truck transport costs. Corn stover transported by pipeline at 20% solids concentration (wet basis) or higher could directly enter an ethanol fermentation plant, and hence the investment in the pipeline inlet end processing facilities displaces comparable investment in the plant. At 20% solids, pipeline transport of corn stover costs less than trucking at capacities in excess of 1.4 M drytonnes/yr when compared to a mid range of truck transport cost (excluding any credit for economies of scale achieved in the ethanol fermentation plant from larger scale due to multiple pipelines). Pipelining of corn stover gives the opportunity to conduct simultaneous transport and saccharification (STS). If current enzymes are used, this would require elevated temperature. Heating of the slurry for STS, which in a fermentation plant is achieved from waste heat, is a significant cost element (more than 5 cents/l of ethanol) if done at the pipeline inlet unless waste heat is available, for example from an electric power plant located adjacent to the pipeline inlet. Heat loss in a 1.26 m pipeline carrying 2 M drytonnes/yr is about 5 degrees C at a distance of 400 km in typical prairie clay soils, and would not likely require insulation; smaller pipelines or different soil conditions might require insulation for STS. Saccharification in the pipeline would reduce the need for investment in the fermentation plant, saving about 0.2 cents/l of ethanol. Transport of corn stover in multiple pipelines offers the opportunity to develop a large ethanol fermentation plant, avoiding some of the diseconomies of scale that arise from smaller plants whose capacities are limited by issues of truck congestion.

49 CFR 192.937 - What is a continual process of evaluation and assessment to maintain a pipeline's integrity?

Code of Federal Regulations, 2012 CFR

2012-10-01

...: MINIMUM FEDERAL SAFETY STANDARDS Gas Transmission Pipeline Integrity Management § 192.937 What is a..., or stress corrosion cracking. An operator must conduct the direct assessment in accordance with the...

49 CFR 192.937 - What is a continual process of evaluation and assessment to maintain a pipeline's integrity?

Code of Federal Regulations, 2011 CFR

2011-10-01

...: MINIMUM FEDERAL SAFETY STANDARDS Gas Transmission Pipeline Integrity Management § 192.937 What is a..., or stress corrosion cracking. An operator must conduct the direct assessment in accordance with the...

49 CFR 192.937 - What is a continual process of evaluation and assessment to maintain a pipeline's integrity?

Code of Federal Regulations, 2013 CFR

2013-10-01

...: MINIMUM FEDERAL SAFETY STANDARDS Gas Transmission Pipeline Integrity Management § 192.937 What is a..., or stress corrosion cracking. An operator must conduct the direct assessment in accordance with the...

49 CFR 192.937 - What is a continual process of evaluation and assessment to maintain a pipeline's integrity?

Code of Federal Regulations, 2014 CFR

2014-10-01

...: MINIMUM FEDERAL SAFETY STANDARDS Gas Transmission Pipeline Integrity Management § 192.937 What is a..., or stress corrosion cracking. An operator must conduct the direct assessment in accordance with the...

Providing Situational Awareness for Pipeline Control Operations

NASA Astrophysics Data System (ADS)

Butts, Jonathan; Kleinhans, Hugo; Chandia, Rodrigo; Papa, Mauricio; Shenoi, Sujeet

A SCADA system for a single 3,000-mile-long strand of oil or gas pipeline may employ several thousand field devices to measure process parameters and operate equipment. Because of the vital tasks performed by these sensors and actuators, pipeline operators need accurate and timely information about their status and integrity. This paper describes a realtime scanner that provides situational awareness about SCADA devices and control operations. The scanner, with the assistance of lightweight, distributed sensors, analyzes SCADA network traffic, verifies the operational status and integrity of field devices, and identifies anomalous activity. Experimental results obtained using real pipeline control traffic demonstrate the utility of the scanner in industrial settings.

From sequencer to supercomputer: an automatic pipeline for managing and processing next generation sequencing data.

PubMed

Camerlengo, Terry; Ozer, Hatice Gulcin; Onti-Srinivasan, Raghuram; Yan, Pearlly; Huang, Tim; Parvin, Jeffrey; Huang, Kun

2012-01-01

Next Generation Sequencing is highly resource intensive. NGS Tasks related to data processing, management and analysis require high-end computing servers or even clusters. Additionally, processing NGS experiments requires suitable storage space and significant manual interaction. At The Ohio State University's Biomedical Informatics Shared Resource, we designed and implemented a scalable architecture to address the challenges associated with the resource intensive nature of NGS secondary analysis built around Illumina Genome Analyzer II sequencers and Illumina's Gerald data processing pipeline. The software infrastructure includes a distributed computing platform consisting of a LIMS called QUEST (http://bisr.osumc.edu), an Automation Server, a computer cluster for processing NGS pipelines, and a network attached storage device expandable up to 40TB. The system has been architected to scale to multiple sequencers without requiring additional computing or labor resources. This platform provides demonstrates how to manage and automate NGS experiments in an institutional or core facility setting.

DKIST visible broadband imager data processing pipeline

NASA Astrophysics Data System (ADS)

Beard, Andrew; Cowan, Bruce; Ferayorni, Andrew

2014-07-01

The Daniel K. Inouye Solar Telescope (DKIST) Data Handling System (DHS) provides the technical framework and building blocks for developing on-summit instrument quality assurance and data reduction pipelines. The DKIST Visible Broadband Imager (VBI) is a first light instrument that alone will create two data streams with a bandwidth of 960 MB/s each. The high data rate and data volume of the VBI require near-real time processing capability for quality assurance and data reduction, and will be performed on-summit using Graphics Processing Unit (GPU) technology. The VBI data processing pipeline (DPP) is the first designed and developed using the DKIST DHS components, and therefore provides insight into the strengths and weaknesses of the framework. In this paper we lay out the design of the VBI DPP, examine how the underlying DKIST DHS components are utilized, and discuss how integration of the DHS framework with GPUs was accomplished. We present our results of the VBI DPP alpha release implementation of the calibration, frame selection reduction, and quality assurance display processing nodes.

Tumor image signatures and habitats: a processing pipeline of multimodality metabolic and physiological images.

PubMed

You, Daekeun; Kim, Michelle M; Aryal, Madhava P; Parmar, Hemant; Piert, Morand; Lawrence, Theodore S; Cao, Yue

2018-01-01

To create tumor "habitats" from the "signatures" discovered from multimodality metabolic and physiological images, we developed a framework of a processing pipeline. The processing pipeline consists of six major steps: (1) creating superpixels as a spatial unit in a tumor volume; (2) forming a data matrix [Formula: see text] containing all multimodality image parameters at superpixels; (3) forming and clustering a covariance or correlation matrix [Formula: see text] of the image parameters to discover major image "signatures;" (4) clustering the superpixels and organizing the parameter order of the [Formula: see text] matrix according to the one found in step 3; (5) creating "habitats" in the image space from the superpixels associated with the "signatures;" and (6) pooling and clustering a matrix consisting of correlation coefficients of each pair of image parameters from all patients to discover subgroup patterns of the tumors. The pipeline was applied to a dataset of multimodality images in glioblastoma (GBM) first, which consisted of 10 image parameters. Three major image "signatures" were identified. The three major "habitats" plus their overlaps were created. To test generalizability of the processing pipeline, a second image dataset from GBM, acquired on the scanners different from the first one, was processed. Also, to demonstrate the clinical association of image-defined "signatures" and "habitats," the patterns of recurrence of the patients were analyzed together with image parameters acquired prechemoradiation therapy. An association of the recurrence patterns with image-defined "signatures" and "habitats" was revealed. These image-defined "signatures" and "habitats" can be used to guide stereotactic tissue biopsy for genetic and mutation status analysis and to analyze for prediction of treatment outcomes, e.g., patterns of failure.

Susceptibility-weighted imaging using inter-echo-variance channel combination for improved contrast at 7 tesla.

PubMed

Hosseini, Zahra; Liu, Junmin; Solovey, Igor; Menon, Ravi S; Drangova, Maria

2017-04-01

To implement and optimize a new approach for susceptibility-weighted image (SWI) generation from multi-echo multi-channel image data and compare its performance against optimized traditional SWI pipelines. Five healthy volunteers were imaged at 7 Tesla. The inter-echo-variance (IEV) channel combination, which uses the variance of the local frequency shift at multiple echo times as a weighting factor during channel combination, was used to calculate multi-echo local phase shift maps. Linear phase masks were combined with the magnitude to generate IEV-SWI. The performance of the IEV-SWI pipeline was compared with that of two accepted SWI pipelines-channel combination followed by (i) Homodyne filtering (HPH-SWI) and (ii) unwrapping and high-pass filtering (SVD-SWI). The filtering steps of each pipeline were optimized. Contrast-to-noise ratio was used as the comparison metric. Qualitative assessment of artifact and vessel conspicuity was performed and processing time of pipelines was evaluated. The optimized IEV-SWI pipeline (σ = 7 mm) resulted in continuous vessel visibility throughout the brain. IEV-SWI had significantly higher contrast compared with HPH-SWI and SVD-SWI (P < 0.001, Friedman nonparametric test). Residual background fields and phase wraps in HPH-SWI and SVD-SWI corrupted the vessel signal and/or generated vessel-mimicking artifact. Optimized implementation of the IEV-SWI pipeline processed a six-echo 16-channel dataset in under 10 min. IEV-SWI benefits from channel-by-channel processing of phase data and results in high contrast images with an optimal balance between contrast and background noise removal, thereby presenting evidence of importance of the order in which postprocessing techniques are applied for multi-channel SWI generation. 2 J. Magn. Reson. Imaging 2017;45:1113-1124. © 2016 International Society for Magnetic Resonance in Medicine.

Processing Shotgun Proteomics Data on the Amazon Cloud with the Trans-Proteomic Pipeline*

PubMed Central

Slagel, Joseph; Mendoza, Luis; Shteynberg, David; Deutsch, Eric W.; Moritz, Robert L.

2015-01-01

Cloud computing, where scalable, on-demand compute cycles and storage are available as a service, has the potential to accelerate mass spectrometry-based proteomics research by providing simple, expandable, and affordable large-scale computing to all laboratories regardless of location or information technology expertise. We present new cloud computing functionality for the Trans-Proteomic Pipeline, a free and open-source suite of tools for the processing and analysis of tandem mass spectrometry datasets. Enabled with Amazon Web Services cloud computing, the Trans-Proteomic Pipeline now accesses large scale computing resources, limited only by the available Amazon Web Services infrastructure, for all users. The Trans-Proteomic Pipeline runs in an environment fully hosted on Amazon Web Services, where all software and data reside on cloud resources to tackle large search studies. In addition, it can also be run on a local computer with computationally intensive tasks launched onto the Amazon Elastic Compute Cloud service to greatly decrease analysis times. We describe the new Trans-Proteomic Pipeline cloud service components, compare the relative performance and costs of various Elastic Compute Cloud service instance types, and present on-line tutorials that enable users to learn how to deploy cloud computing technology rapidly with the Trans-Proteomic Pipeline. We provide tools for estimating the necessary computing resources and costs given the scale of a job and demonstrate the use of cloud enabled Trans-Proteomic Pipeline by performing over 1100 tandem mass spectrometry files through four proteomic search engines in 9 h and at a very low cost. PMID:25418363

Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline.

PubMed

Slagel, Joseph; Mendoza, Luis; Shteynberg, David; Deutsch, Eric W; Moritz, Robert L

2015-02-01

Cloud computing, where scalable, on-demand compute cycles and storage are available as a service, has the potential to accelerate mass spectrometry-based proteomics research by providing simple, expandable, and affordable large-scale computing to all laboratories regardless of location or information technology expertise. We present new cloud computing functionality for the Trans-Proteomic Pipeline, a free and open-source suite of tools for the processing and analysis of tandem mass spectrometry datasets. Enabled with Amazon Web Services cloud computing, the Trans-Proteomic Pipeline now accesses large scale computing resources, limited only by the available Amazon Web Services infrastructure, for all users. The Trans-Proteomic Pipeline runs in an environment fully hosted on Amazon Web Services, where all software and data reside on cloud resources to tackle large search studies. In addition, it can also be run on a local computer with computationally intensive tasks launched onto the Amazon Elastic Compute Cloud service to greatly decrease analysis times. We describe the new Trans-Proteomic Pipeline cloud service components, compare the relative performance and costs of various Elastic Compute Cloud service instance types, and present on-line tutorials that enable users to learn how to deploy cloud computing technology rapidly with the Trans-Proteomic Pipeline. We provide tools for estimating the necessary computing resources and costs given the scale of a job and demonstrate the use of cloud enabled Trans-Proteomic Pipeline by performing over 1100 tandem mass spectrometry files through four proteomic search engines in 9 h and at a very low cost. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Image Registration to Compensate for EPI Distortion in Patients with Brain Tumors: An Evaluation of Tract-Specific Effects.

PubMed

Albi, Angela; Meola, Antonio; Zhang, Fan; Kahali, Pegah; Rigolo, Laura; Tax, Chantal M W; Ciris, Pelin Aksit; Essayed, Walid I; Unadkat, Prashin; Norton, Isaiah; Rathi, Yogesh; Olubiyi, Olutayo; Golby, Alexandra J; O'Donnell, Lauren J

2018-03-01

Diffusion magnetic resonance imaging (dMRI) provides preoperative maps of neurosurgical patients' white matter tracts, but these maps suffer from echo-planar imaging (EPI) distortions caused by magnetic field inhomogeneities. In clinical neurosurgical planning, these distortions are generally not corrected and thus contribute to the uncertainty of fiber tracking. Multiple image processing pipelines have been proposed for image-registration-based EPI distortion correction in healthy subjects. In this article, we perform the first comparison of such pipelines in neurosurgical patient data. Five pipelines were tested in a retrospective clinical dMRI dataset of 9 patients with brain tumors. Pipelines differed in the choice of fixed and moving images and the similarity metric for image registration. Distortions were measured in two important tracts for neurosurgery, the arcuate fasciculus and corticospinal tracts. Significant differences in distortion estimates were found across processing pipelines. The most successful pipeline used dMRI baseline and T2-weighted images as inputs for distortion correction. This pipeline gave the most consistent distortion estimates across image resolutions and brain hemispheres. Quantitative results of mean tract distortions on the order of 1-2 mm are in line with other recent studies, supporting the potential need for distortion correction in neurosurgical planning. Novel results include significantly higher distortion estimates in the tumor hemisphere and greater effect of image resolution choice on results in the tumor hemisphere. Overall, this study demonstrates possible pitfalls and indicates that care should be taken when implementing EPI distortion correction in clinical settings. Copyright © 2018 by the American Society of Neuroimaging.

Determine new design and construction techniques for transportation of ethanol and ethanol/gasoline blends in new pipelines.

DOT National Transportation Integrated Search

2013-02-15

The technical tasks in this study included activities to characterize the impact of selected : metallurgical processing and fabrication variables on ethanol stress corrosion cracking (ethanol : SCC) of new pipeline steels, develop a better understand...

Guidelines for Constructing Natural Gas and Liquid Hydrocarbon Pipelines Through Areas Prone to Landslide and Subsidence Hazards

DOT National Transportation Integrated Search

2009-01-01

These guidelines provide recommendations for the assessment of new and existing natural gas and liquid hydrocarbon pipelines subjected to potential ground displacements resulting from landslides and subsidence. The process of defining landslide and s...

Bio-Docklets: virtualization containers for single-step execution of NGS pipelines.

PubMed

Kim, Baekdoo; Ali, Thahmina; Lijeron, Carlos; Afgan, Enis; Krampis, Konstantinos

2017-08-01

Processing of next-generation sequencing (NGS) data requires significant technical skills, involving installation, configuration, and execution of bioinformatics data pipelines, in addition to specialized postanalysis visualization and data mining software. In order to address some of these challenges, developers have leveraged virtualization containers toward seamless deployment of preconfigured bioinformatics software and pipelines on any computational platform. We present an approach for abstracting the complex data operations of multistep, bioinformatics pipelines for NGS data analysis. As examples, we have deployed 2 pipelines for RNA sequencing and chromatin immunoprecipitation sequencing, preconfigured within Docker virtualization containers we call Bio-Docklets. Each Bio-Docklet exposes a single data input and output endpoint and from a user perspective, running the pipelines as simply as running a single bioinformatics tool. This is achieved using a "meta-script" that automatically starts the Bio-Docklets and controls the pipeline execution through the BioBlend software library and the Galaxy Application Programming Interface. The pipeline output is postprocessed by integration with the Visual Omics Explorer framework, providing interactive data visualizations that users can access through a web browser. Our goal is to enable easy access to NGS data analysis pipelines for nonbioinformatics experts on any computing environment, whether a laboratory workstation, university computer cluster, or a cloud service provider. Beyond end users, the Bio-Docklets also enables developers to programmatically deploy and run a large number of pipeline instances for concurrent analysis of multiple datasets. © The Authors 2017. Published by Oxford University Press.

Bio-Docklets: virtualization containers for single-step execution of NGS pipelines

PubMed Central

Kim, Baekdoo; Ali, Thahmina; Lijeron, Carlos; Afgan, Enis

2017-01-01

Abstract Processing of next-generation sequencing (NGS) data requires significant technical skills, involving installation, configuration, and execution of bioinformatics data pipelines, in addition to specialized postanalysis visualization and data mining software. In order to address some of these challenges, developers have leveraged virtualization containers toward seamless deployment of preconfigured bioinformatics software and pipelines on any computational platform. We present an approach for abstracting the complex data operations of multistep, bioinformatics pipelines for NGS data analysis. As examples, we have deployed 2 pipelines for RNA sequencing and chromatin immunoprecipitation sequencing, preconfigured within Docker virtualization containers we call Bio-Docklets. Each Bio-Docklet exposes a single data input and output endpoint and from a user perspective, running the pipelines as simply as running a single bioinformatics tool. This is achieved using a “meta-script” that automatically starts the Bio-Docklets and controls the pipeline execution through the BioBlend software library and the Galaxy Application Programming Interface. The pipeline output is postprocessed by integration with the Visual Omics Explorer framework, providing interactive data visualizations that users can access through a web browser. Our goal is to enable easy access to NGS data analysis pipelines for nonbioinformatics experts on any computing environment, whether a laboratory workstation, university computer cluster, or a cloud service provider. Beyond end users, the Bio-Docklets also enables developers to programmatically deploy and run a large number of pipeline instances for concurrent analysis of multiple datasets. PMID:28854616

PyEmir: Data Reduction Pipeline for EMIR, the GTC Near-IR Multi-Object Spectrograph

NASA Astrophysics Data System (ADS)

Pascual, S.; Gallego, J.; Cardiel, N.; Eliche-Moral, M. C.

2010-12-01

EMIR is the near-infrared wide-field camera and multi-slit spectrograph being built for Gran Telescopio Canarias. We present here the work being done on its data processing pipeline. PyEmir is based on Python and it will process automatically data taken in both imaging and spectroscopy mode. PyEmir is begin developed by the UCM Group of Extragalactic Astrophysics and Astronomical Instrumentation.

High-throughput Analysis of Large Microscopy Image Datasets on CPU-GPU Cluster Platforms

PubMed Central

Teodoro, George; Pan, Tony; Kurc, Tahsin M.; Kong, Jun; Cooper, Lee A. D.; Podhorszki, Norbert; Klasky, Scott; Saltz, Joel H.

2014-01-01

Analysis of large pathology image datasets offers significant opportunities for the investigation of disease morphology, but the resource requirements of analysis pipelines limit the scale of such studies. Motivated by a brain cancer study, we propose and evaluate a parallel image analysis application pipeline for high throughput computation of large datasets of high resolution pathology tissue images on distributed CPU-GPU platforms. To achieve efficient execution on these hybrid systems, we have built runtime support that allows us to express the cancer image analysis application as a hierarchical data processing pipeline. The application is implemented as a coarse-grain pipeline of stages, where each stage may be further partitioned into another pipeline of fine-grain operations. The fine-grain operations are efficiently managed and scheduled for computation on CPUs and GPUs using performance aware scheduling techniques along with several optimizations, including architecture aware process placement, data locality conscious task assignment, data prefetching, and asynchronous data copy. These optimizations are employed to maximize the utilization of the aggregate computing power of CPUs and GPUs and minimize data copy overheads. Our experimental evaluation shows that the cooperative use of CPUs and GPUs achieves significant improvements on top of GPU-only versions (up to 1.6×) and that the execution of the application as a set of fine-grain operations provides more opportunities for runtime optimizations and attains better performance than coarser-grain, monolithic implementations used in other works. An implementation of the cancer image analysis pipeline using the runtime support was able to process an image dataset consisting of 36,848 4Kx4K-pixel image tiles (about 1.8TB uncompressed) in less than 4 minutes (150 tiles/second) on 100 nodes of a state-of-the-art hybrid cluster system. PMID:25419546

MetaDB a Data Processing Workflow in Untargeted MS-Based Metabolomics Experiments.

PubMed

Franceschi, Pietro; Mylonas, Roman; Shahaf, Nir; Scholz, Matthias; Arapitsas, Panagiotis; Masuero, Domenico; Weingart, Georg; Carlin, Silvia; Vrhovsek, Urska; Mattivi, Fulvio; Wehrens, Ron

2014-01-01

Due to their sensitivity and speed, mass-spectrometry based analytical technologies are widely used to in metabolomics to characterize biological phenomena. To address issues like metadata organization, quality assessment, data processing, data storage, and, finally, submission to public repositories, bioinformatic pipelines of a non-interactive nature are often employed, complementing the interactive software used for initial inspection and visualization of the data. These pipelines often are created as open-source software allowing the complete and exhaustive documentation of each step, ensuring the reproducibility of the analysis of extensive and often expensive experiments. In this paper, we will review the major steps which constitute such a data processing pipeline, discussing them in the context of an open-source software for untargeted MS-based metabolomics experiments recently developed at our institute. The software has been developed by integrating our metaMS R package with a user-friendly web-based application written in Grails. MetaMS takes care of data pre-processing and annotation, while the interface deals with the creation of the sample lists, the organization of the data storage, and the generation of survey plots for quality assessment. Experimental and biological metadata are stored in the ISA-Tab format making the proposed pipeline fully integrated with the Metabolights framework.

Failure modes for pipelines in landslide areas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bruschi, R.; Spinazze, M.; Tomassini, D.

1995-12-31

In recent years a number of incidences of pipelines affected by slow soil movements have been reported in the relevant literature. Further related issues such as soil-pipe interaction have been studied both theoretically and through experimental surveys, along with the environmental conditions which are responsible for hazard to the pipeline integrity. A suitable design criteria under these circumstances has been discussed by several authors, in particular in relation to a limit state approach and hence a strain based criteria. The scope of this paper is to describe the failure mechanisms which may affect the pipeline in the presence of slowmore » soil movements impacting on the pipeline, both in the longitudinal and transverse direction. Particular attention is paid to environmental, geometric and structural parameters which steer the process towards one or other failure mechanism. Criteria for deciding upon remedial measures required to guarantee the structural integrity of the pipeline, both in the short and in the long term, are discussed.« less

Framework for the Integration of Multi-Instrument Pipelines in the BepiColombo Science Operations Control System

NASA Astrophysics Data System (ADS)

Pérez-López, F.; Vallejo, J. C.; Martínez, S.; Ortiz, I.; Macfarlane, A.; Osuna, P.; Gill, R.; Casale, M.

2015-09-01

BepiColombo is an interdisciplinary ESA mission to explore the planet Mercury in cooperation with JAXA. The mission consists of two separate orbiters: ESA's Mercury Planetary Orbiter (MPO) and JAXA's Mercury Magnetospheric Orbiter (MMO), which are dedicated to the detailed study of the planet and its magnetosphere. The MPO scientific payload comprises eleven instruments packages covering different disciplines developed by several European teams. This paper describes the design and development approach of the framework required to support the operation of the distributed BepiColombo MPO instruments pipelines, developed and operated from different locations, but designed as a single entity. An architecture based on primary-redundant configuration, fully integrated into the BepiColombo Science Operations Control System (BSCS), has been selected, where some instrument pipelines will be operated from the instrument team's data processing centres, having a pipeline replica that can be run from the Science Ground Segment (SGS), while others will be executed as primary pipelines from the SGS, adopting the SGS the pipeline orchestration role.

Demonstrating the Effects of Shop Flow Process Variability on the Air Force Depot Level Reparable Item Pipeline

DTIC Science & Technology

1992-09-01

Crawford found that pipeline contents are extremely variable about their mean (10:24) and Kettner and Wheatley said that "a statistical analysis of data...write the results from this replication "* to the ANOVA files for later analysis . The first set outputs points "* for overall pipeline contents . The...families and friends for their unselfishness and support. Marvin A. Arostegui and Jon A. Larvick ii Table of Contents Page Preface

Study on Failure of Third-Party Damage for Urban Gas Pipeline Based on Fuzzy Comprehensive Evaluation

PubMed Central

Li, Jun; Zhang, Hong; Han, Yinshan; Wang, Baodong

2016-01-01

Focusing on the diversity, complexity and uncertainty of the third-party damage accident, the failure probability of third-party damage to urban gas pipeline was evaluated on the theory of analytic hierarchy process and fuzzy mathematics. The fault tree of third-party damage containing 56 basic events was built by hazard identification of third-party damage. The fuzzy evaluation of basic event probabilities were conducted by the expert judgment method and using membership function of fuzzy set. The determination of the weight of each expert and the modification of the evaluation opinions were accomplished using the improved analytic hierarchy process, and the failure possibility of the third-party to urban gas pipeline was calculated. Taking gas pipelines of a certain large provincial capital city as an example, the risk assessment structure of the method was proved to conform to the actual situation, which provides the basis for the safety risk prevention. PMID:27875545

Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public Repositories.

PubMed

Chockalingam, Sriram; Aluru, Maneesha; Aluru, Srinivas

2016-09-19

Pre-processing of microarray data is a well-studied problem. Furthermore, all popular platforms come with their own recommended best practices for differential analysis of genes. However, for genome-scale network inference using microarray data collected from large public repositories, these methods filter out a considerable number of genes. This is primarily due to the effects of aggregating a diverse array of experiments with different technical and biological scenarios. Here we introduce a pre-processing pipeline suitable for inferring genome-scale gene networks from large microarray datasets. We show that partitioning of the available microarray datasets according to biological relevance into tissue- and process-specific categories significantly extends the limits of downstream network construction. We demonstrate the effectiveness of our pre-processing pipeline by inferring genome-scale networks for the model plant Arabidopsis thaliana using two different construction methods and a collection of 11,760 Affymetrix ATH1 microarray chips. Our pre-processing pipeline and the datasets used in this paper are made available at http://alurulab.cc.gatech.edu/microarray-pp.

Theory and Application of Magnetic Flux Leakage Pipeline Detection.

PubMed

Shi, Yan; Zhang, Chao; Li, Rui; Cai, Maolin; Jia, Guanwei

2015-12-10

Magnetic flux leakage (MFL) detection is one of the most popular methods of pipeline inspection. It is a nondestructive testing technique which uses magnetic sensitive sensors to detect the magnetic leakage field of defects on both the internal and external surfaces of pipelines. This paper introduces the main principles, measurement and processing of MFL data. As the key point of a quantitative analysis of MFL detection, the identification of the leakage magnetic signal is also discussed. In addition, the advantages and disadvantages of different identification methods are analyzed. Then the paper briefly introduces the expert systems used. At the end of this paper, future developments in pipeline MFL detection are predicted.

Theory and Application of Magnetic Flux Leakage Pipeline Detection

PubMed Central

Shi, Yan; Zhang, Chao; Li, Rui; Cai, Maolin; Jia, Guanwei

2015-01-01

Magnetic flux leakage (MFL) detection is one of the most popular methods of pipeline inspection. It is a nondestructive testing technique which uses magnetic sensitive sensors to detect the magnetic leakage field of defects on both the internal and external surfaces of pipelines. This paper introduces the main principles, measurement and processing of MFL data. As the key point of a quantitative analysis of MFL detection, the identification of the leakage magnetic signal is also discussed. In addition, the advantages and disadvantages of different identification methods are analyzed. Then the paper briefly introduces the expert systems used. At the end of this paper, future developments in pipeline MFL detection are predicted. PMID:26690435

Simulation of pipeline in the area of the underwater crossing

NASA Astrophysics Data System (ADS)

Burkov, P.; Chernyavskiy, D.; Burkova, S.; Konan, E. C.

2014-08-01

The article studies stress-strain behavior of the main oil-pipeline section Alexandrovskoye-Anzhero-Sudzhensk using software system Ansys. This method of examination and assessment of technical conditions of objects of pipeline transport studies the objects and the processes that affect the technical condition of these facilities, including the research on the basis of computer simulation. Such approach allows to develop the theory, methods of calculations and designing of objects of pipeline transport, units and parts of machines, regardless of their industry and destination with a view to improve the existing constructions and create new structures, machines of high performance, durability and reliability, maintainability, low material capacity and cost, which have competitiveness on the world market.

CLAMP - a toolkit for efficiently building customized clinical natural language processing pipelines.

PubMed

Soysal, Ergin; Wang, Jingqi; Jiang, Min; Wu, Yonghui; Pakhomov, Serguei; Liu, Hongfang; Xu, Hua

2017-11-24

Existing general clinical natural language processing (NLP) systems such as MetaMap and Clinical Text Analysis and Knowledge Extraction System have been successfully applied to information extraction from clinical text. However, end users often have to customize existing systems for their individual tasks, which can require substantial NLP skills. Here we present CLAMP (Clinical Language Annotation, Modeling, and Processing), a newly developed clinical NLP toolkit that provides not only state-of-the-art NLP components, but also a user-friendly graphic user interface that can help users quickly build customized NLP pipelines for their individual applications. Our evaluation shows that the CLAMP default pipeline achieved good performance on named entity recognition and concept encoding. We also demonstrate the efficiency of the CLAMP graphic user interface in building customized, high-performance NLP pipelines with 2 use cases, extracting smoking status and lab test values. CLAMP is publicly available for research use, and we believe it is a unique asset for the clinical NLP community. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Parallel processing considerations for image recognition tasks

NASA Astrophysics Data System (ADS)

Simske, Steven J.

2011-01-01

Many image recognition tasks are well-suited to parallel processing. The most obvious example is that many imaging tasks require the analysis of multiple images. From this standpoint, then, parallel processing need be no more complicated than assigning individual images to individual processors. However, there are three less trivial categories of parallel processing that will be considered in this paper: parallel processing (1) by task; (2) by image region; and (3) by meta-algorithm. Parallel processing by task allows the assignment of multiple workflows-as diverse as optical character recognition [OCR], document classification and barcode reading-to parallel pipelines. This can substantially decrease time to completion for the document tasks. For this approach, each parallel pipeline is generally performing a different task. Parallel processing by image region allows a larger imaging task to be sub-divided into a set of parallel pipelines, each performing the same task but on a different data set. This type of image analysis is readily addressed by a map-reduce approach. Examples include document skew detection and multiple face detection and tracking. Finally, parallel processing by meta-algorithm allows different algorithms to be deployed on the same image simultaneously. This approach may result in improved accuracy.

Scaling-up NLP Pipelines to Process Large Corpora of Clinical Notes.

PubMed

Divita, G; Carter, M; Redd, A; Zeng, Q; Gupta, K; Trautner, B; Samore, M; Gundlapalli, A

2015-01-01

This article is part of the Focus Theme of Methods of Information in Medicine on "Big Data and Analytics in Healthcare". This paper describes the scale-up efforts at the VA Salt Lake City Health Care System to address processing large corpora of clinical notes through a natural language processing (NLP) pipeline. The use case described is a current project focused on detecting the presence of an indwelling urinary catheter in hospitalized patients and subsequent catheter-associated urinary tract infections. An NLP algorithm using v3NLP was developed to detect the presence of an indwelling urinary catheter in hospitalized patients. The algorithm was tested on a small corpus of notes on patients for whom the presence or absence of a catheter was already known (reference standard). In planning for a scale-up, we estimated that the original algorithm would have taken 2.4 days to run on a larger corpus of notes for this project (550,000 notes), and 27 days for a corpus of 6 million records representative of a national sample of notes. We approached scaling-up NLP pipelines through three techniques: pipeline replication via multi-threading, intra-annotator threading for tasks that can be further decomposed, and remote annotator services which enable annotator scale-out. The scale-up resulted in reducing the average time to process a record from 206 milliseconds to 17 milliseconds or a 12- fold increase in performance when applied to a corpus of 550,000 notes. Purposely simplistic in nature, these scale-up efforts are the straight forward evolution from small scale NLP processing to larger scale extraction without incurring associated complexities that are inherited by the use of the underlying UIMA framework. These efforts represent generalizable and widely applicable techniques that will aid other computationally complex NLP pipelines that are of need to be scaled out for processing and analyzing big data.

49 CFR 192.243 - Nondestructive testing.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 3 2010-10-01 2010-10-01 false Nondestructive testing. 192.243 Section 192.243... BY PIPELINE: MINIMUM FEDERAL SAFETY STANDARDS Welding of Steel in Pipelines § 192.243 Nondestructive testing. (a) Nondestructive testing of welds must be performed by any process, other than trepanning, that...

State Regulators Promote Consumer Choice in Retail Gas Markets

EIA Publications

1996-01-01

Restructuring of interstate pipeline companies has created new choices and challenges for local distribution companies (LDCs), their regulators, and their customers. The process of separating interstate pipeline gas sales from transportation service has been completed and has resulted in greater gas procurement options for LDCs.

DALiuGE: A graph execution framework for harnessing the astronomical data deluge

NASA Astrophysics Data System (ADS)

Wu, C.; Tobar, R.; Vinsen, K.; Wicenec, A.; Pallot, D.; Lao, B.; Wang, R.; An, T.; Boulton, M.; Cooper, I.; Dodson, R.; Dolensky, M.; Mei, Y.; Wang, F.

2017-07-01

The Data Activated Liu Graph Engine - DALiuGE- is an execution framework for processing large astronomical datasets at a scale required by the Square Kilometre Array Phase 1 (SKA1). It includes an interface for expressing complex data reduction pipelines consisting of both datasets and algorithmic components and an implementation run-time to execute such pipelines on distributed resources. By mapping the logical view of a pipeline to its physical realisation, DALiuGE separates the concerns of multiple stakeholders, allowing them to collectively optimise large-scale data processing solutions in a coherent manner. The execution in DALiuGE is data-activated, where each individual data item autonomously triggers the processing on itself. Such decentralisation also makes the execution framework very scalable and flexible, supporting pipeline sizes ranging from less than ten tasks running on a laptop to tens of millions of concurrent tasks on the second fastest supercomputer in the world. DALiuGE has been used in production for reducing interferometry datasets from the Karl E. Jansky Very Large Array and the Mingantu Ultrawide Spectral Radioheliograph; and is being developed as the execution framework prototype for the Science Data Processor (SDP) consortium of the Square Kilometre Array (SKA) telescope. This paper presents a technical overview of DALiuGE and discusses case studies from the CHILES and MUSER projects that use DALiuGE to execute production pipelines. In a companion paper, we provide in-depth analysis of DALiuGE's scalability to very large numbers of tasks on two supercomputing facilities.

Bifrost: a Modular Python/C++ Framework for Development of High-Throughput Data Analysis Pipelines

NASA Astrophysics Data System (ADS)

Cranmer, Miles; Barsdell, Benjamin R.; Price, Danny C.; Garsden, Hugh; Taylor, Gregory B.; Dowell, Jayce; Schinzel, Frank; Costa, Timothy; Greenhill, Lincoln J.

2017-01-01

Large radio interferometers have data rates that render long-term storage of raw correlator data infeasible, thus motivating development of real-time processing software. For high-throughput applications, processing pipelines are challenging to design and implement. Motivated by science efforts with the Long Wavelength Array, we have developed Bifrost, a novel Python/C++ framework that eases the development of high-throughput data analysis software by packaging algorithms as black box processes in a directed graph. This strategy to modularize code allows astronomers to create parallelism without code adjustment. Bifrost uses CPU/GPU ’circular memory’ data buffers that enable ready introduction of arbitrary functions into the processing path for ’streams’ of data, and allow pipelines to automatically reconfigure in response to astrophysical transient detection or input of new observing settings. We have deployed and tested Bifrost at the latest Long Wavelength Array station, in Sevilleta National Wildlife Refuge, NM, where it handles throughput exceeding 10 Gbps per CPU core.

Gathering pipeline methane emissions in Fayetteville shale pipelines and scoping guidelines for future pipeline measurement campaigns

DOE PAGES

Zimmerle, Daniel J.; Pickering, Cody K.; Bell, Clay S.; ...

2017-11-24

Gathering pipelines, which transport gas from well pads to downstream processing, are a sector of the natural gas supply chain for which little measured methane emissions data are available. This study performed leak detection and measurement on 96 km of gathering pipeline and the associated 56 pigging facilities and 39 block valves. The study found one underground leak accounting for 83% (4.0 kg CH 4/hr) of total measured emissions. Methane emissions for the 4684 km of gathering pipeline in the study area were estimated at 402 kg CH 4/hr [95 to 1065 kg CH 4/hr, 95% CI], or 1% [0.2%more » to 2.6%] of all methane emissions measured during a prior aircraft study of the same area. Emissions estimated by this study fall within the uncertainty range of emissions estimated using emission factors from EPA's 2015 Greenhouse Inventory and study activity estimates. While EPA's current inventory is based upon emission factors from distribution mains measured in the 1990s, this study indicates that using emission factors from more recent distribution studies could significantly underestimate emissions from gathering pipelines. To guide broader studies of pipeline emissions, we also estimate the fraction of the pipeline length within a basin that must be measured to constrain uncertainty of pipeline emissions estimates to within 1% of total basin emissions. The study provides both substantial insight into the mix of emission sources and guidance for future gathering pipeline studies, but since measurements were made in a single basin, the results are not sufficiently representative to provide methane emission factors at the regional or national level.« less

Gathering pipeline methane emissions in Fayetteville shale pipelines and scoping guidelines for future pipeline measurement campaigns

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zimmerle, Daniel J.; Pickering, Cody K.; Bell, Clay S.

Gathering pipelines, which transport gas from well pads to downstream processing, are a sector of the natural gas supply chain for which little measured methane emissions data are available. This study performed leak detection and measurement on 96 km of gathering pipeline and the associated 56 pigging facilities and 39 block valves. The study found one underground leak accounting for 83% (4.0 kg CH 4/hr) of total measured emissions. Methane emissions for the 4684 km of gathering pipeline in the study area were estimated at 402 kg CH 4/hr [95 to 1065 kg CH 4/hr, 95% CI], or 1% [0.2%more » to 2.6%] of all methane emissions measured during a prior aircraft study of the same area. Emissions estimated by this study fall within the uncertainty range of emissions estimated using emission factors from EPA's 2015 Greenhouse Inventory and study activity estimates. While EPA's current inventory is based upon emission factors from distribution mains measured in the 1990s, this study indicates that using emission factors from more recent distribution studies could significantly underestimate emissions from gathering pipelines. To guide broader studies of pipeline emissions, we also estimate the fraction of the pipeline length within a basin that must be measured to constrain uncertainty of pipeline emissions estimates to within 1% of total basin emissions. The study provides both substantial insight into the mix of emission sources and guidance for future gathering pipeline studies, but since measurements were made in a single basin, the results are not sufficiently representative to provide methane emission factors at the regional or national level.« less

A method for simulating the release of natural gas from the rupture of high-pressure pipelines in any terrain.

PubMed

Deng, Yajun; Hu, Hongbing; Yu, Bo; Sun, Dongliang; Hou, Lei; Liang, Yongtu

2018-01-15

The rupture of a high-pressure natural gas pipeline can pose a serious threat to human life and environment. In this research, a method has been proposed to simulate the release of natural gas from the rupture of high-pressure pipelines in any terrain. The process of gas releases from the rupture of a high-pressure pipeline is divided into three stages, namely the discharge, jet, and dispersion stages. Firstly, a discharge model is established to calculate the release rate of the orifice. Secondly, an improved jet model is proposed to obtain the parameters of the pseudo source. Thirdly, a fast-modeling method applicable to any terrain is introduced. Finally, based upon these three steps, a dispersion model, which can take any terrain into account, is established. Then, the dispersion scenarios of released gas in four different terrains are studied. Moreover, the effects of pipeline pressure, pipeline diameter, wind speed and concentration of hydrogen sulfide on the dispersion scenario in real terrain are systematically analyzed. The results provide significant guidance for risk assessment and contingency planning of a ruptured natural gas pipeline. Copyright © 2017. Published by Elsevier B.V.

Fully automated processing of fMRI data in SPM: from MRI scanner to PACS.

PubMed

Maldjian, Joseph A; Baer, Aaron H; Kraft, Robert A; Laurienti, Paul J; Burdette, Jonathan H

2009-01-01

Here we describe the Wake Forest University Pipeline, a fully automated method for the processing of fMRI data using SPM. The method includes fully automated data transfer and archiving from the point of acquisition, real-time batch script generation, distributed grid processing, interface to SPM in MATLAB, error recovery and data provenance, DICOM conversion and PACS insertion. It has been used for automated processing of fMRI experiments, as well as for the clinical implementation of fMRI and spin-tag perfusion imaging. The pipeline requires no manual intervention, and can be extended to any studies requiring offline processing.

Natural gas and CO2 price variation: impact on the relative cost-efficiency of LNG and pipelines.

PubMed

Ulvestad, Marte; Overland, Indra

2012-06-01

THIS ARTICLE DEVELOPS A FORMAL MODEL FOR COMPARING THE COST STRUCTURE OF THE TWO MAIN TRANSPORT OPTIONS FOR NATURAL GAS: liquefied natural gas (LNG) and pipelines. In particular, it evaluates how variations in the prices of natural gas and greenhouse gas emissions affect the relative cost-efficiency of these two options. Natural gas is often promoted as the most environmentally friendly of all fossil fuels, and LNG as a modern and efficient way of transporting it. Some research has been carried out into the local environmental impact of LNG facilities, but almost none into aspects related to climate change. This paper concludes that at current price levels for natural gas and CO 2 emissions the distance from field to consumer and the volume of natural gas transported are the main determinants of transport costs. The pricing of natural gas and greenhouse emissions influence the relative cost-efficiency of LNG and pipeline transport, but only to a limited degree at current price levels. Because more energy is required for the LNG process (especially for fuelling the liquefaction process) than for pipelines at distances below 9100 km, LNG is more exposed to variability in the price of natural gas and greenhouse gas emissions up to this distance. If the prices of natural gas and/or greenhouse gas emission rise dramatically in the future, this will affect the choice between pipelines and LNG. Such a price increase will be favourable for pipelines relative to LNG.

Natural gas and CO2 price variation: impact on the relative cost-efficiency of LNG and pipelines

PubMed Central

Ulvestad, Marte; Overland, Indra

2012-01-01

This article develops a formal model for comparing the cost structure of the two main transport options for natural gas: liquefied natural gas (LNG) and pipelines. In particular, it evaluates how variations in the prices of natural gas and greenhouse gas emissions affect the relative cost-efficiency of these two options. Natural gas is often promoted as the most environmentally friendly of all fossil fuels, and LNG as a modern and efficient way of transporting it. Some research has been carried out into the local environmental impact of LNG facilities, but almost none into aspects related to climate change. This paper concludes that at current price levels for natural gas and CO2 emissions the distance from field to consumer and the volume of natural gas transported are the main determinants of transport costs. The pricing of natural gas and greenhouse emissions influence the relative cost-efficiency of LNG and pipeline transport, but only to a limited degree at current price levels. Because more energy is required for the LNG process (especially for fuelling the liquefaction process) than for pipelines at distances below 9100 km, LNG is more exposed to variability in the price of natural gas and greenhouse gas emissions up to this distance. If the prices of natural gas and/or greenhouse gas emission rise dramatically in the future, this will affect the choice between pipelines and LNG. Such a price increase will be favourable for pipelines relative to LNG. PMID:24683269

A novel joint-processing adaptive nonlinear equalizer using a modular recurrent neural network for chaotic communication systems.

PubMed

Zhao, Haiquan; Zeng, Xiangping; Zhang, Jiashu; Liu, Yangguang; Wang, Xiaomin; Li, Tianrui

2011-01-01

To eliminate nonlinear channel distortion in chaotic communication systems, a novel joint-processing adaptive nonlinear equalizer based on a pipelined recurrent neural network (JPRNN) is proposed, using a modified real-time recurrent learning (RTRL) algorithm. Furthermore, an adaptive amplitude RTRL algorithm is adopted to overcome the deteriorating effect introduced by the nesting process. Computer simulations illustrate that the proposed equalizer outperforms the pipelined recurrent neural network (PRNN) and recurrent neural network (RNN) equalizers. Copyright © 2010 Elsevier Ltd. All rights reserved.

A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines

PubMed Central

2011-01-01

Background Bioinformatic analyses typically proceed as chains of data-processing tasks. A pipeline, or 'workflow', is a well-defined protocol, with a specific structure defined by the topology of data-flow interdependencies, and a particular functionality arising from the data transformations applied at each step. In computer science, the dataflow programming (DFP) paradigm defines software systems constructed in this manner, as networks of message-passing components. Thus, bioinformatic workflows can be naturally mapped onto DFP concepts. Results To enable the flexible creation and execution of bioinformatics dataflows, we have written a modular framework for parallel pipelines in Python ('PaPy'). A PaPy workflow is created from re-usable components connected by data-pipes into a directed acyclic graph, which together define nested higher-order map functions. The successive functional transformations of input data are evaluated on flexibly pooled compute resources, either local or remote. Input items are processed in batches of adjustable size, all flowing one to tune the trade-off between parallelism and lazy-evaluation (memory consumption). An add-on module ('NuBio') facilitates the creation of bioinformatics workflows by providing domain specific data-containers (e.g., for biomolecular sequences, alignments, structures) and functionality (e.g., to parse/write standard file formats). Conclusions PaPy offers a modular framework for the creation and deployment of parallel and distributed data-processing workflows. Pipelines derive their functionality from user-written, data-coupled components, so PaPy also can be viewed as a lightweight toolkit for extensible, flow-based bioinformatics data-processing. The simplicity and flexibility of distributed PaPy pipelines may help users bridge the gap between traditional desktop/workstation and grid computing. PaPy is freely distributed as open-source Python code at http://muralab.org/PaPy, and includes extensive documentation and annotated usage examples. PMID:21352538

A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines.

PubMed

Cieślik, Marcin; Mura, Cameron

2011-02-25

Bioinformatic analyses typically proceed as chains of data-processing tasks. A pipeline, or 'workflow', is a well-defined protocol, with a specific structure defined by the topology of data-flow interdependencies, and a particular functionality arising from the data transformations applied at each step. In computer science, the dataflow programming (DFP) paradigm defines software systems constructed in this manner, as networks of message-passing components. Thus, bioinformatic workflows can be naturally mapped onto DFP concepts. To enable the flexible creation and execution of bioinformatics dataflows, we have written a modular framework for parallel pipelines in Python ('PaPy'). A PaPy workflow is created from re-usable components connected by data-pipes into a directed acyclic graph, which together define nested higher-order map functions. The successive functional transformations of input data are evaluated on flexibly pooled compute resources, either local or remote. Input items are processed in batches of adjustable size, all flowing one to tune the trade-off between parallelism and lazy-evaluation (memory consumption). An add-on module ('NuBio') facilitates the creation of bioinformatics workflows by providing domain specific data-containers (e.g., for biomolecular sequences, alignments, structures) and functionality (e.g., to parse/write standard file formats). PaPy offers a modular framework for the creation and deployment of parallel and distributed data-processing workflows. Pipelines derive their functionality from user-written, data-coupled components, so PaPy also can be viewed as a lightweight toolkit for extensible, flow-based bioinformatics data-processing. The simplicity and flexibility of distributed PaPy pipelines may help users bridge the gap between traditional desktop/workstation and grid computing. PaPy is freely distributed as open-source Python code at http://muralab.org/PaPy, and includes extensive documentation and annotated usage examples.

27 CFR 20.94 - Statement of process.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 5150.19 shall also contain the following information: (i) Flow diagrams shall be submitted with the... connecting pipelines and valves. All major equipment shall be identified as to its use. The direction of flow through the pipelines shall be indicated in the flow diagram. The flow diagram, shall be accompanied by a...

27 CFR 20.94 - Statement of process.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 5150.19 shall also contain the following information: (i) Flow diagrams shall be submitted with the... connecting pipelines and valves. All major equipment shall be identified as to its use. The direction of flow through the pipelines shall be indicated in the flow diagram. The flow diagram, shall be accompanied by a...

27 CFR 20.94 - Statement of process.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 5150.19 shall also contain the following information: (i) Flow diagrams shall be submitted with the... connecting pipelines and valves. All major equipment shall be identified as to its use. The direction of flow through the pipelines shall be indicated in the flow diagram. The flow diagram, shall be accompanied by a...

27 CFR 20.94 - Statement of process.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 5150.19 shall also contain the following information: (i) Flow diagrams shall be submitted with the... connecting pipelines and valves. All major equipment shall be identified as to its use. The direction of flow through the pipelines shall be indicated in the flow diagram. The flow diagram, shall be accompanied by a...

27 CFR 20.94 - Statement of process.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 5150.19 shall also contain the following information: (i) Flow diagrams shall be submitted with the... connecting pipelines and valves. All major equipment shall be identified as to its use. The direction of flow through the pipelines shall be indicated in the flow diagram. The flow diagram, shall be accompanied by a...

The Application of PVDF in Converter Cooling Pipeline

NASA Astrophysics Data System (ADS)

Geng, Man; Lu, Zhimin

2017-11-01

The structure, mechanical property, thermodynamics property, electrical aspects, radiation property and chemical property were introduced, and PVDF could satisfy the requirement of converter cooling pipe. PVDF department and pipe of distribution pipeline of converter cooling system in Debao HVDC project are used to introduce the molding process of PVDF.

Basic overview towards the assessment of landslide and subsidence risks along a geothermal pipeline network

NASA Astrophysics Data System (ADS)

Astisiasari; Van Westen, Cees; Jetten, Victor; van der Meer, Freek; Rahmawati Hizbaron, Dyah

2017-12-01

An operating geothermal power plant consists of installation units that work systematically in a network. The pipeline network connects various engineering structures, e.g. well pads, separator, scrubber, and power station, in the process of transferring geothermal fluids to generate electricity. Besides, a pipeline infrastructure also delivers the brine back to earth, through the injection well-pads. Despite of its important functions, a geothermal pipeline may bear a threat to its vicinity through a pipeline failure. The pipeline can be impacted by perilous events like landslides, earthquakes, and subsidence. The pipeline failure itself may relate to physical deterioration over time, e.g. due to corrosion and fatigue. The geothermal reservoirs are usually located in mountainous areas that are associated with steep slopes, complex geology, and weathered soil. Geothermal areas record a noteworthy number of disasters, especially due to landslide and subsidence. Therefore, a proper multi-risk assessment along the geothermal pipeline is required, particularly for these two types of hazard. This is also to mention that the impact on human fatality and injury is not presently discussed here. This paper aims to give a basic overview on the existing approaches for the assessment of multi-risk assessment along geothermal pipelines. It delivers basic principles on the analysis of risks and its contributing variables, in order to model the loss consequences. By considering the loss consequences, as well as the alternatives for mitigation measures, the environmental safety in geothermal working area could be enforced.

First Retrieval of Surface Lambert Albedos From Mars Reconnaissance Orbiter CRISM Data

NASA Astrophysics Data System (ADS)

McGuire, P. C.; Arvidson, R. E.; Murchie, S. L.; Wolff, M. J.; Smith, M. D.; Martin, T. Z.; Milliken, R. E.; Mustard, J. F.; Pelkey, S. M.; Lichtenberg, K. A.; Cavender, P. J.; Humm, D. C.; Titus, T. N.; Malaret, E. R.

2006-12-01

We have developed a pipeline-processing software system to convert radiance-on-sensor for each of 72 out of 544 CRISM spectral bands used in global mapping to the corresponding surface Lambert albedo, accounting for atmospheric, thermal, and photoclinometric effects. We will present and interpret first results from this software system for the retrieval of Lambert albedos from CRISM data. For the multispectral mapping modes, these pipeline-processed 72 spectral bands constitute all of the available bands, for wavelengths from 0.362-3.920 μm, at 100-200 m/pixel spatial resolution, and ~ 0.006\\spaceμm spectral resolution. For the hyperspectral targeted modes, these pipeline-processed 72 spectral bands are only a selection of all of the 544 spectral bands, but at a resolution of 15-38 m/pixel. The pipeline processing for both types of observing modes (multispectral and hyperspectral) will use climatology, based on data from MGS/TES, in order to estimate ice- and dust-aerosol optical depths, prior to the atmospheric correction with lookup tables based upon radiative-transport calculations via DISORT. There is one DISORT atmospheric-correction lookup table for converting radiance-on-sensor to Lambert albedo for each of the 72 spectral bands. The measurements of the Emission Phase Function (EPF) during targeting will not be employed in this pipeline processing system. We are developing a separate system for extracting more accurate aerosol optical depths and surface scattering properties. This separate system will use direct calls (instead of lookup tables) to the DISORT code for all 544 bands, and it will use the EPF data directly, bootstrapping from the climatology data for the aerosol optical depths. The pipeline processing will thermally correct the albedos for the spectral bands above ~ 2.6 μm, by a choice between 4 different techniques for determining surface temperature: 1) climatology, 2) empirical estimation of the albedo at 3.9 μm from the measured albedo at 2.5 μm, 3) a physical thermal model (PTM) based upon maps of thermal inertia from TES and coarse-resolution surface slopes (SS) from MOLA, and 4) a photoclinometric extension to the PTM that uses CRISM albedos at 0.41 μm to compute the SS at CRISM spatial resolution. For the thermal correction, we expect that each of these 4 different techniques will be valuable for some fraction of the observations.

Smart Sound Processing for Defect Sizing in Pipelines Using EMAT Actuator Based Multi-Frequency Lamb Waves

PubMed Central

García-Gómez, Joaquín; Rosa-Zurera, Manuel; Romero-Camacho, Antonio; Jiménez-Garrido, Jesús Antonio; García-Benavides, Víctor

2018-01-01

Pipeline inspection is a topic of particular interest to the companies. Especially important is the defect sizing, which allows them to avoid subsequent costly repairs in their equipment. A solution for this issue is using ultrasonic waves sensed through Electro-Magnetic Acoustic Transducer (EMAT) actuators. The main advantage of this technology is the absence of the need to have direct contact with the surface of the material under investigation, which must be a conductive one. Specifically interesting is the meander-line-coil based Lamb wave generation, since the directivity of the waves allows a study based in the circumferential wrap-around received signal. However, the variety of defect sizes changes the behavior of the signal when it passes through the pipeline. Because of that, it is necessary to apply advanced techniques based on Smart Sound Processing (SSP). These methods involve extracting useful information from the signals sensed with EMAT at different frequencies to obtain nonlinear estimations of the depth of the defect, and to select the features that better estimate the profile of the pipeline. The proposed technique has been tested using both simulated and real signals in steel pipelines, obtaining good results in terms of Root Mean Square Error (RMSE). PMID:29518927

A homology-based pipeline for global prediction of post-translational modification sites

NASA Astrophysics Data System (ADS)

Chen, Xiang; Shi, Shao-Ping; Xu, Hao-Dong; Suo, Sheng-Bao; Qiu, Jian-Ding

2016-05-01

The pathways of protein post-translational modifications (PTMs) have been shown to play particularly important roles for almost any biological process. Identification of PTM substrates along with information on the exact sites is fundamental for fully understanding or controlling biological processes. Alternative computational strategies would help to annotate PTMs in a high-throughput manner. Traditional algorithms are suited for identifying the common organisms and tissues that have a complete PTM atlas or extensive experimental data. While annotation of rare PTMs in most organisms is a clear challenge. In this work, to this end we have developed a novel homology-based pipeline named PTMProber that allows identification of potential modification sites for most of the proteomes lacking PTMs data. Cross-promotion E-value (CPE) as stringent benchmark has been used in our pipeline to evaluate homology to known modification sites. Independent-validation tests show that PTMProber achieves over 58.8% recall with high precision by CPE benchmark. Comparisons with other machine-learning tools show that PTMProber pipeline performs better on general predictions. In addition, we developed a web-based tool to integrate this pipeline at http://bioinfo.ncu.edu.cn/PTMProber/index.aspx. In addition to pre-constructed prediction models of PTM, the website provides an extensional functionality to allow users to customize models.

Image processing and Quality Control for the first 10,000 brain imaging datasets from UK Biobank.

PubMed

Alfaro-Almagro, Fidel; Jenkinson, Mark; Bangerter, Neal K; Andersson, Jesper L R; Griffanti, Ludovica; Douaud, Gwenaëlle; Sotiropoulos, Stamatios N; Jbabdi, Saad; Hernandez-Fernandez, Moises; Vallee, Emmanuel; Vidaurre, Diego; Webster, Matthew; McCarthy, Paul; Rorden, Christopher; Daducci, Alessandro; Alexander, Daniel C; Zhang, Hui; Dragonu, Iulius; Matthews, Paul M; Miller, Karla L; Smith, Stephen M

2018-02-01

UK Biobank is a large-scale prospective epidemiological study with all data accessible to researchers worldwide. It is currently in the process of bringing back 100,000 of the original participants for brain, heart and body MRI, carotid ultrasound and low-dose bone/fat x-ray. The brain imaging component covers 6 modalities (T1, T2 FLAIR, susceptibility weighted MRI, Resting fMRI, Task fMRI and Diffusion MRI). Raw and processed data from the first 10,000 imaged subjects has recently been released for general research access. To help convert this data into useful summary information we have developed an automated processing and QC (Quality Control) pipeline that is available for use by other researchers. In this paper we describe the pipeline in detail, following a brief overview of UK Biobank brain imaging and the acquisition protocol. We also describe several quantitative investigations carried out as part of the development of both the imaging protocol and the processing pipeline. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Generation of Custom DSP Transform IP Cores: Case Study Walsh-Hadamard Transform

DTIC Science & Technology

2002-09-01

mathematics and hardware design What I know: Finite state machine Pipelining Systolic array … What I know: Linear algebra Digital signal processing...state machine Pipelining Systolic array … What I know: Linear algebra Digital signal processing Adaptive filter theory … A math guy A hardware engineer...Synthesis Technology Libary Bit-width (8) HF factor (1,2,3,6) VF factor (1,2,4, ... 32) Xilinx FPGA Place&Route Xilinx FPGA Place&Route Performance

Optimal Energy Consumption Analysis of Natural Gas Pipeline

PubMed Central

Liu, Enbin; Li, Changjun; Yang, Yi

2014-01-01

There are many compressor stations along long-distance natural gas pipelines. Natural gas can be transported using different boot programs and import pressures, combined with temperature control parameters. Moreover, different transport methods have correspondingly different energy consumptions. At present, the operating parameters of many pipelines are determined empirically by dispatchers, resulting in high energy consumption. This practice does not abide by energy reduction policies. Therefore, based on a full understanding of the actual needs of pipeline companies, we introduce production unit consumption indicators to establish an objective function for achieving the goal of lowering energy consumption. By using a dynamic programming method for solving the model and preparing calculation software, we can ensure that the solution process is quick and efficient. Using established optimization methods, we analyzed the energy savings for the XQ gas pipeline. By optimizing the boot program, the import station pressure, and the temperature parameters, we achieved the optimal energy consumption. By comparison with the measured energy consumption, the pipeline now has the potential to reduce energy consumption by 11 to 16 percent. PMID:24955410

Risk analysis of urban gas pipeline network based on improved bow-tie model

NASA Astrophysics Data System (ADS)

Hao, M. J.; You, Q. J.; Yue, Z.

2017-11-01

Gas pipeline network is a major hazard source in urban areas. In the event of an accident, there could be grave consequences. In order to understand more clearly the causes and consequences of gas pipeline network accidents, and to develop prevention and mitigation measures, the author puts forward the application of improved bow-tie model to analyze risks of urban gas pipeline network. The improved bow-tie model analyzes accident causes from four aspects: human, materials, environment and management; it also analyzes the consequences from four aspects: casualty, property loss, environment and society. Then it quantifies the causes and consequences. Risk identification, risk analysis, risk assessment, risk control, and risk management will be clearly shown in the model figures. Then it can suggest prevention and mitigation measures accordingly to help reduce accident rate of gas pipeline network. The results show that the whole process of an accident can be visually investigated using the bow-tie model. It can also provide reasons for and predict consequences of an unfortunate event. It is of great significance in order to analyze leakage failure of gas pipeline network.

Time-Distance Helioseismology Data-Analysis Pipeline for Helioseismic and Magnetic Imager Onboard Solar Dynamics Observatory (SDO-HMI) and Its Initial Results

NASA Technical Reports Server (NTRS)

Zhao, J.; Couvidat, S.; Bogart, R. S.; Parchevsky, K. V.; Birch, A. C.; Duvall, Thomas L., Jr.; Beck, J. G.; Kosovichev, A. G.; Scherrer, P. H.

2011-01-01

The Helioseismic and Magnetic Imager onboard the Solar Dynamics Observatory (SDO/HMI) provides continuous full-disk observations of solar oscillations. We develop a data-analysis pipeline based on the time-distance helioseismology method to measure acoustic travel times using HMI Doppler-shift observations, and infer solar interior properties by inverting these measurements. The pipeline is used for routine production of near-real-time full-disk maps of subsurface wave-speed perturbations and horizontal flow velocities for depths ranging from 0 to 20 Mm, every eight hours. In addition, Carrington synoptic maps for the subsurface properties are made from these full-disk maps. The pipeline can also be used for selected target areas and time periods. We explain details of the pipeline organization and procedures, including processing of the HMI Doppler observations, measurements of the travel times, inversions, and constructions of the full-disk and synoptic maps. Some initial results from the pipeline, including full-disk flow maps, sunspot subsurface flow fields, and the interior rotation and meridional flow speeds, are presented.

Research on Submarine Pipeline Steel with High Performance

NASA Astrophysics Data System (ADS)

Ren, Yi; Liu, Wenyue; Zhang, Shuai; Wang, Shuang; Gao, Hong

Submarine pipeline steel has largely uniform elongation, low yield ratio and good balance between high strength and high plasticity because of the microstructure with dual phase. In this work, the microstructure and properties of the submarine pipeline steel are studied. The results show that the matrix structure is consisted of ferrite, bainite and martensite -austenite islands. The structure has a tight relationship with the thermal-mechanical controlled process. Fine dual phase shows good plasticity and low yield ratio, which can support the good balance between high strength and high plasticity.

Vector processing efficiency of plasma MHD codes by use of the FACOM 230-75 APU

NASA Astrophysics Data System (ADS)

Matsuura, T.; Tanaka, Y.; Naraoka, K.; Takizuka, T.; Tsunematsu, T.; Tokuda, S.; Azumi, M.; Kurita, G.; Takeda, T.

1982-06-01

In the framework of pipelined vector architecture, the efficiency of vector processing is assessed with respect to plasma MHD codes in nuclear fusion research. By using a vector processor, the FACOM 230-75 APU, the limit of the enhancement factor due to parallelism of current vector machines is examined for three numerical codes based on a fluid model. Reasonable speed-up factors of approximately 6,6 and 4 times faster than the highly optimized scalar version are obtained for ERATO (linear stability code), AEOLUS-R1 (nonlinear stability code) and APOLLO (1-1/2D transport code), respectively. Problems of the pipelined vector processors are discussed from the viewpoint of restructuring, optimization and choice of algorithms. In conclusion, the important concept of "concurrency within pipelined parallelism" is emphasized.

Effect of Cooling Mode on Microstructure and Mechanical Properties of Pipeline Steel for Strain Based Design and Research on its Deformation Mechanism

NASA Astrophysics Data System (ADS)

Hesong, Zhang; Yonglin, Kang

With the rapid development of oil and gas industry long distance pipelines inevitably pass through regions with complex geological activities. In order to avoid large deformation the pipelines must be designed based on strain criteria. In this paper the alloy system of X80 high deformability pipeline steel was designed which was 0.25%Mo-0.05%C-1.75%Mn. The effect of controlled cooling process on microstructure and mechanical properties of X80 high deformability pipeline steel were systematically investigated. Through the two-stage controlled cooling process the microstructure of the X80 high deformability pipeline steel were ferrite, bainite and M/A island. There were two kinds of ferrite which were polygonal ferrite (PF) and quasi-polygonal ferrite (QF). The bainite was granular bainite ferrite (GF). Along with the decrease of the start cooling temperature, the volume fraction of ferrite and M/A both increased, the yield ratio (Y/T) decreased, the uniform elongation (uEl) increased firstly with the content of ferrite increased but then decreased with the content and size of M/A increased. When the finish cooling temperature decreasing, the size of M/A became finer. As the start cooling temperature was 690 °C and the finish cooling temperature was 450 °C the volume fraction of ferrite was 23%, the size of ferrite grain was 5μm, the size of M/A island was below 1μm and the structure uniformity was the best. The deformation mechanism of X80 high deformability pipeline steel was analyzed. The best way to improve the work hardening rate was reducing the size of M/A islands on the premise of a certain volume fraction. The decreasing path of instantaneous strain hardening index (n*-value) showed three stages in the deformation process. The n*-value kept stable in the second stage, the reason was that the retained austenite transformed into martensite and the phase transition improved the strain hardening ability of the microstructure. This phenomenon was called transformation induced plasticity effect (TRIP).

Full image-processing pipeline in field-programmable gate array for a small endoscopic camera

NASA Astrophysics Data System (ADS)

Mostafa, Sheikh Shanawaz; Sousa, L. Natércia; Ferreira, Nuno Fábio; Sousa, Ricardo M.; Santos, Joao; Wäny, Martin; Morgado-Dias, F.

2017-01-01

Endoscopy is an imaging procedure used for diagnosis as well as for some surgical purposes. The camera used for the endoscopy should be small and able to produce a good quality image or video, to reduce discomfort of the patients, and to increase the efficiency of the medical team. To achieve these fundamental goals, a small endoscopy camera with a footprint of 1 mm×1 mm×1.65 mm is used. Due to the physical properties of the sensors and human vision system limitations, different image-processing algorithms, such as noise reduction, demosaicking, and gamma correction, among others, are needed to faithfully reproduce the image or video. A full image-processing pipeline is implemented using a field-programmable gate array (FPGA) to accomplish a high frame rate of 60 fps with minimum processing delay. Along with this, a viewer has also been developed to display and control the image-processing pipeline. The control and data transfer are done by a USB 3.0 end point in the computer. The full developed system achieves real-time processing of the image and fits in a Xilinx Spartan-6LX150 FPGA.

78 FR 35658 - Spectra Energy Corp., Application for a New or Amended Presidential Permit

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-13

... transactions. Spectra Energy owns and operates a large diversified portfolio of natural gas-related energy assets in the areas of gathering and processing, transmission, and distribution. Its natural gas pipeline..., to Caster, Wyoming and includes five pump stations. The Express Pipeline has been in operation since...

49 CFR 192.227 - Qualification of welders.

Code of Federal Regulations, 2010 CFR

2010-10-01

... BY PIPELINE: MINIMUM FEDERAL SAFETY STANDARDS Welding of Steel in Pipelines § 192.227 Qualification... earlier edition. (b) A welder may qualify to perform welding on pipe to be operated at a pressure that... process to be used, under the test set forth in section I of Appendix C of this part. Each welder who is...

Disrupting the Pipeline: The Role of School Leadership in Mitigating Exclusion and Criminalization of Students

ERIC Educational Resources Information Center

Wilson, Michael G.

2013-01-01

Recently, the effects of school exclusion and criminalization of youth misbehavior has garnered much attention from the research community. The process associated with school exclusion and criminalization has been described popularly as a school to prison pipeline (STPP). Studies of school exclusion and criminalization repeatedly report evidence…

Improved Photometry for the DASCH Pipeline

NASA Astrophysics Data System (ADS)

Tang, Sumin; Grindlay, Jonathan; Los, Edward; Servillat, Mathieu

2013-07-01

The Digital Access to a Sky Century@Harvard (DASCH) project is digitizing the ˜500,000 glass plate images obtained (full sky) by the Harvard College Observatory from 1885 to 1992. Astrometry and photometry for each resolved object are derived with photometric rms values of ˜0.15 mag for the initial photometry analysis pipeline. Here we describe new developments for DASCH photometry, applied to the Kepler field, that have yielded further improvements, including better identification of image blends and plate defects by measuring image profiles and astrometric deviations. A local calibration procedure using nearby stars in a similar magnitude range as the program star (similar to what has been done for visual photometry from the plates) yields additional improvement for a net photometric rms of ˜0.1 mag. We also describe statistical measures of light curves that are now used in the DASCH pipeline processing to identify new variables autonomously. The DASCH photometry methods described here are used in the pipeline processing for the data releases of DASCH data,5 as well as for a forthcoming paper on the long-term variables discovered by DASCH in the Kepler field.

Accelerating root system phenotyping of seedlings through a computer-assisted processing pipeline.

PubMed

Dupuy, Lionel X; Wright, Gladys; Thompson, Jacqueline A; Taylor, Anna; Dekeyser, Sebastien; White, Christopher P; Thomas, William T B; Nightingale, Mark; Hammond, John P; Graham, Neil S; Thomas, Catherine L; Broadley, Martin R; White, Philip J

2017-01-01

There are numerous systems and techniques to measure the growth of plant roots. However, phenotyping large numbers of plant roots for breeding and genetic analyses remains challenging. One major difficulty is to achieve high throughput and resolution at a reasonable cost per plant sample. Here we describe a cost-effective root phenotyping pipeline, on which we perform time and accuracy benchmarking to identify bottlenecks in such pipelines and strategies for their acceleration. Our root phenotyping pipeline was assembled with custom software and low cost material and equipment. Results show that sample preparation and handling of samples during screening are the most time consuming task in root phenotyping. Algorithms can be used to speed up the extraction of root traits from image data, but when applied to large numbers of images, there is a trade-off between time of processing the data and errors contained in the database. Scaling-up root phenotyping to large numbers of genotypes will require not only automation of sample preparation and sample handling, but also efficient algorithms for error detection for more reliable replacement of manual interventions.

Grid Computing Application for Brain Magnetic Resonance Image Processing

NASA Astrophysics Data System (ADS)

Valdivia, F.; Crépeault, B.; Duchesne, S.

2012-02-01

This work emphasizes the use of grid computing and web technology for automatic post-processing of brain magnetic resonance images (MRI) in the context of neuropsychiatric (Alzheimer's disease) research. Post-acquisition image processing is achieved through the interconnection of several individual processes into pipelines. Each process has input and output data ports, options and execution parameters, and performs single tasks such as: a) extracting individual image attributes (e.g. dimensions, orientation, center of mass), b) performing image transformations (e.g. scaling, rotation, skewing, intensity standardization, linear and non-linear registration), c) performing image statistical analyses, and d) producing the necessary quality control images and/or files for user review. The pipelines are built to perform specific sequences of tasks on the alphanumeric data and MRIs contained in our database. The web application is coded in PHP and allows the creation of scripts to create, store and execute pipelines and their instances either on our local cluster or on high-performance computing platforms. To run an instance on an external cluster, the web application opens a communication tunnel through which it copies the necessary files, submits the execution commands and collects the results. We present result on system tests for the processing of a set of 821 brain MRIs from the Alzheimer's Disease Neuroimaging Initiative study via a nonlinear registration pipeline composed of 10 processes. Our results show successful execution on both local and external clusters, and a 4-fold increase in performance if using the external cluster. However, the latter's performance does not scale linearly as queue waiting times and execution overhead increase with the number of tasks to be executed.

The Chandra Source Catalog: Processing and Infrastructure

NASA Astrophysics Data System (ADS)

Evans, Janet; Evans, Ian N.; Glotfelty, Kenny J.; Hain, Roger; Hall, Diane M.; Miller, Joseph B.; Plummer, David A.; Zografou, Panagoula; Primini, Francis A.; Anderson, Craig S.; Bonaventura, Nina R.; Chen, Judy C.; Davis, John E.; Doe, Stephen M.; Fabbiano, Giuseppina; Galle, Elizabeth C.; Gibbs, Danny G., II; Grier, John D.; Harbo, Peter N.; He, Xiang Qun (Helen); Houck, John C.; Karovska, Margarita; Kashyap, Vinay L.; Lauer, Jennifer; McCollough, Michael L.; McDowell, Jonathan C.; Mitschang, Arik W.; Morgan, Douglas L.; Mossman, Amy E.; Nichols, Joy S.; Nowak, Michael A.; Refsdal, Brian L.; Rots, Arnold H.; Siemiginowska, Aneta L.; Sundheim, Beth A.; Tibbetts, Michael S.; van Stone, David W.; Winkelman, Sherry L.

2009-09-01

Chandra Source Catalog processing recalibrates each observation using the latest available calibration data, and employs a wavelet-based source detection algorithm to identify all the X-ray sources in the field of view. Source properties are then extracted from each detected source that is a candidate for inclusion in the catalog. Catalog processing is completed by matching sources across multiple observations, merging common detections, and applying quality assurance checks. The Chandra Source Catalog processing system shares a common processing infrastructure and utilizes much of the functionality that is built into the Standard Data Processing (SDP) pipeline system that provides calibrated Chandra data to end-users. Other key components of the catalog processing system have been assembled from the portable CIAO data analysis package. Minimal new software tool development has been required to support the science algorithms needed for catalog production. Since processing pipelines must be instantiated for each detected source, the number of pipelines that are run during catalog construction is a factor of order 100 times larger than for SDP. The increased computational load, and inherent parallel nature of the processing, is handled by distributing the workload across a multi-node Beowulf cluster. Modifications to the SDP automated processing application to support catalog processing, and extensions to Chandra Data Archive software to ingest and retrieve catalog products, complete the upgrades to the infrastructure to support catalog processing.

Comparative coal transportation costs: an economic and engineering analysis of truck, belt, rail, barge and coal slurry and pneumatic pipelines. Volume 3. Coal slurry pipelines. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rieber, M.; Soo, S.L.

1977-08-01

A coal slurry pipeline system requires that the coal go through a number of processing stages before it is used by the power plant. Once mined, the coal is delivered to a preparation plant where it is pulverized to sizes between 18 and 325 mesh and then suspended in about an equal weight of water. This 50-50 slurry mixture has a consistency approximating toothpaste. It is pushed through the pipeline via electric pumping stations 70 to 100 miles apart. Flow velocity through the line must be maintained within a narrow range. For example, if a 3.5 mph design is usedmore » at 5 mph, the system must be able to withstand double the horsepower, peak pressure, and wear. Minimum flowrate must be maintained to avoid particle settling and plugging. However, in general, once a pipeline system has been designed, because of economic considerations on the one hand and design limits on the other, flowrate is rather inflexible. Pipelines that have a slowly moving throughput and a water carrier may be subject to freezing in northern areas during periods of severe cold. One of the problems associated with slurry pipeline analyses is the lack of operating experience.« less

ToTem: a tool for variant calling pipeline optimization.

PubMed

Tom, Nikola; Tom, Ondrej; Malcikova, Jitka; Pavlova, Sarka; Kubesova, Blanka; Rausch, Tobias; Kolarik, Miroslav; Benes, Vladimir; Bystry, Vojtech; Pospisilova, Sarka

2018-06-26

High-throughput bioinformatics analyses of next generation sequencing (NGS) data often require challenging pipeline optimization. The key problem is choosing appropriate tools and selecting the best parameters for optimal precision and recall. Here we introduce ToTem, a tool for automated pipeline optimization. ToTem is a stand-alone web application with a comprehensive graphical user interface (GUI). ToTem is written in Java and PHP with an underlying connection to a MySQL database. Its primary role is to automatically generate, execute and benchmark different variant calling pipeline settings. Our tool allows an analysis to be started from any level of the process and with the possibility of plugging almost any tool or code. To prevent an over-fitting of pipeline parameters, ToTem ensures the reproducibility of these by using cross validation techniques that penalize the final precision, recall and F-measure. The results are interpreted as interactive graphs and tables allowing an optimal pipeline to be selected, based on the user's priorities. Using ToTem, we were able to optimize somatic variant calling from ultra-deep targeted gene sequencing (TGS) data and germline variant detection in whole genome sequencing (WGS) data. ToTem is a tool for automated pipeline optimization which is freely available as a web application at  https://totem.software .

Ultrasonic wave based pressure measurement in small diameter pipeline.

PubMed

Wang, Dan; Song, Zhengxiang; Wu, Yuan; Jiang, Yuan

2015-12-01

An effective non-intrusive method of ultrasound-based technique that allows monitoring liquid pressure in small diameter pipeline (less than 10mm) is presented in this paper. Ultrasonic wave could penetrate medium, through the acquisition of representative information from the echoes, properties of medium can be reflected. This pressure measurement is difficult due to that echoes' information is not easy to obtain in small diameter pipeline. The proposed method is a study on pipeline with Kneser liquid and is based on the principle that the transmission speed of ultrasonic wave in pipeline liquid correlates with liquid pressure and transmission speed of ultrasonic wave in pipeline liquid is reflected through ultrasonic propagation time providing that acoustic distance is fixed. Therefore, variation of ultrasonic propagation time can reflect variation of pressure in pipeline. Ultrasonic propagation time is obtained by electric processing approach and is accurately measured to nanosecond through high resolution time measurement module. We used ultrasonic propagation time difference to reflect actual pressure in this paper to reduce the environmental influences. The corresponding pressure values are finally obtained by acquiring the relationship between variation of ultrasonic propagation time difference and pressure with the use of neural network analysis method, the results show that this method is accurate and can be used in practice. Copyright © 2015 Elsevier B.V. All rights reserved.

Nanosurveyor: a framework for real-time data processing

DOE PAGES

Daurer, Benedikt J.; Krishnan, Hari; Perciano, Talita; ...

2017-01-31

Background: The ever improving brightness of accelerator based sources is enabling novel observations and discoveries with faster frame rates, larger fields of view, higher resolution, and higher dimensionality. Results: Here we present an integrated software/algorithmic framework designed to capitalize on high-throughput experiments through efficient kernels, load-balanced workflows, which are scalable in design. We describe the streamlined processing pipeline of ptychography data analysis. Conclusions: The pipeline provides throughput, compression, and resolution as well as rapid feedback to the microscope operators.

Workflows for microarray data processing in the Kepler environment.

PubMed

Stropp, Thomas; McPhillips, Timothy; Ludäscher, Bertram; Bieda, Mark

2012-05-17

Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis demands, including integration with new data sources. Bioinformatics pipelines are usually custom built for different applications, making them typically difficult to modify, extend and repurpose. Scientific workflow systems are intended to address these issues by providing general-purpose frameworks in which to develop and execute such pipelines. The Kepler workflow environment is a well-established system under continual development that is employed in several areas of scientific research. Kepler provides a flexible graphical interface, featuring clear display of parameter values, for design and modification of workflows. It has capabilities for developing novel computational components in the R, Python, and Java programming languages, all of which are widely used for bioinformatics algorithm development, along with capabilities for invoking external applications and using web services. We developed a series of fully functional bioinformatics pipelines addressing common tasks in microarray processing in the Kepler workflow environment. These pipelines consist of a set of tools for GFF file processing of NimbleGen chromatin immunoprecipitation on microarray (ChIP-chip) datasets and more comprehensive workflows for Affymetrix gene expression microarray bioinformatics and basic primer design for PCR experiments, which are often used to validate microarray results. Although functional in themselves, these workflows can be easily customized, extended, or repurposed to match the needs of specific projects and are designed to be a toolkit and starting point for specific applications. These workflows illustrate a workflow programming paradigm focusing on local resources (programs and data) and therefore are close to traditional shell scripting or R/BioConductor scripting approaches to pipeline design. Finally, we suggest that microarray data processing task workflows may provide a basis for future example-based comparison of different workflow systems. We provide a set of tools and complete workflows for microarray data analysis in the Kepler environment, which has the advantages of offering graphical, clear display of conceptual steps and parameters and the ability to easily integrate other resources such as remote data and web services.

Kepler Science Operations Center Pipeline Framework

NASA Technical Reports Server (NTRS)

Klaus, Todd C.; McCauliff, Sean; Cote, Miles T.; Girouard, Forrest R.; Wohler, Bill; Allen, Christopher; Middour, Christopher; Caldwell, Douglas A.; Jenkins, Jon M.

2010-01-01

The Kepler mission is designed to continuously monitor up to 170,000 stars at a 30 minute cadence for 3.5 years searching for Earth-size planets. The data are processed at the Science Operations Center (SOC) at NASA Ames Research Center. Because of the large volume of data and the memory and CPU-intensive nature of the analysis, significant computing hardware is required. We have developed generic pipeline framework software that is used to distribute and synchronize the processing across a cluster of CPUs and to manage the resulting products. The framework is written in Java and is therefore platform-independent, and scales from a single, standalone workstation (for development and research on small data sets) to a full cluster of homogeneous or heterogeneous hardware with minimal configuration changes. A plug-in architecture provides customized control of the unit of work without the need to modify the framework itself. Distributed transaction services provide for atomic storage of pipeline products for a unit of work across a relational database and the custom Kepler DB. Generic parameter management and data accountability services are provided to record the parameter values, software versions, and other meta-data used for each pipeline execution. A graphical console allows for the configuration, execution, and monitoring of pipelines. An alert and metrics subsystem is used to monitor the health and performance of the pipeline. The framework was developed for the Kepler project based on Kepler requirements, but the framework itself is generic and could be used for a variety of applications where these features are needed.

Comparison of carbon footprints of steel versus concrete pipelines for water transmission.

PubMed

Chilana, Lalit; Bhatt, Arpita H; Najafi, Mohammad; Sattler, Melanie

2016-05-01

The global demand for water transmission and service pipelines is expected to more than double between 2012 and 2022. This study compared the carbon footprint of the two most common materials used for large-diameter water transmission pipelines, steel pipe (SP) and prestressed concrete cylinder pipe (PCCP). A planned water transmission pipeline in Texas was used as a case study. Four life-cycle phases for each material were considered: material production and pipeline fabrication, pipe transportation to the job site, pipe installation in the trench, and operation of the pipeline. In each phase, the energy consumed and the CO2-equivalent emissions were quantified. It was found that pipe manufacturing consumed a large amount of energy, and thus contributed more than 90% of life cycle carbon emissions for both kinds of pipe. Steel pipe had 64% larger CO2-eq emissions from manufacturing compared to PCCP. For the transportation phase, PCCP consumed more fuel due to its heavy weight, and therefore had larger CO2-eq emissions. Fuel consumption by construction equipment for installation of pipe was found to be similar for steel pipe and PCCP. Overall, steel had a 32% larger footprint due to greater energy used during manufacturing. This study compared the carbon footprint of two large-diameter water transmission pipeline materials, steel and prestressed concrete cylinder, considering four life-cycle phases for each. The study provides information that project managers can incorporate into their decision-making process concerning pipeline materials. It also provides information concerning the most important phases of the pipeline life cycle to target for emission reductions.

Application of graphics processing units to search pipelines for gravitational waves from coalescing binaries of compact objects

NASA Astrophysics Data System (ADS)

Chung, Shin Kee; Wen, Linqing; Blair, David; Cannon, Kipp; Datta, Amitava

2010-07-01

We report a novel application of a graphics processing unit (GPU) for the purpose of accelerating the search pipelines for gravitational waves from coalescing binaries of compact objects. A speed-up of 16-fold in total has been achieved with an NVIDIA GeForce 8800 Ultra GPU card compared with one core of a 2.5 GHz Intel Q9300 central processing unit (CPU). We show that substantial improvements are possible and discuss the reduction in CPU count required for the detection of inspiral sources afforded by the use of GPUs.

Canary: an atomic pipeline for clinical amplicon assays.

PubMed

Doig, Kenneth D; Ellul, Jason; Fellowes, Andrew; Thompson, Ella R; Ryland, Georgina; Blombery, Piers; Papenfuss, Anthony T; Fox, Stephen B

2017-12-15

High throughput sequencing requires bioinformatics pipelines to process large volumes of data into meaningful variants that can be translated into a clinical report. These pipelines often suffer from a number of shortcomings: they lack robustness and have many components written in multiple languages, each with a variety of resource requirements. Pipeline components must be linked together with a workflow system to achieve the processing of FASTQ files through to a VCF file of variants. Crafting these pipelines requires considerable bioinformatics and IT skills beyond the reach of many clinical laboratories. Here we present Canary, a single program that can be run on a laptop, which takes FASTQ files from amplicon assays through to an annotated VCF file ready for clinical analysis. Canary can be installed and run with a single command using Docker containerization or run as a single JAR file on a wide range of platforms. Although it is a single utility, Canary performs all the functions present in more complex and unwieldy pipelines. All variants identified by Canary are 3' shifted and represented in their most parsimonious form to provide a consistent nomenclature, irrespective of sequencing variation. Further, proximate in-phase variants are represented as a single HGVS 'delins' variant. This allows for correct nomenclature and consequences to be ascribed to complex multi-nucleotide polymorphisms (MNPs), which are otherwise difficult to represent and interpret. Variants can also be annotated with hundreds of attributes sourced from MyVariant.info to give up to date details on pathogenicity, population statistics and in-silico predictors. Canary has been used at the Peter MacCallum Cancer Centre in Melbourne for the last 2 years for the processing of clinical sequencing data. By encapsulating clinical features in a single, easily installed executable, Canary makes sequencing more accessible to all pathology laboratories. Canary is available for download as source or a Docker image at https://github.com/PapenfussLab/Canary under a GPL-3.0 License.

DOE Office of Scientific and Technical Information (OSTI.GOV)

SADE is a software package for rapidly assembling analytic pipelines to manipulate data. The packages consists of the engine that manages the data and coordinates the movement of data between the tasks performing a function? a set of core libraries consisting of plugins that perform common tasks? and a framework to extend the system supporting the development of new plugins. Currently through configuration files, a pipeline can be defined that maps the routing of data through a series of plugins. Pipelines can be run in a batch mode or can process streaming data? they can be executed from the commandmore » line or run through a Windows background service. There currently exists over a hundred plugins, over fifty pipeline configurations? and the software is now being used by about a half-dozen projects.« less

Extending the Fermi-LAT data processing pipeline to the grid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zimmer, S.; Arrabito, L.; Glanzman, T.

2015-05-12

The Data Handling Pipeline ("Pipeline") has been developed for the Fermi Gamma-Ray Space Telescope (Fermi) Large Area Telescope (LAT) which launched in June 2008. Since then it has been in use to completely automate the production of data quality monitoring quantities, reconstruction and routine analysis of all data received from the satellite and to deliver science products to the collaboration and the Fermi Science Support Center. Aside from the reconstruction of raw data from the satellite (Level 1), data reprocessing and various event-level analyses are also reasonably heavy loads on the pipeline and computing resources. These other loads, unlike Levelmore » 1, can run continuously for weeks or months at a time. Additionally, it receives heavy use in performing production Monte Carlo tasks.« less

Applications of the pipeline environment for visual informatics and genomics computations

PubMed Central

2011-01-01

Background Contemporary informatics and genomics research require efficient, flexible and robust management of large heterogeneous data, advanced computational tools, powerful visualization, reliable hardware infrastructure, interoperability of computational resources, and detailed data and analysis-protocol provenance. The Pipeline is a client-server distributed computational environment that facilitates the visual graphical construction, execution, monitoring, validation and dissemination of advanced data analysis protocols. Results This paper reports on the applications of the LONI Pipeline environment to address two informatics challenges - graphical management of diverse genomics tools, and the interoperability of informatics software. Specifically, this manuscript presents the concrete details of deploying general informatics suites and individual software tools to new hardware infrastructures, the design, validation and execution of new visual analysis protocols via the Pipeline graphical interface, and integration of diverse informatics tools via the Pipeline eXtensible Markup Language syntax. We demonstrate each of these processes using several established informatics packages (e.g., miBLAST, EMBOSS, mrFAST, GWASS, MAQ, SAMtools, Bowtie) for basic local sequence alignment and search, molecular biology data analysis, and genome-wide association studies. These examples demonstrate the power of the Pipeline graphical workflow environment to enable integration of bioinformatics resources which provide a well-defined syntax for dynamic specification of the input/output parameters and the run-time execution controls. Conclusions The LONI Pipeline environment http://pipeline.loni.ucla.edu provides a flexible graphical infrastructure for efficient biomedical computing and distributed informatics research. The interactive Pipeline resource manager enables the utilization and interoperability of diverse types of informatics resources. The Pipeline client-server model provides computational power to a broad spectrum of informatics investigators - experienced developers and novice users, user with or without access to advanced computational-resources (e.g., Grid, data), as well as basic and translational scientists. The open development, validation and dissemination of computational networks (pipeline workflows) facilitates the sharing of knowledge, tools, protocols and best practices, and enables the unbiased validation and replication of scientific findings by the entire community. PMID:21791102

Remaining Sites Verification Package for the 100-F-44:2, Discovery Pipeline Near 108-F Building, Waste Site Reclassification Form 2007-006

DOE Office of Scientific and Technical Information (OSTI.GOV)

J. M. Capron

2008-05-30

The 100-F-44:2 waste site is a steel pipeline that was discovered in a junction box during confirmatory sampling of the 100-F-26:4 pipeline from December 2004 through January 2005. The 100-F-44:2 pipeline feeds into the 100-F-26:4 subsite vitrified clay pipe (VCP) process sewer pipeline from the 108-F Biology Laboratory at the junction box. In accordance with this evaluation, the confirmatory sampling results support a reclassification of this site to No Action. The current site conditions achieve the remedial action objectives and the corresponding remedial action goals established in the Remaining Sites ROD. The results of confirmatory sampling show that residual contaminantmore » concentrations do not preclude any future uses and allow for unrestricted use of shallow zone soils. The results also demonstrate that residual contaminant concentrations are protective of groundwater and the Columbia River.« less

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

NASA Technical Reports Server (NTRS)

Donato, Davide; Angelini, Lorella; Padgett, C.A.; Reichard, T.; Gehrels, Neil; Marshall, Francis E.; Sakamoto, Takanori

2012-01-01

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.

Application of Morphological Segmentation to Leaking Defect Detection in Sewer Pipelines

PubMed Central

Su, Tung-Ching; Yang, Ming-Der

2014-01-01

As one of major underground pipelines, sewerage is an important infrastructure in any modern city. The most common problem occurring in sewerage is leaking, whose position and failure level is typically idengified through closed circuit television (CCTV) inspection in order to facilitate rehabilitation process. This paper proposes a novel method of computer vision, morphological segmentation based on edge detection (MSED), to assist inspectors in detecting pipeline defects in CCTV inspection images. In addition to MSED, other mathematical morphology-based image segmentation methods, including opening top-hat operation (OTHO) and closing bottom-hat operation (CBHO), were also applied to the defect detection in vitrified clay sewer pipelines. The CCTV inspection images of the sewer system in the 9th district, Taichung City, Taiwan were selected as the experimental materials. The segmentation results demonstrate that MSED and OTHO are useful for the detection of cracks and open joints, respectively, which are the typical leakage defects found in sewer pipelines. PMID:24841247

Diagnostic layer integration in FPGA-based pipeline measurement systems for HEP experiments

NASA Astrophysics Data System (ADS)

Pozniak, Krzysztof T.

2007-08-01

Integrated triggering and data acquisition systems for high energy physics experiments may be considered as fast, multichannel, synchronous, distributed, pipeline measurement systems. A considerable extension of functional, technological and monitoring demands, which has recently been imposed on them, forced a common usage of large field-programmable gate array (FPGA), digital signal processing-enhanced matrices and fast optical transmission for their realization. This paper discusses modelling, design, realization and testing of pipeline measurement systems. A distribution of synchronous data stream flows is considered in the network. A general functional structure of a single network node is presented. A suggested, novel block structure of the node model facilitates full implementation in the FPGA chip, circuit standardization and parametrization, as well as integration of functional and diagnostic layers. A general method for pipeline system design was derived. This method is based on a unified model of the synchronous data network node. A few examples of practically realized, FPGA-based, pipeline measurement systems were presented. The described systems were applied in ZEUS and CMS.

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

NASA Astrophysics Data System (ADS)

Donato, D.; Angelini, L.; Padgett, C. A.; Reichard, T.; Gehrels, N.; Marshall, F. E.; Sakamoto, T.

2012-11-01

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.

Reclamation of the Wahsatch gathering system pipeline in southwestern Wyoming and northeastern Utah

DOE Office of Scientific and Technical Information (OSTI.GOV)

Strickland, D.; Dern, G.; Johnson, G.

1996-12-31

The Union Pacific Resources Company (UPRC) constructed a 40.4 mile pipeline in 1993 in Summit and Rich Countries, Utah and Uinta County, Wyoming. The pipeline collects and delivers natural gas from six existing wells to the Whitney Canyon Processing Plant north of Evanston, Wyoming. We describe reclamation of the pipeline, the cooperation received from landowners along the right-of-way, and mitigation measures implemented by UPRC to minimize impacts to wildlife. The reclamation procedure combines a 2 step topsoil separation, mulching with natural vegetation, native seed mixes, and measures designed to reduce the visual impacts of the pipeline. Topsoil is separated intomore » the top 4 inches of soil material, when present. The resulting top dressing is rich in native seed and rhizomes allowing a reduced seeding rate. The borders of the right-of-way are mowed in a curvilinear pattern to reduce the straight line effects of landowner cooperation on revegetation. Specifically, following 2 years of monitoring, significant differences in plant cover (0.01« less

Pipeline enhances Norman Wells potential

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

Approval of an oil pipeline from halfway down Canada's MacKenzie River Valley at Norman Wells to N. Alberta has raised the potential for development of large reserves along with controversy over native claims. The project involves 2 closely related proposals. One, by Esso Resources, the exploration and production unit of Imperial Oil, will increase oil production from the Norman Wells field from 3000 bpd currently to 25,000 bpd. The other proposal, by Interprovincial Pipeline (N.W) Ltd., calls for construction of an underground pipeline to transport the additional production from Norman Wells to Alberta. The 560-mile, 12-in. pipeline will extend frommore » Norman Wells, which is 90 miles south of the Arctic Circle on the north shore of the Mackenzie River, south to the end of an existing line at Zama in N. Alberta. There will be 3 pumping stations en route. This work also discusses recovery, potential, drilling limitations, the processing plant, positive impact, and further development of the Norman Wells project.« less

Enhanced Automated Guidance System for Horizontal Auger Boring Based on Image Processing

PubMed Central

Wu, Lingling; Wen, Guojun; Wang, Yudan; Huang, Lei; Zhou, Jiang

2018-01-01

Horizontal auger boring (HAB) is a widely used trenchless technology for the high-accuracy installation of gravity or pressure pipelines on line and grade. Differing from other pipeline installations, HAB requires a more precise and automated guidance system for use in a practical project. This paper proposes an economic and enhanced automated optical guidance system, based on optimization research of light-emitting diode (LED) light target and five automated image processing bore-path deviation algorithms. An LED target was optimized for many qualities, including light color, filter plate color, luminous intensity, and LED layout. The image preprocessing algorithm, feature extraction algorithm, angle measurement algorithm, deflection detection algorithm, and auto-focus algorithm, compiled in MATLAB, are used to automate image processing for deflection computing and judging. After multiple indoor experiments, this guidance system is applied in a project of hot water pipeline installation, with accuracy controlled within 2 mm in 48-m distance, providing accurate line and grade controls and verifying the feasibility and reliability of the guidance system. PMID:29462855

Query-Driven Visualization and Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruebel, Oliver; Bethel, E. Wes; Prabhat, Mr.

2012-11-01

This report focuses on an approach to high performance visualization and analysis, termed query-driven visualization and analysis (QDV). QDV aims to reduce the amount of data that needs to be processed by the visualization, analysis, and rendering pipelines. The goal of the data reduction process is to separate out data that is "scientifically interesting'' and to focus visualization, analysis, and rendering on that interesting subset. The premise is that for any given visualization or analysis task, the data subset of interest is much smaller than the larger, complete data set. This strategy---extracting smaller data subsets of interest and focusing ofmore » the visualization processing on these subsets---is complementary to the approach of increasing the capacity of the visualization, analysis, and rendering pipelines through parallelism. This report discusses the fundamental concepts in QDV, their relationship to different stages in the visualization and analysis pipelines, and presents QDV's application to problems in diverse areas, ranging from forensic cybersecurity to high energy physics.« less

Enhanced Automated Guidance System for Horizontal Auger Boring Based on Image Processing.

PubMed

Wu, Lingling; Wen, Guojun; Wang, Yudan; Huang, Lei; Zhou, Jiang

2018-02-15

Horizontal auger boring (HAB) is a widely used trenchless technology for the high-accuracy installation of gravity or pressure pipelines on line and grade. Differing from other pipeline installations, HAB requires a more precise and automated guidance system for use in a practical project. This paper proposes an economic and enhanced automated optical guidance system, based on optimization research of light-emitting diode (LED) light target and five automated image processing bore-path deviation algorithms. An LED light target was optimized for many qualities, including light color, filter plate color, luminous intensity, and LED layout. The image preprocessing algorithm, direction location algorithm, angle measurement algorithm, deflection detection algorithm, and auto-focus algorithm, compiled in MATLAB, are used to automate image processing for deflection computing and judging. After multiple indoor experiments, this guidance system is applied in a project of hot water pipeline installation, with accuracy controlled within 2 mm in 48-m distance, providing accurate line and grade controls and verifying the feasibility and reliability of the guidance system.

Real-time multiple objects tracking on Raspberry-Pi-based smart embedded camera

NASA Astrophysics Data System (ADS)

Dziri, Aziz; Duranton, Marc; Chapuis, Roland

2016-07-01

Multiple-object tracking constitutes a major step in several computer vision applications, such as surveillance, advanced driver assistance systems, and automatic traffic monitoring. Because of the number of cameras used to cover a large area, these applications are constrained by the cost of each node, the power consumption, the robustness of the tracking, the processing time, and the ease of deployment of the system. To meet these challenges, the use of low-power and low-cost embedded vision platforms to achieve reliable tracking becomes essential in networks of cameras. We propose a tracking pipeline that is designed for fixed smart cameras and which can handle occlusions between objects. We show that the proposed pipeline reaches real-time processing on a low-cost embedded smart camera composed of a Raspberry-Pi board and a RaspiCam camera. The tracking quality and the processing speed obtained with the proposed pipeline are evaluated on publicly available datasets and compared to the state-of-the-art methods.

Pipeline active filter utilizing a booth type multiplier

NASA Technical Reports Server (NTRS)

Nathan, Robert (Inventor)

1987-01-01

Multiplier units of the modified Booth decoder and carry-save adder/full adder combination are used to implement a pipeline active filter wherein pixel data is processed sequentially, and each pixel need only be accessed once and multiplied by a predetermined number of weights simultaneously, one multiplier unit for each weight. Each multiplier unit uses only one row of carry-save adders, and the results are shifted to less significant multiplier positions and one row of full adders to add the carry to the sum in order to provide the correct binary number for the product Wp. The full adder is also used to add this product Wp to the sum of products .SIGMA.Wp from preceding multiply units. If m.times.m multiplier units are pipelined, the system would be capable of processing a kernel array of m.times.m weighting factors.

A novel pipeline based FPGA implementation of a genetic algorithm

NASA Astrophysics Data System (ADS)

Thirer, Nonel

2014-05-01

To solve problems when an analytical solution is not available, more and more bio-inspired computation techniques have been applied in the last years. Thus, an efficient algorithm is the Genetic Algorithm (GA), which imitates the biological evolution process, finding the solution by the mechanism of "natural selection", where the strong has higher chances to survive. A genetic algorithm is an iterative procedure which operates on a population of individuals called "chromosomes" or "possible solutions" (usually represented by a binary code). GA performs several processes with the population individuals to produce a new population, like in the biological evolution. To provide a high speed solution, pipelined based FPGA hardware implementations are used, with a nstages pipeline for a n-phases genetic algorithm. The FPGA pipeline implementations are constraints by the different execution time of each stage and by the FPGA chip resources. To minimize these difficulties, we propose a bio-inspired technique to modify the crossover step by using non identical twins. Thus two of the chosen chromosomes (parents) will build up two new chromosomes (children) not only one as in classical GA. We analyze the contribution of this method to reduce the execution time in the asynchronous and synchronous pipelines and also the possibility to a cheaper FPGA implementation, by using smaller populations. The full hardware architecture for a FPGA implementation to our target ALTERA development card is presented and analyzed.

A new segmentation strategy for processing magnetic anomaly detection data of shallow depth ferromagnetic pipeline

NASA Astrophysics Data System (ADS)

Feng, Shuo; Liu, Dejun; Cheng, Xing; Fang, Huafeng; Li, Caifang

2017-04-01

Magnetic anomalies produced by underground ferromagnetic pipelines because of the polarization of earth's magnetic field are used to obtain the information on the location, buried depth and other parameters of pipelines. In order to achieve a fast inversion and interpretation of measured data, it is necessary to develop a fast and stable forward method. Magnetic dipole reconstruction (MDR), as a kind of integration numerical method, is well suited for simulating a thin pipeline anomaly. In MDR the pipeline model must be cut into small magnetic dipoles through different segmentation methods. The segmentation method has an impact on the stability and speed of forward calculation. Rapid and accurate simulation of deep-buried pipelines has been achieved by exciting segmentation method. However, in practical measurement, the depth of underground pipe is uncertain. When it comes to the shallow-buried pipeline, the present segmentation may generate significant errors. This paper aims at solving this problem in three stages. First, the cause of inaccuracy is analyzed by simulation experiment. Secondly, new variable interval section segmentation is proposed based on the existing segmentation. It can help MDR method to obtain simulation results in a fast way under the premise of ensuring the accuracy of different depth models. Finally, the measured data is inversed based on new segmentation method. The result proves that the inversion based on the new segmentation can achieve fast and accurate inversion of depth parameters of underground pipes without being limited by pipeline depth.

2dx_automator: implementation of a semiautomatic high-throughput high-resolution cryo-electron crystallography pipeline.

PubMed

Scherer, Sebastian; Kowal, Julia; Chami, Mohamed; Dandey, Venkata; Arheit, Marcel; Ringler, Philippe; Stahlberg, Henning

2014-05-01

The introduction of direct electron detectors (DED) to cryo-electron microscopy has tremendously increased the signal-to-noise ratio (SNR) and quality of the recorded images. We discuss the optimal use of DEDs for cryo-electron crystallography, introduce a new automatic image processing pipeline, and demonstrate the vast improvement in the resolution achieved by the use of both together, especially for highly tilted samples. The new processing pipeline (now included in the software package 2dx) exploits the high SNR and frame readout frequency of DEDs to automatically correct for beam-induced sample movement, and reliably processes individual crystal images without human interaction as data are being acquired. A new graphical user interface (GUI) condenses all information required for quality assessment in one window, allowing the imaging conditions to be verified and adjusted during the data collection session. With this new pipeline an automatically generated unit cell projection map of each recorded 2D crystal is available less than 5 min after the image was recorded. The entire processing procedure yielded a three-dimensional reconstruction of the 2D-crystallized ion-channel membrane protein MloK1 with a much-improved resolution of 5Å in-plane and 7Å in the z-direction, within 2 days of data acquisition and simultaneous processing. The results obtained are superior to those delivered by conventional photographic film-based methodology of the same sample, and demonstrate the importance of drift-correction. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Quantification of diffusion tensor imaging in normal white matter maturation of early childhood using an automated processing pipeline.

PubMed

Loh, K B; Ramli, N; Tan, L K; Roziah, M; Rahmat, K; Ariffin, H

2012-07-01

The degree and status of white matter myelination can be sensitively monitored using diffusion tensor imaging (DTI). This study looks at the measurement of fractional anistropy (FA) and mean diffusivity (MD) using an automated ROI with an existing DTI atlas. Anatomical MRI and structural DTI were performed cross-sectionally on 26 normal children (newborn to 48 months old), using 1.5-T MRI. The automated processing pipeline was implemented to convert diffusion-weighted images into the NIfTI format. DTI-TK software was used to register the processed images to the ICBM DTI-81 atlas, while AFNI software was used for automated atlas-based volumes of interest (VOIs) and statistical value extraction. DTI exhibited consistent grey-white matter contrast. Triphasic temporal variation of the FA and MD values was noted, with FA increasing and MD decreasing rapidly early in the first 12 months. The second phase lasted 12-24 months during which the rate of FA and MD changes was reduced. After 24 months, the FA and MD values plateaued. DTI is a superior technique to conventional MR imaging in depicting WM maturation. The use of the automated processing pipeline provides a reliable environment for quantitative analysis of high-throughput DTI data. Diffusion tensor imaging outperforms conventional MRI in depicting white matter maturation. • DTI will become an important clinical tool for diagnosing paediatric neurological diseases. • DTI appears especially helpful for developmental abnormalities, tumours and white matter disease. • An automated processing pipeline assists quantitative analysis of high throughput DTI data.

On the VLSI design of a pipeline Reed-Solomon decoder using systolic arrays

NASA Technical Reports Server (NTRS)

Shao, H. M.; Deutsch, L. J.; Reed, I. S.

1987-01-01

A new very large scale integration (VLSI) design of a pipeline Reed-Solomon decoder is presented. The transform decoding technique used in a previous article is replaced by a time domain algorithm through a detailed comparison of their VLSI implementations. A new architecture that implements the time domain algorithm permits efficient pipeline processing with reduced circuitry. Erasure correction capability is also incorporated with little additional complexity. By using a multiplexing technique, a new implementation of Euclid's algorithm maintains the throughput rate with less circuitry. Such improvements result in both enhanced capability and significant reduction in silicon area.

An approximate inverse scattering technique for reconstructing blockage profiles in water pipelines using acoustic transients.

PubMed

Jing, Liwen; Li, Zhao; Wang, Wenjie; Dubey, Amartansh; Lee, Pedro; Meniconi, Silvia; Brunone, Bruno; Murch, Ross D

2018-05-01

An approximate inverse scattering technique is proposed for reconstructing cross-sectional area variation along water pipelines to deduce the size and position of blockages. The technique allows the reconstructed blockage profile to be written explicitly in terms of the measured acoustic reflectivity. It is based upon the Born approximation and provides good accuracy, low computational complexity, and insight into the reconstruction process. Numerical simulations and experimental results are provided for long pipelines with mild and severe blockages of different lengths. Good agreement is found between the inverse result and the actual pipe condition for mild blockages.

On the VLSI design of a pipeline Reed-Solomon decoder using systolic arrays

NASA Technical Reports Server (NTRS)

Shao, Howard M.; Reed, Irving S.

1988-01-01

A new very large scale integration (VLSI) design of a pipeline Reed-Solomon decoder is presented. The transform decoding technique used in a previous article is replaced by a time domain algorithm through a detailed comparison of their VLSI implementations. A new architecture that implements the time domain algorithm permits efficient pipeline processing with reduced circuitry. Erasure correction capability is also incorporated with little additional complexity. By using multiplexing technique, a new implementation of Euclid's algorithm maintains the throughput rate with less circuitry. Such improvements result in both enhanced capability and significant reduction in silicon area.

A-Track: A new approach for detection of moving objects in FITS images

NASA Astrophysics Data System (ADS)

Atay, T.; Kaplan, M.; Kilic, Y.; Karapinar, N.

2016-10-01

We have developed a fast, open-source, cross-platform pipeline, called A-Track, for detecting the moving objects (asteroids and comets) in sequential telescope images in FITS format. The pipeline is coded in Python 3. The moving objects are detected using a modified line detection algorithm, called MILD. We tested the pipeline on astronomical data acquired by an SI-1100 CCD with a 1-meter telescope. We found that A-Track performs very well in terms of detection efficiency, stability, and processing time. The code is hosted on GitHub under the GNU GPL v3 license.

76 FR 52654 - Millennium Pipeline Company, LLC; Notice of Intent To Prepare an Environmental Assessment for the...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-23

... proposes to construct and operate one new compressor station in Minisink, New York. The Minisink Compressor... at the new Minisink Compressor Station; Approximately 1,090 feet of 36-inch-diameter pipeline for... would be maintained permanently for operation of the Minisink Compressor Station. The EA Process The...

Reed-Solomon decoder

NASA Technical Reports Server (NTRS)

Lahmeyer, Charles R. (Inventor)

1987-01-01

A Reed-Solomon decoder with dedicated hardware for five sequential algorithms was designed with overall pipelining by memory swapping between input, processing and output memories, and internal pipelining through the five algorithms. The code definition used in decoding is specified by a keyword received with each block of data so that a number of different code formats may be decoded by the same hardware.

Study on the Control of Cleanliness for X90 Pipeline in the Secondary Refining Process

NASA Astrophysics Data System (ADS)

Chu, Ren Sheng; Liu, Jin Gang; Li, Zhan Jun

X90 pipeline steel requires ultra low for sulfur content and gas content in the smelting process. The secondary refining process is very important for X90 pipeline in smelting process and the control of cleanliness is the key for the secondary refining process in the steelmaking process for Pretreatment of hot metal → LD → LF refining → RH refining → Calcium treatment → CC. In the current paper, the cleanliness control method of secondary refining was analyzed for the evolution of non-metallic inclusions in the secondary refining prcess and related changes for composition in steel. The size, composition and the type of the non-metallic inclusions were analyzed by aspex explorer automated scanning electron microscope in X90 pipeline samples for 20mm * 25mm * 25mm by the line cutting. The results show that the number of non-metallic inclusions in steel decrease from the beginning of the LF refining to the RH refining. In the composition of the Non-metallic inclusions, the initial non-metallic inclusions of alumina is converted to two comple-type non-metallic inclusions. Most of them, the non-metallic inclusions were composed by the calcium aluminate and CaS. The others are that the spinel is the core, peripheral parcels calcium aluminate nonmetallic inclusions for complex-type non-metallic inclusions. For the size of the non-metallic inclusions, the non-metallic inclusions for size larger than 100µm is converted to 5 20µm based small size non-metallic inclusions. While the S content of the steel decreased from 0.012% to 0.0012% or less, Al content is kept at between 0.025% to 0.035% and the quality for the casting slab satisfies the requirement of the steel. The ratings for various types of the non-metallic inclusions are 1.5 or less. The control strategy for the inclusions in 90 pipeline is small size, diffuse distribution and little amount of the deformation after rolling. On the contrary, the specific chemical composition of the inclusions is not important, single component in the inclusions is better.

The Minimal Preprocessing Pipelines for the Human Connectome Project

PubMed Central

Glasser, Matthew F.; Sotiropoulos, Stamatios N; Wilson, J Anthony; Coalson, Timothy S; Fischl, Bruce; Andersson, Jesper L; Xu, Junqian; Jbabdi, Saad; Webster, Matthew; Polimeni, Jonathan R; Van Essen, David C; Jenkinson, Mark

2013-01-01

The Human Connectome Project (HCP) faces the challenging task of bringing multiple magnetic resonance imaging (MRI) modalities together in a common automated preprocessing framework across a large cohort of subjects. The MRI data acquired by the HCP differ in many ways from data acquired on conventional 3 Tesla scanners and often require newly developed preprocessing methods. We describe the minimal preprocessing pipelines for structural, functional, and diffusion MRI that were developed by the HCP to accomplish many low level tasks, including spatial artifact/distortion removal, surface generation, cross-modal registration, and alignment to standard space. These pipelines are specially designed to capitalize on the high quality data offered by the HCP. The final standard space makes use of a recently introduced CIFTI file format and the associated grayordinates spatial coordinate system. This allows for combined cortical surface and subcortical volume analyses while reducing the storage and processing requirements for high spatial and temporal resolution data. Here, we provide the minimum image acquisition requirements for the HCP minimal preprocessing pipelines and additional advice for investigators interested in replicating the HCP’s acquisition protocols or using these pipelines. Finally, we discuss some potential future improvements for the pipelines. PMID:23668970

High-throughput bioinformatics with the Cyrille2 pipeline system

PubMed Central

Fiers, Mark WEJ; van der Burgt, Ate; Datema, Erwin; de Groot, Joost CW; van Ham, Roeland CHJ

2008-01-01

Background Modern omics research involves the application of high-throughput technologies that generate vast volumes of data. These data need to be pre-processed, analyzed and integrated with existing knowledge through the use of diverse sets of software tools, models and databases. The analyses are often interdependent and chained together to form complex workflows or pipelines. Given the volume of the data used and the multitude of computational resources available, specialized pipeline software is required to make high-throughput analysis of large-scale omics datasets feasible. Results We have developed a generic pipeline system called Cyrille2. The system is modular in design and consists of three functionally distinct parts: 1) a web based, graphical user interface (GUI) that enables a pipeline operator to manage the system; 2) the Scheduler, which forms the functional core of the system and which tracks what data enters the system and determines what jobs must be scheduled for execution, and; 3) the Executor, which searches for scheduled jobs and executes these on a compute cluster. Conclusion The Cyrille2 system is an extensible, modular system, implementing the stated requirements. Cyrille2 enables easy creation and execution of high throughput, flexible bioinformatics pipelines. PMID:18269742

Aerial surveillance for gas and liquid hydrocarbon pipelines using a flame ionization detector (FID)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Riquetti, P.V.; Fletcher, J.I.; Minty, C.D.

1996-12-31

A novel application for the detection of airborne hydrocarbons has been successfully developed by means of a highly sensitive, fast responding Flame Ionization Detector (FID). The traditional way to monitor pipeline leaks has been by ground crews using specific sensors or by airborne crews highly trained to observe anomalies associated with leaks during periodic surveys of the pipeline right-of-way. The goal has been to detect leaks in a fast and cost effective way before the associated spill becomes a costly and hazardous problem. This paper describes a leak detection system combined with a global positioning system (GPS) and a computerizedmore » data output designed to pinpoint the presence of hydrocarbons in the air space of the pipeline`s right of way. Fixed wing aircraft as well as helicopters have been successfully used as airborne platforms. Natural gas, crude oil and finished products pipelines in Canada and the US have been surveyed using this technology with excellent correlation between the aircraft detection and in situ ground detection. The information obtained is processed with a proprietary software and reduced to simple coordinates. Results are transferred to ground crews to effect the necessary repairs.« less

Color correction pipeline optimization for digital cameras

NASA Astrophysics Data System (ADS)

Bianco, Simone; Bruna, Arcangelo R.; Naccari, Filippo; Schettini, Raimondo

2013-04-01

The processing pipeline of a digital camera converts the RAW image acquired by the sensor to a representation of the original scene that should be as faithful as possible. There are mainly two modules responsible for the color-rendering accuracy of a digital camera: the former is the illuminant estimation and correction module, and the latter is the color matrix transformation aimed to adapt the color response of the sensor to a standard color space. These two modules together form what may be called the color correction pipeline. We design and test new color correction pipelines that exploit different illuminant estimation and correction algorithms that are tuned and automatically selected on the basis of the image content. Since the illuminant estimation is an ill-posed problem, illuminant correction is not error-free. An adaptive color matrix transformation module is optimized, taking into account the behavior of the first module in order to alleviate the amplification of color errors. The proposed pipelines are tested on a publicly available dataset of RAW images. Experimental results show that exploiting the cross-talks between the modules of the pipeline can lead to a higher color-rendition accuracy.

Use of a GIS-based hybrid artificial neural network to prioritize the order of pipe replacement in a water distribution network.

PubMed

Ho, Cheng-I; Lin, Min-Der; Lo, Shang-Lien

2010-07-01

A methodology based on the integration of a seismic-based artificial neural network (ANN) model and a geographic information system (GIS) to assess water leakage and to prioritize pipeline replacement is developed in this work. Qualified pipeline break-event data derived from the Taiwan Water Corporation Pipeline Leakage Repair Management System were analyzed. "Pipe diameter," "pipe material," and "the number of magnitude-3( + ) earthquakes" were employed as the input factors of ANN, while "the number of monthly breaks" was used for the prediction output. This study is the first attempt to manipulate earthquake data in the break-event ANN prediction model. Spatial distribution of the pipeline break-event data was analyzed and visualized by GIS. Through this, the users can swiftly figure out the hotspots of the leakage areas. A northeastern township in Taiwan, frequently affected by earthquakes, is chosen as the case study. Compared to the traditional processes for determining the priorities of pipeline replacement, the methodology developed is more effective and efficient. Likewise, the methodology can overcome the difficulty of prioritizing pipeline replacement even in situations where the break-event records are unavailable.

MEASURING TRANSIT SIGNAL RECOVERY IN THE KEPLER PIPELINE. I. INDIVIDUAL EVENTS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Christiansen, Jessie L.; Clarke, Bruce D.; Burke, Christopher J.

The Kepler mission was designed to measure the frequency of Earth-size planets in the habitable zone of Sun-like stars. A crucial component for recovering the underlying planet population from a sample of detected planets is understanding the completeness of that sample-the fraction of the planets that could have been discovered in a given data set that actually were detected. Here, we outline the information required to determine the sample completeness, and describe an experiment to address a specific aspect of that question, i.e., the issue of transit signal recovery. We investigate the extent to which the Kepler pipeline preserves individualmore » transit signals by injecting simulated transits into the pixel-level data, processing the modified pixels through the pipeline, and comparing the measured transit signal-to-noise ratio (S/N) to that expected without perturbation by the pipeline. We inject simulated transit signals across the full focal plane for a set of observations for a duration of 89 days. On average, we find that the S/N of the injected signal is recovered at MS = 0.9973({+-} 0.0012) Multiplication-Sign BS - 0.0151({+-} 0.0049), where MS is the measured S/N and BS is the baseline, or expected, S/N. The 1{sigma} width of the distribution around this correlation is {+-}2.64%. This indicates an extremely high fidelity in reproducing the expected detection statistics for single transit events, and provides teams performing their own periodic transit searches the confidence that there is no systematic reduction in transit signal strength introduced by the pipeline. We discuss the pipeline processes that cause the measured S/N to deviate significantly from the baseline S/N for a small fraction of targets; these are primarily the handling of data adjacent to spacecraft re-pointings and the removal of harmonics prior to the measurement of the S/N. Finally, we outline the further work required to characterize the completeness of the Kepler pipeline.« less

WFIRST: User and mission support at ISOC - IPAC Science Operations Center

NASA Astrophysics Data System (ADS)

Akeson, Rachel; Armus, Lee; Bennett, Lee; Colbert, James; Helou, George; Kirkpatrick, J. Davy; Laine, Seppo; Meshkat, Tiffany; Paladini, Roberta; Ramirez, Solange; Wang, Yun; Xie, Joan; Yan, Lin

2018-01-01

The science center for WFIRST is distributed between the Goddard Space Flight Center, the Infrared Processing and Analysis Center (IPAC) and the Space Telescope Science Institute (STScI). The main functions of the IPAC Science Operations Center (ISOC) are:* Conduct the GO, archival and theory proposal submission and evaluation process* Support the coronagraph instrument, including observation planning, calibration and data processing pipeline, generation of data products, and user support* Microlensing survey data processing pipeline, generation of data products, and user support* Community engagement including conferences, workshops and general support of the WFIRST exoplanet communityWe will describe the components planned to support these functions and the community of WFIRST users.

Cathodic Protection Measurement Through Inline Inspection Technology Uses and Observations

NASA Astrophysics Data System (ADS)

Ferguson, Briana Ley

This research supports the evaluation of an impressed current cathodic protection (CP) system of a buried coated steel pipeline through alternative technology and methods, via an inline inspection device (ILI, CP ILI tool, or tool), in order to prevent and mitigate external corrosion. This thesis investigates the ability to measure the current density of a pipeline's CP system from inside of a pipeline rather than manually from outside, and then convert that CP ILI tool reading into a pipe-to-soil potential as required by regulations and standards. This was demonstrated through a mathematical model that utilizes applications of Ohm's Law, circuit concepts, and attenuation principles in order to match the results of the ILI sample data by varying parameters of the model (i.e., values for over potential and coating resistivity). This research has not been conducted previously in order to determine if the protected potential range can be achieved with respect to the predicted current density from the CP ILI device. Kirchhoff's method was explored, but certain principals could not be used in the model as manual measurements were required. This research was based on circuit concepts which indirectly affected electrochemical processes. Through Ohm's law, the results show that a constant current density is possible in the protected potential range; therefore, indicates polarization of the pipeline, which leads to calcareous deposit development with respect to electrochemistry. Calcareous deposit is desirable in industry since it increases the resistance of the pipeline coating and lowers current, thus slowing the oxygen diffusion process. This research conveys that an alternative method for CP evaluation from inside of the pipeline is possible where the pipe-to-soil potential can be estimated (as required by regulations) from the ILI tool's current density measurement.

Characterization and Validation of Transiting Planets in the TESS SPOC Pipeline

NASA Astrophysics Data System (ADS)

Twicken, Joseph D.; Caldwell, Douglas A.; Davies, Misty; Jenkins, Jon Michael; Li, Jie; Morris, Robert L.; Rose, Mark; Smith, Jeffrey C.; Tenenbaum, Peter; Ting, Eric; Wohler, Bill

2018-06-01

Light curves for Transiting Exoplanet Survey Satellite (TESS) target stars will be extracted and searched for transiting planet signatures in the Science Processing Operations Center (SPOC) Science Pipeline at NASA Ames Research Center. Targets for which the transiting planet detection threshold is exceeded will be processed in the Data Validation (DV) component of the Pipeline. The primary functions of DV are to (1) characterize planets identified in the transiting planet search, (2) search for additional transiting planet signatures in light curves after modeled transit signatures have been removed, and (3) perform a comprehensive suite of diagnostic tests to aid in discrimination between true transiting planets and false positive detections. DV data products include extensive reports by target, one-page summaries by planet candidate, and tabulated transit model fit and diagnostic test results. DV products may be employed by humans and automated systems to vet planet candidates identified in the Pipeline. TESS will launch in 2018 and survey the full sky for transiting exoplanets over a period of two years. The SPOC pipeline was ported from the Kepler Science Operations Center (SOC) codebase and extended for TESS after the mission was selected for flight in the NASA Astrophysics Explorer program. We describe the Data Validation component of the SPOC Pipeline. The diagnostic tests exploit the flux (i.e., light curve) and pixel time series associated with each target to support the determination of the origin of each purported transiting planet signature. We also highlight the differences between the DV components for Kepler and TESS. Candidate planet detections and data products will be delivered to the Mikulski Archive for Space Telescopes (MAST); the MAST URL is archive.stsci.edu/tess. Funding for the TESS Mission has been provided by the NASA Science Mission Directorate.

Visual analysis of trash bin processing on garbage trucks in low resolution video

NASA Astrophysics Data System (ADS)

Sidla, Oliver; Loibner, Gernot

2015-03-01

We present a system for trash can detection and counting from a camera which is mounted on a garbage collection truck. A working prototype has been successfully implemented and tested with several hours of real-world video. The detection pipeline consists of HOG detectors for two trash can sizes, and meanshift tracking and low level image processing for the analysis of the garbage disposal process. Considering the harsh environment and unfavorable imaging conditions, the process works already good enough so that very useful measurements from video data can be extracted. The false positive/false negative rate of the full processing pipeline is about 5-6% at fully automatic operation. Video data of a full day (about 8 hrs) can be processed in about 30 minutes on a standard PC.

With simple gasoline stripping devices, a problem of gas transportation by pipeline is resolved (in Spanish)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Couto, J.A.

1975-06-01

Liquid hydrocarbons contained in Argentina's Pico Truncade natural gas caused a number of serious pipeline transmission and gas processing problems. Gas del Estado has installed a series of efficient liquid removal devices at the producing fields. A flow chart of the gasoline stripping process is illustrated, as are 2 types of heat exchangers. This process of gasoline stripping (gas condensate recovery) integrates various operations which normally are performed independently: separation of the poor condensate in the gas, stabilization of the same, and incorporation of the light components (products of the stabilization) in the main gas flow.

30 CFR 250.1003 - Installation, testing, and repair requirements for DOI pipelines.

Code of Federal Regulations, 2010 CFR

2010-07-01

.... (a)(1) Pipelines greater than 8-5/8 inches in diameter and installed in water depths of less than 200... shall be pressure tested with water at a stabilized pressure of at least 1.25 times the MAOP for at... pressure tested with water or processed natural gas at a minimum stabilized pressure of at least 1.25 times...

Development of an optical character recognition pipeline for handwritten form fields from an electronic health record.

PubMed

Rasmussen, Luke V; Peissig, Peggy L; McCarty, Catherine A; Starren, Justin

2012-06-01

Although the penetration of electronic health records is increasing rapidly, much of the historical medical record is only available in handwritten notes and forms, which require labor-intensive, human chart abstraction for some clinical research. The few previous studies on automated extraction of data from these handwritten notes have focused on monolithic, custom-developed recognition systems or third-party systems that require proprietary forms. We present an optical character recognition processing pipeline, which leverages the capabilities of existing third-party optical character recognition engines, and provides the flexibility offered by a modular custom-developed system. The system was configured and run on a selected set of form fields extracted from a corpus of handwritten ophthalmology forms. The processing pipeline allowed multiple configurations to be run, with the optimal configuration consisting of the Nuance and LEADTOOLS engines running in parallel with a positive predictive value of 94.6% and a sensitivity of 13.5%. While limitations exist, preliminary experience from this project yielded insights on the generalizability and applicability of integrating multiple, inexpensive general-purpose third-party optical character recognition engines in a modular pipeline.

Development of an optical character recognition pipeline for handwritten form fields from an electronic health record

PubMed Central

Peissig, Peggy L; McCarty, Catherine A; Starren, Justin

2011-01-01

Background Although the penetration of electronic health records is increasing rapidly, much of the historical medical record is only available in handwritten notes and forms, which require labor-intensive, human chart abstraction for some clinical research. The few previous studies on automated extraction of data from these handwritten notes have focused on monolithic, custom-developed recognition systems or third-party systems that require proprietary forms. Methods We present an optical character recognition processing pipeline, which leverages the capabilities of existing third-party optical character recognition engines, and provides the flexibility offered by a modular custom-developed system. The system was configured and run on a selected set of form fields extracted from a corpus of handwritten ophthalmology forms. Observations The processing pipeline allowed multiple configurations to be run, with the optimal configuration consisting of the Nuance and LEADTOOLS engines running in parallel with a positive predictive value of 94.6% and a sensitivity of 13.5%. Discussion While limitations exist, preliminary experience from this project yielded insights on the generalizability and applicability of integrating multiple, inexpensive general-purpose third-party optical character recognition engines in a modular pipeline. PMID:21890871

Low-level processing for real-time image analysis

NASA Technical Reports Server (NTRS)

Eskenazi, R.; Wilf, J. M.

1979-01-01

A system that detects object outlines in television images in real time is described. A high-speed pipeline processor transforms the raw image into an edge map and a microprocessor, which is integrated into the system, clusters the edges, and represents them as chain codes. Image statistics, useful for higher level tasks such as pattern recognition, are computed by the microprocessor. Peak intensity and peak gradient values are extracted within a programmable window and are used for iris and focus control. The algorithms implemented in hardware and the pipeline processor architecture are described. The strategy for partitioning functions in the pipeline was chosen to make the implementation modular. The microprocessor interface allows flexible and adaptive control of the feature extraction process. The software algorithms for clustering edge segments, creating chain codes, and computing image statistics are also discussed. A strategy for real time image analysis that uses this system is given.

Auto-rickshaw: an automated crystal structure determination platform as an efficient tool for the validation of an X-ray diffraction experiment.

PubMed

Panjikar, Santosh; Parthasarathy, Venkataraman; Lamzin, Victor S; Weiss, Manfred S; Tucker, Paul A

2005-04-01

The EMBL-Hamburg Automated Crystal Structure Determination Platform is a system that combines a number of existing macromolecular crystallographic computer programs and several decision-makers into a software pipeline for automated and efficient crystal structure determination. The pipeline can be invoked as soon as X-ray data from derivatized protein crystals have been collected and processed. It is controlled by a web-based graphical user interface for data and parameter input, and for monitoring the progress of structure determination. A large number of possible structure-solution paths are encoded in the system and the optimal path is selected by the decision-makers as the structure solution evolves. The processes have been optimized for speed so that the pipeline can be used effectively for validating the X-ray experiment at a synchrotron beamline.

TRAPR: R Package for Statistical Analysis and Visualization of RNA-Seq Data.

PubMed

Lim, Jae Hyun; Lee, Soo Youn; Kim, Ju Han

2017-03-01

High-throughput transcriptome sequencing, also known as RNA sequencing (RNA-Seq), is a standard technology for measuring gene expression with unprecedented accuracy. Numerous bioconductor packages have been developed for the statistical analysis of RNA-Seq data. However, these tools focus on specific aspects of the data analysis pipeline, and are difficult to appropriately integrate with one another due to their disparate data structures and processing methods. They also lack visualization methods to confirm the integrity of the data and the process. In this paper, we propose an R-based RNA-Seq analysis pipeline called TRAPR, an integrated tool that facilitates the statistical analysis and visualization of RNA-Seq expression data. TRAPR provides various functions for data management, the filtering of low-quality data, normalization, transformation, statistical analysis, data visualization, and result visualization that allow researchers to build customized analysis pipelines.

Pipeline oil fire detection with MODIS active fire products

NASA Astrophysics Data System (ADS)

Ogungbuyi, M. G.; Martinez, P.; Eckardt, F. D.

2017-12-01

We investigate 85 129 MODIS satellite active fire events from 2007 to 2015 in the Niger Delta of Nigeria. The region is the oil base for Nigerian economy and the hub of oil exploration where oil facilities (i.e. flowlines, flow stations, trunklines, oil wells and oil fields) are domiciled, and from where crude oil and refined products are transported to different Nigerian locations through a network of pipeline systems. Pipeline and other oil facilities are consistently susceptible to oil leaks due to operational or maintenance error, and by acts of deliberate sabotage of the pipeline equipment which often result in explosions and fire outbreaks. We used ground oil spill reports obtained from the National Oil Spill Detection and Response Agency (NOSDRA) database (see www.oilspillmonitor.ng) to validate MODIS satellite data. NOSDRA database shows an estimate of 10 000 spill events from 2007 - 2015. The spill events were filtered to include largest spills by volume and events occurring only in the Niger Delta (i.e. 386 spills). By projecting both MODIS fire and spill as `input vector' layers with `Points' geometry, and the Nigerian pipeline networks as `from vector' layers with `LineString' geometry in a geographical information system, we extracted the nearest MODIS events (i.e. 2192) closed to the pipelines by 1000m distance in spatial vector analysis. The extraction process that defined the nearest distance to the pipelines is based on the global practices of the Right of Way (ROW) in pipeline management that earmarked 30m strip of land to the pipeline. The KML files of the extracted fires in a Google map validated their source origin to be from oil facilities. Land cover mapping confirmed fire anomalies. The aim of the study is to propose a near-real-time monitoring of spill events along pipeline routes using 250 m spatial resolution of MODIS active fire detection sensor when such spills are accompanied by fire events in the study location.

BALBES: a molecular-replacement pipeline.

PubMed

Long, Fei; Vagin, Alexei A; Young, Paul; Murshudov, Garib N

2008-01-01

The number of macromolecular structures solved and deposited in the Protein Data Bank (PDB) is higher than 40 000. Using this information in macromolecular crystallography (MX) should in principle increase the efficiency of MX structure solution. This paper describes a molecular-replacement pipeline, BALBES, that makes extensive use of this repository. It uses a reorganized database taken from the PDB with multimeric as well as domain organization. A system manager written in Python controls the workflow of the process. Testing the current version of the pipeline using entries from the PDB has shown that this approach has huge potential and that around 75% of structures can be solved automatically without user intervention.

A single chip VLSI Reed-Solomon decoder

NASA Technical Reports Server (NTRS)

Shao, H. M.; Truong, T. K.; Hsu, I. S.; Deutsch, L. J.; Reed, I. S.

1986-01-01

A new VLSI design of a pipeline Reed-Solomon decoder is presented. The transform decoding technique used in a previous design is replaced by a time domain algorithm. A new architecture that implements such an algorithm permits efficient pipeline processing with minimum circuitry. A systolic array is also developed to perform erasure corrections in the new design. A modified form of Euclid's algorithm is implemented by a new architecture that maintains the throughput rate with less circuitry. Such improvements result in both enhanced capability and a significant reduction in silicon area, therefore making it possible to build a pipeline (31,15)RS decoder on a single VLSI chip.

Design and analysis of quantitative differential proteomics investigations using LC-MS technology.

PubMed

Bukhman, Yury V; Dharsee, Moyez; Ewing, Rob; Chu, Peter; Topaloglou, Thodoros; Le Bihan, Thierry; Goh, Theo; Duewel, Henry; Stewart, Ian I; Wisniewski, Jacek R; Ng, Nancy F

2008-02-01

Liquid chromatography-mass spectrometry (LC-MS)-based proteomics is becoming an increasingly important tool in characterizing the abundance of proteins in biological samples of various types and across conditions. Effects of disease or drug treatments on protein abundance are of particular interest for the characterization of biological processes and the identification of biomarkers. Although state-of-the-art instrumentation is available to make high-quality measurements and commercially available software is available to process the data, the complexity of the technology and data presents challenges for bioinformaticians and statisticians. Here, we describe a pipeline for the analysis of quantitative LC-MS data. Key components of this pipeline include experimental design (sample pooling, blocking, and randomization) as well as deconvolution and alignment of mass chromatograms to generate a matrix of molecular abundance profiles. An important challenge in LC-MS-based quantitation is to be able to accurately identify and assign abundance measurements to members of protein families. To address this issue, we implement a novel statistical method for inferring the relative abundance of related members of protein families from tryptic peptide intensities. This pipeline has been used to analyze quantitative LC-MS data from multiple biomarker discovery projects. We illustrate our pipeline here with examples from two of these studies, and show that the pipeline constitutes a complete workable framework for LC-MS-based differential quantitation. Supplementary material is available at http://iec01.mie.utoronto.ca/~thodoros/Bukhman/.

AmeriFlux Data Processing: Integrating automated and manual data management across software technologies and an international network to generate timely data products

NASA Astrophysics Data System (ADS)

Christianson, D. S.; Beekwilder, N.; Chan, S.; Cheah, Y. W.; Chu, H.; Dengel, S.; O'Brien, F.; Pastorello, G.; Sandesh, M.; Torn, M. S.; Agarwal, D.

2017-12-01

AmeriFlux is a network of scientists who independently collect eddy covariance and related environmental observations at over 250 locations across the Americas. As part of the AmeriFlux Management Project, the AmeriFlux Data Team manages standardization, collection, quality assurance / quality control (QA/QC), and distribution of data submitted by network members. To generate data products that are timely, QA/QC'd, and repeatable, and have traceable provenance, we developed a semi-automated data processing pipeline. The new pipeline consists of semi-automated format and data QA/QC checks. Results are communicated via on-line reports as well as an issue-tracking system. Data processing time has been reduced from 2-3 days to a few hours of manual review time, resulting in faster data availability from the time of data submission. The pipeline is scalable to the network level and has the following key features. (1) On-line results of the format QA/QC checks are available immediately for data provider review. This enables data providers to correct and resubmit data quickly. (2) The format QA/QC assessment includes an automated attempt to fix minor format errors. Data submissions that are formatted in the new AmeriFlux FP-In standard can be queued for the data QA/QC assessment, often with minimal delay. (3) Automated data QA/QC checks identify and communicate potentially erroneous data via online, graphical quick views that highlight observations with unexpected values, incorrect units, time drifts, invalid multivariate correlations, and/or radiation shadows. (4) Progress through the pipeline is integrated with an issue-tracking system that facilitates communications between data providers and the data processing team in an organized and searchable fashion. Through development of these and other features of the pipeline, we present solutions to challenges that include optimizing automated with manual processing, bridging legacy data management infrastructure with various software tools, and working across interdisciplinary and international science cultures. Additionally, we discuss results from community member feedback that helped refine QA/QC communications for efficient data submission and revision.

An evolutionary approach to the architecture of effective healthcare delivery systems.

PubMed

Towill, D R; Christopher, M

2005-01-01

Aims to show that material flow concepts developed and successfully applied to commercial products and services can form equally well the architectural infrastructure of effective healthcare delivery systems. The methodology is based on the "power of analogy" which demonstrates that healthcare pipelines may be classified via the Time-Space Matrix. A small number (circa 4) of substantially different healthcare delivery pipelines will cover the vast majority of patient needs and simultaneously create adequate added value from their perspective. The emphasis is firmly placed on total process mapping and analysis via established identification techniques. Healthcare delivery pipelines must be properly engineered and matched to life cycle phase if the service is to be effective. This small family of healthcare delivery pipelines needs to be designed via adherence to very specific-to-purpose principles. These vary from "lean production" through to "agile delivery". The proposition for a strategic approach to healthcare delivery pipeline design is novel and positions much currently isolated research into a comprehensive organisational framework. It therefore provides a synthesis of the needs of global healthcare.

DIORAMA Communications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Galassi, Mark C.

Diorama is written as a collection of modules that can run in separate threads or in separate processes. This defines a clear interface between the modules and also allows concurrent processing of different parts of the pipeline. The pipeline is determined by a description in a scenario file[Norman and Tornga, 2012, Tornga and Norman, 2014]. The scenario manager parses the XML scenario and sets up the sequence of modules which will generate an event, propagate the signal to a set of sensors, and then run processing modules on the results provided by those sensor simulations. During a run a varietymore » of “observer” and “processor” modules can be invoked to do interim analysis of results. Observers do not modify the simulation results, while processors may affect the final result. At the end of a run results are collated and final reports are put out. A detailed description of the scenario file and how it puts together a simulation are given in [Tornga and Norman, 2014]. The processing pipeline and how to program it with the Diorama API is described in Tornga et al. [2015] and Tornga and Wakeford [2015]. In this report I describe the communications infrastructure that is used.« less

Falco: a quick and flexible single-cell RNA-seq processing framework on the cloud.

PubMed

Yang, Andrian; Troup, Michael; Lin, Peijie; Ho, Joshua W K

2017-03-01

Single-cell RNA-seq (scRNA-seq) is increasingly used in a range of biomedical studies. Nonetheless, current RNA-seq analysis tools are not specifically designed to efficiently process scRNA-seq data due to their limited scalability. Here we introduce Falco, a cloud-based framework to enable paralellization of existing RNA-seq processing pipelines using big data technologies of Apache Hadoop and Apache Spark for performing massively parallel analysis of large scale transcriptomic data. Using two public scRNA-seq datasets and two popular RNA-seq alignment/feature quantification pipelines, we show that the same processing pipeline runs 2.6-145.4 times faster using Falco than running on a highly optimized standalone computer. Falco also allows users to utilize low-cost spot instances of Amazon Web Services, providing a ∼65% reduction in cost of analysis. Falco is available via a GNU General Public License at https://github.com/VCCRI/Falco/. j.ho@victorchang.edu.au. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data.

PubMed

Graña, Osvaldo; López-Fernández, Hugo; Fdez-Riverola, Florentino; González Pisano, David; Glez-Peña, Daniel

2018-04-15

High-throughput sequencing of bisulfite-converted DNA is a technique used to measure DNA methylation levels. Although a considerable number of computational pipelines have been developed to analyze such data, none of them tackles all the peculiarities of the analysis together, revealing limitations that can force the user to manually perform additional steps needed for a complete processing of the data. This article presents bicycle, an integrated, flexible analysis pipeline for bisulfite sequencing data. Bicycle analyzes whole genome bisulfite sequencing data, targeted bisulfite sequencing data and hydroxymethylation data. To show how bicycle overtakes other available pipelines, we compared them on a defined number of features that are summarized in a table. We also tested bicycle with both simulated and real datasets, to show its level of performance, and compared it to different state-of-the-art methylation analysis pipelines. Bicycle is publicly available under GNU LGPL v3.0 license at http://www.sing-group.org/bicycle. Users can also download a customized Ubuntu LiveCD including bicycle and other bisulfite sequencing data pipelines compared here. In addition, a docker image with bicycle and its dependencies, which allows a straightforward use of bicycle in any platform (e.g. Linux, OS X or Windows), is also available. ograna@cnio.es or dgpena@uvigo.es. Supplementary data are available at Bioinformatics online.

Illumina GA IIx& HiSeq 2000 Production Sequenccing and QC Analysis Pipelines at the DOE Joint Genome Institute

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daum, Christopher; Zane, Matthew; Han, James

2011-01-31

The U.S. Department of Energy (DOE) Joint Genome Institute's (JGI) Production Sequencing group is committed to the generation of high-quality genomic DNA sequence to support the mission areas of renewable energy generation, global carbon management, and environmental characterization and clean-up. Within the JGI's Production Sequencing group, a robust Illumina Genome Analyzer and HiSeq pipeline has been established. Optimization of the sesequencer pipelines has been ongoing with the aim of continual process improvement of the laboratory workflow, reducing operational costs and project cycle times to increases ample throughput, and improving the overall quality of the sequence generated. A sequence QC analysismore » pipeline has been implemented to automatically generate read and assembly level quality metrics. The foremost of these optimization projects, along with sequencing and operational strategies, throughput numbers, and sequencing quality results will be presented.« less

An Investigation of the Cryogenic Freezing of Water in Non-Metallic Pipelines

NASA Astrophysics Data System (ADS)

Martin, C. I.; Richardson, R. N.; Bowen, R. J.

2004-06-01

Pipe freezing is increasingly used in a range of industries to solve otherwise intractable pipe line maintenance and servicing problems. This paper presents the interim results from an experimental study on deliberate freezing of polymeric pipelines. Previous and contemporary works are reviewed. The object of the current research is to confirm the feasibility of ice plug formation within a polymeric pipe as a method of isolation. Tests have been conducted on a range of polymeric pipes of various sizes. The results reported here all relate to freezing of horizontal pipelines. In each case the process of plug formation was photographed, the frozen plug pressure tested and the pipe inspected for signs of damage resulting from the freeze procedure. The time to freeze was recorded and various temperatures logged. These tests have demonstrated that despite the poor thermal and mechanical properties of the polymers, freezing offers a viable alternative method of isolation in polymeric pipelines.

Photometer Performance Assessment in TESS SPOC Pipeline

NASA Astrophysics Data System (ADS)

Li, Jie; Caldwell, Douglas A.; Jenkins, Jon Michael; Twicken, Joseph D.; Wohler, Bill; Chen, Xiaolan; Rose, Mark; TESS Science Processing Operations Center

2018-06-01

This poster describes the Photometer Performance Assessment (PPA) software component in the Transiting Exoplanet Survey Satellite (TESS) Science Processing Operations Center (SPOC) pipeline, which is developed based on the Kepler science pipeline. The PPA component performs two tasks: the first task is to assess the health and performance of the instrument based on the science data sets collected during each observation sector, identifying out of bounds conditions and generating alerts. The second is to combine the astrometric data collected for each CCD readout channel to construct a high fidelity record of the pointing history for each of the 4 cameras and an attitude solution for the TESS spacecraft for each 2-min data collection interval. PPA is implemented with multiple pipeline modules: PPA Metrics Determination (PMD), PMD Aggregator (PAG), and PPA Attitude Determination (PAD). The TESS Mission is funded by NASA's Science Mission Directorate. The SPOC is managed and operated by NASA Ames Research Center.

Detection of underground pipeline based on Golay waveform design

NASA Astrophysics Data System (ADS)

Dai, Jingjing; Xu, Dazhuan

2017-08-01

The detection of underground pipeline is an important problem in the development of the city, but the research about it is not mature at present. In this paper, based on the principle of waveform design in wireless communication, we design an acoustic signal detection system to detect the location of underground pipelines. According to the principle of acoustic localization, we chose DSP-F28335 as the development board, and use DA and AD module as the master control chip. The DA module uses complementary Golay sequence as emission signal. The AD module acquisiting data synchronously, so that the echo signals which containing position information of the target is recovered through the signal processing. The test result shows that the method in this paper can not only calculate the sound velocity of the soil, but also can locate the location of underground pipelines accurately.

The LCOGT Science Archive and Data Pipeline

NASA Astrophysics Data System (ADS)

Lister, Tim; Walker, Z.; Ciardi, D.; Gelino, C. R.; Good, J.; Laity, A.; Swain, M.

2013-01-01

Las Cumbres Observatory Global Telescope (LCOGT) is building and deploying a world-wide network of optical telescopes dedicated to time-domain astronomy. In the past year, we have deployed and commissioned four new 1m telescopes at McDonald Observatory, Texas and at CTIO, Chile, with more to come at SAAO, South Africa and Siding Spring Observatory, Australia. To handle these new data sources coming from the growing LCOGT network, and to serve them to end users, we have constructed a new data pipeline and Science Archive. We describe the new LCOGT pipeline, currently under development and testing, which makes use of the ORAC-DR automated recipe-based data reduction pipeline and illustrate some of the new data products. We also present the new Science Archive, which is being developed in partnership with the Infrared Processing and Analysis Center (IPAC) and show some of the new features the Science Archive provides.

GPU-Powered Coherent Beamforming

NASA Astrophysics Data System (ADS)

Magro, A.; Adami, K. Zarb; Hickish, J.

2015-03-01

Graphics processing units (GPU)-based beamforming is a relatively unexplored area in radio astronomy, possibly due to the assumption that any such system will be severely limited by the PCIe bandwidth required to transfer data to the GPU. We have developed a CUDA-based GPU implementation of a coherent beamformer, specifically designed and optimized for deployment at the BEST-2 array which can generate an arbitrary number of synthesized beams for a wide range of parameters. It achieves ˜1.3 TFLOPs on an NVIDIA Tesla K20, approximately 10x faster than an optimized, multithreaded CPU implementation. This kernel has been integrated into two real-time, GPU-based time-domain software pipelines deployed at the BEST-2 array in Medicina: a standalone beamforming pipeline and a transient detection pipeline. We present performance benchmarks for the beamforming kernel as well as the transient detection pipeline with beamforming capabilities as well as results of test observation.

Enabling a high throughput real time data pipeline for a large radio telescope array with GPUs

NASA Astrophysics Data System (ADS)

Edgar, R. G.; Clark, M. A.; Dale, K.; Mitchell, D. A.; Ord, S. M.; Wayth, R. B.; Pfister, H.; Greenhill, L. J.

2010-10-01

The Murchison Widefield Array (MWA) is a next-generation radio telescope currently under construction in the remote Western Australia Outback. Raw data will be generated continuously at 5 GiB s-1, grouped into 8 s cadences. This high throughput motivates the development of on-site, real time processing and reduction in preference to archiving, transport and off-line processing. Each batch of 8 s data must be completely reduced before the next batch arrives. Maintaining real time operation will require a sustained performance of around 2.5 TFLOP s-1 (including convolutions, FFTs, interpolations and matrix multiplications). We describe a scalable heterogeneous computing pipeline implementation, exploiting both the high computing density and FLOP-per-Watt ratio of modern GPUs. The architecture is highly parallel within and across nodes, with all major processing elements performed by GPUs. Necessary scatter-gather operations along the pipeline are loosely synchronized between the nodes hosting the GPUs. The MWA will be a frontier scientific instrument and a pathfinder for planned peta- and exa-scale facilities.

Rainfall-ground movement modelling for natural gas pipelines through landslide terrain

DOE Office of Scientific and Technical Information (OSTI.GOV)

O`Neil, G.D.; Simmonds, G.R.; Grivas, D.A.

1996-12-31

Perhaps the greatest challenge to geotechnical engineers is to maintain the integrity of pipelines at river crossings where landslide terrain dominates the approach slopes. The current design process at NOVA Gas Transmission Ltd. (NGTL) has developed to the point where this impact can be reasonably estimated using in-house models of pipeline-soil interaction. To date, there has been no method to estimate ground movements within unexplored slopes at the outset of the design process. To address this problem, rainfall and slope instrumentation data have been processed to derive rainfall-ground movement relationships. Early results indicate that the ground movements exhibit two components:more » a steady, small rate of movement independent of the rainfall, and, increased rates over short periods of time following heavy amounts of rainfall. Evidence exists of a definite threshold value of rainfall which has to be exceeded before any incremental movement is induced. Additional evidence indicates a one-month lag between rainfall and ground movement. While these models are in the preliminary stage, results indicate a potential to estimate ground movements for both initial design and planned maintenance actions.« less

A Pipeline for Large Data Processing Using Regular Sampling for Unstructured Grids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berres, Anne Sabine; Adhinarayanan, Vignesh; Turton, Terece

2017-05-12

Large simulation data requires a lot of time and computational resources to compute, store, analyze, visualize, and run user studies. Today, the largest cost of a supercomputer is not hardware but maintenance, in particular energy consumption. Our goal is to balance energy consumption and cognitive value of visualizations of resulting data. This requires us to go through the entire processing pipeline, from simulation to user studies. To reduce the amount of resources, data can be sampled or compressed. While this adds more computation time, the computational overhead is negligible compared to the simulation time. We built a processing pipeline atmore » the example of regular sampling. The reasons for this choice are two-fold: using a simple example reduces unnecessary complexity as we know what to expect from the results. Furthermore, it provides a good baseline for future, more elaborate sampling methods. We measured time and energy for each test we did, and we conducted user studies in Amazon Mechanical Turk (AMT) for a range of different results we produced through sampling.« less

Data Pre-Processing for Label-Free Multiple Reaction Monitoring (MRM) Experiments

PubMed Central

Chung, Lisa M.; Colangelo, Christopher M.; Zhao, Hongyu

2014-01-01

Multiple Reaction Monitoring (MRM) conducted on a triple quadrupole mass spectrometer allows researchers to quantify the expression levels of a set of target proteins. Each protein is often characterized by several unique peptides that can be detected by monitoring predetermined fragment ions, called transitions, for each peptide. Concatenating large numbers of MRM transitions into a single assay enables simultaneous quantification of hundreds of peptides and proteins. In recognition of the important role that MRM can play in hypothesis-driven research and its increasing impact on clinical proteomics, targeted proteomics such as MRM was recently selected as the Nature Method of the Year. However, there are many challenges in MRM applications, especially data pre‑processing where many steps still rely on manual inspection of each observation in practice. In this paper, we discuss an analysis pipeline to automate MRM data pre‑processing. This pipeline includes data quality assessment across replicated samples, outlier detection, identification of inaccurate transitions, and data normalization. We demonstrate the utility of our pipeline through its applications to several real MRM data sets. PMID:24905083

Data Pre-Processing for Label-Free Multiple Reaction Monitoring (MRM) Experiments.

PubMed

Chung, Lisa M; Colangelo, Christopher M; Zhao, Hongyu

2014-06-05

Multiple Reaction Monitoring (MRM) conducted on a triple quadrupole mass spectrometer allows researchers to quantify the expression levels of a set of target proteins. Each protein is often characterized by several unique peptides that can be detected by monitoring predetermined fragment ions, called transitions, for each peptide. Concatenating large numbers of MRM transitions into a single assay enables simultaneous quantification of hundreds of peptides and proteins. In recognition of the important role that MRM can play in hypothesis-driven research and its increasing impact on clinical proteomics, targeted proteomics such as MRM was recently selected as the Nature Method of the Year. However, there are many challenges in MRM applications, especially data pre‑processing where many steps still rely on manual inspection of each observation in practice. In this paper, we discuss an analysis pipeline to automate MRM data pre‑processing. This pipeline includes data quality assessment across replicated samples, outlier detection, identification of inaccurate transitions, and data normalization. We demonstrate the utility of our pipeline through its applications to several real MRM data sets.

Online image classification under monotonic decision boundary constraint

NASA Astrophysics Data System (ADS)

Lu, Cheng; Allebach, Jan; Wagner, Jerry; Pitta, Brandi; Larson, David; Guo, Yandong

2015-01-01

Image classification is a prerequisite for copy quality enhancement in all-in-one (AIO) device that comprises a printer and scanner, and which can be used to scan, copy and print. Different processing pipelines are provided in an AIO printer. Each of the processing pipelines is designed specifically for one type of input image to achieve the optimal output image quality. A typical approach to this problem is to apply Support Vector Machine to classify the input image and feed it to its corresponding processing pipeline. The online training SVM can help users to improve the performance of classification as input images accumulate. At the same time, we want to make quick decision on the input image to speed up the classification which means sometimes the AIO device does not need to scan the entire image to make a final decision. These two constraints, online SVM and quick decision, raise questions regarding: 1) what features are suitable for classification; 2) how we should control the decision boundary in online SVM training. This paper will discuss the compatibility of online SVM and quick decision capability.

Hydrocarbonaceous material processing methods and apparatus

DOEpatents

Brecher, Lee E [Laramie, WY

2011-07-12

Methods and apparatus are disclosed for possibly producing pipeline-ready heavy oil from substantially non-pumpable oil feeds. The methods and apparatus may be designed to produce such pipeline-ready heavy oils in the production field. Such methods and apparatus may involve thermal soaking of liquid hydrocarbonaceous inputs in thermal environments (2) to generate, though chemical reaction, an increased distillate amount as compared with conventional boiling technologies.

A Pervasive Parallel Processing Framework for Data Visualization and Analysis at Extreme Scale

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, Kwan-Liu

Most of today’s visualization libraries and applications are based off of what is known today as the visualization pipeline. In the visualization pipeline model, algorithms are encapsulated as “filtering” components with inputs and outputs. These components can be combined by connecting the outputs of one filter to the inputs of another filter. The visualization pipeline model is popular because it provides a convenient abstraction that allows users to combine algorithms in powerful ways. Unfortunately, the visualization pipeline cannot run effectively on exascale computers. Experts agree that the exascale machine will comprise processors that contain many cores. Furthermore, physical limitations willmore » prevent data movement in and out of the chip (that is, between main memory and the processing cores) from keeping pace with improvements in overall compute performance. To use these processors to their fullest capability, it is essential to carefully consider memory access. This is where the visualization pipeline fails. Each filtering component in the visualization library is expected to take a data set in its entirety, perform some computation across all of the elements, and output the complete results. The process of iterating over all elements must be repeated in each filter, which is one of the worst possible ways to traverse memory when trying to maximize the number of executions per memory access. This project investigates a new type of visualization framework that exhibits a pervasive parallelism necessary to run on exascale machines. Our framework achieves this by defining algorithms in terms of functors, which are localized, stateless operations. Functors can be composited in much the same way as filters in the visualization pipeline. But, functors’ design allows them to be concurrently running on massive amounts of lightweight threads. Only with such fine-grained parallelism can we hope to fill the billions of threads we expect will be necessary for efficient computation on an exascale computer. This project concludes with a functional prototype containing pervasively parallel algorithms that perform demonstratively well on many-core processors. These algorithms are fundamental for performing data analysis and visualization at extreme scale.« less

Effects of EPI distortion correction pipelines on the connectome in Parkinson's Disease

NASA Astrophysics Data System (ADS)

Galvis, Justin; Mezher, Adam F.; Ragothaman, Anjanibhargavi; Villalon-Reina, Julio E.; Fletcher, P. Thomas; Thompson, Paul M.; Prasad, Gautam

2016-03-01

Echo-planar imaging (EPI) is commonly used for diffusion-weighted imaging (DWI) but is susceptible to nonlinear geometric distortions arising from inhomogeneities in the static magnetic field. These inhomogeneities can be measured and corrected using a fieldmap image acquired during the scanning process. In studies where the fieldmap image is not collected, these distortions can be corrected, to some extent, by nonlinearly registering the diffusion image to a corresponding anatomical image, either a T1- or T2-weighted image. Here we compared two EPI distortion correction pipelines, both based on nonlinear registration, which were optimized for the particular weighting of the structural image registration target. The first pipeline used a 3D nonlinear registration to a T1-weighted target, while the second pipeline used a 1D nonlinear registration to a T2-weighted target. We assessed each pipeline in its ability to characterize high-level measures of brain connectivity in Parkinson's disease (PD) in 189 individuals (58 healthy controls, 131 people with PD) from the Parkinson's Progression Markers Initiative (PPMI) dataset. We computed a structural connectome (connectivity map) for each participant using regions of interest from a cortical parcellation combined with DWI-based whole-brain tractography. We evaluated test-retest reliability of the connectome for each EPI distortion correction pipeline using a second diffusion scan acquired directly after the participants' first. Finally, we used support vector machine (SVM) classification to assess how accurately each pipeline classified PD versus healthy controls using each participants' structural connectome.

Simplified Technique for Predicting Offshore Pipeline Expansion

NASA Astrophysics Data System (ADS)

Seo, J. H.; Kim, D. K.; Choi, H. S.; Yu, S. Y.; Park, K. S.

2018-06-01

In this study, we propose a method for estimating the amount of expansion that occurs in subsea pipelines, which could be applied in the design of robust structures that transport oil and gas from offshore wells. We begin with a literature review and general discussion of existing estimation methods and terminologies with respect to subsea pipelines. Due to the effects of high pressure and high temperature, the production of fluid from offshore wells is typically caused by physical deformation of subsea structures, e.g., expansion and contraction during the transportation process. In severe cases, vertical and lateral buckling occurs, which causes a significant negative impact on structural safety, and which is related to on-bottom stability, free-span, structural collapse, and many other factors. In addition, these factors may affect the production rate with respect to flow assurance, wax, and hydration, to name a few. In this study, we developed a simple and efficient method for generating a reliable pipe expansion design in the early stage, which can lead to savings in both cost and computation time. As such, in this paper, we propose an applicable diagram, which we call the standard dimensionless ratio (SDR) versus virtual anchor length (L A ) diagram, that utilizes an efficient procedure for estimating subsea pipeline expansion based on applied reliable scenarios. With this user guideline, offshore pipeline structural designers can reliably determine the amount of subsea pipeline expansion and the obtained results will also be useful for the installation, design, and maintenance of the subsea pipeline.

Application of Technology of Hydrodynamic Cavitation Processing High-Viscosity Oils for the Purpose of Improving the Rheological Characteristics of Oils

NASA Astrophysics Data System (ADS)

Zemenkov, Y. D.; Zemenkova, M. Y.; Vengerov, A. A.; Brand, A. E.

2016-10-01

There is investigated the technology of hydrodynamic cavitational processing viscous and high-viscosity oils and the possibility of its application in the pipeline transport system for the purpose of increasing of rheological properties of the transported oils, including dynamic viscosity shear stress in the article. It is considered the possibility of application of the combined hydrodynamic cavitational processing with addition of depressor additive for identification of effect of a synergism. It is developed the laboratory bench and they are presented results of modeling and laboratory researches. It is developed the hardware and technological scheme of application of the developed equipment at industrial objects of pipeline transport.

VizieR Online Data Catalog: Kepler planetary candidates. VII. 48-month (Coughlin+, 2016)

NASA Astrophysics Data System (ADS)

Coughlin, J. L.; Mullally, F.; Thompson, S. E.; Rowe, J. F.; Burke, C. J.; Latham, D. W.; Batalha, N. M.; Ofir, A.; Quarles, B. L.; Henze, C. E.; Wolfgang, A.; Caldwell, D. A.; Bryson, S. T.; Shporer, A.; Catanzarite, J.; Akeson, R.; Barclay, T.; Borucki, W. J.; Boyajian, T. S.; Campbell, J. R.; Christiansen, J. L.; Girouard, F. R.; Haas, M. R.; Howell, S. B.; Huber, D.; Jenkins, J. M.; Li, J.; Patil-Sabale, A.; Quintana, E. V.; Ramirez, S.; Seader, S.; Smith, J. C.; Tenenbaum, P.; Twicken, J. D.; Zamudio, K. A.

2016-07-01

This catalog is based on Kepler's 24th data release (DR24), which includes the processing of all data utilizing version 9.2 of the Kepler pipeline (Jenkins et al. 2010ApJ...724.1108J). This marks the first time that all of the Kepler mission data have been processed consistently with the same version of the Kepler pipeline. Over a period of 48 months (2009 May 13 to 2013 May 11), subdivided into 17 quarters (Q1-Q17), a total of 198646 targets were observed. (7 data files).

Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case.

PubMed

Amar, David; Frades, Itziar; Danek, Agnieszka; Goldberg, Tatyana; Sharma, Sanjeev K; Hedley, Pete E; Proux-Wera, Estelle; Andreasson, Erik; Shamir, Ron; Tzfadia, Oren; Alexandersson, Erik

2014-12-05

For most organisms, even if their genome sequence is available, little functional information about individual genes or proteins exists. Several annotation pipelines have been developed for functional analysis based on sequence, 'omics', and literature data. However, researchers encounter little guidance on how well they perform. Here, we used the recently sequenced potato genome as a case study. The potato genome was selected since its genome is newly sequenced and it is a non-model plant even if there is relatively ample information on individual potato genes, and multiple gene expression profiles are available. We show that the automatic gene annotations of potato have low accuracy when compared to a "gold standard" based on experimentally validated potato genes. Furthermore, we evaluate six state-of-the-art annotation pipelines and show that their predictions are markedly dissimilar (Jaccard similarity coefficient of 0.27 between pipelines on average). To overcome this discrepancy, we introduce a simple GO structure-based algorithm that reconciles the predictions of the different pipelines. We show that the integrated annotation covers more genes, increases by over 50% the number of highly co-expressed GO processes, and obtains much higher agreement with the gold standard. We find that different annotation pipelines produce different results, and show how to integrate them into a unified annotation that is of higher quality than each single pipeline. We offer an improved functional annotation of both PGSC and ITAG potato gene models, as well as tools that can be applied to additional pipelines and improve annotation in other organisms. This will greatly aid future functional analysis of '-omics' datasets from potato and other organisms with newly sequenced genomes. The new potato annotations are available with this paper.

SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read

PubMed Central

2010-01-01

Background High-throughput automated sequencing has enabled an exponential growth rate of sequencing data. This requires increasing sequence quality and reliability in order to avoid database contamination with artefactual sequences. The arrival of pyrosequencing enhances this problem and necessitates customisable pre-processing algorithms. Results SeqTrim has been implemented both as a Web and as a standalone command line application. Already-published and newly-designed algorithms have been included to identify sequence inserts, to remove low quality, vector, adaptor, low complexity and contaminant sequences, and to detect chimeric reads. The availability of several input and output formats allows its inclusion in sequence processing workflows. Due to its specific algorithms, SeqTrim outperforms other pre-processors implemented as Web services or standalone applications. It performs equally well with sequences from EST libraries, SSH libraries, genomic DNA libraries and pyrosequencing reads and does not lead to over-trimming. Conclusions SeqTrim is an efficient pipeline designed for pre-processing of any type of sequence read, including next-generation sequencing. It is easily configurable and provides a friendly interface that allows users to know what happened with sequences at every pre-processing stage, and to verify pre-processing of an individual sequence if desired. The recommended pipeline reveals more information about each sequence than previously described pre-processors and can discard more sequencing or experimental artefacts. PMID:20089148

An acceleration system for Laplacian image fusion based on SoC

NASA Astrophysics Data System (ADS)

Gao, Liwen; Zhao, Hongtu; Qu, Xiujie; Wei, Tianbo; Du, Peng

2018-04-01

Based on the analysis of Laplacian image fusion algorithm, this paper proposes a partial pipelining and modular processing architecture, and a SoC based acceleration system is implemented accordingly. Full pipelining method is used for the design of each module, and modules in series form the partial pipelining with unified data formation, which is easy for management and reuse. Integrated with ARM processor, DMA and embedded bare-mental program, this system achieves 4 layers of Laplacian pyramid on the Zynq-7000 board. Experiments show that, with small resources consumption, a couple of 256×256 images can be fused within 1ms, maintaining a fine fusion effect at the same time.

On the VLSI design of a pipeline Reed-Solomon decoder using systolic arrays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shao, H.M.; Reed, I.S.

A new VLSI design of a pipeline Reed-Solomon decoder is presented. The transform decoding technique used in a previous paper is replaced by a time domain algorithm through a detailed comparison of their VLSI implementations. A new architecture that implements the time domain algorithm permits efficient pipeline processing with reduced circuitry. Erasure correction capability is also incorporated with little additional complexity. By using a multiplexing technique, a new implementation of Euclid's algorithm maintains the throughput rate with less circuitry. Such improvements result in both enhanced capability and significant reduction in silicon area, therefore making it possible to build a pipelinemore » Reed-Solomon decoder on a single VLSI chip.« less

A Pipeline Software Architecture for NMR Spectrum Data Translation

PubMed Central

Ellis, Heidi J.C.; Weatherby, Gerard; Nowling, Ronald J.; Vyas, Jay; Fenwick, Matthew; Gryk, Michael R.

2012-01-01

The problem of formatting data so that it conforms to the required input for scientific data processing tools pervades scientific computing. The CONNecticut Joint University Research Group (CONNJUR) has developed a data translation tool based on a pipeline architecture that partially solves this problem. The CONNJUR Spectrum Translator supports data format translation for experiments that use Nuclear Magnetic Resonance to determine the structure of large protein molecules. PMID:24634607

A Parallel Pipelined Renderer for the Time-Varying Volume Data

NASA Technical Reports Server (NTRS)

Chiueh, Tzi-Cker; Ma, Kwan-Liu

1997-01-01

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.

Demons registration for in vivo and deformable laser scanning confocal endomicroscopy.

PubMed

Chiew, Wei-Ming; Lin, Feng; Seah, Hock Soon

2017-09-01

A critical effect found in noninvasive in vivo endomicroscopic imaging modalities is image distortions due to sporadic movement exhibited by living organisms. In three-dimensional confocal imaging, this effect results in a dataset that is tilted across deeper slices. Apart from that, the sequential flow of the imaging-processing pipeline restricts real-time adjustments due to the unavailability of information obtainable only from subsequent stages. To solve these problems, we propose an approach to render Demons-registered datasets as they are being captured, focusing on the coupling between registration and visualization. To improve the acquisition process, we also propose a real-time visual analytics tool, which complements the imaging pipeline and the Demons registration pipeline with useful visual indicators to provide real-time feedback for immediate adjustments. We highlight the problem of deformation within the visualization pipeline for object-ordered and image-ordered rendering. Visualizations of critical information including registration forces and partial renderings of the captured data are also presented in the analytics system. We demonstrate the advantages of the algorithmic design through experimental results with both synthetically deformed datasets and actual in vivo, time-lapse tissue datasets expressing natural deformations. Remarkably, this algorithm design is for embedded implementation in intelligent biomedical imaging instrumentation with customizable circuitry. (2017) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

East Spar: Alliance approach for offshore gasfield development

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1998-04-01

East spar is a gas/condensate field 25 miles west of Barrow Island, offshore Western Australia. Proved plus probable reserves at the time of development were estimated at 430 Bcf gas and 28 million bbl of condensate. The field was discovered in early 1993 when the Western Australia gas market was deregulated and the concept of a gas pipeline to the gold fields was proposed. This created a window of opportunity for East Spar, but only if plans could be established quickly. A base-case development plan was established to support gas marketing while alternative plans could be developed in parallel. Themore » completed East Spar facilities comprise two subsea wells, a subsea gathering system, and a multiphase (gas/condensate/water) pipeline to new gas-processing facilities. The subsea facilities are controlled through a navigation, communication, and control (NCC) buoy. The control room and gas-processing plant are 39 miles east of the field on Varanus Island. Sales gas is exported through a pre-existing gas-sales pipeline to the Dampier-Bunbury and Goldfields Gas Transmission pipelines. Condensate is stored in and exported by use of pre-existing facilities on Varanus Island. Field development from approval to first production took 22 months. The paper describes its field development.« less

Demons registration for in vivo and deformable laser scanning confocal endomicroscopy

NASA Astrophysics Data System (ADS)

Chiew, Wei Ming; Lin, Feng; Seah, Hock Soon

2017-09-01

A critical effect found in noninvasive in vivo endomicroscopic imaging modalities is image distortions due to sporadic movement exhibited by living organisms. In three-dimensional confocal imaging, this effect results in a dataset that is tilted across deeper slices. Apart from that, the sequential flow of the imaging-processing pipeline restricts real-time adjustments due to the unavailability of information obtainable only from subsequent stages. To solve these problems, we propose an approach to render Demons-registered datasets as they are being captured, focusing on the coupling between registration and visualization. To improve the acquisition process, we also propose a real-time visual analytics tool, which complements the imaging pipeline and the Demons registration pipeline with useful visual indicators to provide real-time feedback for immediate adjustments. We highlight the problem of deformation within the visualization pipeline for object-ordered and image-ordered rendering. Visualizations of critical information including registration forces and partial renderings of the captured data are also presented in the analytics system. We demonstrate the advantages of the algorithmic design through experimental results with both synthetically deformed datasets and actual in vivo, time-lapse tissue datasets expressing natural deformations. Remarkably, this algorithm design is for embedded implementation in intelligent biomedical imaging instrumentation with customizable circuitry.

Latest Development and Application of High Strength and Heavy Gauge Pipeline Steel in China

NASA Astrophysics Data System (ADS)

Yongqing, Zhang; Aimin, Guo; Chengjia, Shang; Qingyou, Liu; Gray, J. Malcolm; Barbaro, Frank

Over the past twenty years, significant advances have been made in the field of microalloying and associated application, among which one of the most successful application cases is HTP practice for heavy gauge, high strength pipeline steels. Combined the strengthening effects of TMCP and retardation effects of austenite recrystallization with increasing Nb in austenite region, HTP conception with low carbon and high niobium alloy design has been successfully applied to develop X80 coil with a thickness of 18.4mm used for China's Second West-East pipeline. During this process, big efforts were made to further develop and enrich the application of microalloying technology, and at the same time the strengthening effects of Nb have been completely unfolded and fully utilized with improved metallurgical quality and quantitative analysis of microstructure. In this paper, the existing status and strengthening effect of Nb during reheating, rolling, cooling and welding have been analyzed and characterized based on mass production samples and laboratory analysis. As confirmed, grain refinement remains the most basic strengthening measure to reduce the microstructure gradient along the thickness, which in turn enlarges the processing window to improve upon low temperature toughness, and finally make it possible to develop heavy gauge, high strength pipeline steels with more challenging fracture toughness requirements.

Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development.

PubMed

Kaczor-Urbanowicz, Karolina Elzbieta; Kim, Yong; Li, Feng; Galeev, Timur; Kitchen, Rob R; Gerstein, Mark; Koyano, Kikuye; Jeong, Sung-Hee; Wang, Xiaoyan; Elashoff, David; Kang, So Young; Kim, Su Mi; Kim, Kyoung; Kim, Sung; Chia, David; Xiao, Xinshu; Rozowsky, Joel; Wong, David T W

2018-01-01

Analysis of RNA sequencing (RNA-Seq) data in human saliva is challenging. Lack of standardization and unification of the bioinformatic procedures undermines saliva's diagnostic potential. Thus, it motivated us to perform this study. We applied principal pipelines for bioinformatic analysis of small RNA-Seq data of saliva of 98 healthy Korean volunteers including either direct or indirect mapping of the reads to the human genome using Bowtie1. Analysis of alignments to exogenous genomes by another pipeline revealed that almost all of the reads map to bacterial genomes. Thus, salivary exRNA has fundamental properties that warrant the design of unique additional steps while performing the bioinformatic analysis. Our pipelines can serve as potential guidelines for processing of RNA-Seq data of human saliva. Processing and analysis results of the experimental data generated by the exceRpt (v4.6.3) small RNA-seq pipeline (github.gersteinlab.org/exceRpt) are available from exRNA atlas (exrna-atlas.org). Alignment to exogenous genomes and their quantification results were used in this paper for the analyses of small RNAs of exogenous origin. dtww@ucla.edu. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Optimizing the TESS Planet Finding Pipeline

NASA Astrophysics Data System (ADS)

Chitamitara, Aerbwong; Smith, Jeffrey C.; Tenenbaum, Peter; TESS Science Processing Operations Center

2017-10-01

The Transiting Exoplanet Survey Satellite (TESS) is a new NASA planet finding all-sky survey that will observe stars within 200 light years and 10-100 times brighter than that of the highly successful Kepler mission. TESS is expected to detect ~1000 planets smaller than Neptune and dozens of Earth size planets. As in the Kepler mission, the Science Processing Operations Center (SPOC) processing pipeline at NASA Ames Research center is tasked with calibrating the raw pixel data, generating systematic error corrected light curves and then detecting and validating transit signals. The Transiting Planet Search (TPS) component of the pipeline must be modified and tuned for the new data characteristics in TESS. For example, due to each sector being viewed for as little as 28 days, the pipeline will be identifying transiting planets based on a minimum of two transit signals rather than three, as in the Kepler mission. This may result in a significantly higher false positive rate. The study presented here is to measure the detection efficiency of the TESS pipeline using simulated data. Transiting planets identified by TPS are compared to transiting planets from the simulated transit model using the measured epochs, periods, transit durations and the expected detection statistic of injected transit signals (expected MES). From the comparisons, the recovery and false positive rates of TPS is measured. Measurements of recovery in TPS are then used to adjust TPS configuration parameters to maximize the planet recovery rate and minimize false detections. The improvements in recovery rate between initial TPS conditions and after various adjustments will be presented and discussed.

Gap-free segmentation of vascular networks with automatic image processing pipeline.

PubMed

Hsu, Chih-Yang; Ghaffari, Mahsa; Alaraj, Ali; Flannery, Michael; Zhou, Xiaohong Joe; Linninger, Andreas

2017-03-01

Current image processing techniques capture large vessels reliably but often fail to preserve connectivity in bifurcations and small vessels. Imaging artifacts and noise can create gaps and discontinuity of intensity that hinders segmentation of vascular trees. However, topological analysis of vascular trees require proper connectivity without gaps, loops or dangling segments. Proper tree connectivity is also important for high quality rendering of surface meshes for scientific visualization or 3D printing. We present a fully automated vessel enhancement pipeline with automated parameter settings for vessel enhancement of tree-like structures from customary imaging sources, including 3D rotational angiography, magnetic resonance angiography, magnetic resonance venography, and computed tomography angiography. The output of the filter pipeline is a vessel-enhanced image which is ideal for generating anatomical consistent network representations of the cerebral angioarchitecture for further topological or statistical analysis. The filter pipeline combined with computational modeling can potentially improve computer-aided diagnosis of cerebrovascular diseases by delivering biometrics and anatomy of the vasculature. It may serve as the first step in fully automatic epidemiological analysis of large clinical datasets. The automatic analysis would enable rigorous statistical comparison of biometrics in subject-specific vascular trees. The robust and accurate image segmentation using a validated filter pipeline would also eliminate operator dependency that has been observed in manual segmentation. Moreover, manual segmentation is time prohibitive given that vascular trees have more than thousands of segments and bifurcations so that interactive segmentation consumes excessive human resources. Subject-specific trees are a first step toward patient-specific hemodynamic simulations for assessing treatment outcomes. Copyright © 2017 Elsevier Ltd. All rights reserved.

ADEPt, a semantically-enriched pipeline for extracting adverse drug events from free-text electronic health records.

PubMed

Iqbal, Ehtesham; Mallah, Robbie; Rhodes, Daniel; Wu, Honghan; Romero, Alvin; Chang, Nynn; Dzahini, Olubanke; Pandey, Chandra; Broadbent, Matthew; Stewart, Robert; Dobson, Richard J B; Ibrahim, Zina M

2017-01-01

Adverse drug events (ADEs) are unintended responses to medical treatment. They can greatly affect a patient's quality of life and present a substantial burden on healthcare. Although Electronic health records (EHRs) document a wealth of information relating to ADEs, they are frequently stored in the unstructured or semi-structured free-text narrative requiring Natural Language Processing (NLP) techniques to mine the relevant information. Here we present a rule-based ADE detection and classification pipeline built and tested on a large Psychiatric corpus comprising 264k patients using the de-identified EHRs of four UK-based psychiatric hospitals. The pipeline uses characteristics specific to Psychiatric EHRs to guide the annotation process, and distinguishes: a) the temporal value associated with the ADE mention (whether it is historical or present), b) the categorical value of the ADE (whether it is assertive, hypothetical, retrospective or a general discussion) and c) the implicit contextual value where the status of the ADE is deduced from surrounding indicators, rather than explicitly stated. We manually created the rulebase in collaboration with clinicians and pharmacists by studying ADE mentions in various types of clinical notes. We evaluated the open-source Adverse Drug Event annotation Pipeline (ADEPt) using 19 ADEs specific to antipsychotics and antidepressants medication. The ADEs chosen vary in severity, regularity and persistence. The average F-measure and accuracy achieved by our tool across all tested ADEs were 0.83 and 0.83 respectively. In addition to annotation power, the ADEPT pipeline presents an improvement to the state of the art context-discerning algorithm, ConText.

Fuzzy-based propagation of prior knowledge to improve large-scale image analysis pipelines

PubMed Central

Mikut, Ralf

2017-01-01

Many automatically analyzable scientific questions are well-posed and a variety of information about expected outcomes is available a priori. Although often neglected, this prior knowledge can be systematically exploited to make automated analysis operations sensitive to a desired phenomenon or to evaluate extracted content with respect to this prior knowledge. For instance, the performance of processing operators can be greatly enhanced by a more focused detection strategy and by direct information about the ambiguity inherent in the extracted data. We present a new concept that increases the result quality awareness of image analysis operators by estimating and distributing the degree of uncertainty involved in their output based on prior knowledge. This allows the use of simple processing operators that are suitable for analyzing large-scale spatiotemporal (3D+t) microscopy images without compromising result quality. On the foundation of fuzzy set theory, we transform available prior knowledge into a mathematical representation and extensively use it to enhance the result quality of various processing operators. These concepts are illustrated on a typical bioimage analysis pipeline comprised of seed point detection, segmentation, multiview fusion and tracking. The functionality of the proposed approach is further validated on a comprehensive simulated 3D+t benchmark data set that mimics embryonic development and on large-scale light-sheet microscopy data of a zebrafish embryo. The general concept introduced in this contribution represents a new approach to efficiently exploit prior knowledge to improve the result quality of image analysis pipelines. The generality of the concept makes it applicable to practically any field with processing strategies that are arranged as linear pipelines. The automated analysis of terabyte-scale microscopy data will especially benefit from sophisticated and efficient algorithms that enable a quantitative and fast readout. PMID:29095927

The Snow Data System at NASA JPL

NASA Astrophysics Data System (ADS)

Laidlaw, R.; Painter, T. H.; Mattmann, C. A.; Ramirez, P.; Bormann, K.; Brodzik, M. J.; Burgess, A. B.; Rittger, K.; Goodale, C. E.; Joyce, M.; McGibbney, L. J.; Zimdars, P.

2014-12-01

NASA JPL's Snow Data System has a data-processing pipeline powered by Apache OODT, an open source software tool. The pipeline has been running for several years and has successfully generated a significant amount of cryosphere data, including MODIS-based products such as MODSCAG, MODDRFS and MODICE, with historical and near-real time windows and covering regions such as the Artic, Western US, Alaska, Central Europe, Asia, South America, Australia and New Zealand. The team continues to improve the pipeline, using monitoring tools such as Ganglia to give an overview of operations, and improving fault-tolerance with automated recovery scripts. Several alternative adaptations of the Snow Covered Area and Grain size (SCAG) algorithm are being investigated. These include using VIIRS and Landsat TM/ETM+ satellite data as inputs. Parallel computing techniques are being considered for core SCAG processing, such as using the PyCUDA Python API to utilize multi-core GPU architectures. An experimental version of MODSCAG is also being developed for the Google Earth Engine platform, a cloud-based service.

Mapping of Brain Activity by Automated Volume Analysis of Immediate Early Genes.

PubMed

Renier, Nicolas; Adams, Eliza L; Kirst, Christoph; Wu, Zhuhao; Azevedo, Ricardo; Kohl, Johannes; Autry, Anita E; Kadiri, Lolahon; Umadevi Venkataraju, Kannan; Zhou, Yu; Wang, Victoria X; Tang, Cheuk Y; Olsen, Olav; Dulac, Catherine; Osten, Pavel; Tessier-Lavigne, Marc

2016-06-16

Understanding how neural information is processed in physiological and pathological states would benefit from precise detection, localization, and quantification of the activity of all neurons across the entire brain, which has not, to date, been achieved in the mammalian brain. We introduce a pipeline for high-speed acquisition of brain activity at cellular resolution through profiling immediate early gene expression using immunostaining and light-sheet fluorescence imaging, followed by automated mapping and analysis of activity by an open-source software program we term ClearMap. We validate the pipeline first by analysis of brain regions activated in response to haloperidol. Next, we report new cortical regions downstream of whisker-evoked sensory processing during active exploration. Last, we combine activity mapping with axon tracing to uncover new brain regions differentially activated during parenting behavior. This pipeline is widely applicable to different experimental paradigms, including animal species for which transgenic activity reporters are not readily available. Copyright © 2016 Elsevier Inc. All rights reserved.

Mapping of brain activity by automated volume analysis of immediate early genes

PubMed Central

Renier, Nicolas; Adams, Eliza L.; Kirst, Christoph; Wu, Zhuhao; Azevedo, Ricardo; Kohl, Johannes; Autry, Anita E.; Kadiri, Lolahon; Venkataraju, Kannan Umadevi; Zhou, Yu; Wang, Victoria X.; Tang, Cheuk Y.; Olsen, Olav; Dulac, Catherine; Osten, Pavel; Tessier-Lavigne, Marc

2016-01-01

Summary Understanding how neural information is processed in physiological and pathological states would benefit from precise detection, localization and quantification of the activity of all neurons across the entire brain, which has not to date been achieved in the mammalian brain. We introduce a pipeline for high speed acquisition of brain activity at cellular resolution through profiling immediate early gene expression using immunostaining and light-sheet fluorescence imaging, followed by automated mapping and analysis of activity by an open-source software program we term ClearMap. We validate the pipeline first by analysis of brain regions activated in response to Haloperidol. Next, we report new cortical regions downstream of whisker-evoked sensory processing during active exploration. Lastly, we combine activity mapping with axon tracing to uncover new brain regions differentially activated during parenting behavior. This pipeline is widely applicable to different experimental paradigms, including animal species for which transgenic activity reporters are not readily available. PMID:27238021

CamBAfx: Workflow Design, Implementation and Application for Neuroimaging

PubMed Central

Ooi, Cinly; Bullmore, Edward T.; Wink, Alle-Meije; Sendur, Levent; Barnes, Anna; Achard, Sophie; Aspden, John; Abbott, Sanja; Yue, Shigang; Kitzbichler, Manfred; Meunier, David; Maxim, Voichita; Salvador, Raymond; Henty, Julian; Tait, Roger; Subramaniam, Naresh; Suckling, John

2009-01-01

CamBAfx is a workflow application designed for both researchers who use workflows to process data (consumers) and those who design them (designers). It provides a front-end (user interface) optimized for data processing designed in a way familiar to consumers. The back-end uses a pipeline model to represent workflows since this is a common and useful metaphor used by designers and is easy to manipulate compared to other representations like programming scripts. As an Eclipse Rich Client Platform application, CamBAfx's pipelines and functions can be bundled with the software or downloaded post-installation. The user interface contains all the workflow facilities expected by consumers. Using the Eclipse Extension Mechanism designers are encouraged to customize CamBAfx for their own pipelines. CamBAfx wraps a workflow facility around neuroinformatics software without modification. CamBAfx's design, licensing and Eclipse Branding Mechanism allow it to be used as the user interface for other software, facilitating exchange of innovative computational tools between originating labs. PMID:19826470

[Character accentuations as a criterion for psychological risks in the professional activity of the builders of main gas pipelines in the conditions of arctic].

PubMed

Korneeva, Ia A; Simonova, N N

2015-01-01

The article is devoted to the study of character accentuations as a criterion for psychological risks in the professional activity of builders of main gas pipelines in the conditions of Arctic. to study the severity of character accentuations in rotation-employed builders of main gas pipelines, stipulated by their professional activities, as well as personal resources to overcome these destructions. The study involved 70 rotation-employed builders of trunk pipelines, working in the Tyumen Region (duration of the shift-in--52 days), aged from 23 to 59 (mean age 34,9 ± 8.1) years, with the experience of work from 0.5 years to 14 years (the average length of 4.42 ± 3.1). Methods of the study: questionnaires, psychological testing, participant observation. One-Sample t-test of Student, multiple regression analysis, incremental analysis. In the work there were revealed differences of expression of character accentuations in builders of trunk pipelines with experience in work on rotation less and more than five years. There was determined that builders of the main gas pipelines, working on the rotation in Arctic, with more pronounced accentuation ofthe character use mainly psychological defenses of compensation, substitution and denial, and have an average level of expression of flexibility as the regulatory process.

Status of the TESS Science Processing Operations Center

NASA Astrophysics Data System (ADS)

Jenkins, Jon Michael; Caldwell, Douglas A.; Davies, Misty; Li, Jie; Morris, Robert L.; Rose, Mark; Smith, Jeffrey C.; Tenenbaum, Peter; Ting, Eric; Twicken, Joseph D.; Wohler, Bill

2018-06-01

The Transiting Exoplanet Survey Satellite (TESS) was selected by NASA’s Explorer Program to conduct a search for Earth’s closest cousins starting in 2018. TESS will conduct an all-sky transit survey of F, G and K dwarf stars between 4 and 12 magnitudes and M dwarf stars within 200 light years. TESS is expected to discover 1,000 small planets less than twice the size of Earth, and to measure the masses of at least 50 of these small worlds. The TESS science pipeline is being developed by the Science Processing Operations Center (SPOC) at NASA Ames Research Center based on the highly successful Kepler science pipeline. Like the Kepler pipeline, the TESS pipeline provides calibrated pixels, simple and systematic error-corrected aperture photometry, and centroid locations for all 200,000+ target stars observed over the 2-year mission, along with associated uncertainties. The pixel and light curve products are modeled on the Kepler archive products and will be archived to the Mikulski Archive for Space Telescopes (MAST). In addition to the nominal science data, the 30-minute Full Frame Images (FFIs) simultaneously collected by TESS will also be calibrated by the SPOC and archived at MAST. The TESS pipeline searches through all light curves for evidence of transits that occur when a planet crosses the disk of its host star. The Data Validation pipeline generates a suite of diagnostic metrics for each transit-like signature, and then extracts planetary parameters by fitting a limb-darkened transit model to each potential planetary signature. The results of the transit search are modeled on the Kepler transit search products (tabulated numerical results, time series products, and pdf reports) all of which will be archived to MAST. Synthetic sample data products are available at https://archive.stsci.edu/tess/ete-6.html.Funding for the TESS Mission has been provided by the NASA Science Mission Directorate.

Study on quantitative risk assessment model of the third party damage for natural gas pipelines based on fuzzy comprehensive assessment

NASA Astrophysics Data System (ADS)

Qiu, Zeyang; Liang, Wei; Wang, Xue; Lin, Yang; Zhang, Meng

2017-05-01

As an important part of national energy supply system, transmission pipelines for natural gas are possible to cause serious environmental pollution, life and property loss in case of accident. The third party damage is one of the most significant causes for natural gas pipeline system accidents, and it is very important to establish an effective quantitative risk assessment model of the third party damage for reducing the number of gas pipelines operation accidents. Against the third party damage accident has the characteristics such as diversity, complexity and uncertainty, this paper establishes a quantitative risk assessment model of the third party damage based on Analytic Hierarchy Process (AHP) and Fuzzy Comprehensive Evaluation (FCE). Firstly, risk sources of third party damage should be identified exactly, and the weight of factors could be determined via improved AHP, finally the importance of each factor is calculated by fuzzy comprehensive evaluation model. The results show that the quantitative risk assessment model is suitable for the third party damage of natural gas pipelines and improvement measures could be put forward to avoid accidents based on the importance of each factor.

Wild Horse 69-kV transmission line environmental assessment

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1996-12-01

Hill County Electric Cooperative Inc. (Hill County) proposes to construct and operate a 69-kV transmission line from its North Gildford Substation in Montana north to the Canadian border. A vicinity project area map is enclosed as a figure. TransCanada Power Corporation (TCP), a Canadian power-marketing company, will own and construct the connecting 69-kV line from the international border to Express Pipeline`s pump station at Wild Horse, Alberta. This Environmental Assessment is prepared for the Department of Energy (DOE) as lead federal agency to comply with the requirements of the National Environmental Policy Act (NEPA), as part of DOE`s review andmore » approval process of the applications filed by Hill County for a DOE Presidential Permit and License to Export Electricity to a foreign country. The purpose of the proposed line is to supply electric energy to a crude oil pump station in Canada, owned by Express Pipeline Ltd. (Express). The pipeline would transport Canadian-produced oil from Hardisty, Alberta, Canada, to Caster, Wyoming. The Express Pipeline is scheduled to be constructed in 1996--97 and will supply crude oil to refineries in Wyoming and the midwest.« less

Ground motion values for use in the seismic design of the Trans-Alaska Pipeline system

USGS Publications Warehouse

Page, Robert A.; Boore, D.M.; Joyner, W.B.; Coulter, H.W.

1972-01-01

The proposed trans-Alaska oil pipeline, which would traverse the state north to south from Prudhoe Bay on the Arctic coast to Valdez on Prince William Sound, will be subject to serious earthquake hazards over much of its length. To be acceptable from an environmental standpoint, the pipeline system is to be designed to minimize the potential of oil leakage resulting from seismic shaking, faulting, and seismically induced ground deformation. The design of the pipeline system must accommodate the effects of earthquakes with magnitudes ranging from 5.5 to 8.5 as specified in the 'Stipulations for Proposed Trans-Alaskan Pipeline System.' This report characterizes ground motions for the specified earthquakes in terms of peak levels of ground acceleration, velocity, and displacement and of duration of shaking. Published strong motion data from the Western United States are critically reviewed to determine the intensity and duration of shaking within several kilometers of the slipped fault. For magnitudes 5 and 6, for which sufficient near-fault records are available, the adopted ground motion values are based on data. For larger earthquakes the values are based on extrapolations from the data for smaller shocks, guided by simplified theoretical models of the faulting process.

Implementation of Cloud based next generation sequencing data analysis in a clinical laboratory.

PubMed

Onsongo, Getiria; Erdmann, Jesse; Spears, Michael D; Chilton, John; Beckman, Kenneth B; Hauge, Adam; Yohe, Sophia; Schomaker, Matthew; Bower, Matthew; Silverstein, Kevin A T; Thyagarajan, Bharat

2014-05-23

The introduction of next generation sequencing (NGS) has revolutionized molecular diagnostics, though several challenges remain limiting the widespread adoption of NGS testing into clinical practice. One such difficulty includes the development of a robust bioinformatics pipeline that can handle the volume of data generated by high-throughput sequencing in a cost-effective manner. Analysis of sequencing data typically requires a substantial level of computing power that is often cost-prohibitive to most clinical diagnostics laboratories. To address this challenge, our institution has developed a Galaxy-based data analysis pipeline which relies on a web-based, cloud-computing infrastructure to process NGS data and identify genetic variants. It provides additional flexibility, needed to control storage costs, resulting in a pipeline that is cost-effective on a per-sample basis. It does not require the usage of EBS disk to run a sample. We demonstrate the validation and feasibility of implementing this bioinformatics pipeline in a molecular diagnostics laboratory. Four samples were analyzed in duplicate pairs and showed 100% concordance in mutations identified. This pipeline is currently being used in the clinic and all identified pathogenic variants confirmed using Sanger sequencing further validating the software.

A big data pipeline: Identifying dynamic gene regulatory networks from time-course Gene Expression Omnibus data with applications to influenza infection.

PubMed

Carey, Michelle; Ramírez, Juan Camilo; Wu, Shuang; Wu, Hulin

2018-07-01

A biological host response to an external stimulus or intervention such as a disease or infection is a dynamic process, which is regulated by an intricate network of many genes and their products. Understanding the dynamics of this gene regulatory network allows us to infer the mechanisms involved in a host response to an external stimulus, and hence aids the discovery of biomarkers of phenotype and biological function. In this article, we propose a modeling/analysis pipeline for dynamic gene expression data, called Pipeline4DGEData, which consists of a series of statistical modeling techniques to construct dynamic gene regulatory networks from the large volumes of high-dimensional time-course gene expression data that are freely available in the Gene Expression Omnibus repository. This pipeline has a consistent and scalable structure that allows it to simultaneously analyze a large number of time-course gene expression data sets, and then integrate the results across different studies. We apply the proposed pipeline to influenza infection data from nine studies and demonstrate that interesting biological findings can be discovered with its implementation.

Investigation of CO2 release pressures in pipeline cracks

NASA Astrophysics Data System (ADS)

Gorenz, Paul; Herzog, Nicoleta; Egbers, Christoph

2013-04-01

The CCS (Carbon Capture and Storage) technology can prevent or reduce the emissions of carbon dioxide. The main idea of this technology is the segregation and collection of CO2 from facilities with a high emission of that greenhouse gas, i.e. power plants which burn fossil fuels. To segregate CO2 from the exhaust gas the power plant must be upgraded. Up to now there are three possible procedures to segregate the carbon dioxide with different advantages and disadvantages. After segregation the carbon dioxide will be transported by pipeline to a subsurface storage location. As CO2 is at normal conditions (1013,25 Pa; 20 °C) in a gaseous phase state it must be set under high pressure to enter denser phase states to make a more efficient pipeline transport possible. Normally the carbon dioxide is set into the liquid or supercritical phase state by compressor stations which compress the gas up to 15 MPa. The pressure drop makes booster stations along the pipeline necessary which keep the CO2 in a dens phase state. Depending on the compression pressure CO2 can be transported over 300km without any booster station. The goal of this work is the investigation of release pressures in pipeline cracks. The high pressurised pipeline system consists of different parts with different failure probabilities. In most cases corrosion or obsolescence is the reason for pipeline damages. In case of a crack CO2 will escape from the pipeline and disperse into the atmosphere. Due to its nature CO2 can remain unattended for a long time. There are some studies of the CO2 dispersion process, e.g. Mazzoldi et al. (2007, 2008 and 2011) and Wang et al. (2008), but with different assumptions concerning the pipeline release pressures. To give an idea of realistic release pressures investigations with the CFD tool OpenFOAM were carried out and are presented within this work. To cover such a scenario with an accidental release of carbon dioxide a pipeline section with different diameters and leakage release holes were modelled. This pipeline section is 10m long with the leakage hole in the middle. Additionally a small environment subdomain is simulated around the crack. For computation a multiphase solver was utilised. In a first step incompressible and isothermal fluids with no phase change were assumed.

The Herschel Data Processing System - Hipe And Pipelines - During The Early Mission Phase

NASA Astrophysics Data System (ADS)

Ardila, David R.; Herschel Science Ground Segment Consortium

2010-01-01

The Herschel Space Observatory, the fourth cornerstone mission in the ESA science program, was launched 14th of May 2009. With a 3.5 m telescope, it is the largest space telescope ever launched. Herschel's three instruments (HIFI, PACS, and SPIRE) perform photometry and spectroscopy in the 55 - 672 micron range and will deliver exciting science for the astronomical community during at least three years of routine observations. Here we summarize the state of the Herschel Data Processing System and give an overview about future development milestones and plans. The development of the Herschel Data Processing System started seven years ago to support the data analysis for Instrument Level Tests. Resources were made available to implement a freely distributable Data Processing System capable of interactively and automatically reduce Herschel data at different processing levels. The system combines data retrieval, pipeline execution and scientific analysis in one single environment. The software is coded in Java and Jython to be platform independent and to avoid the need for commercial licenses. The Herschel Interactive Processing Environment (HIPE) is the user-friendly face of Herschel Data Processing. The first PACS preview observation of M51 was processed with HIPE, using basic pipeline scripts to a fantastic image within 30 minutes of data reception. Also the first HIFI observations on DR-21 were successfully reduced to high quality spectra, followed by SPIRE observations on M66 and M74. The Herschel Data Processing System is a joint development by the Herschel Science Ground Segment Consortium, consisting of ESA, the NASA Herschel Science Center, and the HIFI, PACS and SPIRE consortium members.

A method for simulating the entire leaking process and calculating the liquid leakage volume of a damaged pressurized pipeline.

PubMed

He, Guoxi; Liang, Yongtu; Li, Yansong; Wu, Mengyu; Sun, Liying; Xie, Cheng; Li, Feng

2017-06-15

The accidental leakage of long-distance pressurized oil pipelines is a major area of risk, capable of causing extensive damage to human health and environment. However, the complexity of the leaking process, with its complex boundary conditions, leads to difficulty in calculating the leakage volume. In this study, the leaking process is divided into 4 stages based on the strength of transient pressure. 3 models are established to calculate the leaking flowrate and volume. First, a negative pressure wave propagation attenuation model is applied to calculate the sizes of orifices. Second, a transient oil leaking model, consisting of continuity, momentum conservation, energy conservation and orifice flow equations, is built to calculate the leakage volume. Third, a steady-state oil leaking model is employed to calculate the leakage after valves and pumps shut down. Moreover, sensitive factors that affect the leak coefficient of orifices and volume are analyzed respectively to determine the most influential one. To validate the numerical simulation, two types of leakage test with different sizes of leakage holes were conducted from Sinopec product pipelines. More validations were carried out by applying commercial software to supplement the experimental insufficiency. Thus, the leaking process under different leaking conditions are described and analyzed. Copyright © 2017 Elsevier B.V. All rights reserved.

PANGEA: pipeline for analysis of next generation amplicons.

PubMed

Giongo, Adriana; Crabb, David B; Davis-Richardson, Austin G; Chauliac, Diane; Mobberley, Jennifer M; Gano, Kelsey A; Mukherjee, Nabanita; Casella, George; Roesch, Luiz F W; Walts, Brandon; Riva, Alberto; King, Gary; Triplett, Eric W

2010-07-01

High-throughput DNA sequencing can identify organisms and describe population structures in many environmental and clinical samples. Current technologies generate millions of reads in a single run, requiring extensive computational strategies to organize, analyze and interpret those sequences. A series of bioinformatics tools for high-throughput sequencing analysis, including pre-processing, clustering, database matching and classification, have been compiled into a pipeline called PANGEA. The PANGEA pipeline was written in Perl and can be run on Mac OSX, Windows or Linux. With PANGEA, sequences obtained directly from the sequencer can be processed quickly to provide the files needed for sequence identification by BLAST and for comparison of microbial communities. Two different sets of bacterial 16S rRNA sequences were used to show the efficiency of this workflow. The first set of 16S rRNA sequences is derived from various soils from Hawaii Volcanoes National Park. The second set is derived from stool samples collected from diabetes-resistant and diabetes-prone rats. The workflow described here allows the investigator to quickly assess libraries of sequences on personal computers with customized databases. PANGEA is provided for users as individual scripts for each step in the process or as a single script where all processes, except the chi(2) step, are joined into one program called the 'backbone'.

High performance pipelined multiplier with fast carry-save adder

NASA Technical Reports Server (NTRS)

Wu, Angus

1990-01-01

A high-performance pipelined multiplier is described. Its high performance results from the fast carry-save adder basic cell which has a simple structure and is suitable for the Gate Forest semi-custom environment. The carry-save adder computes the sum and carry within two gate delay. Results show that the proposed adder can operate at 200 MHz for a 2-micron CMOS process; better performance is expected in a Gate Forest realization.

A Spatial Risk Analysis of Oil Refineries within the United States

DTIC Science & Technology

2012-03-01

regulator and consumer. This is especially true within the energy sector which is composed of electrical power, oil , and gas infrastructure [10...Naphtali, "Analysis of Electrical Power and Oil and Gas Pipeline Failures," in International Federation for Information Processing, E. Goetz and S...61-67, September 1999. [5] J. Simonoff, C. Restrepo, R. Zimmerman, and Z. Naphtali, "Analysis of Electrical Power and Oil and Gas Pipeline Failures

Turning Noise into Signal: Utilizing Impressed Pipeline Currents for EM Exploration

NASA Astrophysics Data System (ADS)

Lindau, Tobias; Becken, Michael

2017-04-01

Impressed Current Cathodic Protection (ICCP) systems are extensively used for the protection of central Europe's dense network of oil-, gas- and water pipelines against destruction by electrochemical corrosion. While ICCP systems usually provide protection by injecting a DC current into the pipeline, mandatory pipeline integrity surveys demand a periodical switching of the current. Consequently, the resulting time varying pipe currents induce secondary electric- and magnetic fields in the surrounding earth. While these fields are usually considered to be unwanted cultural noise in electromagnetic exploration, this work aims at utilizing the fields generated by the ICCP system for determining the electrical resistivity of the subsurface. The fundamental period of the switching cycles typically amounts to 15 seconds in Germany and thereby roughly corresponds to periods used in controlled source EM applications (CSEM). For detailed studies we chose an approximately 30km long pipeline segment near Herford, Germany as a test site. The segment is located close to the southern margin of the Lower Saxony Basin (LSB) and part of a larger gas pipeline composed of multiple segments. The current injected into the pipeline segment originates in a rectified 50Hz AC signal which is periodically switched on and off. In contrast to the usual dipole sources used in CSEM surveys, the current distribution along the pipeline is unknown and expected to be non-uniform due to coating defects that cause current to leak into the surrounding soil. However, an accurate current distribution is needed to model the fields generated by the pipeline source. We measured the magnetic fields at several locations above the pipeline and used Biot-Savarts-Law to estimate the currents decay function. The resulting frequency dependent current distribution shows a current decay away from the injection point as well as a frequency dependent phase shift which is increasing with distance from the injection point. Electric field data were recorded at 45 stations located in an area of about 60 square kilometers in the vicinity to the pipeline. Additionally, the injected source current was recorded directly at the injection point. Transfer functions between the local electric fields and the injected source current are estimated for frequencies ranging from 0.03Hz to 15Hz using robust time series processing techniques. The resulting transfer functions are inverted for a 3D conductivity model of the subsurface using an elaborate pipeline model. We interpret the model with regards to the local geologic setting, demonstrating the methods capabilities to image the subsurface.

dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments.

PubMed

Petukhov, Viktor; Guo, Jimin; Baryawno, Ninib; Severe, Nicolas; Scadden, David T; Samsonova, Maria G; Kharchenko, Peter V

2018-06-19

Recent single-cell RNA-seq protocols based on droplet microfluidics use massively multiplexed barcoding to enable simultaneous measurements of transcriptomes for thousands of individual cells. The increasing complexity of such data creates challenges for subsequent computational processing and troubleshooting of these experiments, with few software options currently available. Here, we describe a flexible pipeline for processing droplet-based transcriptome data that implements barcode corrections, classification of cell quality, and diagnostic information about the droplet libraries. We introduce advanced methods for correcting composition bias and sequencing errors affecting cellular and molecular barcodes to provide more accurate estimates of molecular counts in individual cells.

Building a common pipeline for rule-based document classification.

PubMed

Patterson, Olga V; Ginter, Thomas; DuVall, Scott L

2013-01-01

Instance-based classification of clinical text is a widely used natural language processing task employed as a step for patient classification, document retrieval, or information extraction. Rule-based approaches rely on concept identification and context analysis in order to determine the appropriate class. We propose a five-step process that enables even small research teams to develop simple but powerful rule-based NLP systems by taking advantage of a common UIMA AS based pipeline for classification. Our proposed methodology coupled with the general-purpose solution provides researchers with access to the data locked in clinical text in cases of limited human resources and compact timelines.

MICCA: a complete and accurate software for taxonomic profiling of metagenomic data.

PubMed

Albanese, Davide; Fontana, Paolo; De Filippo, Carlotta; Cavalieri, Duccio; Donati, Claudio

2015-05-19

The introduction of high throughput sequencing technologies has triggered an increase of the number of studies in which the microbiota of environmental and human samples is characterized through the sequencing of selected marker genes. While experimental protocols have undergone a process of standardization that makes them accessible to a large community of scientist, standard and robust data analysis pipelines are still lacking. Here we introduce MICCA, a software pipeline for the processing of amplicon metagenomic datasets that efficiently combines quality filtering, clustering of Operational Taxonomic Units (OTUs), taxonomy assignment and phylogenetic tree inference. MICCA provides accurate results reaching a good compromise among modularity and usability. Moreover, we introduce a de-novo clustering algorithm specifically designed for the inference of Operational Taxonomic Units (OTUs). Tests on real and synthetic datasets shows that thanks to the optimized reads filtering process and to the new clustering algorithm, MICCA provides estimates of the number of OTUs and of other common ecological indices that are more accurate and robust than currently available pipelines. Analysis of public metagenomic datasets shows that the higher consistency of results improves our understanding of the structure of environmental and human associated microbial communities. MICCA is an open source project.

MICCA: a complete and accurate software for taxonomic profiling of metagenomic data

PubMed Central

Albanese, Davide; Fontana, Paolo; De Filippo, Carlotta; Cavalieri, Duccio; Donati, Claudio

2015-01-01

The introduction of high throughput sequencing technologies has triggered an increase of the number of studies in which the microbiota of environmental and human samples is characterized through the sequencing of selected marker genes. While experimental protocols have undergone a process of standardization that makes them accessible to a large community of scientist, standard and robust data analysis pipelines are still lacking. Here we introduce MICCA, a software pipeline for the processing of amplicon metagenomic datasets that efficiently combines quality filtering, clustering of Operational Taxonomic Units (OTUs), taxonomy assignment and phylogenetic tree inference. MICCA provides accurate results reaching a good compromise among modularity and usability. Moreover, we introduce a de-novo clustering algorithm specifically designed for the inference of Operational Taxonomic Units (OTUs). Tests on real and synthetic datasets shows that thanks to the optimized reads filtering process and to the new clustering algorithm, MICCA provides estimates of the number of OTUs and of other common ecological indices that are more accurate and robust than currently available pipelines. Analysis of public metagenomic datasets shows that the higher consistency of results improves our understanding of the structure of environmental and human associated microbial communities. MICCA is an open source project. PMID:25988396

Infrared thermography for inspecting of pipeline specimen

NASA Astrophysics Data System (ADS)

Chen, Dapeng; Li, Xiaoli; Sun, Zuoming; Zhang, Xiaolong

2018-02-01

Infrared thermography is a fast and effective non-destructive testing method, which has an increasing application in the field of Aeronautics, Astronautic, architecture and medical, et al. Most of the reports about the application of this technology are focus on the specimens of planar, pulse light is often used as the heat stimulation and a plane heat source is generated on the surface of the specimen by the using of a lampshade, however, this method is not suitable for the specimen of non-planar, such as the pipeline. Therefore, in this paper, according the NDT problem of a steel and composite pipeline specimen, ultrasonic and hot water are applied as the heat source respectively, and an IR camera is used to record the temperature varies of the surface of the specimen, defects are revealed by the thermal images sequence processing. Furthermore, the results of light pulse thermography are also shown as comparison, it is indicated that choose the right stimulation method, can get a more effective NDT results for the pipeline specimen.

Leakage detection in galvanized iron pipelines using ensemble empirical mode decomposition analysis

NASA Astrophysics Data System (ADS)

Amin, Makeen; Ghazali, M. Fairusham

2015-05-01

There are many numbers of possible approaches to detect leaks. Some leaks are simply noticeable when the liquids or water appears on the surface. However many leaks do not find their way to the surface and the existence has to be check by analysis of fluid flow in the pipeline. The first step is to determine the approximate position of leak. This can be done by isolate the sections of the mains in turn and noting which section causes a drop in the flow. Next approach is by using sensor to locate leaks. This approach are involves strain gauge pressure transducers and piezoelectric sensor. the occurrence of leaks and know its exact location in the pipeline by using specific method which are Acoustic leak detection method and transient method. The objective is to utilize the signal processing technique in order to analyse leaking in the pipeline. With this, an EEMD method will be applied as the analysis method to collect and analyse the data.

Crystallographic data processing for free-electron laser sources

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Thomas A., E-mail: taw@physics.org; Barty, Anton; Stellato, Francesco

2013-07-01

A processing pipeline for diffraction data acquired using the ‘serial crystallography’ methodology with a free-electron laser source is described with reference to the crystallographic analysis suite CrystFEL and the pre-processing program Cheetah. A processing pipeline for diffraction data acquired using the ‘serial crystallography’ methodology with a free-electron laser source is described with reference to the crystallographic analysis suite CrystFEL and the pre-processing program Cheetah. A detailed analysis of the nature and impact of indexing ambiguities is presented. Simulations of the Monte Carlo integration scheme, which accounts for the partially recorded nature of the diffraction intensities, are presented and show thatmore » the integration of partial reflections could be made to converge more quickly if the bandwidth of the X-rays were to be increased by a small amount or if a slight convergence angle were introduced into the incident beam.« less

Thunder Energy Inc. applications to modify an existing sweet gas processing facility to a sour gas processing facility and increase the hydrogen sulfide concentration of existing pipelines, Kelsey area: Examiner report 98-2, application numbers 1007719 and 1013399

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

Thunder Energy Inc. received approval from the Alberta Energy and Utilities Board for modification of an existing gas plant to process sour gas, and also applied for permission to increase the hydrogen sulfide content of its existing pipelines in the Kelsey area. This report presents the views of Thunder Energy, the Board, and various intervenors at a hearing held to consider objections to the plant approval and matters related to the application. Issues considered include the need for sour gas processing, the need for the plant modification as opposed to the feasibility of using existing sour gas processing facilities, environmentalmore » impacts, and the requirements for notification of industry in the area. The report concludes with the Board`s decision.« less

Developing an ESIP-wide Process "Pipeline" to Extract Data-driven Stories from Compelling Agriculture and Energy Research on Climate Resilience

NASA Astrophysics Data System (ADS)

Hoebelheinrich, N. J.; Eckman, R.; Teng, W. L.; Beltz, C.

2016-12-01

The classic approach to scientific storytelling, especially for publication, is to establish the research problem, describe the potential solution and the efforts to solve the problem, and end with the results - whether "successful" or not - as the "Ta Da!" of the story. This classic approach, however, does not necessarily adapt well to the kind of storytelling that policy-making and general public end-users find more compelling, i.e., with the "Ta Da!" element of the story immediately evident. Working with the U.S. Climate Resilience Toolkit (CRT) staff, two collaborative groups of the Earth Science Information Partners (ESIP), Agriculture and Climate and Energy and Climate, have begun to assist agriculture and energy researchers in making the switch in story telling approach and, thus, get more easily understood and actionable information out to potential end-users about how the research data produced can help them. The CRT is a platform for telling stories based on both end-user needs and the data that are used to meet those needs. The ESIP groups are establishing an ESIP-wide process "pipeline," through which research results and data, with the help of group discussions and the use of CRT templates, are transformed into potential stories. When appropriate, the stories are handed off to the CRT staff to be fully developed. Two case studies that are in the process of being added to the CRT involve (1) the use of the RETScreen tool by Natural Resources Canada and (2) a fallow lands mapping project with the California Department of Water Resources to monitor ongoing drought conditions in California. These two case studies will be used to illustrate the process pipeline being developed, discuss lessons learned to date, and suggest future plans for further refining and expanding the process "pipeline."

High-throughput neuroimaging-genetics computational infrastructure

PubMed Central

Dinov, Ivo D.; Petrosyan, Petros; Liu, Zhizhong; Eggert, Paul; Hobel, Sam; Vespa, Paul; Woo Moon, Seok; Van Horn, John D.; Franco, Joseph; Toga, Arthur W.

2014-01-01

Many contemporary neuroscientific investigations face significant challenges in terms of data management, computational processing, data mining, and results interpretation. These four pillars define the core infrastructure necessary to plan, organize, orchestrate, validate, and disseminate novel scientific methods, computational resources, and translational healthcare findings. Data management includes protocols for data acquisition, archival, query, transfer, retrieval, and aggregation. Computational processing involves the necessary software, hardware, and networking infrastructure required to handle large amounts of heterogeneous neuroimaging, genetics, clinical, and phenotypic data and meta-data. Data mining refers to the process of automatically extracting data features, characteristics and associations, which are not readily visible by human exploration of the raw dataset. Result interpretation includes scientific visualization, community validation of findings and reproducible findings. In this manuscript we describe the novel high-throughput neuroimaging-genetics computational infrastructure available at the Institute for Neuroimaging and Informatics (INI) and the Laboratory of Neuro Imaging (LONI) at University of Southern California (USC). INI and LONI include ultra-high-field and standard-field MRI brain scanners along with an imaging-genetics database for storing the complete provenance of the raw and derived data and meta-data. In addition, the institute provides a large number of software tools for image and shape analysis, mathematical modeling, genomic sequence processing, and scientific visualization. A unique feature of this architecture is the Pipeline environment, which integrates the data management, processing, transfer, and visualization. Through its client-server architecture, the Pipeline environment provides a graphical user interface for designing, executing, monitoring validating, and disseminating of complex protocols that utilize diverse suites of software tools and web-services. These pipeline workflows are represented as portable XML objects which transfer the execution instructions and user specifications from the client user machine to remote pipeline servers for distributed computing. Using Alzheimer's and Parkinson's data, we provide several examples of translational applications using this infrastructure1. PMID:24795619

Automatic detection of surface changes on Mars - a status report

NASA Astrophysics Data System (ADS)

Sidiropoulos, Panagiotis; Muller, Jan-Peter

2016-10-01

Orbiter missions have acquired approximately 500,000 high-resolution visible images of the Martian surface, covering an area approximately 6 times larger than the overall area of Mars. This data abundance allows the scientific community to examine the Martian surface thoroughly and potentially make exciting new discoveries. However, the increased data volume, as well as its complexity, generate problems at the data processing stages, which are mainly related to a number of unresolved issues that batch-mode planetary data processing presents. As a matter of fact, the scientific community is currently struggling to scale the common ("one-at-a-time" processing of incoming products by expert scientists) paradigm to tackle the large volumes of input data. Moreover, expert scientists are more or less forced to use complex software in order to extract input information for their research from raw data, even though they are not data scientists themselves.Our work within the STFC and EU FP7 i-Mars projects aims at developing automated software that will process all of the acquired data, leaving domain expert planetary scientists to focus on their final analysis and interpretation. Moreover, after completing the development of a fully automated pipeline that processes automatically the co-registration of high-resolution NASA images to ESA/DLR HRSC baseline, our main goal has shifted to the automated detection of surface changes on Mars. In particular, we are developing a pipeline that uses as an input multi-instrument image pairs, which are processed by an automated pipeline, in order to identify changes that are correlated with Mars surface dynamic phenomena. The pipeline has currently been tested in anger on 8,000 co-registered images and by the time of DPS/EPSC we expect to have processed many tens of thousands of image pairs, producing a set of change detection results, a subset of which will be shown in the presentation.The research leading to these results has received funding from the STFC "MSSL Consolidated Grant under "Planetary Surface Data Mining" ST/K000977/1 and partial support from the European Union's Seventh Framework Programme (FP7/2007-2013) under iMars grant agreement number 607379

The Next Generation of HLA Image Products

NASA Astrophysics Data System (ADS)

Gaffney, N. I.; Casertano, S.; Ferguson, B.

2012-09-01

We present the re-engineered pipeline based on existing and improved algorithms with the aim of improving processing quality, cross-instrument portability, data flow management, and software maintenance. The Hubble Legacy Archive (HLA) is a project to add value to the Hubble Space Telescope data archive by producing and delivering science-ready drizzled data products and source lists derived from these products. Initially, ACS, NICMOS, and WFCP2 data were combined using instrument-specific pipelines based on scripts developed to process the ACS GOODS data and a separate set of scripts to generate source extractor and DAOPhot source lists. The new pipeline, initially designed for WFC3 data, isolates instrument-specific processing and is easily extendable to other instruments and to generating wide-area mosaics. Significant improvements have been made in image combination using improved alignment, source detection, and background equalization routines. It integrates improved alignment procedures, better noise model, and source list generation within a single code base. Wherever practical, PyRAF based routines have been replaced with non-IRAF based python libraries (e.g. NumPy and PyFITS). The data formats have been modified to handle better and more consistent propagation of information from individual exposures to the combined products. A new exposure layer stores the effective exposure time for each pixel in the sky which is key in properly interpreting combined images from diverse data that were not initially planned to be mosaiced. We worked to improve the validity of the metadata within our FITS headers for these products relative to standard IRAF/PyRAF processing. Any keywords that pertain to individual exposures have been removed from the primary and extension headers and placed in a table extension for more direct and efficient perusal. This mechanism also allows for more detailed information on the processing of individual images to be stored and propagated providing a more hierarchical metadata storage system than key value pair FITS headers provide. In this poster we will discuss the changes to the pipeline processing and source list generation and the lessons learned which may be applicable to other archive projects as well as discuss our new metadata curation and preservation process.

Detection of Legionella, L. pneumophila and Mycobacterium Avium Complex (MAC) along Potable Water Distribution Pipelines

PubMed Central

Whiley, Harriet; Keegan, Alexandra; Fallowfield, Howard; Bentham, Richard

2014-01-01

Inhalation of potable water presents a potential route of exposure to opportunistic pathogens and hence warrants significant public health concern. This study used qPCR to detect opportunistic pathogens Legionella spp., L. pneumophila and MAC at multiple points along two potable water distribution pipelines. One used chlorine disinfection and the other chloramine disinfection. Samples were collected four times over the year to provide seasonal variation and the chlorine or chloramine residual was measured during collection. Legionella spp., L. pneumophila and MAC were detected in both distribution systems throughout the year and were all detected at a maximum concentration of 103 copies/mL in the chlorine disinfected system and 106, 103 and 104 copies/mL respectively in the chloramine disinfected system. The concentrations of these opportunistic pathogens were primarily controlled throughout the distribution network through the maintenance of disinfection residuals. At a dead-end and when the disinfection residual was not maintained significant (p < 0.05) increases in concentration were observed when compared to the concentration measured closest to the processing plant in the same pipeline and sampling period. Total coliforms were not present in any water sample collected. This study demonstrates the ability of Legionella spp., L. pneumophila and MAC to survive the potable water disinfection process and highlights the need for greater measures to control these organisms along the distribution pipeline and at point of use. PMID:25046636

Transiting exoplanet candidates from K2 Campaigns 5 and 6

NASA Astrophysics Data System (ADS)

Pope, Benjamin J. S.; Parviainen, Hannu; Aigrain, Suzanne

2016-10-01

We introduce a new transit search and vetting pipeline for observations from the K2 mission, and present the candidate transiting planets identified by this pipeline out of the targets in Campaigns 5 and 6. Our pipeline uses the Gaussian process-based K2SC code to correct for the K2 pointing systematics and simultaneously model stellar variability. The systematics-corrected, variability-detrended light curves are searched for transits with the box-least-squares method, and a period-dependent detection threshold is used to generate a preliminary candidate list. Two or three individuals vet each candidate manually to produce the final candidate list, using a set of automatically generated transit fits and assorted diagnostic tests to inform the vetting. We detect 145 single-planet system candidates and 5 multi-planet systems, independently recovering the previously published hot Jupiters EPIC 212110888b, WASP-55b (EPIC 212300977b) and Qatar-2b (EPIC 212756297b). We also report the outcome of reconnaissance spectroscopy carried out for all candidates with Kepler magnitude Kp ≤ 13, identifying 12 targets as likely false positives. We compare our results to those of other K2 transit search pipelines, noting that ours performs particularly well for variable and/or active stars, but that the results are very similar overall. All the light curves and code used in the transit search and vetting process are publicly available, as are the follow-up spectra.

Detection of Legionella, L. pneumophila and Mycobacterium avium complex (MAC) along potable water distribution pipelines.

PubMed

Whiley, Harriet; Keegan, Alexandra; Fallowfield, Howard; Bentham, Richard

2014-07-18

Inhalation of potable water presents a potential route of exposure to opportunistic pathogens and hence warrants significant public health concern. This study used qPCR to detect opportunistic pathogens Legionella spp., L. pneumophila and MAC at multiple points along two potable water distribution pipelines. One used chlorine disinfection and the other chloramine disinfection. Samples were collected four times over the year to provide seasonal variation and the chlorine or chloramine residual was measured during collection. Legionella spp., L. pneumophila and MAC were detected in both distribution systems throughout the year and were all detected at a maximum concentration of 103 copies/mL in the chlorine disinfected system and 106, 103 and 104 copies/mL respectively in the chloramine disinfected system. The concentrations of these opportunistic pathogens were primarily controlled throughout the distribution network through the maintenance of disinfection residuals. At a dead-end and when the disinfection residual was not maintained significant (p < 0.05) increases in concentration were observed when compared to the concentration measured closest to the processing plant in the same pipeline and sampling period. Total coliforms were not present in any water sample collected. This study demonstrates the ability of Legionella spp., L. pneumophila and MAC to survive the potable water disinfection process and highlights the need for greater measures to control these organisms along the distribution pipeline and at point of use.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pallesen, T.R.; Braestrup, M.W.; Jorgensen, O.

Development of Danish North Sea hydrocarbon resources includes the 17-km Rolf pipeline installed in 1985. This one consists of an insulated 8-in. two-phase flow product line with a 3-in. piggyback gas lift line. A practical solution to design of this insulated pipeline, including the small diameter, piggyback injection line was corrosion coating of fusion bonded epoxy (FBE) and polyethylene (PE) sleeve pipe. The insulation design prevents hydrate formation under the most conservative flow regime during gas lift production. Also, the required minimum flow rate during the initial natural lift period is well below the value anticipiated at the initiation ofmore » gas lift. The weight coating design ensures stability on the seabed during the summer months only; thus trenching was required during the same installation season. Installation of insulated flowlines serving marginal fields is a significant feature of North Sea hydrocarbon development projects. The Skjold field is connected to Gorm by a 6-in., two-phase-flow line. The 11-km line was installed in 1982 as the first insulated pipeline in the North Sea. The Rolf field, located 17 km west of Gorm, went on stream Jan. 2. The development includes an unmanned wellhead platform and an insulated, two-phase-flow pipeline to the Gorm E riser platform. After separation on the Gorm C process platform, the oil and condensate are transported to shore through the 20-in. oil pipeline, and the natural gas is piped to Tyra for transmission through the 30-in. gas pipeline. Oil production at Rolf is assisted by the injection of lift gas, transported from Gorm through a 3-in. pipeline, installed piggyback on the insulated 8-in. product line. The seabed is smooth and sandy, the water depth varying between 33.7 m (110.5 ft) at Rolf and 39.1 m (128 ft) at Gorm.« less

An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.

PubMed

Wang, Zichen; Ma'ayan, Avi

2016-01-01

RNA-seq analysis is becoming a standard method for global gene expression profiling. However, open and standard pipelines to perform RNA-seq analysis by non-experts remain challenging due to the large size of the raw data files and the hardware requirements for running the alignment step. Here we introduce a reproducible open source RNA-seq pipeline delivered as an IPython notebook and a Docker image. The pipeline uses state-of-the-art tools and can run on various platforms with minimal configuration overhead. The pipeline enables the extraction of knowledge from typical RNA-seq studies by generating interactive principal component analysis (PCA) and hierarchical clustering (HC) plots, performing enrichment analyses against over 90 gene set libraries, and obtaining lists of small molecules that are predicted to either mimic or reverse the observed changes in mRNA expression. We apply the pipeline to a recently published RNA-seq dataset collected from human neuronal progenitors infected with the Zika virus (ZIKV). In addition to confirming the presence of cell cycle genes among the genes that are downregulated by ZIKV, our analysis uncovers significant overlap with upregulated genes that when knocked out in mice induce defects in brain morphology. This result potentially points to the molecular processes associated with the microcephaly phenotype observed in newborns from pregnant mothers infected with the virus. In addition, our analysis predicts small molecules that can either mimic or reverse the expression changes induced by ZIKV. The IPython notebook and Docker image are freely available at:  http://nbviewer.jupyter.org/github/maayanlab/Zika-RNAseq-Pipeline/blob/master/Zika.ipynb and  https://hub.docker.com/r/maayanlab/zika/.

Education biographies from the science pipeline: An analysis of Latino/a student perspectives on ethnic and gender identity in higher education

NASA Astrophysics Data System (ADS)

Lujan, Vanessa Beth

This study is a qualitative narrative analysis on the importance and relevance of the ethnic and gender identities of 17 Latino/a (Hispanic) college students in the biological sciences. This research study asks the question of how one's higher education experience within the science pipeline shapes an individual's direction of study, attitudes toward science, and cultural/ethnic and gender identity development. By understanding the ideologies of these students, we are able to better comprehend the world-makings that these students bring with them to the learning process in the sciences. Informed by life history narrative analysis, this study examines Latino/as and their persisting involvement within the science pipeline in higher education and is based on qualitative observations and interviews of student perspectives on the importance of the college science experience on their ethnic identity and gender identity. The findings in this study show the multiple interrelationships from both Latino male and Latina female narratives, separate and intersecting, to reveal the complexities of the Latino/a group experience in college science. By understanding from a student perspective how the science pipeline affects one's cultural, ethnic, or gender identity, we can create a thought-provoking discussion on why and how underrepresented student populations persist in the science pipeline in higher education. The conditions created in the science pipeline and how they affect Latino/a undergraduate pathways may further be used to understand and improve the quality of the undergraduate learning experience.

Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains.

PubMed

O'Farrell, Brian; Haase, Jana K; Velayudhan, Vimalkumar; Murphy, Ronan A; Achtman, Mark

2012-01-01

Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST) of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS) consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of < €25 per strain. Since developing this pipeline, >200,000 items were processed by two to three people. Our sophisticated automated pipeline can be implemented by a small microbiology group without extensive external support, and provides a general framework for semi-automated bacterial genotyping of large numbers of samples at low cost.

Learning normalized inputs for iterative estimation in medical image segmentation.

PubMed

Drozdzal, Michal; Chartrand, Gabriel; Vorontsov, Eugene; Shakeri, Mahsa; Di Jorio, Lisa; Tang, An; Romero, Adriana; Bengio, Yoshua; Pal, Chris; Kadoury, Samuel

2018-02-01

In this paper, we introduce a simple, yet powerful pipeline for medical image segmentation that combines Fully Convolutional Networks (FCNs) with Fully Convolutional Residual Networks (FC-ResNets). We propose and examine a design that takes particular advantage of recent advances in the understanding of both Convolutional Neural Networks as well as ResNets. Our approach focuses upon the importance of a trainable pre-processing when using FC-ResNets and we show that a low-capacity FCN model can serve as a pre-processor to normalize medical input data. In our image segmentation pipeline, we use FCNs to obtain normalized images, which are then iteratively refined by means of a FC-ResNet to generate a segmentation prediction. As in other fully convolutional approaches, our pipeline can be used off-the-shelf on different image modalities. We show that using this pipeline, we exhibit state-of-the-art performance on the challenging Electron Microscopy benchmark, when compared to other 2D methods. We improve segmentation results on CT images of liver lesions, when contrasting with standard FCN methods. Moreover, when applying our 2D pipeline on a challenging 3D MRI prostate segmentation challenge we reach results that are competitive even when compared to 3D methods. The obtained results illustrate the strong potential and versatility of the pipeline by achieving accurate segmentations on a variety of image modalities and different anatomical regions. Copyright © 2017 Elsevier B.V. All rights reserved.

Characterization of Microbial Communities in Gas Industry Pipelines

PubMed Central

Zhu, Xiang Y.; Lubeck, John; Kilbane, John J.

2003-01-01

Culture-independent techniques, denaturing gradient gel electrophoresis (DGGE) analysis, and random cloning of 16S rRNA gene sequences amplified from community DNA were used to determine the diversity of microbial communities in gas industry pipelines. Samples obtained from natural gas pipelines were used directly for DNA extraction, inoculated into sulfate-reducing bacterium medium, or used to inoculate a reactor that simulated a natural gas pipeline environment. The variable V2-V3 (average size, 384 bp) and V3-V6 (average size, 648 bp) regions of bacterial and archaeal 16S rRNA genes, respectively, were amplified from genomic DNA isolated from nine natural gas pipeline samples and analyzed. A total of 106 bacterial 16S rDNA sequences were derived from DGGE bands, and these formed three major clusters: beta and gamma subdivisions of Proteobacteria and gram-positive bacteria. The most frequently encountered bacterial species was Comamonas denitrificans, which was not previously reported to be associated with microbial communities found in gas pipelines or with microbially influenced corrosion. The 31 archaeal 16S rDNA sequences obtained in this study were all related to those of methanogens and phylogenetically fall into three clusters: order I, Methanobacteriales; order III, Methanomicrobiales; and order IV, Methanosarcinales. Further microbial ecology studies are needed to better understand the relationship among bacterial and archaeal groups and the involvement of these groups in the process of microbially influenced corrosion in order to develop improved ways of monitoring and controlling microbially influenced corrosion. PMID:12957923

Transforming Microbial Genotyping: A Robotic Pipeline for Genotyping Bacterial Strains

PubMed Central

Velayudhan, Vimalkumar; Murphy, Ronan A.; Achtman, Mark

2012-01-01

Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST) of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS) consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of < €25 per strain. Since developing this pipeline, >200,000 items were processed by two to three people. Our sophisticated automated pipeline can be implemented by a small microbiology group without extensive external support, and provides a general framework for semi-automated bacterial genotyping of large numbers of samples at low cost. PMID:23144721

Algorithms for parallel flow solvers on message passing architectures

NASA Technical Reports Server (NTRS)

Vanderwijngaart, Rob F.

1995-01-01

The purpose of this project has been to identify and test suitable technologies for implementation of fluid flow solvers -- possibly coupled with structures and heat equation solvers -- on MIMD parallel computers. In the course of this investigation much attention has been paid to efficient domain decomposition strategies for ADI-type algorithms. Multi-partitioning derives its efficiency from the assignment of several blocks of grid points to each processor in the parallel computer. A coarse-grain parallelism is obtained, and a near-perfect load balance results. In uni-partitioning every processor receives responsibility for exactly one block of grid points instead of several. This necessitates fine-grain pipelined program execution in order to obtain a reasonable load balance. Although fine-grain parallelism is less desirable on many systems, especially high-latency networks of workstations, uni-partition methods are still in wide use in production codes for flow problems. Consequently, it remains important to achieve good efficiency with this technique that has essentially been superseded by multi-partitioning for parallel ADI-type algorithms. Another reason for the concentration on improving the performance of pipeline methods is their applicability in other types of flow solver kernels with stronger implied data dependence. Analytical expressions can be derived for the size of the dynamic load imbalance incurred in traditional pipelines. From these it can be determined what is the optimal first-processor retardation that leads to the shortest total completion time for the pipeline process. Theoretical predictions of pipeline performance with and without optimization match experimental observations on the iPSC/860 very well. Analysis of pipeline performance also highlights the effect of uncareful grid partitioning in flow solvers that employ pipeline algorithms. If grid blocks at boundaries are not at least as large in the wall-normal direction as those immediately adjacent to them, then the first processor in the pipeline will receive a computational load that is less than that of subsequent processors, magnifying the pipeline slowdown effect. Extra compensation is needed for grid boundary effects, even if all grid blocks are equally sized.

Enabling Earth Science Through Cloud Computing

NASA Technical Reports Server (NTRS)

Hardman, Sean; Riofrio, Andres; Shams, Khawaja; Freeborn, Dana; Springer, Paul; Chafin, Brian

2012-01-01

Cloud Computing holds tremendous potential for missions across the National Aeronautics and Space Administration. Several flight missions are already benefiting from an investment in cloud computing for mission critical pipelines and services through faster processing time, higher availability, and drastically lower costs available on cloud systems. However, these processes do not currently extend to general scientific algorithms relevant to earth science missions. The members of the Airborne Cloud Computing Environment task at the Jet Propulsion Laboratory have worked closely with the Carbon in Arctic Reservoirs Vulnerability Experiment (CARVE) mission to integrate cloud computing into their science data processing pipeline. This paper details the efforts involved in deploying a science data system for the CARVE mission, evaluating and integrating cloud computing solutions with the system and porting their science algorithms for execution in a cloud environment.

Renaissance of protein crystallization and precipitation in biopharmaceuticals purification.

PubMed

Dos Santos, Raquel; Carvalho, Ana Luísa; Roque, A Cecília A

The current chromatographic approaches used in protein purification are not keeping pace with the increasing biopharmaceutical market demand. With the upstream improvements, the bottleneck shifted towards the downstream process. New approaches rely in Anything But Chromatography methodologies and revisiting former techniques with a bioprocess perspective. Protein crystallization and precipitation methods are already implemented in the downstream process of diverse therapeutic biological macromolecules, overcoming the current chromatographic bottlenecks. Promising work is being developed in order to implement crystallization and precipitation in the purification pipeline of high value therapeutic molecules. This review focuses in the role of these two methodologies in current industrial purification processes, and highlights their potential implementation in the purification pipeline of high value therapeutic molecules, overcoming chromatographic holdups. Copyright © 2016 Elsevier Inc. All rights reserved.

SIMPLEX: Cloud-Enabled Pipeline for the Comprehensive Analysis of Exome Sequencing Data

PubMed Central

Fischer, Maria; Snajder, Rene; Pabinger, Stephan; Dander, Andreas; Schossig, Anna; Zschocke, Johannes; Trajanoski, Zlatko; Stocker, Gernot

2012-01-01

In recent studies, exome sequencing has proven to be a successful screening tool for the identification of candidate genes causing rare genetic diseases. Although underlying targeted sequencing methods are well established, necessary data handling and focused, structured analysis still remain demanding tasks. Here, we present a cloud-enabled autonomous analysis pipeline, which comprises the complete exome analysis workflow. The pipeline combines several in-house developed and published applications to perform the following steps: (a) initial quality control, (b) intelligent data filtering and pre-processing, (c) sequence alignment to a reference genome, (d) SNP and DIP detection, (e) functional annotation of variants using different approaches, and (f) detailed report generation during various stages of the workflow. The pipeline connects the selected analysis steps, exposes all available parameters for customized usage, performs required data handling, and distributes computationally expensive tasks either on a dedicated high-performance computing infrastructure or on the Amazon cloud environment (EC2). The presented application has already been used in several research projects including studies to elucidate the role of rare genetic diseases. The pipeline is continuously tested and is publicly available under the GPL as a VirtualBox or Cloud image at http://simplex.i-med.ac.at; additional supplementary data is provided at http://www.icbi.at/exome. PMID:22870267

Design Improvements and Analysis of Innovative High-Level Waste Pipeline Unplugging Technologies - 12171

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pribanic, Tomas; Awwad, Amer; Crespo, Jairo

2012-07-01

Transferring high-level waste (HLW) between storage tanks or to treatment facilities is a common practice performed at the Department of Energy (DoE) sites. Changes in the chemical and/or physical properties of the HLW slurry during the transfer process may lead to the formation of blockages inside the pipelines resulting in schedule delays and increased costs. To improve DoE's capabilities in the event of a pipeline plugging incident, FIU has continued to develop two novel unplugging technologies: an asynchronous pulsing system and a peristaltic crawler. The asynchronous pulsing system uses a hydraulic pulse generator to create pressure disturbances at two oppositemore » inlet locations of the pipeline to dislodge blockages by attacking the plug from both sides remotely. The peristaltic crawler is a pneumatic/hydraulic operated crawler that propels itself by a sequence of pressurization/depressurization of cavities (inner tubes). The crawler includes a frontal attachment that has a hydraulically powered unplugging tool. In this paper, details of the asynchronous pulsing system's ability to unplug a pipeline on a small-scale test-bed and results from the experimental testing of the second generation peristaltic crawler are provided. The paper concludes with future improvements for the third generation crawler and a recommended path forward for the asynchronous pulsing testing. (authors)« less

Development of a Dmt Monitor for Statistical Tracking of Gravitational-Wave Burst Triggers Generated from the Omega Pipeline

NASA Astrophysics Data System (ADS)

Li, Jun-Wei; Cao, Jun-Wei

2010-04-01

One challenge in large-scale scientific data analysis is to monitor data in real-time in a distributed environment. For the LIGO (Laser Interferometer Gravitational-wave Observatory) project, a dedicated suit of data monitoring tools (DMT) has been developed, yielding good extensibility to new data type and high flexibility to a distributed environment. Several services are provided, including visualization of data information in various forms and file output of monitoring results. In this work, a DMT monitor, OmegaMon, is developed for tracking statistics of gravitational-wave (OW) burst triggers that are generated from a specific OW burst data analysis pipeline, the Omega Pipeline. Such results can provide diagnostic information as reference of trigger post-processing and interferometer maintenance.

The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)

DOE PAGES

Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos; ...

2016-02-24

The DOE-JGI Metagenome Annotation Pipeline (MAP v.4) performs structural and functional annotation for metagenomic sequences that are submitted to the Integrated Microbial Genomes with Microbiomes (IMG/M) system for comparative analysis. The pipeline runs on nucleotide sequences provide d via the IMG submission site. Users must first define their analysis projects in GOLD and then submit the associated sequence datasets consisting of scaffolds/contigs with optional coverage information and/or unassembled reads in fasta and fastq file formats. The MAP processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNAs, as well as CRISPR elements. Structural annotation ismore » followed by functional annotation including assignment of protein product names and connection to various protein family databases.« less

The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos

The DOE-JGI Metagenome Annotation Pipeline (MAP v.4) performs structural and functional annotation for metagenomic sequences that are submitted to the Integrated Microbial Genomes with Microbiomes (IMG/M) system for comparative analysis. The pipeline runs on nucleotide sequences provide d via the IMG submission site. Users must first define their analysis projects in GOLD and then submit the associated sequence datasets consisting of scaffolds/contigs with optional coverage information and/or unassembled reads in fasta and fastq file formats. The MAP processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNAs, as well as CRISPR elements. Structural annotation ismore » followed by functional annotation including assignment of protein product names and connection to various protein family databases.« less

A-Track: A New Approach for Detection of Moving Objects in FITS Images

NASA Astrophysics Data System (ADS)

Kılıç, Yücel; Karapınar, Nurdan; Atay, Tolga; Kaplan, Murat

2016-07-01

Small planet and asteroid observations are important for understanding the origin and evolution of the Solar System. In this work, we have developed a fast and robust pipeline, called A-Track, for detecting asteroids and comets in sequential telescope images. The moving objects are detected using a modified line detection algorithm, called ILDA. We have coded the pipeline in Python 3, where we have made use of various scientific modules in Python to process the FITS images. We tested the code on photometrical data taken by an SI-1100 CCD with a 1-meter telescope at TUBITAK National Observatory, Antalya. The pipeline can be used to analyze large data archives or daily sequential data. The code is hosted on GitHub under the GNU GPL v3 license.

IDCDACS: IDC's Distributed Application Control System

NASA Astrophysics Data System (ADS)

Ertl, Martin; Boresch, Alexander; Kianička, Ján; Sudakov, Alexander; Tomuta, Elena

2015-04-01

The Preparatory Commission for the CTBTO is an international organization based in Vienna, Austria. Its mission is to establish a global verification regime to monitor compliance with the Comprehensive Nuclear-Test-Ban Treaty (CTBT), which bans all nuclear explosions. For this purpose time series data from a global network of seismic, hydro-acoustic and infrasound (SHI) sensors are transmitted to the International Data Centre (IDC) in Vienna in near-real-time, where it is processed to locate events that may be nuclear explosions. We newly designed the distributed application control system that glues together the various components of the automatic waveform data processing system at the IDC (IDCDACS). Our highly-scalable solution preserves the existing architecture of the IDC processing system that proved successful over many years of operational use, but replaces proprietary components with open-source solutions and custom developed software. Existing code was refactored and extended to obtain a reusable software framework that is flexibly adaptable to different types of processing workflows. Automatic data processing is organized in series of self-contained processing steps, each series being referred to as a processing pipeline. Pipelines process data by time intervals, i.e. the time-series data received from monitoring stations is organized in segments based on the time when the data was recorded. So-called data monitor applications queue the data for processing in each pipeline based on specific conditions, e.g. data availability, elapsed time or completion states of preceding processing pipelines. IDCDACS consists of a configurable number of distributed monitoring and controlling processes, a message broker and a relational database. All processes communicate through message queues hosted on the message broker. Persistent state information is stored in the database. A configurable processing controller instantiates and monitors all data processing applications. Due to decoupling by message queues the system is highly versatile and failure tolerant. The implementation utilizes the RabbitMQ open-source messaging platform that is based upon the Advanced Message Queuing Protocol (AMQP), an on-the-wire protocol (like HTML) and open industry standard. IDCDACS uses high availability capabilities provided by RabbitMQ and is equipped with failure recovery features to survive network and server outages. It is implemented in C and Python and is operated in a Linux environment at the IDC. Although IDCDACS was specifically designed for the existing IDC processing system its architecture is generic and reusable for different automatic processing workflows, e.g. similar to those described in (Olivieri et al. 2012, Kværna et al. 2012). Major advantages are its independence of the specific data processing applications used and the possibility to reconfigure IDCDACS for different types of processing, data and trigger logic. A possible future development would be to use the IDCDACS framework for different scientific domains, e.g. for processing of Earth observation satellite data extending the one-dimensional time-series intervals to spatio-temporal data cubes. REFERENCES Olivieri M., J. Clinton (2012) An almost fair comparison between Earthworm and SeisComp3, Seismological Research Letters, 83(4), 720-727. Kværna, T., S. J. Gibbons, D. B. Harris, D. A. Dodge (2012) Adapting pipeline architectures to track developing aftershock sequences and recurrent explosions, Proceedings of the 2012 Monitoring Research Review: Ground-Based Nuclear Explosion Monitoring Technologies, 776-785.

Fully Automated Atlas-Based Hippocampus Volumetry for Clinical Routine: Validation in Subjects with Mild Cognitive Impairment from the ADNI Cohort.

PubMed

Suppa, Per; Hampel, Harald; Spies, Lothar; Fiebach, Jochen B; Dubois, Bruno; Buchert, Ralph

2015-01-01

Hippocampus volumetry based on magnetic resonance imaging (MRI) has not yet been translated into everyday clinical diagnostic patient care, at least in part due to limited availability of appropriate software tools. In the present study, we evaluate a fully-automated and computationally efficient processing pipeline for atlas based hippocampal volumetry using freely available Statistical Parametric Mapping (SPM) software in 198 amnestic mild cognitive impairment (MCI) subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI1). Subjects were grouped into MCI stable and MCI to probable Alzheimer's disease (AD) converters according to follow-up diagnoses at 12, 24, and 36 months. Hippocampal grey matter volume (HGMV) was obtained from baseline T1-weighted MRI and then corrected for total intracranial volume and age. Average processing time per subject was less than 4 minutes on a standard PC. The area under the receiver operator characteristic curve of the corrected HGMV for identification of MCI to probable AD converters within 12, 24, and 36 months was 0.78, 0.72, and 0.71, respectively. Thus, hippocampal volume computed with the fully-automated processing pipeline provides similar power for prediction of MCI to probable AD conversion as computationally more expensive methods. The whole processing pipeline has been made freely available as an SPM8 toolbox. It is easily set up and integrated into everyday clinical patient care.

A Design Verification of the Parallel Pipelined Image Processings

NASA Astrophysics Data System (ADS)

Wasaki, Katsumi; Harai, Toshiaki

2008-11-01

This paper presents a case study of the design and verification of a parallel and pipe-lined image processing unit based on an extended Petri net, which is called a Logical Colored Petri net (LCPN). This is suitable for Flexible-Manufacturing System (FMS) modeling and discussion of structural properties. LCPN is another family of colored place/transition-net(CPN) with the addition of the following features: integer value assignment of marks, representation of firing conditions as marks' value based formulae, and coupling of output procedures with transition firing. Therefore, to study the behavior of a system modeled with this net, we provide a means of searching the reachability tree for markings.

77 FR 70543 - Pipeline Safety: Meeting of the Gas Pipeline Advisory Committee and the Liquid Pipeline Advisory...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-26

.... PHMSA-2009-0203] Pipeline Safety: Meeting of the Gas Pipeline Advisory Committee and the Liquid Pipeline..., and safety policies for natural gas pipelines and for hazardous liquid pipelines. Both committees were...: Notice of advisory committee meeting. SUMMARY: This notice announces a public meeting of the Gas Pipeline...

Safety and Offshore Oil: Background Papers of the Committee on Assessment of Safety of OCS Activities.

DTIC Science & Technology

1981-01-01

areas in the world. Data to gauge the effects of drilling are unavailable, and technology not only to develop, produce and transport hydrocarbons but to...spills associated with drillng operations and the transport of oil ashore for processing and refining--whether by tanker or pipeline --can and do pose...associated with each of these forms of transport . In the past, pipeline accidents released more oil to the marine environment than any other source directly

Long Range Spoil Disposal Study. Part I. General Data for the Delaware River,

DTIC Science & Technology

1969-01-01

estimated approximately four and a half miles off- annual saving of $2,400,000. shore in the vicinity of Big Stone Beach, The feasibility plan for the ter...portioned to the rates of inflow to assure a In the case of pipeline dredging, also long detention period and presumably good bucket or dipper dredging, the...District is in process owned pipeline, dipper , and bucket dredges, of reducing the 13 ppt limitation to 8 ppt in also specially designed plant for the

Synthetic natural gas in California: When and why. [from coal

NASA Technical Reports Server (NTRS)

Wood, W. B.

1978-01-01

A coal gasification plant planned for northwestern New Mexico to produce 250 MMCFD of pipeline quality gas (SNG) using the German Lurgi process is discussed. The SNG will be commingled with natural gas in existing pipelines for delivery to southern California and the Midwest. Cost of the plant is figured at more than $1.4 billion in January 1978 dollars with a current inflation rate of $255,000 for each day of delay. Plant start-up is now scheduled for 1984.

Merged GIS, GPS data assist siting for gulf gas line

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scott, D.R.; Schmidt, J.A.

1998-06-29

A GIS-based decision-support system was developed for a US Gulf of Mexico onshore and offshore pipeline that has assisted in locating a cost-effective pipeline route based on landcover type, wetland distribution, and proximity to other environmentally sensitive resources. Described here are the methods used to integrate various sources of available GIS data with satellite imagery and surveyed information. Costs of collecting and processing these data are compared with benefits of the system over use of manual methods.

Realtime processing of LOFAR data for the detection of nano-second pulses from the Moon

NASA Astrophysics Data System (ADS)

Winchen, T.; Bonardi, A.; Buitink, S.; Corstanje, A.; Enriquez, J. E.; Falcke, H.; Hörandel, J. R.; Mitra, P.; Mulrey, K.; Nelles, A.; Rachen, J. P.; Rossetto, L.; Schellart, P.; Scholten, O.; Thoudam, S.; Trinh, T. N. G.; ter Veen, S.; KSP, The LOFAR Cosmic Ray

2017-10-01

The low flux of the ultra-high energy cosmic rays (UHECR) at the highest energies provides a challenge to answer the long standing question about their origin and nature. Even lower fluxes of neutrinos with energies above 1022 eV are predicted in certain Grand-Unifying-Theories (GUTs) and e.g. models for super-heavy dark matter (SHDM). The significant increase in detector volume required to detect these particles can be achieved by searching for the nanosecond radio pulses that are emitted when a particle interacts in Earth’s moon with current and future radio telescopes. In this contribution we present the design of an online analysis and trigger pipeline for the detection of nano-second pulses with the LOFAR radio telescope. The most important steps of the processing pipeline are digital focusing of the antennas towards the Moon, correction of the signal for ionospheric dispersion, and synthesis of the time-domain signal from the polyphased-filtered signal in frequency domain. The implementation of the pipeline on a GPU/CPU cluster will be discussed together with the computing performance of the prototype.

Parameters of Solidifying Mixtures Transporting at Underground Ore Mining

NASA Astrophysics Data System (ADS)

Golik, Vladimir; Dmitrak, Yury

2017-11-01

The article is devoted to the problem of providing mining enterprises with solidifying filling mixtures at underground mining. The results of analytical studies using the data of foreign and domestic practice of solidifying mixtures delivery to stopes are given. On the basis of experimental practice the parameters of transportation of solidifying filling mixtures are given with an increase in their quality due to the effect of vibration in the pipeline. The mechanism of the delivery process and the procedure for determining the parameters of the forced oscillations of the pipeline, the characteristics of the transporting processes, the rigidity of the elastic elements of pipeline section supports and the magnitude of vibrator' driving force are detailed. It is determined that the quality of solidifying filling mixtures can be increased due to the rational use of technical resources during the transportation of mixtures, and as a result the mixtures are characterized by a more even distribution of the aggregate. The algorithm for calculating the parameters of the pipe vibro-transport of solidifying filling mixtures can be in demand in the design of mineral deposits underground mining technology.

Parallel algorithms for mapping pipelined and parallel computations

NASA Technical Reports Server (NTRS)

Nicol, David M.

1988-01-01

Many computational problems in image processing, signal processing, and scientific computing are naturally structured for either pipelined or parallel computation. When mapping such problems onto a parallel architecture it is often necessary to aggregate an obvious problem decomposition. Even in this context the general mapping problem is known to be computationally intractable, but recent advances have been made in identifying classes of problems and architectures for which optimal solutions can be found in polynomial time. Among these, the mapping of pipelined or parallel computations onto linear array, shared memory, and host-satellite systems figures prominently. This paper extends that work first by showing how to improve existing serial mapping algorithms. These improvements have significantly lower time and space complexities: in one case a published O(nm sup 3) time algorithm for mapping m modules onto n processors is reduced to an O(nm log m) time complexity, and its space requirements reduced from O(nm sup 2) to O(m). Run time complexity is further reduced with parallel mapping algorithms based on these improvements, which run on the architecture for which they create the mappings.

The ALFALFA Extragalactic Catalog and Data Processing Pipeline

NASA Astrophysics Data System (ADS)

Kent, Brian R.; Haynes, Martha P.; Giovanelli, Riccardo; ALFALFA Team

2018-06-01

The Arecibo Legacy Fast ALFA 21cm HI Survey has reached completion. The observations and data are used by team members and the astronomical community in a variety of scientific initiatives with gas-rich galaxies, cluster environments, and studies of low redshift cosmology. The survey covers nearly 7000 square degrees of high galactic latitude sky visible from Arecibo, Puerto Rico and ~4400 hours of observations from 2005 to 2011. We present the extragalactic HI source catalog of over ~31,000 detections, their measured properties, and associated derived parameters. The observations were carefully reduced using a custom made data reduction pipeline and interface. Team members interacted with this pipeline through observation planning, calibration, imaging, source extraction, and cataloging. We describe this processing workflow as it pertains to the complexities of the single-dish multi-feed data reduction as well as known caveats of the source catalog and spectra for use in future astronomical studies and analysis. The ALFALFA team at Cornell has been supported by NSF grants AST-0607007, AST-1107390 and AST-1714828 and by grants from the Brinson Foundation.

Control structures for high speed processors

NASA Technical Reports Server (NTRS)

Maki, G. K.; Mankin, R.; Owsley, P. A.; Kim, G. M.

1982-01-01

A special processor was designed to function as a Reed Solomon decoder with throughput data rate in the Mhz range. This data rate is significantly greater than is possible with conventional digital architectures. To achieve this rate, the processor design includes sequential, pipelined, distributed, and parallel processing. The processor was designed using a high level language register transfer language. The RTL can be used to describe how the different processes are implemented by the hardware. One problem of special interest was the development of dependent processes which are analogous to software subroutines. For greater flexibility, the RTL control structure was implemented in ROM. The special purpose hardware required approximately 1000 SSI and MSI components. The data rate throughput is 2.5 megabits/second. This data rate is achieved through the use of pipelined and distributed processing. This data rate can be compared with 800 kilobits/second in a recently proposed very large scale integration design of a Reed Solomon encoder.

Kepler Planet Detection Metrics: Per-Target Flux-Level Transit Injection Tests of TPS for Data Release 25

NASA Technical Reports Server (NTRS)

Burke, Christopher J.; Catanzarite, Joseph

2017-01-01

Quantifying the ability of a transiting planet survey to recover transit signals has commonly been accomplished through Monte-Carlo injection of transit signals into the observed data and subsequent running of the signal search algorithm (Gilliland et al., 2000; Weldrake et al., 2005; Burke et al., 2006). In order to characterize the performance of the Kepler pipeline (Twicken et al., 2016; Jenkins et al., 2017) on a sample of over 200,000 stars, two complementary injection and recovery tests are utilized:1. Injection of a single transit signal per target into the image or pixel-level data, hereafter referred to as pixel-level transit injection (PLTI), with subsequent processing through the Photometric Analysis (PA), Presearch Data Conditioning (PDC), Transiting Planet Search (TPS), and Data Validation (DV) modules of the Kepler pipeline. The PLTI quantification of the Kepler pipeline's completeness has been described previously by Christiansen et al. (2015, 2016); the completeness of the final SOC 9.3 Kepler pipeline acting on the Data Release 25 (DR25) light curves is described by Christiansen (2017).2. Injection of multiple transit signals per target into the normalized flux time series data with a subsequent transit search using a stream-lined version of the Transiting Planet Search (TPS) module. This test, hereafter referred to as flux-level transit injection (FLTI), is the subject of this document. By running a heavily modified version of TPS, FLTI is able to perform many injections on selected targets and determine in some detail which injected signals are recoverable. Significant numerical efficiency gains are enabled by precomputing the data conditioning steps at the onset of TPS and limiting the search parameter space (i.e., orbital period, transit duration, and ephemeris zero-point) to a small region around each injected transit signal.The PLTI test has the advantage that it follows transit signals through all processing steps of the Kepler pipeline, and the recovered signals can be further classified as planet candidates or false positives in the exact same manner as detections from the nominal (i.e., observed) pipeline run (Twicken et al., 2016, Thompson et al., in preparation). To date, the PLTI test has been the standard means of measuring pipeline completeness averaged over large samples of targets (Christiansen et al., 2015, 2016; Christiansen, 2017). However, since the PLTI test uses only one injection per target, it does not elucidate individual-target variations in pipeline completeness due to differences in stellar properties or astrophysical variability. Thus, we developed the FLTI test to provide a numerically efficient way to fully map individual targets and explore the performance of the pipeline in greater detail. The FLTI tests thereby allow a thorough validation of the pipeline completeness models (such as window function (Burke and Catanzarite, 2017a), detection efficiency (Burke Catanzarite, 2017b), etc.) across the spectrum of Kepler targets (i.e., various astrophysical phenomena and differences in instrumental noise). Tests during development of the FLTI capability revealed that there are significant target-to-target variations in the detection efficiency.

The economics of energy from animal manure for greenhouse gas mitigation

NASA Astrophysics Data System (ADS)

Ghafoori, Emad

2007-12-01

Anaerobic digestion (AD) has significant economies of scale, i.e. per unit processing costs decrease with increasing size. The economics of AD to produce biogas and in turn electric power in farm or feedlot based units as well as centralized plants is evaluated for two settings in Alberta: a mixed farming area, Red Deer County, and an area of concentrated beef cattle feedlots, Lethbridge County. A centralized plant drawing manure from 61 sources in the mixed farming area could produce power at a cost of 218 MWh-1 (2005 US). A centralized plant drawing manure from 560,000 beef cattle in Lethbridge County, can produce power at a cost of 138 MWh-1. Digestate processing, if commercially available, shifts the balance in favor of centralized processing. At larger scales, pipelines could be used to deliver manure to a centralized plant and return the processed digestate back to the manure source for spreading. Pipeline transport of beef cattle manure is more economic than truck transport for the manure produced by more than 90,000 animals. Pipeline transport of digestate is more economic when manure from more than 21,000 beef cattle is available and two-way pipelining of manure plus digestate is more economic when manure from more than 29,000 beef cattle is available. The value of carbon credits necessary to make AD profitable in a mixed farming region is also calculated based on a detailed analysis of manure and digestate transport and processing costs at an AD plant. Carbon emission reductions from power generation are calculated for displacement of power from coal and natural gas. The required carbon credit to cover the cost of AD processing of manure is greater than 150 per tonne of CO2. These results show that AD treatment of manure from mixed farming areas is not economic given current values of carbon credits. Power from biogas has a high cost relative to current power prices and to the cost of power from other large scale renewable sources. Power from biogas would need to be justified by other factors than energy value alone, such as phosphate, pathogen or odor control.

PANDA: a pipeline toolbox for analyzing brain diffusion images.

PubMed

Cui, Zaixu; Zhong, Suyu; Xu, Pengfei; He, Yong; Gong, Gaolang

2013-01-01

Diffusion magnetic resonance imaging (dMRI) is widely used in both scientific research and clinical practice in in-vivo studies of the human brain. While a number of post-processing packages have been developed, fully automated processing of dMRI datasets remains challenging. Here, we developed a MATLAB toolbox named "Pipeline for Analyzing braiN Diffusion imAges" (PANDA) for fully automated processing of brain diffusion images. The processing modules of a few established packages, including FMRIB Software Library (FSL), Pipeline System for Octave and Matlab (PSOM), Diffusion Toolkit and MRIcron, were employed in PANDA. Using any number of raw dMRI datasets from different subjects, in either DICOM or NIfTI format, PANDA can automatically perform a series of steps to process DICOM/NIfTI to diffusion metrics [e.g., fractional anisotropy (FA) and mean diffusivity (MD)] that are ready for statistical analysis at the voxel-level, the atlas-level and the Tract-Based Spatial Statistics (TBSS)-level and can finish the construction of anatomical brain networks for all subjects. In particular, PANDA can process different subjects in parallel, using multiple cores either in a single computer or in a distributed computing environment, thus greatly reducing the time cost when dealing with a large number of datasets. In addition, PANDA has a friendly graphical user interface (GUI), allowing the user to be interactive and to adjust the input/output settings, as well as the processing parameters. As an open-source package, PANDA is freely available at http://www.nitrc.org/projects/panda/. This novel toolbox is expected to substantially simplify the image processing of dMRI datasets and facilitate human structural connectome studies.

PANDA: a pipeline toolbox for analyzing brain diffusion images

PubMed Central

Cui, Zaixu; Zhong, Suyu; Xu, Pengfei; He, Yong; Gong, Gaolang

2013-01-01

Diffusion magnetic resonance imaging (dMRI) is widely used in both scientific research and clinical practice in in-vivo studies of the human brain. While a number of post-processing packages have been developed, fully automated processing of dMRI datasets remains challenging. Here, we developed a MATLAB toolbox named “Pipeline for Analyzing braiN Diffusion imAges” (PANDA) for fully automated processing of brain diffusion images. The processing modules of a few established packages, including FMRIB Software Library (FSL), Pipeline System for Octave and Matlab (PSOM), Diffusion Toolkit and MRIcron, were employed in PANDA. Using any number of raw dMRI datasets from different subjects, in either DICOM or NIfTI format, PANDA can automatically perform a series of steps to process DICOM/NIfTI to diffusion metrics [e.g., fractional anisotropy (FA) and mean diffusivity (MD)] that are ready for statistical analysis at the voxel-level, the atlas-level and the Tract-Based Spatial Statistics (TBSS)-level and can finish the construction of anatomical brain networks for all subjects. In particular, PANDA can process different subjects in parallel, using multiple cores either in a single computer or in a distributed computing environment, thus greatly reducing the time cost when dealing with a large number of datasets. In addition, PANDA has a friendly graphical user interface (GUI), allowing the user to be interactive and to adjust the input/output settings, as well as the processing parameters. As an open-source package, PANDA is freely available at http://www.nitrc.org/projects/panda/. This novel toolbox is expected to substantially simplify the image processing of dMRI datasets and facilitate human structural connectome studies. PMID:23439846

The Pan-STARRS PS1 Image Processing Pipeline

NASA Astrophysics Data System (ADS)

Magnier, E.

The Pan-STARRS PS1 Image Processing Pipeline (IPP) performs the image processing and data analysis tasks needed to enable the scientific use of the images obtained by the Pan-STARRS PS1 prototype telescope. The primary goals of the IPP are to process the science images from the Pan-STARRS telescopes and make the results available to other systems within Pan-STARRS. It also is responsible for combining all of the science images in a given filter into a single representation of the non-variable component of the night sky defined as the "Static Sky". To achieve these goals, the IPP also performs other analysis functions to generate the calibrations needed in the science image processing, and to occasionally use the derived data to generate improved astrometric and photometric reference catalogs. It also provides the infrastructure needed to store the incoming data and the resulting data products. The IPP inherits lessons learned, and in some cases code and prototype code, from several other astronomy image analysis systems, including Imcat (Kaiser), the Sloan Digital Sky Survey (REF), the Elixir system (Magnier & Cuillandre), and Vista (Tonry). Imcat and Vista have a large number of robust image processing functions. SDSS has demonstrated a working analysis pipeline and large-scale databasesystem for a dedicated project. The Elixir system has demonstrated an automatic image processing system and an object database system for operational usage. This talk will present an overview of the IPP architecture, functional flow, code development structure, and selected analysis algorithms. Also discussed is the HW highly parallel HW configuration necessary to support PS1 operational requirements. Finally, results are presented of the processing of images collected during PS1 early commissioning tasks utilizing the Pan-STARRS Test Camera #3.

Sentinel-1 Archive and Processing in the Cloud using the Hybrid Pluggable Processing Pipeline (HyP3) at the ASF DAAC

NASA Astrophysics Data System (ADS)

Arko, S. A.; Hogenson, R.; Geiger, A.; Herrmann, J.; Buechler, B.; Hogenson, K.

2016-12-01

In the coming years there will be an unprecedented amount of SAR data available on a free and open basis to research and operational users around the globe. The Alaska Satellite Facility (ASF) DAAC hosts, through an international agreement, data from the Sentinel-1 spacecraft and will be hosting data from the upcoming NASA ISRO SAR (NISAR) mission. To more effectively manage and exploit these vast datasets, ASF DAAC has begun moving portions of the archive to the cloud and utilizing cloud services to provide higher-level processing on the data. The Hybrid Pluggable Processing Pipeline (HyP3) project is designed to support higher-level data processing in the cloud and extend the capabilities of researchers to larger scales. Built upon a set of core Amazon cloud services, the HyP3 system allows users to request data processing using a number of canned algorithms or their own algorithms once they have been uploaded to the cloud. The HyP3 system automatically accesses the ASF cloud-based archive through the DAAC RESTful application programming interface and processes the data on Amazon's elastic compute cluster (EC2). Final products are distributed through Amazon's simple storage service (S3) and are available for user download. This presentation will provide an overview of ASF DAAC's activities moving the Sentinel-1 archive into the cloud and developing the integrated HyP3 system, covering both the benefits and difficulties of working in the cloud. Additionally, we will focus on the utilization of HyP3 for higher-level processing of SAR data. Two example algorithms, for sea-ice tracking and change detection, will be discussed as well as the mechanism for integrating new algorithms into the pipeline for community use.

Simultaneous Analysis and Quality Assurance for Diffusion Tensor Imaging

PubMed Central

Lauzon, Carolyn B.; Asman, Andrew J.; Esparza, Michael L.; Burns, Scott S.; Fan, Qiuyun; Gao, Yurui; Anderson, Adam W.; Davis, Nicole; Cutting, Laurie E.; Landman, Bennett A.

2013-01-01

Diffusion tensor imaging (DTI) enables non-invasive, cyto-architectural mapping of in vivo tissue microarchitecture through voxel-wise mathematical modeling of multiple magnetic resonance imaging (MRI) acquisitions, each differently sensitized to water diffusion. DTI computations are fundamentally estimation processes and are sensitive to noise and artifacts. Despite widespread adoption in the neuroimaging community, maintaining consistent DTI data quality remains challenging given the propensity for patient motion, artifacts associated with fast imaging techniques, and the possibility of hardware changes/failures. Furthermore, the quantity of data acquired per voxel, the non-linear estimation process, and numerous potential use cases complicate traditional visual data inspection approaches. Currently, quality inspection of DTI data has relied on visual inspection and individual processing in DTI analysis software programs (e.g. DTIPrep, DTI-studio). However, recent advances in applied statistical methods have yielded several different metrics to assess noise level, artifact propensity, quality of tensor fit, variance of estimated measures, and bias in estimated measures. To date, these metrics have been largely studied in isolation. Herein, we select complementary metrics for integration into an automatic DTI analysis and quality assurance pipeline. The pipeline completes in 24 hours, stores statistical outputs, and produces a graphical summary quality analysis (QA) report. We assess the utility of this streamlined approach for empirical quality assessment on 608 DTI datasets from pediatric neuroimaging studies. The efficiency and accuracy of quality analysis using the proposed pipeline is compared with quality analysis based on visual inspection. The unified pipeline is found to save a statistically significant amount of time (over 70%) while improving the consistency of QA between a DTI expert and a pool of research associates. Projection of QA metrics to a low dimensional manifold reveal qualitative, but clear, QA-study associations and suggest that automated outlier/anomaly detection would be feasible. PMID:23637895

WASS: An open-source pipeline for 3D stereo reconstruction of ocean waves

NASA Astrophysics Data System (ADS)

Bergamasco, Filippo; Torsello, Andrea; Sclavo, Mauro; Barbariol, Francesco; Benetazzo, Alvise

2017-10-01

Stereo 3D reconstruction of ocean waves is gaining more and more popularity in the oceanographic community and industry. Indeed, recent advances of both computer vision algorithms and computer processing power now allow the study of the spatio-temporal wave field with unprecedented accuracy, especially at small scales. Even if simple in theory, multiple details are difficult to be mastered for a practitioner, so that the implementation of a sea-waves 3D reconstruction pipeline is in general considered a complex task. For instance, camera calibration, reliable stereo feature matching and mean sea-plane estimation are all factors for which a well designed implementation can make the difference to obtain valuable results. For this reason, we believe that the open availability of a well tested software package that automates the reconstruction process from stereo images to a 3D point cloud would be a valuable addition for future researches in this area. We present WASS (http://www.dais.unive.it/wass), an Open-Source stereo processing pipeline for sea waves 3D reconstruction. Our tool completely automates all the steps required to estimate dense point clouds from stereo images. Namely, it computes the extrinsic parameters of the stereo rig so that no delicate calibration has to be performed on the field. It implements a fast 3D dense stereo reconstruction procedure based on the consolidated OpenCV library and, lastly, it includes set of filtering techniques both on the disparity map and the produced point cloud to remove the vast majority of erroneous points that can naturally arise while analyzing the optically complex nature of the water surface. In this paper, we describe the architecture of WASS and the internal algorithms involved. The pipeline workflow is shown step-by-step and demonstrated on real datasets acquired at sea.

Fast in-database cross-matching of high-cadence, high-density source lists with an up-to-date sky model

NASA Astrophysics Data System (ADS)

Scheers, B.; Bloemen, S.; Mühleisen, H.; Schellart, P.; van Elteren, A.; Kersten, M.; Groot, P. J.

2018-04-01

Coming high-cadence wide-field optical telescopes will image hundreds of thousands of sources per minute. Besides inspecting the near real-time data streams for transient and variability events, the accumulated data archive is a wealthy laboratory for making complementary scientific discoveries. The goal of this work is to optimise column-oriented database techniques to enable the construction of a full-source and light-curve database for large-scale surveys, that is accessible by the astronomical community. We adopted LOFAR's Transients Pipeline as the baseline and modified it to enable the processing of optical images that have much higher source densities. The pipeline adds new source lists to the archive database, while cross-matching them with the known cataloguedsources in order to build a full light-curve archive. We investigated several techniques of indexing and partitioning the largest tables, allowing for faster positional source look-ups in the cross matching algorithms. We monitored all query run times in long-term pipeline runs where we processed a subset of IPHAS data that have image source density peaks over 170,000 per field of view (500,000 deg-2). Our analysis demonstrates that horizontal table partitions of declination widths of one-degree control the query run times. Usage of an index strategy where the partitions are densely sorted according to source declination yields another improvement. Most queries run in sublinear time and a few (< 20%) run in linear time, because of dependencies on input source-list and result-set size. We observed that for this logical database partitioning schema the limiting cadence the pipeline achieved with processing IPHAS data is 25 s.

Fast, accurate and easy-to-pipeline methods for amplicon sequence processing

NASA Astrophysics Data System (ADS)

Antonielli, Livio; Sessitsch, Angela

2016-04-01

Next generation sequencing (NGS) technologies established since years as an essential resource in microbiology. While on the one hand metagenomic studies can benefit from the continuously increasing throughput of the Illumina (Solexa) technology, on the other hand the spreading of third generation sequencing technologies (PacBio, Oxford Nanopore) are getting whole genome sequencing beyond the assembly of fragmented draft genomes, making it now possible to finish bacterial genomes even without short read correction. Besides (meta)genomic analysis next-gen amplicon sequencing is still fundamental for microbial studies. Amplicon sequencing of the 16S rRNA gene and ITS (Internal Transcribed Spacer) remains a well-established widespread method for a multitude of different purposes concerning the identification and comparison of archaeal/bacterial (16S rRNA gene) and fungal (ITS) communities occurring in diverse environments. Numerous different pipelines have been developed in order to process NGS-derived amplicon sequences, among which Mothur, QIIME and USEARCH are the most well-known and cited ones. The entire process from initial raw sequence data through read error correction, paired-end read assembly, primer stripping, quality filtering, clustering, OTU taxonomic classification and BIOM table rarefaction as well as alternative "normalization" methods will be addressed. An effective and accurate strategy will be presented using the state-of-the-art bioinformatic tools and the example of a straightforward one-script pipeline for 16S rRNA gene or ITS MiSeq amplicon sequencing will be provided. Finally, instructions on how to automatically retrieve nucleotide sequences from NCBI and therefore apply the pipeline to targets other than 16S rRNA gene (Greengenes, SILVA) and ITS (UNITE) will be discussed.

Simultaneous analysis and quality assurance for diffusion tensor imaging.

PubMed

Lauzon, Carolyn B; Asman, Andrew J; Esparza, Michael L; Burns, Scott S; Fan, Qiuyun; Gao, Yurui; Anderson, Adam W; Davis, Nicole; Cutting, Laurie E; Landman, Bennett A

2013-01-01

Diffusion tensor imaging (DTI) enables non-invasive, cyto-architectural mapping of in vivo tissue microarchitecture through voxel-wise mathematical modeling of multiple magnetic resonance imaging (MRI) acquisitions, each differently sensitized to water diffusion. DTI computations are fundamentally estimation processes and are sensitive to noise and artifacts. Despite widespread adoption in the neuroimaging community, maintaining consistent DTI data quality remains challenging given the propensity for patient motion, artifacts associated with fast imaging techniques, and the possibility of hardware changes/failures. Furthermore, the quantity of data acquired per voxel, the non-linear estimation process, and numerous potential use cases complicate traditional visual data inspection approaches. Currently, quality inspection of DTI data has relied on visual inspection and individual processing in DTI analysis software programs (e.g. DTIPrep, DTI-studio). However, recent advances in applied statistical methods have yielded several different metrics to assess noise level, artifact propensity, quality of tensor fit, variance of estimated measures, and bias in estimated measures. To date, these metrics have been largely studied in isolation. Herein, we select complementary metrics for integration into an automatic DTI analysis and quality assurance pipeline. The pipeline completes in 24 hours, stores statistical outputs, and produces a graphical summary quality analysis (QA) report. We assess the utility of this streamlined approach for empirical quality assessment on 608 DTI datasets from pediatric neuroimaging studies. The efficiency and accuracy of quality analysis using the proposed pipeline is compared with quality analysis based on visual inspection. The unified pipeline is found to save a statistically significant amount of time (over 70%) while improving the consistency of QA between a DTI expert and a pool of research associates. Projection of QA metrics to a low dimensional manifold reveal qualitative, but clear, QA-study associations and suggest that automated outlier/anomaly detection would be feasible.

Massive stereo-based DTM production for Mars on cloud computers

NASA Astrophysics Data System (ADS)

Tao, Y.; Muller, J.-P.; Sidiropoulos, P.; Xiong, Si-Ting; Putri, A. R. D.; Walter, S. H. G.; Veitch-Michaelis, J.; Yershov, V.

2018-05-01

Digital Terrain Model (DTM) creation is essential to improving our understanding of the formation processes of the Martian surface. Although there have been previous demonstrations of open-source or commercial planetary 3D reconstruction software, planetary scientists are still struggling with creating good quality DTMs that meet their science needs, especially when there is a requirement to produce a large number of high quality DTMs using "free" software. In this paper, we describe a new open source system to overcome many of these obstacles by demonstrating results in the context of issues found from experience with several planetary DTM pipelines. We introduce a new fully automated multi-resolution DTM processing chain for NASA Mars Reconnaissance Orbiter (MRO) Context Camera (CTX) and High Resolution Imaging Science Experiment (HiRISE) stereo processing, called the Co-registration Ames Stereo Pipeline (ASP) Gotcha Optimised (CASP-GO), based on the open source NASA ASP. CASP-GO employs tie-point based multi-resolution image co-registration, and Gotcha sub-pixel refinement and densification. CASP-GO pipeline is used to produce planet-wide CTX and HiRISE DTMs that guarantee global geo-referencing compliance with respect to High Resolution Stereo Colour imaging (HRSC), and thence to the Mars Orbiter Laser Altimeter (MOLA); providing refined stereo matching completeness and accuracy. All software and good quality products introduced in this paper are being made open-source to the planetary science community through collaboration with NASA Ames, United States Geological Survey (USGS) and the Jet Propulsion Laboratory (JPL), Advanced Multi-Mission Operations System (AMMOS) Planetary Data System (PDS) Pipeline Service (APPS-PDS4), as well as browseable and visualisable through the iMars web based Geographic Information System (webGIS) system.

78 FR 70623 - Pipeline Safety: Meeting of the Gas Pipeline Advisory Committee and the Liquid Pipeline Advisory...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-26

... DEPARTMENT OF TRANSPORTATION Pipeline and Hazardous Materials Safety Administration [Docket No. PHMSA-2009-0203] Pipeline Safety: Meeting of the Gas Pipeline Advisory Committee and the Liquid Pipeline Advisory Committee AGENCY: Pipeline and Hazardous Materials Safety Administration (PHMSA), DOT. [[Page...

Investigation of the motion processes of wastewater in sewerage of high-rise buildings

NASA Astrophysics Data System (ADS)

Pomogaeva, Valentina; Metechko, Lyudmila; Prokofiev, Dmitry; Narezhnaya, Tamara

2018-03-01

When designing, constructing and operating sewage pipelines in high-rise buildings, issues of failure-free operation of a network arise. Investigation of the processes of wastewater moving allows identifying problem areas during operation, assessing the possibility of obstructions and breakdowns of plumbing traps on the gravity drainage sections of the pipeline. The article performs the schemes of the water outflow from the floor sewer into the riser, including the places where the riser is bent, of air delivery to the working riser under the change of the direction of drain movement with the dropout line set-up, with the installation of an automatic anti-vacuum valve, with the installation of the ventilation pipeline. Investigations of the process of sewage waste flow in a sewage riser were carried out, in order to select the appropriate structure. The authors consider structure features of some sections of sewerage in high-rise buildings. The exhaustion value in the riser is determined from the rarefactions that occur below the compressed cross-section of the riser and the loss of the air flow pressure coming from the atmosphere into the riser during the deflooding of the liquid. Preventing the formation of obstructions and breakdowns of plumbing traps is an integral part of sewage networks.

The Performance of the Robo-AO Laser Guide Star Adaptive Optics System at the Kitt Peak 2.1 m Telescope

NASA Astrophysics Data System (ADS)

Jensen-Clem, Rebecca; Duev, Dmitry A.; Riddle, Reed; Salama, Maïssa; Baranec, Christoph; Law, Nicholas M.; Kulkarni, S. R.; Ramprakash, A. N.

2018-01-01

Robo-AO is an autonomous laser guide star adaptive optics (AO) system recently commissioned at the Kitt Peak 2.1 m telescope. With the ability to observe every clear night, Robo-AO at the 2.1 m telescope is the first dedicated AO observatory. This paper presents the imaging performance of the AO system in its first 18 months of operations. For a median seeing value of 1.″44, the average Strehl ratio is 4% in the i\\prime band. After post processing, the contrast ratio under sub-arcsecond seeing for a 2≤slant i\\prime ≤slant 16 primary star is five and seven magnitudes at radial offsets of 0.″5 and 1.″0, respectively. The data processing and archiving pipelines run automatically at the end of each night. The first stage of the processing pipeline shifts and adds the rapid frame rate data using techniques optimized for different signal-to-noise ratios. The second “high-contrast” stage of the pipeline is eponymously well suited to finding faint stellar companions. Currently, a range of scientific programs, including the synthetic tracking of near-Earth asteroids, the binarity of stars in young clusters, and weather on solar system planets are being undertaken with Robo-AO.

PANGEA: pipeline for analysis of next generation amplicons

PubMed Central

Giongo, Adriana; Crabb, David B; Davis-Richardson, Austin G; Chauliac, Diane; Mobberley, Jennifer M; Gano, Kelsey A; Mukherjee, Nabanita; Casella, George; Roesch, Luiz FW; Walts, Brandon; Riva, Alberto; King, Gary; Triplett, Eric W

2010-01-01

High-throughput DNA sequencing can identify organisms and describe population structures in many environmental and clinical samples. Current technologies generate millions of reads in a single run, requiring extensive computational strategies to organize, analyze and interpret those sequences. A series of bioinformatics tools for high-throughput sequencing analysis, including preprocessing, clustering, database matching and classification, have been compiled into a pipeline called PANGEA. The PANGEA pipeline was written in Perl and can be run on Mac OSX, Windows or Linux. With PANGEA, sequences obtained directly from the sequencer can be processed quickly to provide the files needed for sequence identification by BLAST and for comparison of microbial communities. Two different sets of bacterial 16S rRNA sequences were used to show the efficiency of this workflow. The first set of 16S rRNA sequences is derived from various soils from Hawaii Volcanoes National Park. The second set is derived from stool samples collected from diabetes-resistant and diabetes-prone rats. The workflow described here allows the investigator to quickly assess libraries of sequences on personal computers with customized databases. PANGEA is provided for users as individual scripts for each step in the process or as a single script where all processes, except the χ2 step, are joined into one program called the ‘backbone’. PMID:20182525

Cloud CPFP: a shotgun proteomics data analysis pipeline using cloud and high performance computing.

PubMed

Trudgian, David C; Mirzaei, Hamid

2012-12-07

We have extended the functionality of the Central Proteomics Facilities Pipeline (CPFP) to allow use of remote cloud and high performance computing (HPC) resources for shotgun proteomics data processing. CPFP has been modified to include modular local and remote scheduling for data processing jobs. The pipeline can now be run on a single PC or server, a local cluster, a remote HPC cluster, and/or the Amazon Web Services (AWS) cloud. We provide public images that allow easy deployment of CPFP in its entirety in the AWS cloud. This significantly reduces the effort necessary to use the software, and allows proteomics laboratories to pay for compute time ad hoc, rather than obtaining and maintaining expensive local server clusters. Alternatively the Amazon cloud can be used to increase the throughput of a local installation of CPFP as necessary. We demonstrate that cloud CPFP allows users to process data at higher speed than local installations but with similar cost and lower staff requirements. In addition to the computational improvements, the web interface to CPFP is simplified, and other functionalities are enhanced. The software is under active development at two leading institutions and continues to be released under an open-source license at http://cpfp.sourceforge.net.

HEP Computing Tools, Grid and Supercomputers for Genome Sequencing Studies

NASA Astrophysics Data System (ADS)

De, K.; Klimentov, A.; Maeno, T.; Mashinistov, R.; Novikov, A.; Poyda, A.; Tertychnyy, I.; Wenaus, T.

2017-10-01

PanDA - Production and Distributed Analysis Workload Management System has been developed to address ATLAS experiment at LHC data processing and analysis challenges. Recently PanDA has been extended to run HEP scientific applications on Leadership Class Facilities and supercomputers. The success of the projects to use PanDA beyond HEP and Grid has drawn attention from other compute intensive sciences such as bioinformatics. Recent advances of Next Generation Genome Sequencing (NGS) technology led to increasing streams of sequencing data that need to be processed, analysed and made available for bioinformaticians worldwide. Analysis of genomes sequencing data using popular software pipeline PALEOMIX can take a month even running it on the powerful computer resource. In this paper we will describe the adaptation the PALEOMIX pipeline to run it on a distributed computing environment powered by PanDA. To run pipeline we split input files into chunks which are run separately on different nodes as separate inputs for PALEOMIX and finally merge output file, it is very similar to what it done by ATLAS to process and to simulate data. We dramatically decreased the total walltime because of jobs (re)submission automation and brokering within PanDA. Using software tools developed initially for HEP and Grid can reduce payload execution time for Mammoths DNA samples from weeks to days.

A detailed comparison of analysis processes for MCC-IMS data in disease classification—Automated methods can replace manual peak annotations

PubMed Central

Horsch, Salome; Kopczynski, Dominik; Kuthe, Elias; Baumbach, Jörg Ingo; Rahmann, Sven

2017-01-01

Motivation Disease classification from molecular measurements typically requires an analysis pipeline from raw noisy measurements to final classification results. Multi capillary column—ion mobility spectrometry (MCC-IMS) is a promising technology for the detection of volatile organic compounds in the air of exhaled breath. From raw measurements, the peak regions representing the compounds have to be identified, quantified, and clustered across different experiments. Currently, several steps of this analysis process require manual intervention of human experts. Our goal is to identify a fully automatic pipeline that yields competitive disease classification results compared to an established but subjective and tedious semi-manual process. Method We combine a large number of modern methods for peak detection, peak clustering, and multivariate classification into analysis pipelines for raw MCC-IMS data. We evaluate all combinations on three different real datasets in an unbiased cross-validation setting. We determine which specific algorithmic combinations lead to high AUC values in disease classifications across the different medical application scenarios. Results The best fully automated analysis process achieves even better classification results than the established manual process. The best algorithms for the three analysis steps are (i) SGLTR (Savitzky-Golay Laplace-operator filter thresholding regions) and LM (Local Maxima) for automated peak identification, (ii) EM clustering (Expectation Maximization) and DBSCAN (Density-Based Spatial Clustering of Applications with Noise) for the clustering step and (iii) RF (Random Forest) for multivariate classification. Thus, automated methods can replace the manual steps in the analysis process to enable an unbiased high throughput use of the technology. PMID:28910313

78 FR 58897 - Pipeline Safety: Administrative Procedures; Updates and Technical Corrections

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-25

... incorporate increased transparency into the decision making process, the regulations must explicitly recognize... certainty, and due process. II. Discussion of Comments The comments received from the trade organizations... assistance through these processes by assisting OPS in the development of written responses to requests for...

PMAnalyzer: a new web interface for bacterial growth curve analysis.

PubMed

Cuevas, Daniel A; Edwards, Robert A

2017-06-15

Bacterial growth curves are essential representations for characterizing bacteria metabolism within a variety of media compositions. Using high-throughput, spectrophotometers capable of processing tens of 96-well plates, quantitative phenotypic information can be easily integrated into the current data structures that describe a bacterial organism. The PMAnalyzer pipeline performs a growth curve analysis to parameterize the unique features occurring within microtiter wells containing specific growth media sources. We have expanded the pipeline capabilities and provide a user-friendly, online implementation of this automated pipeline. PMAnalyzer version 2.0 provides fast automatic growth curve parameter analysis, growth identification and high resolution figures of sample-replicate growth curves and several statistical analyses. PMAnalyzer v2.0 can be found at https://edwards.sdsu.edu/pmanalyzer/ . Source code for the pipeline can be found on GitHub at https://github.com/dacuevas/PMAnalyzer . Source code for the online implementation can be found on GitHub at https://github.com/dacuevas/PMAnalyzerWeb . dcuevas08@gmail.com. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Robust, open-source removal of systematics in Kepler data

NASA Astrophysics Data System (ADS)

Aigrain, S.; Parviainen, H.; Roberts, S.; Reece, S.; Evans, T.

2017-10-01

We present ARC2 (Astrophysically Robust Correction 2), an open-source python-based systematics-correction pipeline, to correct for the Kepler prime mission long-cadence light curves. The ARC2 pipeline identifies and corrects any isolated discontinuities in the light curves and then removes trends common to many light curves. These trends are modelled using the publicly available co-trending basis vectors, within an (approximate) Bayesian framework with 'shrinkage' priors to minimize the risk of overfitting and the injection of any additional noise into the corrected light curves, while keeping any astrophysical signals intact. We show that the ARC2 pipeline's performance matches that of the standard Kepler PDC-MAP data products using standard noise metrics, and demonstrate its ability to preserve astrophysical signals using injection tests with simulated stellar rotation and planetary transit signals. Although it is not identical, the ARC2 pipeline can thus be used as an open-source alternative to PDC-MAP, whenever the ability to model the impact of the systematics removal process on other kinds of signal is important.

Community Based Informatics: Geographical Information Systems, Remote Sensing and Ontology collaboration - A technical hands-on approach

NASA Astrophysics Data System (ADS)

Branch, B. D.; Raskin, R. G.; Rock, B.; Gagnon, M.; Lecompte, M. A.; Hayden, L. B.

2009-12-01

With the nation challenged to comply with Executive Order 12906 and its needs to augment the Science, Technology, Engineering and Mathematics (STEM) pipeline, applied focus on geosciences pipelines issue may be at risk. The Geosciences pipeline may require intentional K-12 standard course of study consideration in the form of project based, science based and evidenced based learning. Thus, the K-12 to geosciences to informatics pipeline may benefit from an earth science experience that utilizes a community based “learning by doing” approach. Terms such as Community GIS, Community Remotes Sensing, and Community Based Ontology development are termed Community Informatics. Here, approaches of interdisciplinary work to promote and earth science literacy are affordable, consisting of low cost equipment that renders GIS/remote sensing data processing skills necessary in the workforce. Hence, informal community ontology development may evolve or mature from a local community towards formal scientific community collaboration. Such consideration may become a means to engage educational policy towards earth science paradigms and needs, specifically linking synergy among Math, Computer Science, and Earth Science disciplines.

An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data.

PubMed

Jun, Goo; Wing, Mary Kate; Abecasis, Gonçalo R; Kang, Hyun Min

2015-06-01

The analysis of next-generation sequencing data is computationally and statistically challenging because of the massive volume of data and imperfect data quality. We present GotCloud, a pipeline for efficiently detecting and genotyping high-quality variants from large-scale sequencing data. GotCloud automates sequence alignment, sample-level quality control, variant calling, filtering of likely artifacts using machine-learning techniques, and genotype refinement using haplotype information. The pipeline can process thousands of samples in parallel and requires less computational resources than current alternatives. Experiments with whole-genome and exome-targeted sequence data generated by the 1000 Genomes Project show that the pipeline provides effective filtering against false positive variants and high power to detect true variants. Our pipeline has already contributed to variant detection and genotyping in several large-scale sequencing projects, including the 1000 Genomes Project and the NHLBI Exome Sequencing Project. We hope it will now prove useful to many medical sequencing studies. © 2015 Jun et al.; Published by Cold Spring Harbor Laboratory Press.

@TOME-2: a new pipeline for comparative modeling of protein-ligand complexes.

PubMed

Pons, Jean-Luc; Labesse, Gilles

2009-07-01

@TOME 2.0 is new web pipeline dedicated to protein structure modeling and small ligand docking based on comparative analyses. @TOME 2.0 allows fold recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation. These tasks are routinely used in sequence analyses for structure prediction. In our pipeline the necessary software is efficiently interconnected in an original manner to accelerate all the processes. Furthermore, we have also connected comparative docking of small ligands that is performed using protein-protein superposition. The input is a simple protein sequence in one-letter code with no comment. The resulting 3D model, protein-ligand complexes and structural alignments can be visualized through dedicated Web interfaces or can be downloaded for further studies. These original features will aid in the functional annotation of proteins and the selection of templates for molecular modeling and virtual screening. Several examples are described to highlight some of the new functionalities provided by this pipeline. The server and its documentation are freely available at http://abcis.cbs.cnrs.fr/AT2/

@TOME-2: a new pipeline for comparative modeling of protein–ligand complexes

PubMed Central

Pons, Jean-Luc; Labesse, Gilles

2009-01-01

@TOME 2.0 is new web pipeline dedicated to protein structure modeling and small ligand docking based on comparative analyses. @TOME 2.0 allows fold recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation. These tasks are routinely used in sequence analyses for structure prediction. In our pipeline the necessary software is efficiently interconnected in an original manner to accelerate all the processes. Furthermore, we have also connected comparative docking of small ligands that is performed using protein–protein superposition. The input is a simple protein sequence in one-letter code with no comment. The resulting 3D model, protein–ligand complexes and structural alignments can be visualized through dedicated Web interfaces or can be downloaded for further studies. These original features will aid in the functional annotation of proteins and the selection of templates for molecular modeling and virtual screening. Several examples are described to highlight some of the new functionalities provided by this pipeline. The server and its documentation are freely available at http://abcis.cbs.cnrs.fr/AT2/ PMID:19443448

Extending the Fermi-LAT Data Processing Pipeline to the Grid

NASA Astrophysics Data System (ADS)

Zimmer, S.; Arrabito, L.; Glanzman, T.; Johnson, T.; Lavalley, C.; Tsaregorodtsev, A.

2012-12-01

The Data Handling Pipeline (“Pipeline”) has been developed for the Fermi Gamma-Ray Space Telescope (Fermi) Large Area Telescope (LAT) which launched in June 2008. Since then it has been in use to completely automate the production of data quality monitoring quantities, reconstruction and routine analysis of all data received from the satellite and to deliver science products to the collaboration and the Fermi Science Support Center. Aside from the reconstruction of raw data from the satellite (Level 1), data reprocessing and various event-level analyses are also reasonably heavy loads on the pipeline and computing resources. These other loads, unlike Level 1, can run continuously for weeks or months at a time. In addition it receives heavy use in performing production Monte Carlo tasks. In daily use it receives a new data download every 3 hours and launches about 2000 jobs to process each download, typically completing the processing of the data before the next download arrives. The need for manual intervention has been reduced to less than 0.01% of submitted jobs. The Pipeline software is written almost entirely in Java and comprises several modules. The software comprises web-services that allow online monitoring and provides charts summarizing work flow aspects and performance information. The server supports communication with several batch systems such as LSF and BQS and recently also Sun Grid Engine and Condor. This is accomplished through dedicated job control services that for Fermi are running at SLAC and the other computing site involved in this large scale framework, the Lyon computing center of IN2P3. While being different in the logic of a task, we evaluate a separate interface to the Dirac system in order to communicate with EGI sites to utilize Grid resources, using dedicated Grid optimized systems rather than developing our own. More recently the Pipeline and its associated data catalog have been generalized for use by other experiments, and are currently being used by the Enriched Xenon Observatory (EXO), Cryogenic Dark Matter Search (CDMS) experiments as well as for Monte Carlo simulations for the future Cherenkov Telescope Array (CTA).

Performance of Transit Model Fitting in Processing Four Years of Kepler Science Data

NASA Astrophysics Data System (ADS)

Li, Jie; Burke, Christopher J.; Jenkins, Jon Michael; Quintana, Elisa V.; Rowe, Jason; Seader, Shawn; Tenenbaum, Peter; Twicken, Joseph D.

2014-06-01

We present transit model fitting performance of the Kepler Science Operations Center (SOC) Pipeline in processing four years of science data, which were collected by the Kepler spacecraft from May 13, 2009 to May 12, 2013. Threshold Crossing Events (TCEs), which represent transiting planet detections, are generated by the Transiting Planet Search (TPS) component of the pipeline and subsequently processed in the Data Validation (DV) component. The transit model is used in DV to fit TCEs and derive parameters that are used in various diagnostic tests to validate planetary candidates. The standard transit model includes five fit parameters: transit epoch time (i.e. central time of first transit), orbital period, impact parameter, ratio of planet radius to star radius and ratio of semi-major axis to star radius. In the latest Kepler SOC pipeline codebase, the light curve of the target for which a TCE is generated is initially fitted by a trapezoidal model with four parameters: transit epoch time, depth, duration and ingress time. The trapezoidal model fit, implemented with repeated Levenberg-Marquardt minimization, provides a quick and high fidelity assessment of the transit signal. The fit parameters of the trapezoidal model with the minimum chi-square metric are converted to set initial values of the fit parameters of the standard transit model. Additional parameters, such as the equilibrium temperature and effective stellar flux of the planet candidate, are derived from the fit parameters of the standard transit model to characterize pipeline candidates for the search of Earth-size planets in the Habitable Zone. The uncertainties of all derived parameters are updated in the latest codebase to take into account for the propagated errors of the fit parameters as well as the uncertainties in stellar parameters. The results of the transit model fitting of the TCEs identified by the Kepler SOC Pipeline, including fitted and derived parameters, fit goodness metrics and diagnostic figures, are included in the DV report and one-page report summary, which are accessible by the science community at NASA Exoplanet Archive. Funding for the Kepler Mission has been provided by the NASA Science Mission Directorate.

Allele-Specific Alternative mRNA processing (ASARP) | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

A software pipeline for prediction of allele-specific alternative RNA processing events using single RNA-seq data. The current version focuses on prediction of alternative splicing and alternative polyadenylation modulated by genetic variants.

National Pipeline Mapping System (NPMS) : repository standards

DOT National Transportation Integrated Search

1997-07-01

This draft document contains 7 sections. They are as follows: 1. General Topics, 2. Data Formats, 3. Metadata, 4. Attribute Data, 5. Data Flow, 6. Descriptive Process, and 7. Validation and Processing of Submitted Data. These standards were created w...

PRIMO: An Interactive Homology Modeling Pipeline.

PubMed

Hatherley, Rowan; Brown, David K; Glenister, Michael; Tastan Bishop, Özlem

2016-01-01

The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduces the workload required by the user, while still allowing engagement from the user during every step. Default parameters are given for each step, which can either be modified or supplemented with additional external input. PRIMO has been designed for users of varying levels of experience with homology modeling. The pipeline incorporates a user-friendly interface that makes it easy to alter parameters used during modeling. During each stage of the modeling process, the site provides suggestions for novice users to improve the quality of their models. PRIMO provides functionality that allows users to also model ligands and ions in complex with their protein targets. Herein, we assess the accuracy of the fully automated capabilities of the server, including a comparative analysis of the available alignment programs, as well as of the refinement levels used during modeling. The tests presented here demonstrate the reliability of the PRIMO server when producing a large number of protein models. While PRIMO does focus on user involvement in the homology modeling process, the results indicate that in the presence of suitable templates, good quality models can be produced even without user intervention. This gives an idea of the base level accuracy of PRIMO, which users can improve upon by adjusting parameters in their modeling runs. The accuracy of PRIMO's automated scripts is being continuously evaluated by the CAMEO (Continuous Automated Model EvaluatiOn) project. The PRIMO site is free for non-commercial use and can be accessed at https://primo.rubi.ru.ac.za/.

A Primer on High-Throughput Computing for Genomic Selection

PubMed Central

Wu, Xiao-Lin; Beissinger, Timothy M.; Bauck, Stewart; Woodward, Brent; Rosa, Guilherme J. M.; Weigel, Kent A.; Gatti, Natalia de Leon; Gianola, Daniel

2011-01-01

High-throughput computing (HTC) uses computer clusters to solve advanced computational problems, with the goal of accomplishing high-throughput over relatively long periods of time. In genomic selection, for example, a set of markers covering the entire genome is used to train a model based on known data, and the resulting model is used to predict the genetic merit of selection candidates. Sophisticated models are very computationally demanding and, with several traits to be evaluated sequentially, computing time is long, and output is low. In this paper, we present scenarios and basic principles of how HTC can be used in genomic selection, implemented using various techniques from simple batch processing to pipelining in distributed computer clusters. Various scripting languages, such as shell scripting, Perl, and R, are also very useful to devise pipelines. By pipelining, we can reduce total computing time and consequently increase throughput. In comparison to the traditional data processing pipeline residing on the central processors, performing general-purpose computation on a graphics processing unit provide a new-generation approach to massive parallel computing in genomic selection. While the concept of HTC may still be new to many researchers in animal breeding, plant breeding, and genetics, HTC infrastructures have already been built in many institutions, such as the University of Wisconsin–Madison, which can be leveraged for genomic selection, in terms of central processing unit capacity, network connectivity, storage availability, and middleware connectivity. Exploring existing HTC infrastructures as well as general-purpose computing environments will further expand our capability to meet increasing computing demands posed by unprecedented genomic data that we have today. We anticipate that HTC will impact genomic selection via better statistical models, faster solutions, and more competitive products (e.g., from design of marker panels to realized genetic gain). Eventually, HTC may change our view of data analysis as well as decision-making in the post-genomic era of selection programs in animals and plants, or in the study of complex diseases in humans. PMID:22303303

Streak detection and analysis pipeline for space-debris optical images

NASA Astrophysics Data System (ADS)

Virtanen, Jenni; Poikonen, Jonne; Säntti, Tero; Komulainen, Tuomo; Torppa, Johanna; Granvik, Mikael; Muinonen, Karri; Pentikäinen, Hanna; Martikainen, Julia; Näränen, Jyri; Lehti, Jussi; Flohrer, Tim

2016-04-01

We describe a novel data-processing and analysis pipeline for optical observations of moving objects, either of natural (asteroids, meteors) or artificial origin (satellites, space debris). The monitoring of the space object populations requires reliable acquisition of observational data, to support the development and validation of population models and to build and maintain catalogues of orbital elements. The orbital catalogues are, in turn, needed for the assessment of close approaches (for asteroids, with the Earth; for satellites, with each other) and for the support of contingency situations or launches. For both types of populations, there is also increasing interest to detect fainter objects corresponding to the small end of the size distribution. The ESA-funded StreakDet (streak detection and astrometric reduction) activity has aimed at formulating and discussing suitable approaches for the detection and astrometric reduction of object trails, or streaks, in optical observations. Our two main focuses are objects in lower altitudes and space-based observations (i.e., high angular velocities), resulting in long (potentially curved) and faint streaks in the optical images. In particular, we concentrate on single-image (as compared to consecutive frames of the same field) and low-SNR detection of objects. Particular attention has been paid to the process of extraction of all necessary information from one image (segmentation), and subsequently, to efficient reduction of the extracted data (classification). We have developed an automated streak detection and processing pipeline and demonstrated its performance with an extensive database of semisynthetic images simulating streak observations both from ground-based and space-based observing platforms. The average processing time per image is about 13 s for a typical 2k-by-2k image. For long streaks (length >100 pixels), primary targets of the pipeline, the detection sensitivity (true positives) is about 90% for both scenarios for the bright streaks (SNR > 1), while in the low-SNR regime, the sensitivity is still 50% at SNR = 0.5 .

PRIMO: An Interactive Homology Modeling Pipeline

PubMed Central

Glenister, Michael

2016-01-01

The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduces the workload required by the user, while still allowing engagement from the user during every step. Default parameters are given for each step, which can either be modified or supplemented with additional external input. PRIMO has been designed for users of varying levels of experience with homology modeling. The pipeline incorporates a user-friendly interface that makes it easy to alter parameters used during modeling. During each stage of the modeling process, the site provides suggestions for novice users to improve the quality of their models. PRIMO provides functionality that allows users to also model ligands and ions in complex with their protein targets. Herein, we assess the accuracy of the fully automated capabilities of the server, including a comparative analysis of the available alignment programs, as well as of the refinement levels used during modeling. The tests presented here demonstrate the reliability of the PRIMO server when producing a large number of protein models. While PRIMO does focus on user involvement in the homology modeling process, the results indicate that in the presence of suitable templates, good quality models can be produced even without user intervention. This gives an idea of the base level accuracy of PRIMO, which users can improve upon by adjusting parameters in their modeling runs. The accuracy of PRIMO’s automated scripts is being continuously evaluated by the CAMEO (Continuous Automated Model EvaluatiOn) project. The PRIMO site is free for non-commercial use and can be accessed at https://primo.rubi.ru.ac.za/. PMID:27855192

Programming the Navier-Stokes computer: An abstract machine model and a visual editor

NASA Technical Reports Server (NTRS)

Middleton, David; Crockett, Tom; Tomboulian, Sherry

1988-01-01

The Navier-Stokes computer is a parallel computer designed to solve Computational Fluid Dynamics problems. Each processor contains several floating point units which can be configured under program control to implement a vector pipeline with several inputs and outputs. Since the development of an effective compiler for this computer appears to be very difficult, machine level programming seems necessary and support tools for this process have been studied. These support tools are organized into a graphical program editor. A programming process is described by which appropriate computations may be efficiently implemented on the Navier-Stokes computer. The graphical editor would support this programming process, verifying various programmer choices for correctness and deducing values such as pipeline delays and network configurations. Step by step details are provided and demonstrated with two example programs.

The design of multi-core DSP parallel model based on message passing and multi-level pipeline

NASA Astrophysics Data System (ADS)

Niu, Jingyu; Hu, Jian; He, Wenjing; Meng, Fanrong; Li, Chuanrong

2017-10-01

Currently, the design of embedded signal processing system is often based on a specific application, but this idea is not conducive to the rapid development of signal processing technology. In this paper, a parallel processing model architecture based on multi-core DSP platform is designed, and it is mainly suitable for the complex algorithms which are composed of different modules. This model combines the ideas of multi-level pipeline parallelism and message passing, and summarizes the advantages of the mainstream model of multi-core DSP (the Master-Slave model and the Data Flow model), so that it has better performance. This paper uses three-dimensional image generation algorithm to validate the efficiency of the proposed model by comparing with the effectiveness of the Master-Slave and the Data Flow model.

75 FR 24655 - Order Finding That the ICE Waha Financial Basis Contract Traded on the IntercontinentalExchange...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-05

... Texas. Pipelines include El Paso Natural Gas, Transwestern Pipeline, Natural Gas Pipeline Co. of America, Northern Natural Gas, Delhi Pipeline, Oasis Pipeline, EPGT Texas and Lone Star Pipeline. The Platt's [[Page... pipelines. These pipelines bring in natural gas from fields in the Gulf Coast region and ship it to major...

Placement of implantable cardioverter-defibrillators in paediatric and congenital heart defect patients: a pipeline for model generation and simulation prediction of optimal configurations

PubMed Central

Rantner, Lukas J; Vadakkumpadan, Fijoy; Spevak, Philip J; Crosson, Jane E; Trayanova, Natalia A

2013-01-01

There is currently no reliable way of predicting the optimal implantable cardioverter-defibrillator (ICD) placement in paediatric and congenital heart defect (CHD) patients. This study aimed to: (1) develop a new image processing pipeline for constructing patient-specific heart–torso models from clinical magnetic resonance images (MRIs); (2) use the pipeline to determine the optimal ICD configuration in a paediatric tricuspid valve atresia patient; (3) establish whether the widely used criterion of shock-induced extracellular potential (Φe) gradients ≥5 V cm−1 in ≥95% of ventricular volume predicts defibrillation success. A biophysically detailed heart–torso model was generated from patient MRIs. Because transvenous access was impossible, three subcutaneous and three epicardial lead placement sites were identified along with five ICD scan locations. Ventricular fibrillation was induced, and defibrillation shocks were applied from 11 ICD configurations to determine defibrillation thresholds (DFTs). Two configurations with epicardial leads resulted in the lowest DFTs overall and were thus considered optimal. Three configurations shared the lowest DFT among subcutaneous lead ICDs. The Φe gradient criterion was an inadequate predictor of defibrillation success, as defibrillation failed in numerous instances even when 100% of the myocardium experienced such gradients. In conclusion, we have developed a new image processing pipeline and applied it to a CHD patient to construct the first active heart–torso model from clinical MRIs. PMID:23798492

Methodology for Image-Based Reconstruction of Ventricular Geometry for Patient-Specific Modeling of Cardiac Electrophysiology

PubMed Central

Prakosa, A.; Malamas, P.; Zhang, S.; Pashakhanloo, F.; Arevalo, H.; Herzka, D. A.; Lardo, A.; Halperin, H.; McVeigh, E.; Trayanova, N.; Vadakkumpadan, F.

2014-01-01

Patient-specific modeling of ventricular electrophysiology requires an interpolated reconstruction of the 3-dimensional (3D) geometry of the patient ventricles from the low-resolution (Lo-res) clinical images. The goal of this study was to implement a processing pipeline for obtaining the interpolated reconstruction, and thoroughly evaluate the efficacy of this pipeline in comparison with alternative methods. The pipeline implemented here involves contouring the epi- and endocardial boundaries in Lo-res images, interpolating the contours using the variational implicit functions method, and merging the interpolation results to obtain the ventricular reconstruction. Five alternative interpolation methods, namely linear, cubic spline, spherical harmonics, cylindrical harmonics, and shape-based interpolation were implemented for comparison. In the thorough evaluation of the processing pipeline, Hi-res magnetic resonance (MR), computed tomography (CT), and diffusion tensor (DT) MR images from numerous hearts were used. Reconstructions obtained from the Hi-res images were compared with the reconstructions computed by each of the interpolation methods from a sparse sample of the Hi-res contours, which mimicked Lo-res clinical images. Qualitative and quantitative comparison of these ventricular geometry reconstructions showed that the variational implicit functions approach performed better than others. Additionally, the outcomes of electrophysiological simulations (sinus rhythm activation maps and pseudo-ECGs) conducted using models based on the various reconstructions were compared. These electrophysiological simulations demonstrated that our implementation of the variational implicit functions-based method had the best accuracy. PMID:25148771

Design and Implementation of Data Reduction Pipelines for the Keck Observatory Archive

NASA Astrophysics Data System (ADS)

Gelino, C. R.; Berriman, G. B.; Kong, M.; Laity, A. C.; Swain, M. A.; Campbell, R.; Goodrich, R. W.; Holt, J.; Lyke, J.; Mader, J. A.; Tran, H. D.; Barlow, T.

2015-09-01

The Keck Observatory Archive (KOA), a collaboration between the NASA Exoplanet Science Institute and the W. M. Keck Observatory, serves science and calibration data for all active and inactive instruments from the twin Keck Telescopes located near the summit of Mauna Kea, Hawaii. In addition to the raw data, we produce and provide quick look reduced data for four instruments (HIRES, LWS, NIRC2, and OSIRIS) so that KOA users can more easily assess the scientific content and the quality of the data, which can often be difficult with raw data. The reduced products derive from both publicly available data reduction packages (when available) and KOA-created reduction scripts. The automation of publicly available data reduction packages has the benefit of providing a good quality product without the additional time and expense of creating a new reduction package, and is easily applied to bulk processing needs. The downside is that the pipeline is not always able to create an ideal product, particularly for spectra, because the processing options for one type of target (eg., point sources) may not be appropriate for other types of targets (eg., extended galaxies and nebulae). In this poster we present the design and implementation for the current pipelines used at KOA and discuss our strategies for handling data for which the nature of the targets and the observers' scientific goals and data taking procedures are unknown. We also discuss our plans for implementing automated pipelines for the remaining six instruments.

zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs.

PubMed

Parekh, Swati; Ziegenhain, Christoph; Vieth, Beate; Enard, Wolfgang; Hellmann, Ines

2018-06-01

Single-cell RNA-sequencing (scRNA-seq) experiments typically analyze hundreds or thousands of cells after amplification of the cDNA. The high throughput is made possible by the early introduction of sample-specific bar codes (BCs), and the amplification bias is alleviated by unique molecular identifiers (UMIs). Thus, the ideal analysis pipeline for scRNA-seq data needs to efficiently tabulate reads according to both BC and UMI. zUMIs is a pipeline that can handle both known and random BCs and also efficiently collapse UMIs, either just for exon mapping reads or for both exon and intron mapping reads. If BC annotation is missing, zUMIs can accurately detect intact cells from the distribution of sequencing reads. Another unique feature of zUMIs is the adaptive downsampling function that facilitates dealing with hugely varying library sizes but also allows the user to evaluate whether the library has been sequenced to saturation. To illustrate the utility of zUMIs, we analyzed a single-nucleus RNA-seq dataset and show that more than 35% of all reads map to introns. Also, we show that these intronic reads are informative about expression levels, significantly increasing the number of detected genes and improving the cluster resolution. zUMIs flexibility makes if possible to accommodate data generated with any of the major scRNA-seq protocols that use BCs and UMIs and is the most feature-rich, fast, and user-friendly pipeline to process such scRNA-seq data.

Software algorithms for false alarm reduction in LWIR hyperspectral chemical agent detection

NASA Astrophysics Data System (ADS)

Manolakis, D.; Model, J.; Rossacci, M.; Zhang, D.; Ontiveros, E.; Pieper, M.; Seeley, J.; Weitz, D.

2008-04-01

The long-wave infrared (LWIR) hyperpectral sensing modality is one that is often used for the problem of detection and identification of chemical warfare agents (CWA) which apply to both military and civilian situations. The inherent nature and complexity of background clutter dictates a need for sophisticated and robust statistical models which are then used in the design of optimum signal processing algorithms that then provide the best exploitation of hyperspectral data to ultimately make decisions on the absence or presence of potentially harmful CWAs. This paper describes the basic elements of an automated signal processing pipeline developed at MIT Lincoln Laboratory. In addition to describing this signal processing architecture in detail, we briefly describe the key signal models that form the foundation of these algorithms as well as some spatial processing techniques used for false alarm mitigation. Finally, we apply this processing pipeline to real data measured by the Telops FIRST hyperspectral (FIRST) sensor to demonstrate its practical utility for the user community.

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

PubMed Central

Li, Junhua; Chen, Weineng; Chen, Hua; Mende, Daniel R.; Arumugam, Manimozhiyan; Pan, Qi; Liu, Binghang; Qin, Junjie; Wang, Jun; Bork, Peer

2012-01-01

MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/. PMID:23082188

OpenCluster: A Flexible Distributed Computing Framework for Astronomical Data Processing

NASA Astrophysics Data System (ADS)

Wei, Shoulin; Wang, Feng; Deng, Hui; Liu, Cuiyin; Dai, Wei; Liang, Bo; Mei, Ying; Shi, Congming; Liu, Yingbo; Wu, Jingping

2017-02-01

The volume of data generated by modern astronomical telescopes is extremely large and rapidly growing. However, current high-performance data processing architectures/frameworks are not well suited for astronomers because of their limitations and programming difficulties. In this paper, we therefore present OpenCluster, an open-source distributed computing framework to support rapidly developing high-performance processing pipelines of astronomical big data. We first detail the OpenCluster design principles and implementations and present the APIs facilitated by the framework. We then demonstrate a case in which OpenCluster is used to resolve complex data processing problems for developing a pipeline for the Mingantu Ultrawide Spectral Radioheliograph. Finally, we present our OpenCluster performance evaluation. Overall, OpenCluster provides not only high fault tolerance and simple programming interfaces, but also a flexible means of scaling up the number of interacting entities. OpenCluster thereby provides an easily integrated distributed computing framework for quickly developing a high-performance data processing system of astronomical telescopes and for significantly reducing software development expenses.

MOCAT: a metagenomics assembly and gene prediction toolkit.

PubMed

Kultima, Jens Roat; Sunagawa, Shinichi; Li, Junhua; Chen, Weineng; Chen, Hua; Mende, Daniel R; Arumugam, Manimozhiyan; Pan, Qi; Liu, Binghang; Qin, Junjie; Wang, Jun; Bork, Peer

2012-01-01

MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/.

Valve For Extracting Samples From A Process Stream

NASA Technical Reports Server (NTRS)

Callahan, Dave

1995-01-01

Valve for extracting samples from process stream includes cylindrical body bolted to pipe that contains stream. Opening in valve body matched and sealed against opening in pipe. Used to sample process streams in variety of facilities, including cement plants, plants that manufacture and reprocess plastics, oil refineries, and pipelines.

76 FR 29333 - Pipeline Safety: Meetings of the Technical Pipeline Safety Standards Committee and the Technical...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-20

... DEPARTMENT OF TRANSPORTATION Pipeline and Hazardous Materials Safety Administration [Docket No... Technical Hazardous Liquid Pipeline Safety Standards Committee AGENCY: Pipeline and Hazardous Materials... for natural gas pipelines and for hazardous liquid pipelines. Both committees were established under...

77 FR 34123 - Pipeline Safety: Public Meeting on Integrity Management of Gas Distribution Pipelines

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-08

... DEPARTMENT OF TRANSPORTATION Pipeline and Hazardous Materials Safety Administration [Docket No. PHMSA-2012-0100] Pipeline Safety: Public Meeting on Integrity Management of Gas Distribution Pipelines AGENCY: Office of Pipeline Safety, Pipeline and Hazardous Materials Safety Administration, DOT. ACTION...

Taming Pipelines, Users, and High Performance Computing with Rector

NASA Astrophysics Data System (ADS)

Estes, N. M.; Bowley, K. S.; Paris, K. N.; Silva, V. H.; Robinson, M. S.

2018-04-01

Rector is a high-performance job management system created by the LROC SOC team to enable processing of thousands of observations and ancillary data products as well as ad-hoc user jobs across a 634 CPU core processing cluster.

76 FR 43743 - Pipeline Safety: Meetings of the Technical Pipeline Safety Standards Committee and the Technical...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-21

... DEPARTMENT OF TRANSPORTATION Pipeline and Hazardous Materials Safety Administration [Docket No. PHMSA-2011-0127] Pipeline Safety: Meetings of the Technical Pipeline Safety Standards Committee and the Technical Hazardous Liquid Pipeline Safety Standards Committee AGENCY: Pipeline and Hazardous Materials...

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms.

PubMed

Puritz, Jonathan B; Hollenbeck, Christopher M; Gold, John R

2014-01-01

Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for non-model organisms with large effective population sizes and high levels of genetic polymorphism. dDocent is an analysis pipeline with a user-friendly, command-line interface designed to process individually barcoded RADseq data (with double cut sites) into informative SNPs/Indels for population-level analyses. The pipeline, written in BASH, uses data reduction techniques and other stand-alone software packages to perform quality trimming and adapter removal, de novo assembly of RAD loci, read mapping, SNP and Indel calling, and baseline data filtering. Double-digest RAD data from population pairings of three different marine fishes were used to compare dDocent with Stacks, the first generally available, widely used pipeline for analysis of RADseq data. dDocent consistently identified more SNPs shared across greater numbers of individuals and with higher levels of coverage. This is due to the fact that dDocent quality trims instead of filtering, incorporates both forward and reverse reads (including reads with INDEL polymorphisms) in assembly, mapping, and SNP calling. The pipeline and a comprehensive user guide can be found at http://dDocent.wordpress.com.

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

PubMed Central

Hollenbeck, Christopher M.; Gold, John R.

2014-01-01

Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for non-model organisms with large effective population sizes and high levels of genetic polymorphism. dDocent is an analysis pipeline with a user-friendly, command-line interface designed to process individually barcoded RADseq data (with double cut sites) into informative SNPs/Indels for population-level analyses. The pipeline, written in BASH, uses data reduction techniques and other stand-alone software packages to perform quality trimming and adapter removal, de novo assembly of RAD loci, read mapping, SNP and Indel calling, and baseline data filtering. Double-digest RAD data from population pairings of three different marine fishes were used to compare dDocent with Stacks, the first generally available, widely used pipeline for analysis of RADseq data. dDocent consistently identified more SNPs shared across greater numbers of individuals and with higher levels of coverage. This is due to the fact that dDocent quality trims instead of filtering, incorporates both forward and reverse reads (including reads with INDEL polymorphisms) in assembly, mapping, and SNP calling. The pipeline and a comprehensive user guide can be found at http://dDocent.wordpress.com. PMID:24949246

Identification of failure type in corroded pipelines: a bayesian probabilistic approach.

PubMed

Breton, T; Sanchez-Gheno, J C; Alamilla, J L; Alvarez-Ramirez, J

2010-07-15

Spillover of hazardous materials from transport pipelines can lead to catastrophic events with serious and dangerous environmental impact, potential fire events and human fatalities. The problem is more serious for large pipelines when the construction material is under environmental corrosion conditions, as in the petroleum and gas industries. In this way, predictive models can provide a suitable framework for risk evaluation, maintenance policies and substitution procedure design that should be oriented to reduce increased hazards. This work proposes a bayesian probabilistic approach to identify and predict the type of failure (leakage or rupture) for steel pipelines under realistic corroding conditions. In the first step of the modeling process, the mechanical performance of the pipe is considered for establishing conditions under which either leakage or rupture failure can occur. In the second step, experimental burst tests are used to introduce a mean probabilistic boundary defining a region where the type of failure is uncertain. In the boundary vicinity, the failure discrimination is carried out with a probabilistic model where the events are considered as random variables. In turn, the model parameters are estimated with available experimental data and contrasted with a real catastrophic event, showing good discrimination capacity. The results are discussed in terms of policies oriented to inspection and maintenance of large-size pipelines in the oil and gas industry. 2010 Elsevier B.V. All rights reserved.

Reconfigurable pipelined processor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saccardi, R.J.

1989-09-19

This patent describes a reconfigurable pipelined processor for processing data. It comprises: a plurality of memory devices for storing bits of data; a plurality of arithmetic units for performing arithmetic functions with the data; cross bar means for connecting the memory devices with the arithmetic units for transferring data therebetween; at least one counter connected with the cross bar means for providing a source of addresses to the memory devices; at least one variable tick delay device connected with each of the memory devices and arithmetic units; and means for providing control bits to the variable tick delay device formore » variably controlling the input and output operations thereof to selectively delay the memory devices and arithmetic units to align the data for processing in a selected sequence.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Childers, M.; Barnes, J.

The phased field development of the Lion and Panthere fields, offshore the Ivory Coast, includes a small floating production, storage, and offloading (FPSO) tanker with minimal processing capability as an early oil production system (EPS). For the long-term production scheme, the FPSO will be replaced by a converted jack up mobile offshore production system (MOPS) with full process equipment. The development also includes guyed-caisson well platforms, pipeline export for natural gas to fuel an onshore power plant, and a floating storage and offloading (FSO) tanker for oil export. Pipeline export for oil is a future possibility. This array of innovativemore » strategies and techniques seldom has been brought together in a single project. The paper describes the development plan, early oil, jack up MOPS, and transport and installation.« less

The Snow Data System at NASA JPL

NASA Astrophysics Data System (ADS)

Horn, J.; Painter, T. H.; Bormann, K. J.; Rittger, K.; Brodzik, M. J.; Skiles, M.; Burgess, A. B.; Mattmann, C. A.; Ramirez, P.; Joyce, M.; Goodale, C. E.; McGibbney, L. J.; Zimdars, P.; Yaghoobi, R.

2017-12-01

The Snow Data System at NASA JPL includes data processing pipelines built with open source software, Apache 'Object Oriented Data Technology' (OODT). Processing is carried out in parallel across a high-powered computing cluster. The pipelines use input data from satellites such as MODIS, VIIRS and Landsat. They apply algorithms to the input data to produce a variety of outputs in GeoTIFF format. These outputs include daily data for SCAG (Snow Cover And Grain size) and DRFS (Dust Radiative Forcing in Snow), along with 8-day composites and MODICE annual minimum snow and ice calculations. This poster will describe the Snow Data System, its outputs and their uses and applications. It will also highlight recent advancements to the system and plans for the future.

The Snow Data System at NASA JPL

NASA Astrophysics Data System (ADS)

Joyce, M.; Laidlaw, R.; Painter, T. H.; Bormann, K. J.; Rittger, K.; Brodzik, M. J.; Skiles, M.; Burgess, A. B.; Mattmann, C. A.; Ramirez, P.; Goodale, C. E.; McGibbney, L. J.; Zimdars, P.; Yaghoobi, R.

2016-12-01

The Snow Data System at NASA JPL includes data processing pipelines built with open source software, Apache 'Object Oriented Data Technology' (OODT). Processing is carried out in parallel across a high-powered computing cluster. The pipelines use input data from satellites such as MODIS, VIIRS and Landsat. They apply algorithms to the input data to produce a variety of outputs in GeoTIFF format. These outputs include daily data for SCAG (Snow Cover And Grain size) and DRFS (Dust Radiative Forcing in Snow), along with 8-day composites and MODICE annual minimum snow and ice calculations. This poster will describe the Snow Data System, its outputs and their uses and applications. It will also highlight recent advancements to the system and plans for the future.

H2A Biomethane Model Documentation and a Case Study for Biogas From Dairy Farms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saur, G.; Jalalzadeh, A.

2010-12-01

The new H2A Biomethane model was developed to estimate the levelized cost of biomethane by using the framework of the vetted original H2A models for hydrogen production and delivery. For biomethane production, biogas from sources such as dairy farms and landfills is upgraded by a cleanup process. The model also estimates the cost to compress and transport the product gas via the pipeline to export it to the natural gas grid or any other potential end-use site. Inputs include feed biogas composition and cost, required biomethane quality, cleanup equipment capital and operations and maintenance costs, process electricity usage and costs,more » and pipeline delivery specifications.« less

77 FR 16471 - Pipeline Safety: Implementation of the National Registry of Pipeline and Liquefied Natural Gas...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-21

... Registry of Pipeline and Liquefied Natural Gas Operators AGENCY: Pipeline and Hazardous Materials Safety... DEPARTMENT OF TRANSPORTATION Pipeline and Hazardous Materials Safety Administration 49 CFR Parts... Register (75 FR 72878) titled: ``Pipeline Safety: Updates to Pipeline and Liquefied Natural Gas Reporting...

NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

PubMed

Delaglio, F; Grzesiek, S; Vuister, G W; Zhu, G; Pfeifer, J; Bax, A

1995-11-01

The NMRPipe system is a UNIX software environment of processing, graphics, and analysis tools designed to meet current routine and research-oriented multidimensional processing requirements, and to anticipate and accommodate future demands and developments. The system is based on UNIX pipes, which allow programs running simultaneously to exchange streams of data under user control. In an NMRPipe processing scheme, a stream of spectral data flows through a pipeline of processing programs, each of which performs one component of the overall scheme, such as Fourier transformation or linear prediction. Complete multidimensional processing schemes are constructed as simple UNIX shell scripts. The processing modules themselves maintain and exploit accurate records of data sizes, detection modes, and calibration information in all dimensions, so that schemes can be constructed without the need to explicitly define or anticipate data sizes or storage details of real and imaginary channels during processing. The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks.

The Harvard Automated Processing Pipeline for Electroencephalography (HAPPE): Standardized Processing Software for Developmental and High-Artifact Data.

PubMed

Gabard-Durnam, Laurel J; Mendez Leal, Adriana S; Wilkinson, Carol L; Levin, April R

2018-01-01

Electroenchephalography (EEG) recordings collected with developmental populations present particular challenges from a data processing perspective. These EEGs have a high degree of artifact contamination and often short recording lengths. As both sample sizes and EEG channel densities increase, traditional processing approaches like manual data rejection are becoming unsustainable. Moreover, such subjective approaches preclude standardized metrics of data quality, despite the heightened importance of such measures for EEGs with high rates of initial artifact contamination. There is presently a paucity of automated resources for processing these EEG data and no consistent reporting of data quality measures. To address these challenges, we propose the Harvard Automated Processing Pipeline for EEG (HAPPE) as a standardized, automated pipeline compatible with EEG recordings of variable lengths and artifact contamination levels, including high-artifact and short EEG recordings from young children or those with neurodevelopmental disorders. HAPPE processes event-related and resting-state EEG data from raw files through a series of filtering, artifact rejection, and re-referencing steps to processed EEG suitable for time-frequency-domain analyses. HAPPE also includes a post-processing report of data quality metrics to facilitate the evaluation and reporting of data quality in a standardized manner. Here, we describe each processing step in HAPPE, perform an example analysis with EEG files we have made freely available, and show that HAPPE outperforms seven alternative, widely-used processing approaches. HAPPE removes more artifact than all alternative approaches while simultaneously preserving greater or equivalent amounts of EEG signal in almost all instances. We also provide distributions of HAPPE's data quality metrics in an 867 file dataset as a reference distribution and in support of HAPPE's performance across EEG data with variable artifact contamination and recording lengths. HAPPE software is freely available under the terms of the GNU General Public License at https://github.com/lcnhappe/happe.

The Harvard Automated Processing Pipeline for Electroencephalography (HAPPE): Standardized Processing Software for Developmental and High-Artifact Data

PubMed Central

Gabard-Durnam, Laurel J.; Mendez Leal, Adriana S.; Wilkinson, Carol L.; Levin, April R.

2018-01-01

Electroenchephalography (EEG) recordings collected with developmental populations present particular challenges from a data processing perspective. These EEGs have a high degree of artifact contamination and often short recording lengths. As both sample sizes and EEG channel densities increase, traditional processing approaches like manual data rejection are becoming unsustainable. Moreover, such subjective approaches preclude standardized metrics of data quality, despite the heightened importance of such measures for EEGs with high rates of initial artifact contamination. There is presently a paucity of automated resources for processing these EEG data and no consistent reporting of data quality measures. To address these challenges, we propose the Harvard Automated Processing Pipeline for EEG (HAPPE) as a standardized, automated pipeline compatible with EEG recordings of variable lengths and artifact contamination levels, including high-artifact and short EEG recordings from young children or those with neurodevelopmental disorders. HAPPE processes event-related and resting-state EEG data from raw files through a series of filtering, artifact rejection, and re-referencing steps to processed EEG suitable for time-frequency-domain analyses. HAPPE also includes a post-processing report of data quality metrics to facilitate the evaluation and reporting of data quality in a standardized manner. Here, we describe each processing step in HAPPE, perform an example analysis with EEG files we have made freely available, and show that HAPPE outperforms seven alternative, widely-used processing approaches. HAPPE removes more artifact than all alternative approaches while simultaneously preserving greater or equivalent amounts of EEG signal in almost all instances. We also provide distributions of HAPPE's data quality metrics in an 867 file dataset as a reference distribution and in support of HAPPE's performance across EEG data with variable artifact contamination and recording lengths. HAPPE software is freely available under the terms of the GNU General Public License at https://github.com/lcnhappe/happe. PMID:29535597

75 FR 13644 - TORP Terminal LP, Bienville Offshore Energy Terminal Liquefied Natural Gas Deepwater Port License...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-22

... interconnect pipelines to four existing offshore pipelines (Dauphin Natural Gas Pipeline, Williams Natural Gas Pipeline, Destin Natural Gas Pipeline, and Viosca Knoll Gathering System [VKGS] Gas Pipeline) that connect to the onshore natural gas transmission pipeline system. Natural gas would be delivered to customers...

Freight pipelines: Current status and anticipated future use

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1998-07-01

This report is issued by the Task Committee on Freight Pipelines, Pipeline Division, ASCE. Freight pipelines of various types (including slurry pipeline, pneumatic pipeline, and capsule pipeline) have been used throughout the world for over a century for transporting solid and sometimes even package products. Recent advancements in pipeline technology, aided by advanced computer control systems and trenchless technologies, have greatly facilitated the transportation of solids by pipelines. Today, in many situations, freight pipelines are not only the most economical and practical means for transporting solids, they are also the most reliable, safest and most environmentally friendly transportation mode. Increasedmore » use of underground pipelines to transport freight is anticipated in the future, especially as the technology continues to improve and surface transportation modes such as highways become more congested. This paper describes the state of the art and expected future uses of various types of freight pipelines. Obstacles hindering the development and use of the most advanced freight pipeline systems, such as the pneumatic capsule pipeline for interstate transport of freight, are discussed.« less

3D surface reconstruction and visualization of the Drosophila wing imaginal disc at cellular resolution

NASA Astrophysics Data System (ADS)

Bai, Linge; Widmann, Thomas; Jülicher, Frank; Dahmann, Christian; Breen, David

2013-01-01

Quantifying and visualizing the shape of developing biological tissues provide information about the morphogenetic processes in multicellular organisms. The size and shape of biological tissues depend on the number, size, shape, and arrangement of the constituting cells. To better understand the mechanisms that guide tissues into their final shape, it is important to investigate the cellular arrangement within tissues. Here we present a data processing pipeline to generate 3D volumetric surface models of epithelial tissues, as well as geometric descriptions of the tissues' apical cell cross-sections. The data processing pipeline includes image acquisition, editing, processing and analysis, 2D cell mesh generation, 3D contourbased surface reconstruction, cell mesh projection, followed by geometric calculations and color-based visualization of morphological parameters. In their first utilization we have applied these procedures to construct a 3D volumetric surface model at cellular resolution of the wing imaginal disc of Drosophila melanogaster. The ultimate goal of the reported effort is to produce tools for the creation of detailed 3D geometric models of the individual cells in epithelial tissues. To date, 3D volumetric surface models of the whole wing imaginal disc have been created, and the apicolateral cell boundaries have been identified, allowing for the calculation and visualization of cell parameters, e.g. apical cross-sectional area of cells. The calculation and visualization of morphological parameters show position-dependent patterns of cell shape in the wing imaginal disc. Our procedures should offer a general data processing pipeline for the construction of 3D volumetric surface models of a wide variety of epithelial tissues.

Adiabatic pipelining: a key to ternary computing with quantum dots.

PubMed

Pečar, P; Ramšak, A; Zimic, N; Mraz, M; Lebar Bajec, I

2008-12-10

The quantum-dot cellular automaton (QCA), a processing platform based on interacting quantum dots, was introduced by Lent in the mid-1990s. What followed was an exhilarating period with the development of the line, the functionally complete set of logic functions, as well as more complex processing structures, however all in the realm of binary logic. Regardless of these achievements, it has to be acknowledged that the use of binary logic is in computing systems mainly the end result of the technological limitations, which the designers had to cope with in the early days of their design. The first advancement of QCAs to multi-valued (ternary) processing was performed by Lebar Bajec et al, with the argument that processing platforms of the future should not disregard the clear advantages of multi-valued logic. Some of the elementary ternary QCAs, necessary for the construction of more complex processing entities, however, lead to a remarkable increase in size when compared to their binary counterparts. This somewhat negates the advantages gained by entering the ternary computing domain. As it turned out, even the binary QCA had its initial hiccups, which have been solved by the introduction of adiabatic switching and the application of adiabatic pipeline approaches. We present here a study that introduces adiabatic switching into the ternary QCA and employs the adiabatic pipeline approach to successfully solve the issues of elementary ternary QCAs. What is more, the ternary QCAs presented here are sizewise comparable to binary QCAs. This in our view might serve towards their faster adoption.

Computational Testing for Automated Preprocessing 2: Practical Demonstration of a System for Scientific Data-Processing Workflow Management for High-Volume EEG

PubMed Central

Cowley, Benjamin U.; Korpela, Jussi

2018-01-01

Existing tools for the preprocessing of EEG data provide a large choice of methods to suitably prepare and analyse a given dataset. Yet it remains a challenge for the average user to integrate methods for batch processing of the increasingly large datasets of modern research, and compare methods to choose an optimal approach across the many possible parameter configurations. Additionally, many tools still require a high degree of manual decision making for, e.g., the classification of artifacts in channels, epochs or segments. This introduces extra subjectivity, is slow, and is not reproducible. Batching and well-designed automation can help to regularize EEG preprocessing, and thus reduce human effort, subjectivity, and consequent error. The Computational Testing for Automated Preprocessing (CTAP) toolbox facilitates: (i) batch processing that is easy for experts and novices alike; (ii) testing and comparison of preprocessing methods. Here we demonstrate the application of CTAP to high-resolution EEG data in three modes of use. First, a linear processing pipeline with mostly default parameters illustrates ease-of-use for naive users. Second, a branching pipeline illustrates CTAP's support for comparison of competing methods. Third, a pipeline with built-in parameter-sweeping illustrates CTAP's capability to support data-driven method parameterization. CTAP extends the existing functions and data structure from the well-known EEGLAB toolbox, based on Matlab, and produces extensive quality control outputs. CTAP is available under MIT open-source licence from https://github.com/bwrc/ctap. PMID:29692705

Computational Testing for Automated Preprocessing 2: Practical Demonstration of a System for Scientific Data-Processing Workflow Management for High-Volume EEG.

PubMed

Cowley, Benjamin U; Korpela, Jussi

2018-01-01

Existing tools for the preprocessing of EEG data provide a large choice of methods to suitably prepare and analyse a given dataset. Yet it remains a challenge for the average user to integrate methods for batch processing of the increasingly large datasets of modern research, and compare methods to choose an optimal approach across the many possible parameter configurations. Additionally, many tools still require a high degree of manual decision making for, e.g., the classification of artifacts in channels, epochs or segments. This introduces extra subjectivity, is slow, and is not reproducible. Batching and well-designed automation can help to regularize EEG preprocessing, and thus reduce human effort, subjectivity, and consequent error. The Computational Testing for Automated Preprocessing (CTAP) toolbox facilitates: (i) batch processing that is easy for experts and novices alike; (ii) testing and comparison of preprocessing methods. Here we demonstrate the application of CTAP to high-resolution EEG data in three modes of use. First, a linear processing pipeline with mostly default parameters illustrates ease-of-use for naive users. Second, a branching pipeline illustrates CTAP's support for comparison of competing methods. Third, a pipeline with built-in parameter-sweeping illustrates CTAP's capability to support data-driven method parameterization. CTAP extends the existing functions and data structure from the well-known EEGLAB toolbox, based on Matlab, and produces extensive quality control outputs. CTAP is available under MIT open-source licence from https://github.com/bwrc/ctap.

High speed quantitative digital microscopy

NASA Technical Reports Server (NTRS)

Castleman, K. R.; Price, K. H.; Eskenazi, R.; Ovadya, M. M.; Navon, M. A.

1984-01-01

Modern digital image processing hardware makes possible quantitative analysis of microscope images at high speed. This paper describes an application to automatic screening for cervical cancer. The system uses twelve MC6809 microprocessors arranged in a pipeline multiprocessor configuration. Each processor executes one part of the algorithm on each cell image as it passes through the pipeline. Each processor communicates with its upstream and downstream neighbors via shared two-port memory. Thus no time is devoted to input-output operations as such. This configuration is expected to be at least ten times faster than previous systems.

Automated Reduction and Calibration of SCUBA Archive Data Using ORAC-DR

NASA Astrophysics Data System (ADS)

Jenness, T.; Stevens, J. A.; Archibald, E. N.; Economou, F.; Jessop, N.; Robson, E. I.; Tilanus, R. P. J.; Holland, W. S.

The Submillimetre Common User Bolometer Array (SCUBA) instrument has been operating on the James Clerk Maxwell Telescope (JCMT) since 1997. The data archive is now sufficiently large that it can be used for investigating instrumental properties and the variability of astronomical sources. This paper describes the automated calibration and reduction scheme used to process the archive data with particular emphasis on the pointing observations. This is made possible by using the ORAC-DR data reduction pipeline, a flexible and extensible data reduction pipeline that is used on UKIRT and the JCMT.

Head-to-Head Comparison of Two Popular Cortical Thickness Extraction Algorithms: A Cross-Sectional and Longitudinal Study

PubMed Central

Redolfi, Alberto; Manset, David; Barkhof, Frederik; Wahlund, Lars-Olof; Glatard, Tristan; Mangin, Jean-François; Frisoni, Giovanni B.

2015-01-01

Background and Purpose The measurement of cortical shrinkage is a candidate marker of disease progression in Alzheimer’s. This study evaluated the performance of two pipelines: Civet-CLASP (v1.1.9) and Freesurfer (v5.3.0). Methods Images from 185 ADNI1 cases (69 elderly controls (CTR), 37 stable MCI (sMCI), 27 progressive MCI (pMCI), and 52 Alzheimer (AD) patients) scanned at baseline, month 12, and month 24 were processed using the two pipelines and two interconnected e-infrastructures: neuGRID (https://neugrid4you.eu) and VIP (http://vip.creatis.insa-lyon.fr). The vertex-by-vertex cross-algorithm comparison was made possible applying the 3D gradient vector flow (GVF) and closest point search (CPS) techniques. Results The cortical thickness measured with Freesurfer was systematically lower by one third if compared to Civet’s. Cross-sectionally, Freesurfer’s effect size was significantly different in the posterior division of the temporal fusiform cortex. Both pipelines were weakly or mildly correlated with the Mini Mental State Examination score (MMSE) and the hippocampal volumetry. Civet differed significantly from Freesurfer in large frontal, parietal, temporal and occipital regions (p<0.05). In a discriminant analysis with cortical ROIs having effect size larger than 0.8, both pipelines gave no significant differences in area under the curve (AUC). Longitudinally, effect sizes were not significantly different in any of the 28 ROIs tested. Both pipelines weakly correlated with MMSE decay, showing no significant differences. Freesurfer mildly correlated with hippocampal thinning rate and differed in the supramarginal gyrus, temporal gyrus, and in the lateral occipital cortex compared to Civet (p<0.05). In a discriminant analysis with ROIs having effect size larger than 0.6, both pipelines yielded no significant differences in the AUC. Conclusions Civet appears slightly more sensitive to the typical AD atrophic pattern at the MCI stage, but both pipelines can accurately characterize the topography of cortical thinning at the dementia stage. PMID:25781983

Zonation and assessment of frozen-ground conditions along the China-Russia Crude Oil Pipeline route from Mo’he to Daqing, Northeastern China

NASA Astrophysics Data System (ADS)

Jin, H.; Hao, J.; Chang, X.

2009-12-01

The proposed China-Russia Crude Oil Pipeline (CRCOP), 813 mm in diameter, is designed to transport 603,000 barrels of Siberian crude oil per day using conventional burial across 1,030 km of frozen-ground. About 500 boreholes, with depths of 5 to 20 m, were drilled and cored for analyses, and the frozen-ground conditions were evaluated. After detailed surveys and analyses of the permafrost conditions along the pipeline route, a conventional burial construction mode at a nominal depth of 1.5 m was adopted. This paper discusses the principles and criteria for the zonation and assessment of the frozen-ground environments and conditions of engineering geology for the design, construction, operation of the pipeline system based on an extensive and in-depth summary and analysis of the survey and exploration data. Full consideration of the characteristics of pipelining crude oil at ambient temperatures in the permafrost regions and the interactive processes between the pipeline and foundation soils were taken into account. Two zones of frozen-ground environment and conditions of engineering geology, i. e. seasonally-frozen-ground and permafrost, were defined on the basis of the regional distribution and differentiations in frozen-ground environments and conditions. Then, four subzones of the permafrost zone were classified according to the areal extent, taking into consideration the temperatures and thicknesses of permafrost, as well as changes in vegetation coverage. In the four subzones, 151 sections of engineering geology were categorized according to the ice/moisture contents of the permafrost, as well as the classes of frost-heaving and thaw-settlement potentials. These 151 sections are comprehensively summarized into four types for engineering construction and operation: good, fair, poor, and very poor, for overall conditions of engineering geology. The zonation, assessment principles and criteria have been applied in the design of the pipeline. They have also been used as the scientific bases for the construction, environmental management, operation and maintenance/contingency plans

The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data.

PubMed

Lammers, Youri; Peelen, Tamara; Vos, Rutger A; Gravendeel, Barbara

2014-02-06

Mixtures of internationally traded organic substances can contain parts of species protected by the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). These mixtures often raise the suspicion of border control and customs offices, which can lead to confiscation, for example in the case of Traditional Chinese medicines (TCMs). High-throughput sequencing of DNA barcoding markers obtained from such samples provides insight into species constituents of mixtures, but manual cross-referencing of results against the CITES appendices is labor intensive. Matching DNA barcodes against NCBI GenBank using BLAST may yield misleading results both as false positives, due to incorrectly annotated sequences, and false negatives, due to spurious taxonomic re-assignment. Incongruence between the taxonomies of CITES and NCBI GenBank can result in erroneous estimates of illegal trade. The HTS barcode checker pipeline is an application for automated processing of sets of 'next generation' barcode sequences to determine whether these contain DNA barcodes obtained from species listed on the CITES appendices. This analytical pipeline builds upon and extends existing open-source applications for BLAST matching against the NCBI GenBank reference database and for taxonomic name reconciliation. In a single operation, reads are converted into taxonomic identifications matched with names on the CITES appendices. By inclusion of a blacklist and additional names databases, the HTS barcode checker pipeline prevents false positives and resolves taxonomic heterogeneity. The HTS barcode checker pipeline can detect and correctly identify DNA barcodes of CITES-protected species from reads obtained from TCM samples in just a few minutes. The pipeline facilitates and improves molecular monitoring of trade in endangered species, and can aid in safeguarding these species from extinction in the wild. The HTS barcode checker pipeline is available at https://github.com/naturalis/HTS-barcode-checker.

The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data

PubMed Central

2014-01-01

Background Mixtures of internationally traded organic substances can contain parts of species protected by the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). These mixtures often raise the suspicion of border control and customs offices, which can lead to confiscation, for example in the case of Traditional Chinese medicines (TCMs). High-throughput sequencing of DNA barcoding markers obtained from such samples provides insight into species constituents of mixtures, but manual cross-referencing of results against the CITES appendices is labor intensive. Matching DNA barcodes against NCBI GenBank using BLAST may yield misleading results both as false positives, due to incorrectly annotated sequences, and false negatives, due to spurious taxonomic re-assignment. Incongruence between the taxonomies of CITES and NCBI GenBank can result in erroneous estimates of illegal trade. Results The HTS barcode checker pipeline is an application for automated processing of sets of 'next generation’ barcode sequences to determine whether these contain DNA barcodes obtained from species listed on the CITES appendices. This analytical pipeline builds upon and extends existing open-source applications for BLAST matching against the NCBI GenBank reference database and for taxonomic name reconciliation. In a single operation, reads are converted into taxonomic identifications matched with names on the CITES appendices. By inclusion of a blacklist and additional names databases, the HTS barcode checker pipeline prevents false positives and resolves taxonomic heterogeneity. Conclusions The HTS barcode checker pipeline can detect and correctly identify DNA barcodes of CITES-protected species from reads obtained from TCM samples in just a few minutes. The pipeline facilitates and improves molecular monitoring of trade in endangered species, and can aid in safeguarding these species from extinction in the wild. The HTS barcode checker pipeline is available at https://github.com/naturalis/HTS-barcode-checker. PMID:24502833

VizieR Online Data Catalog: Galaxy structural parameters from 3.6um images (Kim+, 2014)

NASA Astrophysics Data System (ADS)

Kim, T.; Gadotti, D. A.; Sheth, K.; Athanassoula, E.; Bosma, A.; Lee, M. G.; Madore, B. F.; Elmegreen, B.; Knapen, J. H.; Zaritsky, D.; Ho, L. C.; Comeron, S.; Holwerda, B.; Hinz, J. L.; Munoz-Mateos, J.-C.; Cisternas, M.; Erroz-Ferrer, S.; Buta, R.; Laurikainen, E.; Salo, H.; Laine, J.; Menendez-Delmestre, K.; Regan, M. W.; de Swardt, B.; Gil de Paz, A.; Seibert, M.; Mizusawa, T.

2016-03-01

We select our samples from the Spitzer Survey of Stellar Structure in Galaxies (S4G; Sheth et al. 2010, cat. J/PASP/122/1397). We chose galaxies that had already been processed by the first three S4G pipelines (Pipelines 1, 2, and 3; Sheth et al. 2010, cat. J/PASP/122/1397) at the moment of this study (2011 November). In brief, Pipeline processes images and provides science-ready images. Pipeline 2 prepares mask images (to exclude foreground and background objects) for further analysis, and Pipeline 3 derives surface brightness profiles and total magnitudes using IRAF ellipse fits. We excluded highly inclined (b/a<0.5), significantly disturbed, very faint, or irregular galaxies. Galaxies were also discarded if their images are unsuitable for decomposition due to contamination such as a bright foreground star or significant stray light from stars in the IRAC scattering zones. Then we chose barred galaxies from all Hubble types from S0 to Sdm using the numerical Hubble types from Hyperleda (Paturel et al. 2003, cat. VII/237, VII/238). The assessment of the presence of a bar was done visually by K. Sheth, T. Kim, and B. de Swardt. Later, we also confirmed the presence of a bar by checking the mid-infrared classification (Buta et al. 2010, cat. J/ApJS/190/147; Buta et al. 2015, cat. J/ApJS/217/32). A total of 144 barred galaxies were selected that satisfy our criteria, and we list our sample in Table1 with basic information. Table2 presents the measures of structural parameters for all galaxies in the sample obtained from the 2D model fit with BUDDA (BUlge/disk Decomposition Analysis, de Souza et al., 2004ApJS..153..411D; Gadotti, 2008MNRAS.384..420G) code. (2 data files).

Characterization and Validation of Transiting Planets in the Kepler and TESS Pipelines

NASA Astrophysics Data System (ADS)

Twicken, Joseph; Brownston, Lee; Catanzarite, Joseph; Clarke, Bruce; Cote, Miles; Girouard, Forrest; Li, Jie; McCauliff, Sean; Seader, Shawn; Tenenbaum, Peter; Wohler, Bill; Jenkins, Jon Michael; Batalha, Natalie; Bryson, Steve; Burke, Christopher; Caldwell, Douglas

2015-08-01

Light curves for Kepler targets are searched for transiting planet signatures in the Transiting Planet Search (TPS) component of the Science Operations Center (SOC) Processing Pipeline. Targets for which the detection threshold is exceeded are subsequently processed in the Data Validation (DV) Pipeline component. The primary functions of DV are to (1) characterize planets identified in the transiting planet search, (2) search for additional transiting planet signatures in light curves after modeled transit signatures have been removed, and (3) perform a comprehensive suite of diagnostic tests to aid in discrimination between true transiting planets and false positive detections. DV output products include extensive reports by target, one-page report summaries by planet candidate, and tabulated planet model fit and diagnostic test results. The DV products are employed by humans and automated systems to vet planet candidates identified in the pipeline. The final revision of the Kepler SOC codebase (9.3) was released in March 2015. It will be utilized to reprocess the complete Q1-Q17 data set later this year. At the same time, the SOC Pipeline codebase is being ported to support the Transiting Exoplanet Survey Satellite (TESS) Mission. TESS is expected to launch in 2017 and survey the entire sky for transiting exoplanets over a period of two years. We describe the final revision of the Kepler Data Validation component with emphasis on the diagnostic tests and reports. This revision also serves as the DV baseline for TESS. The diagnostic tests exploit the flux (i.e., light curve), centroid and pixel time series associated with each target to facilitate the determination of the true origin of each purported transiting planet signature. Candidate planet detections and DV products for Kepler are delivered to the Exoplanet Archive at the NASA Exoplanet Science Institute (NExScI). The Exoplanet Archive is located at exoplanetarchive.ipac.caltech.edu. Funding for the Kepler and TESS Missions has been provided by the NASA Science Mission Directorate.

Molgenis-impute: imputation pipeline in a box.

PubMed

Kanterakis, Alexandros; Deelen, Patrick; van Dijk, Freerk; Byelas, Heorhiy; Dijkstra, Martijn; Swertz, Morris A

2015-08-19

Genotype imputation is an important procedure in current genomic analysis such as genome-wide association studies, meta-analyses and fine mapping. Although high quality tools are available that perform the steps of this process, considerable effort and expertise is required to set up and run a best practice imputation pipeline, particularly for larger genotype datasets, where imputation has to scale out in parallel on computer clusters. Here we present MOLGENIS-impute, an 'imputation in a box' solution that seamlessly and transparently automates the set up and running of all the steps of the imputation process. These steps include genome build liftover (liftovering), genotype phasing with SHAPEIT2, quality control, sample and chromosomal chunking/merging, and imputation with IMPUTE2. MOLGENIS-impute builds on MOLGENIS-compute, a simple pipeline management platform for submission and monitoring of bioinformatics tasks in High Performance Computing (HPC) environments like local/cloud servers, clusters and grids. All the required tools, data and scripts are downloaded and installed in a single step. Researchers with diverse backgrounds and expertise have tested MOLGENIS-impute on different locations and imputed over 30,000 samples so far using the 1,000 Genomes Project and new Genome of the Netherlands data as the imputation reference. The tests have been performed on PBS/SGE clusters, cloud VMs and in a grid HPC environment. MOLGENIS-impute gives priority to the ease of setting up, configuring and running an imputation. It has minimal dependencies and wraps the pipeline in a simple command line interface, without sacrificing flexibility to adapt or limiting the options of underlying imputation tools. It does not require knowledge of a workflow system or programming, and is targeted at researchers who just want to apply best practices in imputation via simple commands. It is built on the MOLGENIS compute workflow framework to enable customization with additional computational steps or it can be included in other bioinformatics pipelines. It is available as open source from: https://github.com/molgenis/molgenis-imputation.

77 FR 37661 - Amended Notice of Intent To Prepare the Environmental Impact Statement for a Proposed Federal...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-22

... natural gas pipelines, the Midwestern Gas Transmission line (3 miles distant) and/or the ANR Pipeline (4.5... Pipeline, Boardwalk/Texas Gas Pipeline, Shell/Capline Oil Pipeline, Panhandle/Trunkline Gas Pipeline, and... Rockport, IN, and CO 2 Pipeline; Conduct Additional Public Scoping Meetings; and Issue a Notice of...

Capsule injection system for a hydraulic capsule pipelining system

DOEpatents

Liu, Henry

1982-01-01

An injection system for injecting capsules into a hydraulic capsule pipelining system, the pipelining system comprising a pipeline adapted for flow of a carrier liquid therethrough, and capsules adapted to be transported through the pipeline by the carrier liquid flowing through the pipeline. The injection system comprises a reservoir of carrier liquid, the pipeline extending within the reservoir and extending downstream out of the reservoir, and a magazine in the reservoir for holding capsules in a series, one above another, for injection into the pipeline in the reservoir. The magazine has a lower end in communication with the pipeline in the reservoir for delivery of capsules from the magazine into the pipeline.

The Chandra Source Catalog 2.0: Building The Catalog

NASA Astrophysics Data System (ADS)

Grier, John D.; Plummer, David A.; Allen, Christopher E.; Anderson, Craig S.; Budynkiewicz, Jamie A.; Burke, Douglas; Chen, Judy C.; Civano, Francesca Maria; D'Abrusco, Raffaele; Doe, Stephen M.; Evans, Ian N.; Evans, Janet D.; Fabbiano, Giuseppina; Gibbs, Danny G., II; Glotfelty, Kenny J.; Graessle, Dale E.; Hain, Roger; Hall, Diane M.; Harbo, Peter N.; Houck, John C.; Lauer, Jennifer L.; Laurino, Omar; Lee, Nicholas P.; Martínez-Galarza, Juan Rafael; McCollough, Michael L.; McDowell, Jonathan C.; Miller, Joseph; McLaughlin, Warren; Morgan, Douglas L.; Mossman, Amy E.; Nguyen, Dan T.; Nichols, Joy S.; Nowak, Michael A.; Paxson, Charles; Primini, Francis Anthony; Rots, Arnold H.; Siemiginowska, Aneta; Sundheim, Beth A.; Tibbetts, Michael; Van Stone, David W.; Zografou, Panagoula

2018-01-01

To build release 2.0 of the Chandra Source Catalog (CSC2), we require scientific software tools and processing pipelines to evaluate and analyze the data. Additionally, software and hardware infrastructure is needed to coordinate and distribute pipeline execution, manage data i/o, and handle data for Quality Assurance (QA) intervention. We also provide data product staging for archive ingestion.Release 2 utilizes a database driven system used for integration and production. Included are four distinct instances of the Automatic Processing (AP) system (Source Detection, Master Match, Source Properties and Convex Hulls) and a high performance computing (HPC) cluster that is managed to provide efficient catalog processing. In this poster we highlight the internal systems developed to meet the CSC2 challenge.This work has been supported by NASA under contract NAS 8-03060 to the Smithsonian Astrophysical Observatory for operation of the Chandra X-ray Center.

Chill Down Process of Hydrogen Transport Pipelines

NASA Technical Reports Server (NTRS)

Mei, Renwei; Klausner, James

2006-01-01

A pseudo-steady model has been developed to predict the chilldown history of pipe wall temperature in the horizontal transport pipeline for cryogenic fluids. A new film boiling heat transfer model is developed by incorporating the stratified flow structure for cryogenic chilldown. A modified nucleate boiling heat transfer correlation for cryogenic chilldown process inside a horizontal pipe is proposed. The efficacy of the correlations is assessed by comparing the model predictions with measured values of wall temperature in several azimuthal positions in a well controlled experiment by Chung et al. (2004). The computed pipe wall temperature histories match well with the measured results. The present model captures important features of thermal interaction between the pipe wall and the cryogenic fluid, provides a simple and robust platform for predicting pipe wall chilldown history in long horizontal pipe at relatively low computational cost, and builds a foundation to incorporate the two-phase hydrodynamic interaction in the chilldown process.

OXSA: An open-source magnetic resonance spectroscopy analysis toolbox in MATLAB.

PubMed

Purvis, Lucian A B; Clarke, William T; Biasiolli, Luca; Valkovič, Ladislav; Robson, Matthew D; Rodgers, Christopher T

2017-01-01

In vivo magnetic resonance spectroscopy provides insight into metabolism in the human body. New acquisition protocols are often proposed to improve the quality or efficiency of data collection. Processing pipelines must also be developed to use these data optimally. Current fitting software is either targeted at general spectroscopy fitting, or for specific protocols. We therefore introduce the MATLAB-based OXford Spectroscopy Analysis (OXSA) toolbox to allow researchers to rapidly develop their own customised processing pipelines. The toolbox aims to simplify development by: being easy to install and use; seamlessly importing Siemens Digital Imaging and Communications in Medicine (DICOM) standard data; allowing visualisation of spectroscopy data; offering a robust fitting routine; flexibly specifying prior knowledge when fitting; and allowing batch processing of spectra. This article demonstrates how each of these criteria have been fulfilled, and gives technical details about the implementation in MATLAB. The code is freely available to download from https://github.com/oxsatoolbox/oxsa.

Real time software tools and methodologies

NASA Technical Reports Server (NTRS)

Christofferson, M. J.

1981-01-01

Real time systems are characterized by high speed processing and throughput as well as asynchronous event processing requirements. These requirements give rise to particular implementations of parallel or pipeline multitasking structures, of intertask or interprocess communications mechanisms, and finally of message (buffer) routing or switching mechanisms. These mechanisms or structures, along with the data structue, describe the essential character of the system. These common structural elements and mechanisms are identified, their implementation in the form of routines, tasks or macros - in other words, tools are formalized. The tools developed support or make available the following: reentrant task creation, generalized message routing techniques, generalized task structures/task families, standardized intertask communications mechanisms, and pipeline and parallel processing architectures in a multitasking environment. Tools development raise some interesting prospects in the areas of software instrumentation and software portability. These issues are discussed following the description of the tools themselves.

Real-time Image Processing for Microscopy-based Label-free Imaging Flow Cytometry in a Microfluidic Chip.

PubMed

Heo, Young Jin; Lee, Donghyeon; Kang, Junsu; Lee, Keondo; Chung, Wan Kyun

2017-09-14

Imaging flow cytometry (IFC) is an emerging technology that acquires single-cell images at high-throughput for analysis of a cell population. Rich information that comes from high sensitivity and spatial resolution of a single-cell microscopic image is beneficial for single-cell analysis in various biological applications. In this paper, we present a fast image-processing pipeline (R-MOD: Real-time Moving Object Detector) based on deep learning for high-throughput microscopy-based label-free IFC in a microfluidic chip. The R-MOD pipeline acquires all single-cell images of cells in flow, and identifies the acquired images as a real-time process with minimum hardware that consists of a microscope and a high-speed camera. Experiments show that R-MOD has the fast and reliable accuracy (500 fps and 93.3% mAP), and is expected to be used as a powerful tool for biomedical and clinical applications.

Research of processes of heat exchange in horizontal pipeline

NASA Astrophysics Data System (ADS)

Nikolaev, A. K.; Dokoukin, V. P.; Lykov, Y. V.; Fetisov, V. G.

2018-03-01

The energy crisis, which becomes more evident in Russia, stems in many respects from unjustified high consumption of energy resources. Development and exploitation of principal oil and gas deposits located in remote areas with severe climatic conditions require considerable investments increasing essentially the cost of power generation. Account should be taken also of the fact that oil and gas resources are nonrenewable. An alternative fuel for heat and power generation is coal, the reserves of which in Russia are quite substantial. For this reason the coal extraction by 2020 will amount to 450-550 million tons. The use of coal, as a solid fuel for heat power plants and heating plants, is complicated by its transportation from extraction to processing and consumption sites. Remoteness of the principal coal mining areas (Kuzbass, Kansk-Achinsk field, Vorkuta) from the main centers of its consumption in the European part of the country, Siberia and Far East makes the problem of coal transportation urgent. Of all possible transportation methods (railway, conveyor, pipeline), the most efficient is hydrotransport which provides continuous transportation at comparatively low capital and working costs, as confirmed by construction and operation of extended coal pipelines in many countries.

Pipeline Processing for VISTA

NASA Astrophysics Data System (ADS)

Lewis, J. R.; Irwin, M.; Bunclark, P.

2010-12-01

The VISTA telescope is a 4 metre instrument which has recently been commissioned at Paranal, Chile. Equipped with an infrared camera, 16 2Kx2K Raytheon detectors and a 1.7 square degree field of view, VISTA represents a huge leap in infrared survey capability in the southern hemisphere. Pipeline processing of IR data is far more technically challenging than for optical data. IR detectors are inherently more unstable, while the sky emission is over 100 times brighter than most objects of interest, and varies in a complex spatial and temporal manner. To compensate for this, exposure times are kept short, leading to high nightly data rates. VISTA is expected to generate an average of 250 GB of data per night over the next 5-10 years, which far exceeds the current total data rate of all 8m-class telescopes. In this presentation we discuss the pipelines that have been developed to deal with IR imaging data from VISTA and discuss the primary issues involved in an end-to-end system capable of: robustly removing instrument and night sky signatures; monitoring data quality and system integrity; providing astrometric and photometric calibration; and generating photon noise-limited images and science-ready astronomical catalogues.

Second Iteration of Photogrammetric Pipeline to Enhance the Accuracy of Image Pose Estimation

NASA Astrophysics Data System (ADS)

Nguyen, T. G.; Pierrot-Deseilligny, M.; Muller, J.-M.; Thom, C.

2017-05-01

In classical photogrammetric processing pipeline, the automatic tie point extraction plays a key role in the quality of achieved results. The image tie points are crucial to pose estimation and have a significant influence on the precision of calculated orientation parameters. Therefore, both relative and absolute orientations of the 3D model can be affected. By improving the precision of image tie point measurement, one can enhance the quality of image orientation. The quality of image tie points is under the influence of several factors such as the multiplicity, the measurement precision and the distribution in 2D images as well as in 3D scenes. In complex acquisition scenarios such as indoor applications and oblique aerial images, tie point extraction is limited while only image information can be exploited. Hence, we propose here a method which improves the precision of pose estimation in complex scenarios by adding a second iteration to the classical processing pipeline. The result of a first iteration is used as a priori information to guide the extraction of new tie points with better quality. Evaluated with multiple case studies, the proposed method shows its validity and its high potiential for precision improvement.

Simulating observations with HARMONI: the integral field spectrograph for the European Extremely Large Telescope

NASA Astrophysics Data System (ADS)

Zieleniewski, Simon; Thatte, Niranjan; Kendrew, Sarah; Houghton, Ryan; Tecza, Matthias; Clarke, Fraser; Fusco, Thierry; Swinbank, Mark

2014-07-01

With the next generation of extremely large telescopes commencing construction, there is an urgent need for detailed quantitative predictions of the scientific observations that these new telescopes will enable. Most of these new telescopes will have adaptive optics fully integrated with the telescope itself, allowing unprecedented spatial resolution combined with enormous sensitivity. However, the adaptive optics point spread function will be strongly wavelength dependent, requiring detailed simulations that accurately model these variations. We have developed a simulation pipeline for the HARMONI integral field spectrograph, a first light instrument for the European Extremely Large Telescope. The simulator takes high-resolution input data-cubes of astrophysical objects and processes them with accurate atmospheric, telescope and instrumental effects, to produce mock observed cubes for chosen observing parameters. The output cubes represent the result of a perfect data reduc- tion process, enabling a detailed analysis and comparison between input and output, showcasing HARMONI's capabilities. The simulations utilise a detailed knowledge of the telescope's wavelength dependent adaptive op- tics point spread function. We discuss the simulation pipeline and present an early example of the pipeline functionality for simulating observations of high redshift galaxies.

PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data.

PubMed

Anslan, Sten; Bahram, Mohammad; Hiiesalu, Indrek; Tedersoo, Leho

2017-11-01

High-throughput sequencing methods have become a routine analysis tool in environmental sciences as well as in public and private sector. These methods provide vast amount of data, which need to be analysed in several steps. Although the bioinformatics may be applied using several public tools, many analytical pipelines allow too few options for the optimal analysis for more complicated or customized designs. Here, we introduce PipeCraft, a flexible and handy bioinformatics pipeline with a user-friendly graphical interface that links several public tools for analysing amplicon sequencing data. Users are able to customize the pipeline by selecting the most suitable tools and options to process raw sequences from Illumina, Pacific Biosciences, Ion Torrent and Roche 454 sequencing platforms. We described the design and options of PipeCraft and evaluated its performance by analysing the data sets from three different sequencing platforms. We demonstrated that PipeCraft is able to process large data sets within 24 hr. The graphical user interface and the automated links between various bioinformatics tools enable easy customization of the workflow. All analytical steps and options are recorded in log files and are easily traceable. © 2017 John Wiley & Sons Ltd.

Development of bacterial biofilms in dairy processing lines.

PubMed

Austin, J W; Bergeron, G

1995-08-01

Adherence of bacteria to various milk contact sites was examined by scanning electron microscopy and transmission electron microscopy. New gaskets, endcaps, vacuum breaker plugs and pipeline inserts were installed in different areas in lines carrying either raw or pasteurized milk, and a routine schedule of cleaning-in-place and sanitizing was followed. Removed cleaned and sanitized gaskets were processed for scanning or transmission electron microscopy. Adherent bacteria were observed on the sides of gaskets removed from both pasteurized and raw milk lines. Some areas of Buna-n gaskets were colonized with a confluent layer of bacterial cells surrounded by an extensive amorphous matrix, while other areas of Buna-n gaskets showed a diffuse adherence over large areas of the surface. Most of the bacteria attached to polytetrafluoroethylene (PTFE or Teflon) gaskets were found in crevices created by insertion of the gasket into the pipeline. Examination of stainless steel endcaps, pipeline inserts, and PTFE vacuum breaker plugs did not reveal the presence of adherent bacteria. The results of this study indicate that biofilms developed on the sides of gaskets in spite of cleaning-in-place procedures. These biofilms may be a source of post-pasteurization contamination.

75 FR 41452 - Withdrawal of the Environmental Impact Statement (EIS) Development Process for the Proposed...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-16

... DEPARTMENT OF DEFENSE Department of the Army, Corps of Engineers Withdrawal of the Environmental Impact Statement (EIS) Development Process for the Proposed Beluga to Fairbanks (B2F) Natural Gas... discontinuing the EIS development process associated with the proposed B2F pipeline. FOR FURTHER INFORMATION...

A pipeline for the de novo assembly of the Themira biloba (Sepsidae: Diptera) transcriptome using a multiple k-mer length approach.

PubMed

Melicher, Dacotah; Torson, Alex S; Dworkin, Ian; Bowsher, Julia H

2014-03-12

The Sepsidae family of flies is a model for investigating how sexual selection shapes courtship and sexual dimorphism in a comparative framework. However, like many non-model systems, there are few molecular resources available. Large-scale sequencing and assembly have not been performed in any sepsid, and the lack of a closely related genome makes investigation of gene expression challenging. Our goal was to develop an automated pipeline for de novo transcriptome assembly, and to use that pipeline to assemble and analyze the transcriptome of the sepsid Themira biloba. Our bioinformatics pipeline uses cloud computing services to assemble and analyze the transcriptome with off-site data management, processing, and backup. It uses a multiple k-mer length approach combined with a second meta-assembly to extend transcripts and recover more bases of transcript sequences than standard single k-mer assembly. We used 454 sequencing to generate 1.48 million reads from cDNA generated from embryo, larva, and pupae of T. biloba and assembled a transcriptome consisting of 24,495 contigs. Annotation identified 16,705 transcripts, including those involved in embryogenesis and limb patterning. We assembled transcriptomes from an additional three non-model organisms to demonstrate that our pipeline assembled a higher-quality transcriptome than single k-mer approaches across multiple species. The pipeline we have developed for assembly and analysis increases contig length, recovers unique transcripts, and assembles more base pairs than other methods through the use of a meta-assembly. The T. biloba transcriptome is a critical resource for performing large-scale RNA-Seq investigations of gene expression patterns, and is the first transcriptome sequenced in this Dipteran family.

76 FR 73570 - Pipeline Safety: Miscellaneous Changes to Pipeline Safety Regulations

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-29

... pipeline facilities to facilitate the removal of liquids and other materials from the gas stream. These... DEPARTMENT OF TRANSPORTATION Pipeline and Hazardous Materials Safety Administration 49 CFR Parts... Changes to Pipeline Safety Regulations AGENCY: Pipeline and Hazardous Materials Safety Administration...

The Chandra Source Catalog : Automated Source Correlation

NASA Astrophysics Data System (ADS)

Hain, Roger; Evans, I. N.; Evans, J. D.; Glotfelty, K. J.; Anderson, C. S.; Bonaventura, N. R.; Chen, J. C.; Davis, J. E.; Doe, S. M.; Fabbiano, G.; Galle, E.; Gibbs, D. G.; Grier, J. D.; Hall, D. M.; Harbo, P. N.; He, X.; Houck, J. C.; Karovska, M.; Lauer, J.; McCollough, M. L.; McDowell, J. C.; Miller, J. B.; Mitschang, A. W.; Morgan, D. L.; Nichols, J. S.; Nowak, M. A.; Plummer, D. A.; Primini, F. A.; Refsdal, B. L.; Rots, A. H.; Siemiginowska, A. L.; Sundheim, B. A.; Tibbetts, M. S.; Van Stone, D. W.; Winkelman, S. L.; Zografou, P.

2009-01-01

Chandra Source Catalog (CSC) master source pipeline processing seeks to automatically detect sources and compute their properties. Since Chandra is a pointed mission and not a sky survey, different sky regions are observed for a different number of times at varying orientations, resolutions, and other heterogeneous conditions. While this provides an opportunity to collect data from a potentially large number of observing passes, it also creates challenges in determining the best way to combine different detection results for the most accurate characterization of the detected sources. The CSC master source pipeline correlates data from multiple observations by updating existing cataloged source information with new data from the same sky region as they become available. This process sometimes leads to relatively straightforward conclusions, such as when single sources from two observations are similar in size and position. Other observation results require more logic to combine, such as one observation finding a single, large source and another identifying multiple, smaller sources at the same position. We present examples of different overlapping source detections processed in the current version of the CSC master source pipeline. We explain how they are resolved into entries in the master source database, and examine the challenges of computing source properties for the same source detected multiple times. Future enhancements are also discussed. This work is supported by NASA contract NAS8-03060 (CXC).

Utilization of protein intrinsic disorder knowledge in structural proteomics

PubMed Central

Oldfield, Christopher J.; Xue, Bin; Van, Ya-Yue; Ulrich, Eldon L.; Markley, John L.; Dunker, A. Keith; Uversky, Vladimir N.

2014-01-01

Intrinsically disordered proteins (IDPs) and proteins with long disordered regions are highly abundant in various proteomes. Despite their lack of well-defined ordered structure, these proteins and regions are frequently involved in crucial biological processes. Although in recent years these proteins have attracted the attention of many researchers, IDPs represent a significant challenge for structural characterization since these proteins can impact many of the processes in the structure determination pipeline. Here we investigate the effects of IDPs on the structure determination process and the utility of disorder prediction in selecting and improving proteins for structural characterization. Examination of the extent of intrinsic disorder in existing crystal structures found that relatively few protein crystal structures contain extensive regions of intrinsic disorder. Although intrinsic disorder is not the only cause of crystallization failures and many structured proteins cannot be crystallized, filtering out highly disordered proteins from structure-determination target lists is still likely to be cost effective. Therefore it is desirable to avoid highly disordered proteins from structure-determination target lists and we show that disorder prediction can be applied effectively to enrich structure determination pipelines with proteins more likely to yield crystal structures. For structural investigation of specific proteins, disorder prediction can be used to improve targets for structure determination. Finally, a framework for considering intrinsic disorder in the structure determination pipeline is proposed. PMID:23232152

esATAC: An Easy-to-use Systematic pipeline for ATAC-seq data analysis.

PubMed

Wei, Zheng; Zhang, Wei; Fang, Huan; Li, Yanda; Wang, Xiaowo

2018-03-07

ATAC-seq is rapidly emerging as one of the major experimental approaches to probe chromatin accessibility genome-wide. Here, we present "esATAC", a highly integrated easy-to-use R/Bioconductor package, for systematic ATAC-seq data analysis. It covers essential steps for full analyzing procedure, including raw data processing, quality control and downstream statistical analysis such as peak calling, enrichment analysis and transcription factor footprinting. esATAC supports one command line execution for preset pipelines, and provides flexible interfaces for building customized pipelines. esATAC package is open source under the GPL-3.0 license. It is implemented in R and C ++. Source code and binaries for Linux, MAC OS X and Windows are available through Bioconductor https://www.bioconductor.org/packages/release/bioc/html/esATAC.html). xwwang@tsinghua.edu.cn. Supplementary data are available at Bioinformatics online.

A New Pipelined Systolic Array-Based Architecture for Matrix Inversion in FPGAs with Kalman Filter Case Study

NASA Astrophysics Data System (ADS)

Bigdeli, Abbas; Biglari-Abhari, Morteza; Salcic, Zoran; Tin Lai, Yat

2006-12-01

A new pipelined systolic array-based (PSA) architecture for matrix inversion is proposed. The pipelined systolic array (PSA) architecture is suitable for FPGA implementations as it efficiently uses available resources of an FPGA. It is scalable for different matrix size and as such allows employing parameterisation that makes it suitable for customisation for application-specific needs. This new architecture has an advantage of[InlineEquation not available: see fulltext.] processing element complexity, compared to the[InlineEquation not available: see fulltext.] in other systolic array structures, where the size of the input matrix is given by[InlineEquation not available: see fulltext.]. The use of the PSA architecture for Kalman filter as an implementation example, which requires different structures for different number of states, is illustrated. The resulting precision error is analysed and shown to be negligible.

Integrated pathway-based transcription regulation network mining and visualization based on gene expression profiles.

PubMed

Kibinge, Nelson; Ono, Naoaki; Horie, Masafumi; Sato, Tetsuo; Sugiura, Tadao; Altaf-Ul-Amin, Md; Saito, Akira; Kanaya, Shigehiko

2016-06-01

Conventionally, workflows examining transcription regulation networks from gene expression data involve distinct analytical steps. There is a need for pipelines that unify data mining and inference deduction into a singular framework to enhance interpretation and hypotheses generation. We propose a workflow that merges network construction with gene expression data mining focusing on regulation processes in the context of transcription factor driven gene regulation. The pipeline implements pathway-based modularization of expression profiles into functional units to improve biological interpretation. The integrated workflow was implemented as a web application software (TransReguloNet) with functions that enable pathway visualization and comparison of transcription factor activity between sample conditions defined in the experimental design. The pipeline merges differential expression, network construction, pathway-based abstraction, clustering and visualization. The framework was applied in analysis of actual expression datasets related to lung, breast and prostrate cancer. Copyright © 2016 Elsevier Inc. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grafe, J.L.

During the past decade many changes have taken place in the natural gas industry, not the least of which is the way information (data) is acquired, moved, compiled, integrated and disseminated within organizations. At El Paso Natural Gas Company (EPNG) the Operations Control Department has been at the center of these changes. The Systems Section within Operations Control has been instrumental in developing the computer programs that acquire and store real-time operational data, and then make it available to not only the Gas Control function, but also to anyone else within the company who might require it and, to amore » limited degree, any supplier or purchaser of gas utilizing the El Paso pipeline. These computer programs which make up the VISA system are, in effect, the tools that help move the data that flows in the pipeline of information within the company. Their integration into this pipeline process is the topic of this paper.« less

A Small Leak Detection Method Based on VMD Adaptive De-Noising and Ambiguity Correlation Classification Intended for Natural Gas Pipelines.

PubMed

Xiao, Qiyang; Li, Jian; Bai, Zhiliang; Sun, Jiedi; Zhou, Nan; Zeng, Zhoumo

2016-12-13

In this study, a small leak detection method based on variational mode decomposition (VMD) and ambiguity correlation classification (ACC) is proposed. The signals acquired from sensors were decomposed using the VMD, and numerous components were obtained. According to the probability density function (PDF), an adaptive de-noising algorithm based on VMD is proposed for noise component processing and de-noised components reconstruction. Furthermore, the ambiguity function image was employed for analysis of the reconstructed signals. Based on the correlation coefficient, ACC is proposed to detect the small leak of pipeline. The analysis of pipeline leakage signals, using 1 mm and 2 mm leaks, has shown that proposed detection method can detect a small leak accurately and effectively. Moreover, the experimental results have shown that the proposed method achieved better performances than support vector machine (SVM) and back propagation neural network (BP) methods.

A Small Leak Detection Method Based on VMD Adaptive De-Noising and Ambiguity Correlation Classification Intended for Natural Gas Pipelines

PubMed Central

Xiao, Qiyang; Li, Jian; Bai, Zhiliang; Sun, Jiedi; Zhou, Nan; Zeng, Zhoumo

2016-01-01

In this study, a small leak detection method based on variational mode decomposition (VMD) and ambiguity correlation classification (ACC) is proposed. The signals acquired from sensors were decomposed using the VMD, and numerous components were obtained. According to the probability density function (PDF), an adaptive de-noising algorithm based on VMD is proposed for noise component processing and de-noised components reconstruction. Furthermore, the ambiguity function image was employed for analysis of the reconstructed signals. Based on the correlation coefficient, ACC is proposed to detect the small leak of pipeline. The analysis of pipeline leakage signals, using 1 mm and 2 mm leaks, has shown that proposed detection method can detect a small leak accurately and effectively. Moreover, the experimental results have shown that the proposed method achieved better performances than support vector machine (SVM) and back propagation neural network (BP) methods. PMID:27983577

Remaining Sites Verification Package for the 100-F-26:13, 108-F Drain Pipelines, Waste Site Reclassification Form 2005-011

DOE Office of Scientific and Technical Information (OSTI.GOV)

L. M. Dittmer

2008-03-03

The 100-F-26:13 waste site is the network of process sewer pipelines that received effluent from the 108-F Biological Laboratory and discharged it to the 188-F Ash Disposal Area (126-F-1 waste site). The pipelines included one 0.15-m (6-in.)-, two 0.2-m (8-in.)-, and one 0.31-m (12-in.)-diameter vitrified clay pipe segments encased in concrete. In accordance with this evaluation, the verification sampling results support a reclassification of this site to Interim Closed Out. The results of verification sampling demonstrated that residual contaminant concentrations do not preclude any future uses and allow for unrestricted use of shallow zone soils. The results also showed thatmore » residual contaminant concentrations are protective of groundwater and the Columbia River.« less

Mathematical modeling of ignition of woodlands resulted from accident on the pipeline

NASA Astrophysics Data System (ADS)

Perminov, V. A.; Loboda, E. L.; Reyno, V. V.

2014-11-01

Accidents occurring at the sites of pipelines, accompanied by environmental damage, economic loss, and sometimes loss of life. In this paper we calculated the sizes of the possible ignition zones in emergency situations on pipelines located close to the forest, accompanied by the appearance of fireballs. In this paper, using the method of mathematical modeling calculates the maximum size of the ignition zones of vegetation as a result of accidental releases of flammable substances. The paper suggested in the context of the general mathematical model of forest fires give a new mathematical setting and method of numerical solution of a problem of a forest fire modeling. The boundary-value problem is solved numerically using the method of splitting according to physical processes. The dependences of the size of the forest fuel for different amounts of leaked flammable substances and moisture content of vegetation.

Pipeline Processing with an Iterative, Context-based Detection Model

DTIC Science & Technology

2014-04-19

stripping the incoming data stream of repeating and irrelevant signals prior to running primary detectors , adaptive beamforming and matched field processing...framework, pattern detectors , correlation detectors , subspace detectors , matched field detectors , nuclear explosion monitoring 16. SECURITY CLASSIFICATION...10 5. Teleseismic paths from earthquakes in

75 FR 63774 - Pipeline Safety: Safety of On-Shore Hazardous Liquid Pipelines

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-18

... DEPARTMENT OF TRANSPORTATION Pipeline and Hazardous Materials Safety Administration 49 CFR Part... Pipelines AGENCY: Pipeline and Hazardous Materials Safety Administration (PHMSA), Department of... Gas Pipeline Safety Act of 1968, Public Law 90-481, delegated to DOT the authority to develop...

49 CFR 195.210 - Pipeline location.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 3 2010-10-01 2010-10-01 false Pipeline location. 195.210 Section 195.210 Transportation Other Regulations Relating to Transportation (Continued) PIPELINE AND HAZARDOUS MATERIALS SAFETY... PIPELINE Construction § 195.210 Pipeline location. (a) Pipeline right-of-way must be selected to avoid, as...

75 FR 5244 - Pipeline Safety: Integrity Management Program for Gas Distribution Pipelines; Correction

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-02

... Management Program for Gas Distribution Pipelines; Correction AGENCY: Pipeline and Hazardous Materials Safety... DEPARTMENT OF TRANSPORTATION Pipeline and Hazardous Materials Safety Administration 49 CFR Part... Regulations to require operators of gas distribution pipelines to develop and implement integrity management...

77 FR 61825 - Pipeline Safety: Notice of Public Meeting on Pipeline Data

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-11

... DEPARTMENT OF TRANSPORTATION Pipeline and Hazardous Materials Safety Administration [Docket ID... program performance measures for gas distribution, gas transmission, and hazardous liquids pipelines. The... distribution pipelines (49 CFR 192.1007(e)), gas transmission pipelines (49 CFR 192.945) and hazardous liquids...

78 FR 41991 - Pipeline Safety: Potential for Damage to Pipeline Facilities Caused by Flooding

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-12

... DEPARTMENT OF TRANSPORTATION Pipeline and Hazardous Materials Safety Administration [Docket No...: Pipeline and Hazardous Materials Safety Administration (PHMSA); DOT. ACTION: Notice; Issuance of Advisory... Gas and Hazardous Liquid Pipeline Systems. Subject: Potential for Damage to Pipeline Facilities Caused...

78 FR 41496 - Pipeline Safety: Meetings of the Gas and Liquid Pipeline Advisory Committees

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-10

... DEPARTMENT OF TRANSPORTATION Pipeline and Hazardous Materials Safety Administration [Docket No. PHMSA-2013-0156] Pipeline Safety: Meetings of the Gas and Liquid Pipeline Advisory Committees AGENCY: Pipeline and Hazardous Materials Safety Administration (PHMSA), DOT. ACTION: Notice of advisory committee...

76 FR 70953 - Pipeline Safety: Safety of Gas Transmission Pipelines

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-16

... DEPARTMENT OF TRANSPORTATION Pipeline and Hazardous Materials Safety Administration 49 CFR Part 192 [Docket ID PHMSA-2011-0023] RIN 2137-AE72 Pipeline Safety: Safety of Gas Transmission Pipelines AGENCY: Pipeline and Hazardous Materials Safety Administration (PHMSA); DOT. ACTION: Advance notice of...

Dynamics of a Pipeline under the Action of Internal Shock Pressure

NASA Astrophysics Data System (ADS)

Il'gamov, M. A.

2017-11-01

The static and dynamic bending of a pipeline in the vertical plane under the action of its own weight is considered with regard to the interaction of the internal pressure with the curvature of the axial line and the axisymmetric deformation. The pressure consists of a constant and timevarying parts and is assumed to be uniformly distributed over the entire span between the supports. The pipeline reaction to the stepwise increase in the pressure is analyzed in the case where it is possible to determine the exact solution of the problem. The initial stage of bending determined by the smallness of elastic forces as compared to the inertial forces is introduced into the consideration. At this stage, the solution is sought in the form of power series and the law of pressure variation can be arbitrary. This solution provides initial conditions for determining the further process. The duration of the inertial stage is compared with the times of sharp changes of the pressure and the shock waves in fluids. The structure parameters are determined in the case where the shock pressure is accepted only by the inertial forces in the pipeline.